subject:(Protein)

Oregon State University

1. Brereton, Andrew E. Exploring Protein Structure: Seeing the Forest and the Trees.

Degree: PhD, 2017, Oregon State University

URL: http://hdl.handle.net/1957/61775

► Life on Earth intimately depends on the function of countless proteins. For the majority of studied proteins, function absolutely depends on conformation (i.e. 3-dimensional shape… (more)

▼ Life on Earth intimately depends on the function of countless proteins. For the majority of studied proteins, function absolutely depends on conformation (i.e. 3-dimensional shape in solution). The exact nature of how a protein goes from an unfolded linear polypeptide chain to an organized folded molecule is still not known, and there is still much uncertainty about the details of folded protein structures. Answering both questions fully, especially by being able to accurately predict protein structures from sequence alone, is known as the protein folding problem. In this dissertation, the nature of protein structure research, especially as it pertains to model-building, entropy, and Boltzmann’s principle, is discussed. Original work is presented in three chapters in the form of primary research reports. In chapter 2, high resolution protein crystal structures are used to describe the details of a high-energy transition conformation that occurs during protein folding. These native structures were found to have stabilized individual residues in conformations that represented “snapshots” along the transition pathway, and could be used to model the transition. In chapter 3, the extent and reliability of observed non-planarity of the peptide bond is assessed, using ultra-high resolution protein crystal structures. This work continues a discussion on peptide planarity that exists in the literature, and sets the record straight on the occurrence of this “non-ideal” geometry. In chapter 4, the “Ensemblator” is described and demonstrated. This software package is capable of comparing and analyzing large numbers of related protein models simultaneously, and represents an invaluable tool to protein structure researchers. Lastly, in chapter 5, impacts and highlights of the reported work are discussed, along with directions for future work. The dissertation concludes with a reflection on the nature of problems being researched in protein structure, and a discussion on how the included original work relates to Boltzmann’s principle and model building in general. Advisors/Committee Members: Karplus, P. Andrew (advisor), Hendrix, David (committee member).

Subjects/Keywords: protein

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APA (6^th Edition):

Brereton, A. E. (2017). Exploring Protein Structure: Seeing the Forest and the Trees. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/61775

Chicago Manual of Style (16^th Edition):

Brereton, Andrew E. “Exploring Protein Structure: Seeing the Forest and the Trees.” 2017. Doctoral Dissertation, Oregon State University. Accessed April 11, 2021. http://hdl.handle.net/1957/61775.

MLA Handbook (7^th Edition):

Brereton, Andrew E. “Exploring Protein Structure: Seeing the Forest and the Trees.” 2017. Web. 11 Apr 2021.

Vancouver:

Brereton AE. Exploring Protein Structure: Seeing the Forest and the Trees. [Internet] [Doctoral dissertation]. Oregon State University; 2017. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/1957/61775.

Council of Science Editors:

Brereton AE. Exploring Protein Structure: Seeing the Forest and the Trees. [Doctoral Dissertation]. Oregon State University; 2017. Available from: http://hdl.handle.net/1957/61775

Hong Kong University of Science and Technology

2. Zhu, Jiawei. The novel role of SLY1 in golgi-ER retrograde protein secretory pathway in budding yeast.

Degree: 2015, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-86332 ; https://doi.org/10.14711/thesis-b1514822 ; http://repository.ust.hk/ir/bitstream/1783.1-86332/1/th_redirect.html

► Bi-directional trafficking in the early protein secretary protein pathway is a universal phenomenon within eukaryotic cells. In yeast, the retrograde trafficking based on COPI coated… (more)

▼ Bi-directional trafficking in the early protein secretary protein pathway is a universal phenomenon within eukaryotic cells. In yeast, the retrograde trafficking based on COPI coated vesicles from Golgi back to ER has essential functions in recycling vesicle components and retrieving escaped ER resident proteins. This retrograde trafficking involves several steps, in which some mechanisms and molecules are still elusive. In previous researches, v-SNARE Sec22p was found mislocalized into vacuole in sec26^PNEE mutant strain. And the Sec26p is one subunit of COPI coatomer complex, which demonstrates a possible interaction between Sec22p and coatomer complex. Also considering the sorting Sec22p into COPI is still elusive, the coatomer complex is suspected to be sorting receptor for Sec22p. However, the SNAREs have little binding affinity to coatomer in bio-chemical experiments. So some other molecules might function as sorting receptors, linking Sec22p and coatomer. On the other hand, our lab’s previous researches found that sly1^T81I is synthetic lethal with sec26^PNEE, indicating the possible link between Sly1p and coatomer. SLY1 belongs to the SM protein family, cycling between ER and Golgi and is involved in bi-directional trafficking and able to bind to free SNAREs such as Sed5p and Bet1p. So a hypothetical model is offered that Sly1p may function as a linker for Sec22p and/or other SNAREs and coatomer. The potential role of Sly1p in interaction between Sec22p and coatomer is the major target to look for. In my study, Sly1p is found to bind to Sec22p in vitro and reduced binding between Sly1p and sec22p mutants that are mislocalized into vacuole is found. Overexpression of Sly1p in vivo seems like to have specific effect in shifting Sec22p to ER while no effect to those sec22p mutants. On the other hand, Sly1p might bind to only two subunits of coatomer: Ret1p and Ret2p, rather than the whole coatomer complex in vitro. The interaction between Sly1p and the two subunits of coatomer cannot be affected by pre-treating Sly1p with t-SNARE Sed5p. So the hypothetical binding model is modified into that Sly1p might function as linker for binding to Sec22p and two subunits of coatomer, which may involves other elusive mechanisms.

Subjects/Keywords: Protein binding ; Protein-protein interactions

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APA (6^th Edition):

Zhu, J. (2015). The novel role of SLY1 in golgi-ER retrograde protein secretory pathway in budding yeast. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-86332 ; https://doi.org/10.14711/thesis-b1514822 ; http://repository.ust.hk/ir/bitstream/1783.1-86332/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhu, Jiawei. “The novel role of SLY1 in golgi-ER retrograde protein secretory pathway in budding yeast.” 2015. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-86332 ; https://doi.org/10.14711/thesis-b1514822 ; http://repository.ust.hk/ir/bitstream/1783.1-86332/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhu, Jiawei. “The novel role of SLY1 in golgi-ER retrograde protein secretory pathway in budding yeast.” 2015. Web. 11 Apr 2021.

Vancouver:

Zhu J. The novel role of SLY1 in golgi-ER retrograde protein secretory pathway in budding yeast. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2015. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-86332 ; https://doi.org/10.14711/thesis-b1514822 ; http://repository.ust.hk/ir/bitstream/1783.1-86332/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhu J. The novel role of SLY1 in golgi-ER retrograde protein secretory pathway in budding yeast. [Thesis]. Hong Kong University of Science and Technology; 2015. Available from: http://repository.ust.hk/ir/Record/1783.1-86332 ; https://doi.org/10.14711/thesis-b1514822 ; http://repository.ust.hk/ir/bitstream/1783.1-86332/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Indian Institute of Science

3. Swapna, L S. Structural And Evolutionary Studies On Protein-Protein Interactions.

Degree: PhD, Faculty of Science, 2014, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/2316

► The last few decades have witnessed an upsurge in the availability of large-scale data on genomes and genome-scale information. The development of methods to understand… (more)

▼ The last few decades have witnessed an upsurge in the availability of large-scale data on genomes and genome-scale information. The development of methods to understand the trends and patterns from large scale data promised potentially to unravel the mechanisms responsible for the enormous diversity observed in biological systems. Of the many mechanisms adopted, protein-protein interactions represent one of the commonly adopted mechanisms to achieve functional diversity using a limited genetic repertoire. Protein-proteins interactions bring about several fundamental cellular processes and also modulate regulation at the cellular level. Different types of protein-protein interactions have evolved to carry out myriad functions in a cell. Mainly, interactions can be permanent or transient in nature, depending on the duration of interaction. In terms of affinity ,they are classified as obligate or non-obligate interactions. Structural studies on the various kinds of complexes have enabled the identification of the distinctive features characterizing the different types of complexes. Further, identifying the mechanisms involved in the evolution of protein-protein interactions are important in understanding the forces involved in their maintenance. Such studies also provide clues for the development of methods to predict protein-protein interactions from the large repertoire of sequence and structural data available. In spite of significant understanding of various aspects of protein-protein interactions, several questions still remain unanswered. The work embodied in this thesis studies two main aspects of protein-protein interactions for various types of complexes: structural and evolutionary features. The first part of the thesis(comprising of chapters 2,3,4 and 5) involves structural studies on the following features of protein-protein interactions: structural change, flexibility, symmetry, and residue conservation. The second part of the thesis(comprising of chapters 6,7,8 and 9) involves study of evolutionary aspects of protein-protein interactions, based on both large-scale data as well as case studies. Chapter1 provides a background and literature survey of the area of protein-protein interactions. The different classification schemes commonly used for describing the various protein-protein interactions are outlined. The key small-scale and large-scale experimental methods used for the identification of protein-protein interactions are described along with the details of the databases storing such experimentally derived information. Further, a comprehensive account of structural and evolutionary studies performed so far using the available data is provided. The computational(prediction)methods developed to address various aspects of protein-protein interactions are also outlined. In addition, the importance of protein-protein interactions in the context of diseases and the development of methods used to inhibit these interactions are discussed. Finally, the efforts towards design of protein-protein interactions… Advisors/Committee Members: Srinivasan, N (advisor).

Subjects/Keywords: Protein-Protein Interactions; Protein-Protein Complexes; Protein-Protein Structure; Homodimeric Proteins; Transient Protein-Protein Complexes; Protein-Protein Interactions - Structure; Protein-Protein Interactions - Evolution; Protein-Protein Interfaces; RNA Polymerase; Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Swapna, L. S. (2014). Structural And Evolutionary Studies On Protein-Protein Interactions. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/2316

Chicago Manual of Style (16^th Edition):

Swapna, L S. “Structural And Evolutionary Studies On Protein-Protein Interactions.” 2014. Doctoral Dissertation, Indian Institute of Science. Accessed April 11, 2021. http://etd.iisc.ac.in/handle/2005/2316.

MLA Handbook (7^th Edition):

Swapna, L S. “Structural And Evolutionary Studies On Protein-Protein Interactions.” 2014. Web. 11 Apr 2021.

Vancouver:

Swapna LS. Structural And Evolutionary Studies On Protein-Protein Interactions. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2014. [cited 2021 Apr 11]. Available from: http://etd.iisc.ac.in/handle/2005/2316.

Council of Science Editors:

Swapna LS. Structural And Evolutionary Studies On Protein-Protein Interactions. [Doctoral Dissertation]. Indian Institute of Science; 2014. Available from: http://etd.iisc.ac.in/handle/2005/2316

University of California – San Diego

4. Kozachenko, Ivan Andrew. Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching.

Degree: Chemistry, 2016, University of California – San Diego

URL: http://www.escholarship.org/uc/item/6wh40797

► This project investigates changes in protein solvation during the folding reaction of Outer membrane protein A (OmpA) of Escherichia Coli, and correlates this dehydration process… (more)

Subjects/Keywords: Biophysics; Chemistry; membrane protein; protein; protein folding

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kozachenko, I. A. (2016). Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/6wh40797

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kozachenko, Ivan Andrew. “Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching.” 2016. Thesis, University of California – San Diego. Accessed April 11, 2021. http://www.escholarship.org/uc/item/6wh40797.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kozachenko, Ivan Andrew. “Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching.” 2016. Web. 11 Apr 2021.

Vancouver:

Kozachenko IA. Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching. [Internet] [Thesis]. University of California – San Diego; 2016. [cited 2021 Apr 11]. Available from: http://www.escholarship.org/uc/item/6wh40797.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kozachenko IA. Studies of Membrane Protein Folding by Bimolecular Fluorescence Quenching. [Thesis]. University of California – San Diego; 2016. Available from: http://www.escholarship.org/uc/item/6wh40797

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Cambridge

5. Zhang, Yuewen. Investigating Protein Properties via Microfluidic Techniques.

Degree: PhD, 2019, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/293020https://www.repository.cam.ac.uk/bitstream/1810/293020/3/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/4/eccef7c7-2090-4b13-87fc-fa98778d425e.zip ; https://www.repository.cam.ac.uk/bitstream/1810/293020/6/YuewenZHANG_thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/10/YuewenZHANG_thesis_redacted.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/7/YuewenZHANG_thesis.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/293020/11/YuewenZHANG_thesis_redacted.pdf.jpg

► Proteins are one of the most abundant biomacromolecules and play important roles in bioactivities within organisms, including key functions in DNA replication, immune system response,… (more)

▼ Proteins are one of the most abundant biomacromolecules and play important roles in bioactivities within organisms, including key functions in DNA replication, immune system response, metabolic reactions and molecular transportation. Proteins fold into their unique compact three-dimensional structures to precisely perform their functions. Knowledge of proteins on their structures and interactions with other molecules or biomacromolecules is fundamental to understand the mechanism of many diseases. Thus, in this thesis, the focus is on studying the physical properties of proteins, and protein interactions using microfluidic techniques. Chapter 1 provides a brief introduction to protein stability and identification as well as their interactions. Then, conventional techniques for studying protein systems are reviewed. Moreover, the principles, designs and applications of microfluidic techniques are introduced. Chapter 2 demonstrates that a microfluidic diffusional sizing device can be employed to study protein interactions with small molecules by measuring the variation of hydrody- namic radius of bovine serum albumin (BSA) in aqueous solution as a function of pH. By simulating the behaviour of folded and unfolded BSA, the relative population of BSA in dif- ferent states can be calculated. In addition, the key residues that regulate the BSA unfolding process are predicted. Furthermore, I utilize a modified microfluidic diffusional sizing device to measure the hydrodynamic radius of Escherichia coli 70S ribosome and study its interactions with antibiotics, such as chloramphenicol. In Chapter 3, a microfluidic device for protein identification is designed to measure the physical parameters of proteins, including the fluorescence intensities of specific amino acids (tryptophan, tyrosine, lysine) and the hydrodynamic radius of proteins. Thus, proteins can be correctly identified in a single microfluidic device. The results have significant implications in development of effective and efficient techniques for precise protein identification in their native state. In Chapter 4, the interactions between a membrane protein (aquaporins) and a small regulator protein (calmodulin) are investigated by detecting the changes of their electrophoretic mobility and diffusivity in microfluidic devices. Then the effective charges of aquaporin0 and its complex with calmodulin are calculated. Finally, the selective binding between calmodulin and different types of aquaporins is investigated based on their relative binding affinities.

Subjects/Keywords: microfluidics; protein-protein interactions; protein physical properties

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhang, Y. (2019). Investigating Protein Properties via Microfluidic Techniques. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/293020https://www.repository.cam.ac.uk/bitstream/1810/293020/3/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/4/eccef7c7-2090-4b13-87fc-fa98778d425e.zip ; https://www.repository.cam.ac.uk/bitstream/1810/293020/6/YuewenZHANG_thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/10/YuewenZHANG_thesis_redacted.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/7/YuewenZHANG_thesis.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/293020/11/YuewenZHANG_thesis_redacted.pdf.jpg

Chicago Manual of Style (16^th Edition):

Zhang, Yuewen. “Investigating Protein Properties via Microfluidic Techniques.” 2019. Doctoral Dissertation, University of Cambridge. Accessed April 11, 2021. https://www.repository.cam.ac.uk/handle/1810/293020https://www.repository.cam.ac.uk/bitstream/1810/293020/3/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/4/eccef7c7-2090-4b13-87fc-fa98778d425e.zip ; https://www.repository.cam.ac.uk/bitstream/1810/293020/6/YuewenZHANG_thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/10/YuewenZHANG_thesis_redacted.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/7/YuewenZHANG_thesis.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/293020/11/YuewenZHANG_thesis_redacted.pdf.jpg.

MLA Handbook (7^th Edition):

Zhang, Yuewen. “Investigating Protein Properties via Microfluidic Techniques.” 2019. Web. 11 Apr 2021.

Vancouver:

Zhang Y. Investigating Protein Properties via Microfluidic Techniques. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Apr 11]. Available from: https://www.repository.cam.ac.uk/handle/1810/293020https://www.repository.cam.ac.uk/bitstream/1810/293020/3/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/4/eccef7c7-2090-4b13-87fc-fa98778d425e.zip ; https://www.repository.cam.ac.uk/bitstream/1810/293020/6/YuewenZHANG_thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/10/YuewenZHANG_thesis_redacted.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/7/YuewenZHANG_thesis.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/293020/11/YuewenZHANG_thesis_redacted.pdf.jpg.

Council of Science Editors:

Zhang Y. Investigating Protein Properties via Microfluidic Techniques. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://www.repository.cam.ac.uk/handle/1810/293020https://www.repository.cam.ac.uk/bitstream/1810/293020/3/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/4/eccef7c7-2090-4b13-87fc-fa98778d425e.zip ; https://www.repository.cam.ac.uk/bitstream/1810/293020/6/YuewenZHANG_thesis.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/10/YuewenZHANG_thesis_redacted.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/293020/7/YuewenZHANG_thesis.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/293020/11/YuewenZHANG_thesis_redacted.pdf.jpg

University of Guelph

6. Zhao, Qianru. Regulation of starch biosynthesis in Arabidopsis thalinan.

Degree: PhD, Department of Molecular and Cellular Biology, 2015, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8787

► Starch is an important carbohydrate in higher plants and is widely used in food and non-food industries. Starch is synthesized in plastids through the actions… (more)

▼ Starch is an important carbohydrate in higher plants and is widely used in food and non-food industries. Starch is synthesized in plastids through the actions of starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (DBE), each with multiple isoforms. This study tested the hypothesis that SSs and SBEs in Arabidopsis thaliana (Arabidopsis) chloroplasts, involved in transient starch biosynthesis in leaves, are regulated by protein phosphorylation and protein-protein interactions. The sub-organelle distribution of starch biosynthetic enzymes was determined and SS2 and SBE2.2 were detected in wild type starch granules at the end of a 16/8h light/dark photoperiod. However, starch granules of ss2- and ss3- mutants also lacked SBE2.2, suggesting an interaction between SS2 and SBE2.2, and also with SS3 in the chloroplast stroma. Formation of protein complexes between SS1, SS2 and SBE was investigated by studying starch granule bound proteins in sbe- mutants and co-immunoprecipitation of interacting enzymes. In wild-type Arabidopsis chloroplasts, SS1 co-immunoprecipitated with SBE2.1 and SBE2.2, and was previously observed in cereal endosperm, suggesting that the interaction mechanisms among starch biosynthetic enzymes are common across species. Recombinant SBE2.1 and SBE2.2 were shown to be phosphorylated by chloroplast protein kinases. Two phosphoserine residues that are highly conserved within the SBEII class of enzyme were identified by site-directed mutagenesis. A phosphorylation-dependent protein complex could be formed in vitro between recombinant Arabidopsis SBE and maize SSI and SSII. However, mutation of the identified SBE phosphorylation sites did not lead to disruption of interactions with SSIIa or SSI, suggesting that these sites are not directly linked to the formation of such protein complexes. When SBE2.2, D653 was mutated to Ser, ATP-dependent protein-protein interaction between maize SSI, SSIIa and Arabidopsis SBE2.2 were lost, suggesting this residue is important in regulating interactions with the SSI and SSII classes of starch synthases. The results of this study provide new insight into the regulation of transient starch biosynthesis in Arabidopsis chloroplasts. Advisors/Committee Members: Emes, Michael (advisor).

Subjects/Keywords: starch; protein phosphorylation; protein-protein interaction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhao, Q. (2015). Regulation of starch biosynthesis in Arabidopsis thalinan. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8787

Chicago Manual of Style (16^th Edition):

Zhao, Qianru. “Regulation of starch biosynthesis in Arabidopsis thalinan.” 2015. Doctoral Dissertation, University of Guelph. Accessed April 11, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8787.

MLA Handbook (7^th Edition):

Zhao, Qianru. “Regulation of starch biosynthesis in Arabidopsis thalinan.” 2015. Web. 11 Apr 2021.

Vancouver:

Zhao Q. Regulation of starch biosynthesis in Arabidopsis thalinan. [Internet] [Doctoral dissertation]. University of Guelph; 2015. [cited 2021 Apr 11]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8787.

Council of Science Editors:

Zhao Q. Regulation of starch biosynthesis in Arabidopsis thalinan. [Doctoral Dissertation]. University of Guelph; 2015. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8787

University of Illinois – Chicago

7. Lin, Meishan. Computational and Experimental Investigations of Folding Principles and Design of Outer Membrane Proteins.

Degree: 2017, University of Illinois – Chicago

URL: http://hdl.handle.net/10027/21818

► Outer membrane proteins are found in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts, and serve essential functions for cell viability. They are also… (more)

▼ Outer membrane proteins are found in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts, and serve essential functions for cell viability. They are also important therapeutic targets of developing drugs, and are the focuses of development of single-molecule sensors. Despite their importance, our understanding of outer membrane protein folding as well as outer membrane protein design have lagged far behind compared to soluble proteins due to the difficulties in studying them in their natural form. Computational methods can compliment experimental methods to expand our knowledge in outer membrane proteins. The main goal of this study is developing computational methods to gain a fundamental understanding of protein structure and function, and in turn using this knowledge to design outer membrane proteins. We first developed a computational approach to assess the folding free energy of outer membrane proteins by combining an empirical energy function with a reduced discrete state space. With this approach, we calculated depth-dependent transfer free energy scales of 20 amino acids, determined the native topology of proteins in the outer membrane, and assessed the effect of asymmetric bacterial outer membranes on the thermodynamic stability of proteins. We then developed a computation-guided strategy to design a novel outer membrane protein. A set of sequence motifs that may be important for the outer membrane protein organization was identified from combinatorial analysis. Strands that are involved in oligomerization have few such motifs, and were replaced with those that are enriched with motifs. Experimental validation proved the success of our design as the resulting protein OmpGF folded into predominant β-sheet structures, and formed a monomeric ion-conducting pore. We also discovered a general mechanism that drives oligomerization of outer membrane proteins. A sequence motif that is specific to trimeric porin family was identified, and was found to form inter-molecular interactions that are conserved in this family. Experimental examination of OmpF and PorB proteins proved that these inter-molecular interactions are essential for trimer formation. Overall, findings from this study provided additional understanding of folding principles of outer membrane proteins, and paved the road for designing novel outer membrane proteins. Advisors/Committee Members: Liang, Jie (advisor), Ma, Ao (committee member), Kenney, Linda J (committee member), Keiderling, Timothy A (committee member), Chen, Min (committee member), Liang, Jie (chair).

Subjects/Keywords: outer membrane protein protein folding protein design

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APA (6^th Edition):

Lin, M. (2017). Computational and Experimental Investigations of Folding Principles and Design of Outer Membrane Proteins. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/21818

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lin, Meishan. “Computational and Experimental Investigations of Folding Principles and Design of Outer Membrane Proteins.” 2017. Thesis, University of Illinois – Chicago. Accessed April 11, 2021. http://hdl.handle.net/10027/21818.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lin, Meishan. “Computational and Experimental Investigations of Folding Principles and Design of Outer Membrane Proteins.” 2017. Web. 11 Apr 2021.

Vancouver:

Lin M. Computational and Experimental Investigations of Folding Principles and Design of Outer Membrane Proteins. [Internet] [Thesis]. University of Illinois – Chicago; 2017. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/10027/21818.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lin M. Computational and Experimental Investigations of Folding Principles and Design of Outer Membrane Proteins. [Thesis]. University of Illinois – Chicago; 2017. Available from: http://hdl.handle.net/10027/21818

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

8. Wang, Chao. Biochemical and structural characterization of ankyrins.

Degree: 2014, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-71766 ; https://doi.org/10.14711/thesis-b1302214 ; http://repository.ust.hk/ir/bitstream/1783.1-71766/1/th_redirect.html

► Ankyrin adaptors together with their spectrin partners coordinate diverse ion channels and cell adhesion molecules within plasma membrane domains and thereby promote physiological activities including… (more)

▼ Ankyrin adaptors together with their spectrin partners coordinate diverse ion channels and cell adhesion molecules within plasma membrane domains and thereby promote physiological activities including fast signaling in the heart and nervous system. Human ankyrins contain three members: ankyrin-R/B/G (AnkR/B/G), encoded by ANK1/2/3, respectively. They all consist of a highly similar N-terminal membrane binding domain composed of 24 ankyrin repeats (ANK repeats), a middle spectrin binding domain comprised of two ZU5 domains and a UPA domain followed by a death domain (DD), and a variable C-terminal regulatory domain. The membrane binding domain and spectrin binding domain are highly conserved among all ankyrins (across isoforms and species), indicating that the two regions are essential for ankyrin’s functions throughout the evolution. Ankyrins specifically bind to unstructured sequences of membrane targets through their 24 ANK repeats, and directly bind to spectrin via the first ZU5 domain in the middle region, although the molecular mechanisms for the facile and independent evolution of these interactions has not been resolved. As an adaptor protein linking membrane proteins to the underlying cytoskeleton, dysfunctions of ankyrins are closely related to serious human diseases. For example, loss-of-function mutations of ankyrins can cause hemolytic anemia, various cardiac diseases including several cardiac arrhythmia syndromes and sinus node dysfunctions, bipolar disorder and autism spectrum disorders, although the underlying molecular bases are poorly understood. In this dissertation, I focus on ankyrin biology mainly from a biochemical and structural view and try to answer these fundamental questions in the ankyrin field by solving atomic structures of ankyrin different domains. Here I will describe three crystal structures of ankyrins combined with detailed biochemical analyses, providing the first structural blueprint for ankyrins. The high resolution structure of the ankyrin-B spectrin binding domain, which is arranged into ZU5-ZU5-UPA-DD (ZZUD) tandem, determined here reveals that the ZU5-ZU5-UPA (ZZU) domains form a tightly packed structural supramodule, whereas DD is freely accessible. Further structural analysis indicates that the ZZU supramodule of ankyrins has two additional surfaces that may bind to targets other than spectrin. The structure of the ankyrin ZZUD provides mechanistic explanations to many disease-causing mutations identified in ankyrin-B&R, and provides a “structural map” for further investigation of the spectrin binding domain of ankyrins. The other two structures of 24 ANK repeats in complex with an inhibitory segment from the C-terminal regulatory domain of ankyrin-R and part of the ANK repeats with a sodium channel Nav1.2 peptide, respectively, show that N-terminal 24 ANK repeats from ankyrins form a superhelical solenoid with an extended, extremely conserved inner groove, which contains multiple quasi-independent target binding sites that can accommodate target proteins with very…

Subjects/Keywords: Proteins ; Protein binding ; Protein-protein interactions

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APA (6^th Edition):

Wang, C. (2014). Biochemical and structural characterization of ankyrins. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-71766 ; https://doi.org/10.14711/thesis-b1302214 ; http://repository.ust.hk/ir/bitstream/1783.1-71766/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wang, Chao. “Biochemical and structural characterization of ankyrins.” 2014. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-71766 ; https://doi.org/10.14711/thesis-b1302214 ; http://repository.ust.hk/ir/bitstream/1783.1-71766/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wang, Chao. “Biochemical and structural characterization of ankyrins.” 2014. Web. 11 Apr 2021.

Vancouver:

Wang C. Biochemical and structural characterization of ankyrins. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2014. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-71766 ; https://doi.org/10.14711/thesis-b1302214 ; http://repository.ust.hk/ir/bitstream/1783.1-71766/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wang C. Biochemical and structural characterization of ankyrins. [Thesis]. Hong Kong University of Science and Technology; 2014. Available from: http://repository.ust.hk/ir/Record/1783.1-71766 ; https://doi.org/10.14711/thesis-b1302214 ; http://repository.ust.hk/ir/bitstream/1783.1-71766/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

9. Chen, Jia. PDZ domain containing proteins in cell polarity.

Degree: 2011, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7617 ; https://doi.org/10.14711/thesis-b1160526 ; http://repository.ust.hk/ir/bitstream/1783.1-7617/1/th_redirect.html

► In my thesis, I’ll use PDZ domain as an example to illustrate how could a small modular domain achieves its specific and diverse binding property… (more)

Subjects/Keywords: Carrier proteins ; Protein binding ; Protein-protein interactions

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APA (6^th Edition):

Chen, J. (2011). PDZ domain containing proteins in cell polarity. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7617 ; https://doi.org/10.14711/thesis-b1160526 ; http://repository.ust.hk/ir/bitstream/1783.1-7617/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chen, Jia. “PDZ domain containing proteins in cell polarity.” 2011. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-7617 ; https://doi.org/10.14711/thesis-b1160526 ; http://repository.ust.hk/ir/bitstream/1783.1-7617/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chen, Jia. “PDZ domain containing proteins in cell polarity.” 2011. Web. 11 Apr 2021.

Vancouver:

Chen J. PDZ domain containing proteins in cell polarity. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2011. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-7617 ; https://doi.org/10.14711/thesis-b1160526 ; http://repository.ust.hk/ir/bitstream/1783.1-7617/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chen J. PDZ domain containing proteins in cell polarity. [Thesis]. Hong Kong University of Science and Technology; 2011. Available from: http://repository.ust.hk/ir/Record/1783.1-7617 ; https://doi.org/10.14711/thesis-b1160526 ; http://repository.ust.hk/ir/bitstream/1783.1-7617/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

10. Zheng, Zhaorong. Structure determination and property characterization of MAGI-3 PDZ4 domain and BDNF prodomain.

Degree: 2012, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7855 ; https://doi.org/10.14711/thesis-b1180093 ; http://repository.ust.hk/ir/bitstream/1783.1-7855/1/th_redirect.html

► As one of the most abundant protein-protein interaction module in the eukaryotic genomes, PDZ domain participates in a variety of cellular activities including neuronal signal… (more)

Subjects/Keywords: Protein binding ; Neurotrophic functions ; Protein-protein interactions

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APA (6^th Edition):

Zheng, Z. (2012). Structure determination and property characterization of MAGI-3 PDZ4 domain and BDNF prodomain. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7855 ; https://doi.org/10.14711/thesis-b1180093 ; http://repository.ust.hk/ir/bitstream/1783.1-7855/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zheng, Zhaorong. “Structure determination and property characterization of MAGI-3 PDZ4 domain and BDNF prodomain.” 2012. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-7855 ; https://doi.org/10.14711/thesis-b1180093 ; http://repository.ust.hk/ir/bitstream/1783.1-7855/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zheng, Zhaorong. “Structure determination and property characterization of MAGI-3 PDZ4 domain and BDNF prodomain.” 2012. Web. 11 Apr 2021.

Vancouver:

Zheng Z. Structure determination and property characterization of MAGI-3 PDZ4 domain and BDNF prodomain. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2012. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-7855 ; https://doi.org/10.14711/thesis-b1180093 ; http://repository.ust.hk/ir/bitstream/1783.1-7855/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zheng Z. Structure determination and property characterization of MAGI-3 PDZ4 domain and BDNF prodomain. [Thesis]. Hong Kong University of Science and Technology; 2012. Available from: http://repository.ust.hk/ir/Record/1783.1-7855 ; https://doi.org/10.14711/thesis-b1180093 ; http://repository.ust.hk/ir/bitstream/1783.1-7855/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

11. Ye, Fei. Structures and target recognition properties of a multi-PDZ domain scaffold protein INAD.

Degree: 2013, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-80943 ; https://doi.org/10.14711/thesis-b1250978 ; http://repository.ust.hk/ir/bitstream/1783.1-80943/1/th_redirect.html

► PDZ domains are highly abundant protein-protein interaction modules and often found in multi-domain scaffold proteins. PDZ-domain-containing scaffold proteins regulate multiple biological processes, including trafficking and… (more)

▼ PDZ domains are highly abundant protein-protein interaction modules and often found in multi-domain scaffold proteins. PDZ-domain-containing scaffold proteins regulate multiple biological processes, including trafficking and clustering receptors and ion-channels at defined membrane regions, organizing and targeting signaling complexes at specific cellular compartments, interfacing cytoskeletal structures with membranes, and maintaining various cellular structures. PDZ domains, each with ~90 amino acid residues folding into a highly similar structure, are best known to bind to short carboxyl tail peptides from their target proteins. A series of recent studies have revealed that, in addition to the canonical target binding mode, many PDZ/target interactions involve amino acid residues beyond the regular PDZ domain fold, which we refer to as extensions. Such extension sequences often form an integral structural and functional unit with the attached PDZ domain, which is defined as a PDZ supramodule. Correspondingly, PDZ domain binding sequences from target proteins are frequently found to require extension sequences beyond canonical short carboxyl tail peptides. Formation of PDZ supramodules not only affords necessary binding specificities and affinities demanded by physiological functions of PDZ domain targets, but also provides regulatory switches to be built in the PDZ/target interactions. Chapter 1 provides an overview introduction of the PDZ domain of the thesis work. I mainly focus on a series of recent studies showing that, in addition to the well-documented, canonical PDZ/target interaction mode, many PDZ domains employ amino acid sequences beyond the canonical PDZ domain fold, which we refer to as “extended PDZ domains”. Such extension sequences often form an integral structural and functional unit with the regular PDZ domains, and we term the “extended PDZ domains” as PDZ supramodules. In Chapter 2, I found a totally unexpected PDZ/target binding mode observed in the interaction between Drosophila scaffold protein INAD and TRP channel. The C-terminal 15 residues of TRP are required for the potent and specific interaction with INAD PDZ3. The structure of the INAD PDZ3/TRP peptide complex reveals that only the extreme C-terminal Leu of the TRP peptide binds to the canonical carboxyl binding pocket of INAD PDZ3. The rest of the TRP peptide, via forming a β-hairpin structure, binds to a surface that is formed by βB, βC and αA, and located away from the canonical target binding groove of INAD PDZ3. As such, the INAD PDZ3/TRP channel interaction is exquisitely specific and represents a new paradigm for PDZ/target recognitions. In Chapter 3, I found the second PDZ domain of INAD, PDZ2, adopts a novel structural and functional “supramodule” for binding to eye-PKC, a key component for light adaptation and deactivation in fly visual signaling. Furthermore, an NMR-based real-time study of PDZ2 eye-PKC phosphorylation provides both kinetic and mechanistic insights into the potential regulation mechanisms of INAD…

Subjects/Keywords: Protein-protein interactions ; Protein binding ; Carrier proteins

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ye, F. (2013). Structures and target recognition properties of a multi-PDZ domain scaffold protein INAD. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-80943 ; https://doi.org/10.14711/thesis-b1250978 ; http://repository.ust.hk/ir/bitstream/1783.1-80943/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ye, Fei. “Structures and target recognition properties of a multi-PDZ domain scaffold protein INAD.” 2013. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-80943 ; https://doi.org/10.14711/thesis-b1250978 ; http://repository.ust.hk/ir/bitstream/1783.1-80943/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ye, Fei. “Structures and target recognition properties of a multi-PDZ domain scaffold protein INAD.” 2013. Web. 11 Apr 2021.

Vancouver:

Ye F. Structures and target recognition properties of a multi-PDZ domain scaffold protein INAD. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2013. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-80943 ; https://doi.org/10.14711/thesis-b1250978 ; http://repository.ust.hk/ir/bitstream/1783.1-80943/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ye F. Structures and target recognition properties of a multi-PDZ domain scaffold protein INAD. [Thesis]. Hong Kong University of Science and Technology; 2013. Available from: http://repository.ust.hk/ir/Record/1783.1-80943 ; https://doi.org/10.14711/thesis-b1250978 ; http://repository.ust.hk/ir/bitstream/1783.1-80943/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

12. Xia, Yitian. Characterization of the interaction between PSD-95 GK domain and MAP1A.

Degree: 2014, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-87481 ; https://doi.org/10.14711/thesis-b1334216 ; http://repository.ust.hk/ir/bitstream/1783.1-87481/1/th_redirect.html

► Nervous system, mainly composed of large numbers of neurons and glia cells, plays central roles in controlling various physiological functions in the metazoan. The normal… (more)

▼ Nervous system, mainly composed of large numbers of neurons and glia cells, plays central roles in controlling various physiological functions in the metazoan. The normal functions of nervous system largely depend on the proper connections between neurons through the specialized structure named synapses. A typical glutamatergic synapse contains three parts: a presynaptic region, which releases glutamate as neurotransmitters; a postsynaptic region, which contains glutamate receptors and can be activated by neurotransmitters; and a synaptic cleft between them. The postsynaptic region is a macromolecular network formed by membranes, receptors, scaffold proteins and enzymes in a highly condensed pattern, shows high electron density under electronic microscopes, and is therefore called postsynaptic density (PSD). PSD-95, a member of membrane-associated guanylate kinases (MAGUKs), mediates varieties of protein-protein interactions through its multiple domains, and plays essential roles in the proper PSD functions, dynamics and plasticity. Microtubule-associated protein 1 A (MAP1A) is a microtubule-stabilizer, and participates in activity-driven dendritic arbor remodeling. Previous studies have found that GK domain of PSD-95 can physically interact with MAP1A, but the detailed binding mechanism remains to be elucidated. Studies in this thesis mainly focused on how the MAP1A interacts with PSD-95 GK domain in an unexpected phosphorylation-independent manner. By using X-ray crystallography, the structure of MAP1A peptide and PSD-95 GK complex was solved. MAP1A peptide adopts a folded conformation to interact with GK. The conformation of MAP1A peptide is different from those of previously reported GK-binding peptides such as p-LGN and p-Lgl. The data in this thesis also shows the conformation of the MAP1A peptide might be binding-induced. Finally, these results contribute to better understanding how GK domains of MAGUKs interact with targets with diverse modes, and provide insights into how PSD-95 and MAP1A can work cooperatively in dendritic remodeling.

Subjects/Keywords: Synapses ; Tubulins ; Protein binding ; Protein-protein interactions

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APA (6^th Edition):

Xia, Y. (2014). Characterization of the interaction between PSD-95 GK domain and MAP1A. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-87481 ; https://doi.org/10.14711/thesis-b1334216 ; http://repository.ust.hk/ir/bitstream/1783.1-87481/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Xia, Yitian. “Characterization of the interaction between PSD-95 GK domain and MAP1A.” 2014. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-87481 ; https://doi.org/10.14711/thesis-b1334216 ; http://repository.ust.hk/ir/bitstream/1783.1-87481/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Xia, Yitian. “Characterization of the interaction between PSD-95 GK domain and MAP1A.” 2014. Web. 11 Apr 2021.

Vancouver:

Xia Y. Characterization of the interaction between PSD-95 GK domain and MAP1A. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2014. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-87481 ; https://doi.org/10.14711/thesis-b1334216 ; http://repository.ust.hk/ir/bitstream/1783.1-87481/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Xia Y. Characterization of the interaction between PSD-95 GK domain and MAP1A. [Thesis]. Hong Kong University of Science and Technology; 2014. Available from: http://repository.ust.hk/ir/Record/1783.1-87481 ; https://doi.org/10.14711/thesis-b1334216 ; http://repository.ust.hk/ir/bitstream/1783.1-87481/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Washington University in St. Louis

13. Borgo, Benjamin. Strategies for Computational Protein Design with Application to the Development of a Biomolecular Tool-kit for Single Molecule Protein Sequencing.

Degree: PhD, Biology and Biomedical Sciences: Computational and Systems Biology, 2014, Washington University in St. Louis

URL: https://openscholarship.wustl.edu/etd/1221

► One of the key properties of proteins is that they exhibit remarkable affinities and specificities for small-molecule and peptide binding partners. To improve the… (more)

Subjects/Keywords: Protein design; Protein engineering; Protein sequencing; Proteomics

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APA (6^th Edition):

Borgo, B. (2014). Strategies for Computational Protein Design with Application to the Development of a Biomolecular Tool-kit for Single Molecule Protein Sequencing. (Doctoral Dissertation). Washington University in St. Louis. Retrieved from https://openscholarship.wustl.edu/etd/1221

Chicago Manual of Style (16^th Edition):

Borgo, Benjamin. “Strategies for Computational Protein Design with Application to the Development of a Biomolecular Tool-kit for Single Molecule Protein Sequencing.” 2014. Doctoral Dissertation, Washington University in St. Louis. Accessed April 11, 2021. https://openscholarship.wustl.edu/etd/1221.

MLA Handbook (7^th Edition):

Borgo, Benjamin. “Strategies for Computational Protein Design with Application to the Development of a Biomolecular Tool-kit for Single Molecule Protein Sequencing.” 2014. Web. 11 Apr 2021.

Vancouver:

Borgo B. Strategies for Computational Protein Design with Application to the Development of a Biomolecular Tool-kit for Single Molecule Protein Sequencing. [Internet] [Doctoral dissertation]. Washington University in St. Louis; 2014. [cited 2021 Apr 11]. Available from: https://openscholarship.wustl.edu/etd/1221.

Council of Science Editors:

Borgo B. Strategies for Computational Protein Design with Application to the Development of a Biomolecular Tool-kit for Single Molecule Protein Sequencing. [Doctoral Dissertation]. Washington University in St. Louis; 2014. Available from: https://openscholarship.wustl.edu/etd/1221

Hong Kong University of Science and Technology

14. Yang, Zhou LIFS. Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.

Degree: 2019, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-101511 ; https://doi.org/10.14711/thesis-991012753260503412 ; http://repository.ust.hk/ir/bitstream/1783.1-101511/1/th_redirect.html

► WW domain tandem-containing proteins such as KIBRA, YAP, and MAGI play critical roles in cell growth and cell polarity via binding to and positioning target… (more)

Subjects/Keywords: Protein-protein interactions ; Protein binding ; Cells ; Growth

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APA (6^th Edition):

Yang, Z. L. (2019). Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-101511 ; https://doi.org/10.14711/thesis-991012753260503412 ; http://repository.ust.hk/ir/bitstream/1783.1-101511/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yang, Zhou LIFS. “Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.” 2019. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-101511 ; https://doi.org/10.14711/thesis-991012753260503412 ; http://repository.ust.hk/ir/bitstream/1783.1-101511/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yang, Zhou LIFS. “Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.” 2019. Web. 11 Apr 2021.

Vancouver:

Yang ZL. Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2019. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-101511 ; https://doi.org/10.14711/thesis-991012753260503412 ; http://repository.ust.hk/ir/bitstream/1783.1-101511/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yang ZL. Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity. [Thesis]. Hong Kong University of Science and Technology; 2019. Available from: http://repository.ust.hk/ir/Record/1783.1-101511 ; https://doi.org/10.14711/thesis-991012753260503412 ; http://repository.ust.hk/ir/bitstream/1783.1-101511/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

15. Fung, Sanderz. Discovering Protein Functional Regions and Protein-Protein Interaction using Co-occurring Aligned Pattern Clusters.

Degree: 2015, University of Waterloo

URL: http://hdl.handle.net/10012/9854

► Bioinformatics is a rapidly expanding field of research due to multiple recent advancements: 1) the advent of machine intelligence, 2) the increase of computing power,… (more)

▼ Bioinformatics is a rapidly expanding field of research due to multiple recent advancements: 1) the advent of machine intelligence, 2) the increase of computing power, 3) our better understanding of the underlying biomolecular mechanisms, and 4) the drastic reduction of biosequencing cost and time. Since wet laboratory approaches to analysing the protein sequencing is still labour intensive and time consuming, more cost-effective computational approaches for analyzing protein sequences and their biochemical interactions are crucial. This is especially true when we encounter a large collection of protein sequences. Aligned Pattern CLustering (APCL), an algorithm which combines machine intelligence methodologies such as pattern recognition, pattern discovery, pattern clustering and alignment, formulated by my research group and myself, is one such technique. APCL discovers, prunes, and clusters aligned statistically significant patterns to assemble a related, or specifically, a homologous group of patterns in the form of an Aligned Pattern Cluster (APC). The APC obtained is found to correspond to statistically and functionally significant association patterns, which corresponds as conserved regions, such as binding segments within and between protein sequences as well as between Protein Transcription Factor (TF) and DNA Transcription Factor Binding Sites (TFBS) in many of our empirical experiments. While several known algorithms also exist to find functionally conserved segments in biosequences, they are less flexible and require more parameters than what APCL requires. Hence, APCL is a powerful tool to analyze biosequences. Because of its effectiveness, the usefulness of APCL is further expanded from the assist of discovering and analyzing functional regions of protein sequences to the exploration of co-occurrence of patterns on the same sequences or on interacting patterns between sequences from the discovered APCs. Two new algorithms are introduced and reported in this thesis in the exploration of 1) APCs containing patterns residing within the same biosequences and 2) APCs containing patterns residing between interacting biosequences. The first algorithm attempts to cluster APCs from APCs that share patterns on the same biosequences. It uses a co-occurrence score between APCs in a co-occurrence APC pair (two APCs containing co-occurrence patterns) to account for the proportion of biosequences of co-occurrence patterns they share against the total number of sequences containing them. Using this score as a similarity measure (or more precisely, as a co-occurring measure), we devise a Co-occurrence APC Clustering Algorithm to cluster APCs obtained from a collection of related biosequences into a Co-Occurrence Cluster of APCs abbreviated by cAPC. It is then analyzed and verified to see whether or not there are essential biological functions associating with the APCs within that cluster. Cytochrome c and ubiquitin families were analyzed in depth, and it was validated that members in the same cAPC do cover…

Subjects/Keywords: Bioinformatics; Protein-Protein Interaction; Protein; Data Mining

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APA (6^th Edition):

Fung, S. (2015). Discovering Protein Functional Regions and Protein-Protein Interaction using Co-occurring Aligned Pattern Clusters. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/9854

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fung, Sanderz. “Discovering Protein Functional Regions and Protein-Protein Interaction using Co-occurring Aligned Pattern Clusters.” 2015. Thesis, University of Waterloo. Accessed April 11, 2021. http://hdl.handle.net/10012/9854.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fung, Sanderz. “Discovering Protein Functional Regions and Protein-Protein Interaction using Co-occurring Aligned Pattern Clusters.” 2015. Web. 11 Apr 2021.

Vancouver:

Fung S. Discovering Protein Functional Regions and Protein-Protein Interaction using Co-occurring Aligned Pattern Clusters. [Internet] [Thesis]. University of Waterloo; 2015. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/10012/9854.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fung S. Discovering Protein Functional Regions and Protein-Protein Interaction using Co-occurring Aligned Pattern Clusters. [Thesis]. University of Waterloo; 2015. Available from: http://hdl.handle.net/10012/9854

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Alberta

16. Alford, Spencer Caleb. Development of fluorogenic fluorescent protein heterodimers.

Degree: PhD, Department of Chemistry, 2012, University of Alberta

URL: https://era.library.ualberta.ca/files/hh63sw19n

► Fluorescent proteins (FPs) are indispensible biochemical tools. The concerted efforts of protein engineers have produced FPs spanning the visible colour spectrum. This wide variety of… (more)

▼ Fluorescent proteins (FPs) are indispensible biochemical tools. The concerted efforts of protein engineers have produced FPs spanning the visible colour spectrum. This wide variety of FPs has greatly facilitated the development of FP-based biosensors. However, researchers rely on relatively few fundamental biosensor design templates. Förster resonance energy transfer and bimolecular complementation are the principal FP-based technologies for live cell imaging of physiological events, such as changes in small molecule concentration, enzymatic activities, and protein-protein interactions. Although widely used, these techniques are often restrictive due to poor signal-to-noise ratios and irreversible sensing, respectively. Furthermore, examples of these biosensor strategies incorporating red FPs are limited. In this thesis we describe our efforts to address this shortcoming in the area of FP-based biosensors. We developed a dimerization-dependent red FP (ddRFP) that serves as an alternative template for biosensor construction. The prototype ddRFP was engineered from a homodimeric variant of a Discosoma red FP. Through extensive directed evolution the homodimer was converted into a fluorogenic obligate heterodimer. The reversible changes in fluorescence intensity that result from association of the ddRFP monomeric constituents, or the irreversible decrease that accompanies dissociation of covalently linked partners following linker cleavage, provides a useful spectroscopic signal for biosensing applications. Specifically, we demonstrated that ddRFP is useful for detecting in vitro protein-protein interactions, as well as imaging changes in calcium ion concentration and activation of caspase-3 in live cells. We also report the expansion of the ddFP colour palette through the development of green (ddGFP) and yellow (ddYFP) ddFP variants. These variants have several improvements relative to the ddRFP prototype including increased in vitro contrast and brightness for ddGFP, and a reduced pKa for ddYFP. While their utility for some live cell imaging applications is restricted due to low dissociation constants, ddGFP proved to be a useful fluorescent label of intermembrane contact sites between the endoplasmic reticulum and the mitochondrial network.

Subjects/Keywords: protein engineering; fluorescent protein; biosensor

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APA (6^th Edition):

Alford, S. C. (2012). Development of fluorogenic fluorescent protein heterodimers. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/hh63sw19n

Chicago Manual of Style (16^th Edition):

Alford, Spencer Caleb. “Development of fluorogenic fluorescent protein heterodimers.” 2012. Doctoral Dissertation, University of Alberta. Accessed April 11, 2021. https://era.library.ualberta.ca/files/hh63sw19n.

MLA Handbook (7^th Edition):

Alford, Spencer Caleb. “Development of fluorogenic fluorescent protein heterodimers.” 2012. Web. 11 Apr 2021.

Vancouver:

Alford SC. Development of fluorogenic fluorescent protein heterodimers. [Internet] [Doctoral dissertation]. University of Alberta; 2012. [cited 2021 Apr 11]. Available from: https://era.library.ualberta.ca/files/hh63sw19n.

Council of Science Editors:

Alford SC. Development of fluorogenic fluorescent protein heterodimers. [Doctoral Dissertation]. University of Alberta; 2012. Available from: https://era.library.ualberta.ca/files/hh63sw19n

University of Illinois – Urbana-Champaign

17. Chan, Tracy Ying. Engineering the interface of cytochrome b5 and myoglobin for in vitro and in vivo applications.

Degree: MS, Chemistry, 2018, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/101364

► Heme-copper oxidases (HCOs) are large membrane proteins found in both bacteria and in eukaryotes. They catalyze about 90% of oxygen reduction in the atmosphere. They… (more)

Subjects/Keywords: metalloproteins; protein-protein interfaces

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APA (6^th Edition):

Chan, T. Y. (2018). Engineering the interface of cytochrome b5 and myoglobin for in vitro and in vivo applications. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/101364

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chan, Tracy Ying. “Engineering the interface of cytochrome b5 and myoglobin for in vitro and in vivo applications.” 2018. Thesis, University of Illinois – Urbana-Champaign. Accessed April 11, 2021. http://hdl.handle.net/2142/101364.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chan, Tracy Ying. “Engineering the interface of cytochrome b5 and myoglobin for in vitro and in vivo applications.” 2018. Web. 11 Apr 2021.

Vancouver:

Chan TY. Engineering the interface of cytochrome b5 and myoglobin for in vitro and in vivo applications. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2018. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/2142/101364.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chan TY. Engineering the interface of cytochrome b5 and myoglobin for in vitro and in vivo applications. [Thesis]. University of Illinois – Urbana-Champaign; 2018. Available from: http://hdl.handle.net/2142/101364

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

18. Muley, Vijaykumar Yogesh. Improved computational prediction and analysis of protein - protein interaction networks.

Degree: 2012, Manipal University

URL: http://shodhganga.inflibnet.ac.in/handle/10603/5399

►

Recent progress in computational methods for predicting physical and functional protein-protein interactions has provided new insights into the complexity of biological processes. Most of these… (more)

▼

Recent progress in computational methods for predicting physical and functional protein-protein interactions has provided new insights into the complexity of biological processes. Most of these methods assume that functionally interacting proteins are likely to have a shared evolutionary history. These methods include phylogenetic profiling (PP),gene neighborhood (GN), gene cluster (GC), and the mirrortree. Expression similarity in various physiological conditions also has been used an indicator of functional linkages between genes. Comprehensive newlinecomparison of these methods has not been frequently reported in literature. In this work, I have shown that the higher performance for predicting protein-protein interactions was achievable even with 100?150 bacterial genomes out of 565 genomes. I find that variants of PP and GN are robust against reference genome selection. This study also reveals that the prediction of metabolic pathway protein interactions continues to be a challenging task for all methods which possibly reflect flexible/independent evolutionary histories of these proteins. On the contrary, genetic information processing pathways are predicted with comparable accuracy. I have also shown that the effective use of a particular prediction method depends on the pathway under investigation. The topological properties of network predicted by each method differ significantly. This study suggests that organization of proteins in the predicted networks ensure the local perturbations in the metabolic pathways and protein complexes should communicate with quickly to other cellular proteins. A set of seven machine learning classifiers also used to predict genome-scale interactome. It is observed that probabilistic classifiers such as naïve bayes are best suitable for PPI prediction task. Finally, I have predicted functions for number of uncharacterized proteins and some of them tested experimentally. A high quality PPIs can be accessible through user friendly interface at http://www.cdfd.org.in/ecofunppi

References p. 138-150, Appendix p. 151-157

Advisors/Committee Members: Ranjan, Akash.

Subjects/Keywords: Protein interaction networks; Protein

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APA (6^th Edition):

Muley, V. Y. (2012). Improved computational prediction and analysis of protein - protein interaction networks. (Thesis). Manipal University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/5399

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Muley, Vijaykumar Yogesh. “Improved computational prediction and analysis of protein - protein interaction networks.” 2012. Thesis, Manipal University. Accessed April 11, 2021. http://shodhganga.inflibnet.ac.in/handle/10603/5399.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Muley, Vijaykumar Yogesh. “Improved computational prediction and analysis of protein - protein interaction networks.” 2012. Web. 11 Apr 2021.

Vancouver:

Muley VY. Improved computational prediction and analysis of protein - protein interaction networks. [Internet] [Thesis]. Manipal University; 2012. [cited 2021 Apr 11]. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/5399.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Muley VY. Improved computational prediction and analysis of protein - protein interaction networks. [Thesis]. Manipal University; 2012. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/5399

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Ottawa

19. Eason, Matthew. A GFP-Based Sensor to Detect Transiently Expressed Proteins .

Degree: 2020, University of Ottawa

URL: http://hdl.handle.net/10393/40500

► Green fluorescent protein (GFP) fusion tags are commonly used to study protein expression and cellular localization in vivo. But, GFP must undergo an autogenic post-translational… (more)

Subjects/Keywords: Biosensor; Fluorescent Protein; Protein Engineering

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APA (6^th Edition):

Eason, M. (2020). A GFP-Based Sensor to Detect Transiently Expressed Proteins . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/40500

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Eason, Matthew. “A GFP-Based Sensor to Detect Transiently Expressed Proteins .” 2020. Thesis, University of Ottawa. Accessed April 11, 2021. http://hdl.handle.net/10393/40500.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Eason, Matthew. “A GFP-Based Sensor to Detect Transiently Expressed Proteins .” 2020. Web. 11 Apr 2021.

Vancouver:

Eason M. A GFP-Based Sensor to Detect Transiently Expressed Proteins . [Internet] [Thesis]. University of Ottawa; 2020. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/10393/40500.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Eason M. A GFP-Based Sensor to Detect Transiently Expressed Proteins . [Thesis]. University of Ottawa; 2020. Available from: http://hdl.handle.net/10393/40500

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Ottawa

20. Simmons, Kateland. Development of a Synthetic Biology Tool to Quantify the Contribution of Protein Components and Protein Interactions Within Transcriptional Regulatory Complexes .

Degree: 2019, University of Ottawa

URL: http://hdl.handle.net/10393/39005

► We have formed the basis for a synthetic gene regulatory network in S. cerevisiae to assess the relative contribution of proteins and protein interactions to… (more)

Subjects/Keywords: Protein components; Protein interactions

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APA (6^th Edition):

Simmons, K. (2019). Development of a Synthetic Biology Tool to Quantify the Contribution of Protein Components and Protein Interactions Within Transcriptional Regulatory Complexes . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/39005

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Simmons, Kateland. “Development of a Synthetic Biology Tool to Quantify the Contribution of Protein Components and Protein Interactions Within Transcriptional Regulatory Complexes .” 2019. Thesis, University of Ottawa. Accessed April 11, 2021. http://hdl.handle.net/10393/39005.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Simmons, Kateland. “Development of a Synthetic Biology Tool to Quantify the Contribution of Protein Components and Protein Interactions Within Transcriptional Regulatory Complexes .” 2019. Web. 11 Apr 2021.

Vancouver:

Simmons K. Development of a Synthetic Biology Tool to Quantify the Contribution of Protein Components and Protein Interactions Within Transcriptional Regulatory Complexes . [Internet] [Thesis]. University of Ottawa; 2019. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/10393/39005.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Simmons K. Development of a Synthetic Biology Tool to Quantify the Contribution of Protein Components and Protein Interactions Within Transcriptional Regulatory Complexes . [Thesis]. University of Ottawa; 2019. Available from: http://hdl.handle.net/10393/39005

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

21. Choi, Yuk Kwan. Regulation of the microtubule-nucleating activity of the β-tubulin ring complex.

Degree: 2011, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7276 ; https://doi.org/10.14711/thesis-b1136631 ; http://repository.ust.hk/ir/bitstream/1783.1-7276/1/th_redirect.html

► Polymerization dynamics enable microtubules to carry out spatial arrangements in response to cellular necessities. Like many other protein polymerization processes, the nucleation steps of microtubule… (more)

▼ Polymerization dynamics enable microtubules to carry out spatial arrangements in response to cellular necessities. Like many other protein polymerization processes, the nucleation steps of microtubule polymerization reactions are slower than the later elongation processes. This allows biological systems to spatially control the reactions. γ-Tubulin complex (γ-TuC) plays a critical role in microtubule nucleation occurring at least at centrosomes, chromatins, and spindle microtubules. However, the control mechanism of γ-TuC-mediated microtubule nucleation remains elusive. CDK5RAP2 is a human microcephaly protein that binds to the γ-TuC and is involved in the centrosomal attachment of γ-tubulin. The γ-TuC-binding domain found in CDK5RAP2 is conserved in Drosophila centrosomin, and Schizosaccharomyces pombe Mto1p and Pcp1p, which are γ-TuC-tethering proteins in the respective organisms. In the first project, I show that this domain within CDK5RAP2 associates with the γ-tubulin ring complex (γ-TuRC) to stimulate its microtubule-nucleating activity and is therefore referred to as the γ-TuRC-mediated nucleation activator (γ-TuNA). The γ-TuNA but not its γ-TuRC-binding deficient mutant stimulates microtubule nucleation by purified γ-TuRC in vitro and induces extensive, γ-TuRC-dependent nucleation of microtubules in a microtubule regrowth assay. γ-TuRC bound to the γ-TuNA contains NME7, FAM128A/B, and actin in addition to γ-tubulin and GCP2-6. RNAi-mediated depletion of CDK5RAP2 impairs both centrosomal and acentrosomal microtubule nucleation, although γ-TuRC assembly is unaffected. Collectively, these results suggest that the γ-TuNA found in CDK5RAP2 has regulatory functions in γ-TuRC-mediated microtubule nucleation. I also investigated the novel γ-TuRC-associated protein NME7 and have found that NME7 is a regulatory component of γ-TuRC and plays an important role in γ-TuRC-mediated microtubule nucleation and ciliogenesis. Immunofluorescence studies show that NME7 localizes to centrosomes throughout all stages of cell cycle, in addition to the basal body and axoneme of the early formed cilium. Furthermore, the NME7 centrosomal localization depends on its incorporation into the γ-TuRC. Although NME7 is not required for γ-TuRC assembly or the assembly of the γ-TuRC into centrosomes, RNAi-mediated depletion of NME7 perturbed the centrosomal microtubule nucleation and ciliogenesis. γ-Tubulin is a GDP/GTP binding protein, however, whether GDP/GTP regulates γ-TuRC-mediated microtubule nucleation remains unknown. In the in vitro assays, the microtubule nucleating-activity of γ-TuRC isolated by γ-TuNA was severely compromised by GDP. In the same settings, NME7 stimulated the microtubule nucleating-activity of GDP-preloaded γ-TuRC and promoted GTP binding to γ-tubulin in γ-TuRC regardless of its autophosphorylating activity. Taken together, these results authenticate that NME7 stimulates the γ-TuRC-mediated microtubule nucleation by facilitating the GTP-bound form of γ-TuRC. In summary, γ-TuRC-mediated microtubule nucleation is…

Subjects/Keywords: Tubulins ; Microtubules ; Protein-protein interactions

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APA (6^th Edition):

Choi, Y. K. (2011). Regulation of the microtubule-nucleating activity of the β-tubulin ring complex. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7276 ; https://doi.org/10.14711/thesis-b1136631 ; http://repository.ust.hk/ir/bitstream/1783.1-7276/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Choi, Yuk Kwan. “Regulation of the microtubule-nucleating activity of the β-tubulin ring complex.” 2011. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-7276 ; https://doi.org/10.14711/thesis-b1136631 ; http://repository.ust.hk/ir/bitstream/1783.1-7276/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Choi, Yuk Kwan. “Regulation of the microtubule-nucleating activity of the β-tubulin ring complex.” 2011. Web. 11 Apr 2021.

Vancouver:

Choi YK. Regulation of the microtubule-nucleating activity of the β-tubulin ring complex. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2011. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-7276 ; https://doi.org/10.14711/thesis-b1136631 ; http://repository.ust.hk/ir/bitstream/1783.1-7276/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Choi YK. Regulation of the microtubule-nucleating activity of the β-tubulin ring complex. [Thesis]. Hong Kong University of Science and Technology; 2011. Available from: http://repository.ust.hk/ir/Record/1783.1-7276 ; https://doi.org/10.14711/thesis-b1136631 ; http://repository.ust.hk/ir/bitstream/1783.1-7276/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

22. Shen, Yuehong. Identification and characterization of various populations of the [gamma]-tubulin ring complex.

Degree: 2012, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7577 ; https://doi.org/10.14711/thesis-b1180086 ; http://repository.ust.hk/ir/bitstream/1783.1-7577/1/th_redirect.html

► The microtubule (MT) network is a major component of the cellular cytoskeleton. Its importance towards cellular function is reflected in its roles in cell proliferation,… (more)

Subjects/Keywords: Tubulins ; Microtubules ; Protein-protein interactions

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APA (6^th Edition):

Shen, Y. (2012). Identification and characterization of various populations of the [gamma]-tubulin ring complex. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7577 ; https://doi.org/10.14711/thesis-b1180086 ; http://repository.ust.hk/ir/bitstream/1783.1-7577/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Shen, Yuehong. “Identification and characterization of various populations of the [gamma]-tubulin ring complex.” 2012. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-7577 ; https://doi.org/10.14711/thesis-b1180086 ; http://repository.ust.hk/ir/bitstream/1783.1-7577/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Shen, Yuehong. “Identification and characterization of various populations of the [gamma]-tubulin ring complex.” 2012. Web. 11 Apr 2021.

Vancouver:

Shen Y. Identification and characterization of various populations of the [gamma]-tubulin ring complex. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2012. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-7577 ; https://doi.org/10.14711/thesis-b1180086 ; http://repository.ust.hk/ir/bitstream/1783.1-7577/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Shen Y. Identification and characterization of various populations of the [gamma]-tubulin ring complex. [Thesis]. Hong Kong University of Science and Technology; 2012. Available from: http://repository.ust.hk/ir/Record/1783.1-7577 ; https://doi.org/10.14711/thesis-b1180086 ; http://repository.ust.hk/ir/bitstream/1783.1-7577/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

23. Hu, Yu. Proteomic profiling and characterization of the γ-tubulin ring complex.

Degree: 2014, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-87483 ; https://doi.org/10.14711/thesis-b1334208 ; http://repository.ust.hk/ir/bitstream/1783.1-87483/1/th_redirect.html

► Microtubules are one of the three major cytoskeletal structures in eukaryotic cells. γ-Tubulin ring complexes (γ-TuRCs) play key roles in microtubule organization by mediating microtubule… (more)

Subjects/Keywords: Tubulins ; Microtubules ; Protein-protein interactions

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hu, Y. (2014). Proteomic profiling and characterization of the γ-tubulin ring complex. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-87483 ; https://doi.org/10.14711/thesis-b1334208 ; http://repository.ust.hk/ir/bitstream/1783.1-87483/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hu, Yu. “Proteomic profiling and characterization of the γ-tubulin ring complex.” 2014. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-87483 ; https://doi.org/10.14711/thesis-b1334208 ; http://repository.ust.hk/ir/bitstream/1783.1-87483/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hu, Yu. “Proteomic profiling and characterization of the γ-tubulin ring complex.” 2014. Web. 11 Apr 2021.

Vancouver:

Hu Y. Proteomic profiling and characterization of the γ-tubulin ring complex. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2014. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-87483 ; https://doi.org/10.14711/thesis-b1334208 ; http://repository.ust.hk/ir/bitstream/1783.1-87483/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hu Y. Proteomic profiling and characterization of the γ-tubulin ring complex. [Thesis]. Hong Kong University of Science and Technology; 2014. Available from: http://repository.ust.hk/ir/Record/1783.1-87483 ; https://doi.org/10.14711/thesis-b1334208 ; http://repository.ust.hk/ir/bitstream/1783.1-87483/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

24. Wu, Min. A preliminary characterization of neuroligin interacting proteins.

Degree: 2014, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-87515 ; https://doi.org/10.14711/thesis-b1333501 ; http://repository.ust.hk/ir/bitstream/1783.1-87515/1/th_redirect.html

► Neuroligins are cell adhesion molecules on the postsynaptic membrane that associate with their presynaptic partners, neurexins. The trans-synaptic neuroligin-neurexin interaction has been extensively investigated in… (more)

Subjects/Keywords: Membrane proteins ; Protein-protein interactions

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APA (6^th Edition):

Wu, M. (2014). A preliminary characterization of neuroligin interacting proteins. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-87515 ; https://doi.org/10.14711/thesis-b1333501 ; http://repository.ust.hk/ir/bitstream/1783.1-87515/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wu, Min. “A preliminary characterization of neuroligin interacting proteins.” 2014. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-87515 ; https://doi.org/10.14711/thesis-b1333501 ; http://repository.ust.hk/ir/bitstream/1783.1-87515/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wu, Min. “A preliminary characterization of neuroligin interacting proteins.” 2014. Web. 11 Apr 2021.

Vancouver:

Wu M. A preliminary characterization of neuroligin interacting proteins. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2014. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-87515 ; https://doi.org/10.14711/thesis-b1333501 ; http://repository.ust.hk/ir/bitstream/1783.1-87515/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wu M. A preliminary characterization of neuroligin interacting proteins. [Thesis]. Hong Kong University of Science and Technology; 2014. Available from: http://repository.ust.hk/ir/Record/1783.1-87515 ; https://doi.org/10.14711/thesis-b1333501 ; http://repository.ust.hk/ir/bitstream/1783.1-87515/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

25. Leung, Sing. Identification of novel interacting partners of regulator of G-protein signaling 19.

Degree: 2014, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-76055 ; https://doi.org/10.14711/thesis-b1432359 ; http://repository.ust.hk/ir/bitstream/1783.1-76055/1/th_redirect.html

► Regulator of G protein signaling 19 (RGS19), previously known as Gα-interacting protein (GAIP), belongs to the RZ/A subfamily of regulators of G protein signaling. RGS19… (more)

▼ Regulator of G protein signaling 19 (RGS19), previously known as Gα-interacting protein (GAIP), belongs to the RZ/A subfamily of regulators of G protein signaling. RGS19 was first isolated from a yeast two-hybrid screening of Gα_i3-interacting proteins. Follow-up functional studies of RGS19 have subsequently revealed that RGS19 serves as a GTPase-activating protein (GAP) for many Gα_i family members, especially Gα_i3, by which it enhances the intrinsic GTPase activity of the Gα subunit. RGS19 has also been demonstrated to associate with other signaling molecules such as GIPN (GAIP-interacting protein N-terminus) and GIPC (GAIP-interacting protein C-terminus). Identification of these interactions diversifies the potential functions of RGS19 in regulating different cellular processes such as autophagy and growth factor signalings. Recent studies have demonstrated that RGS19 inhibits tumor growth of transformed NIH3T3 cells whereas it promotes cell proliferation in HEK293 cells. Yet, the known RGS19-interacting proteins cannot fully account for its functional roles in these cellular events. Hence, a yeast-two-hybrid screen was embarked in an attempt to isolate additional molecules that directly interact with RGS19. Two rounds of yeast two-hybrid (Y2H) screening were performed by using the full-length RGS19 bait protein against a human liver cDNA library. The first and the second Y2H screens yielded 162 and 411 HIS3⁺ADE2⁺lacZ⁺ clones, respectively. cDNA constructs isolated from these positive clones were categorized and analyzed by a combination of multiple techniques and analysis including restriction digestion (HindIII and HaeIII) and direct DNA sequencing. Thus duplicated clones were eliminated and the remaining clones were segregated into different groups prior to downstream verification steps such as yeast retransformation assay as well as colony lift β-galactosidase assay. By the above categorizations and verifications, 19 unique clones appear to be potential binding partners of RGS19 among the total of 573 clones. The identification of these novel RGS19-binding partners suggests that RGS19 may play a regulatory role in proteosomal degradation, autophagy, growth factor signaling, cellular metabolism and immune response. My present study also validated one of the positive clones, AKAP-Lbc. Co-immunoprecipitation studies between RGS19 and AKAP-Lbc further confirmed their interaction upon overexpressing the two tagged proteins in HEK293 cells. It is envisioned that future validation of the identified proteins as true RGS19-interacting partners will shed light on a better understanding on the non-canonical functions of RGS19 beyond its well-defined GAP activity.

Subjects/Keywords: G proteins ; Protein-protein interactions

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APA (6^th Edition):

Leung, S. (2014). Identification of novel interacting partners of regulator of G-protein signaling 19. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-76055 ; https://doi.org/10.14711/thesis-b1432359 ; http://repository.ust.hk/ir/bitstream/1783.1-76055/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Leung, Sing. “Identification of novel interacting partners of regulator of G-protein signaling 19.” 2014. Thesis, Hong Kong University of Science and Technology. Accessed April 11, 2021. http://repository.ust.hk/ir/Record/1783.1-76055 ; https://doi.org/10.14711/thesis-b1432359 ; http://repository.ust.hk/ir/bitstream/1783.1-76055/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Leung, Sing. “Identification of novel interacting partners of regulator of G-protein signaling 19.” 2014. Web. 11 Apr 2021.

Vancouver:

Leung S. Identification of novel interacting partners of regulator of G-protein signaling 19. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2014. [cited 2021 Apr 11]. Available from: http://repository.ust.hk/ir/Record/1783.1-76055 ; https://doi.org/10.14711/thesis-b1432359 ; http://repository.ust.hk/ir/bitstream/1783.1-76055/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Leung S. Identification of novel interacting partners of regulator of G-protein signaling 19. [Thesis]. Hong Kong University of Science and Technology; 2014. Available from: http://repository.ust.hk/ir/Record/1783.1-76055 ; https://doi.org/10.14711/thesis-b1432359 ; http://repository.ust.hk/ir/bitstream/1783.1-76055/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Queens University

26. Wathen, Brent. Sequence and Structure Based Protein Folding Studies With Implications .

Degree: Biochemistry, 2011, Queens University

URL: http://hdl.handle.net/1974/6802

► As the expression of the genetic blueprint, proteins are at the heart of all biological systems. The ever increasing set of available protein structures has… (more)

▼ As the expression of the genetic blueprint, proteins are at the heart of all biological systems. The ever increasing set of available protein structures has taught us that diversity is the hallmark of their architecture, a fundamental characteristic that enables them to perform the vast array of functionality upon which all of life depends. This diversity, however, is central to one of the most challenging problems in molecular biology: how does a folding polypeptide chain navigate its way through all of the myriad of possible conformations to find its own particular biologically active form? With few overarching structural principles to draw upon that can be applied to all protein architecture, the search for a solution to the protein folding problem has yet to produce an algorithm that can explain and duplicate this fundamental biological process. In this thesis, we take a two-pronged approach for investigating the protein folding process. Our initial statistical studies of the distributions of hydrophobic and hydrophilic residues within α-helices and β-sheets suggest (i) that hydrophobicity plays a critical role in helix and sheet formation; and (ii) that the nucleation of these motifs may result in largely unidirectional growth. Most tellingly, from an examination of the amino acids found in the smallest β-sheets, we do not find any evidence of a β-nucleating code in the primary protein sequence. Complementing these statistical analyses, we have analyzed the structural environments of several ever-widening aspects of protein topology. Our examination of the gaps between strands in the smallest β-sheets reveals a common organizational principle underlying β-formation involving strands separated by large sequential gaps: with very few exceptions, these large gaps fold into single, compact structural modules, bringing the β-strands that are otherwise far apart in the sequence close together in space. We conclude, therefore, that β-nucleation in the smallest sheets results from the co-location of two strands that are either local in sequence, or local in space following prior folding events. A second study of larger β-sheets both corroborates and extends these findings: virtually all large sequential gaps between pairs of β-strands organize themselves into an hierarchical arrangement, creating a bread-crumb model of go-and-come-back structural organization that ultimately juxtaposes two strands of a parental β-structure that are far apart in the sequence in close spatial proximity. In a final study, we have formalized this go-and-come-back notion into the concept of anti-parallel double-strandedness (DS), and measure this property across protein architecture in general. With over 90% of all residues in a large, non-redundant set of protein structures classified as DS, we conclude that DS is a unifying structural principle that underpins all globular proteins. We postulate, moreover, that this one simple principle, anti-parallel double-strandedness, unites protein structure, protein folding and protein…

Subjects/Keywords: Protein Structure ; Protein Folding

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APA (6^th Edition):

Wathen, B. (2011). Sequence and Structure Based Protein Folding Studies With Implications . (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/6802

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wathen, Brent. “Sequence and Structure Based Protein Folding Studies With Implications .” 2011. Thesis, Queens University. Accessed April 11, 2021. http://hdl.handle.net/1974/6802.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wathen, Brent. “Sequence and Structure Based Protein Folding Studies With Implications .” 2011. Web. 11 Apr 2021.

Vancouver:

Wathen B. Sequence and Structure Based Protein Folding Studies With Implications . [Internet] [Thesis]. Queens University; 2011. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/1974/6802.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wathen B. Sequence and Structure Based Protein Folding Studies With Implications . [Thesis]. Queens University; 2011. Available from: http://hdl.handle.net/1974/6802

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Massey University

27. Ramesh, Rashmi. Unraveling the dynamics of protein-protein interactions in the Gcn2 signal transduction pathway : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics, Massey University, Albany, New Zealand .

Degree: 2016, Massey University

URL: http://hdl.handle.net/10179/10003

► Eukaryotic cells regulate protein synthesis (translation) for a rapid response to various types of stress, and this involves several protein-protein interactions (PPIs) and protein phosphorylation.… (more)

▼ Eukaryotic cells regulate protein synthesis (translation) for a rapid response to various types of stress, and this involves several protein-protein interactions (PPIs) and protein phosphorylation. Phosphorylation of eukaryotic initiation factor-2 α (eIF2α) is a common regulatory mechanism to adjust protein synthesis in response to various stimuli. Gcn2 (General Control Non-derepressible) is an eIF2α kinase that is conserved from yeast to mammals, that is activated in response to amino acid starvation. Gcn2 activation leads to a reduction in global protein synthesis and simultaneous augmented translation of GCN4, a transcriptional activator of genes that are necessary to overcome stress. This cascade of events that allows cells in stress adaptation constitutes the General Amino Acid control (GAAC) pathway in yeast. Gcn2 activity is controlled by a large array of proteins that directly or indirectly regulate Gcn2. Gcn2 has to bind another protein called Gcn1, in order to be activated in response to amino acid starvation. Yih1 (Yeast IMPACT homolog 1) in yeast and its counterpart IMPACT (IMPrinted and AnCienT) in mammals are homologous proteins that indirectly regulate Gcn2. Yih1/IMPACT inhibit Gcn2 by competing for Gcn1 binding. Yih1 associates with Actin, and studies so far have suggested that Yih1 only inhibits Gcn2 when it dissociates from Actin. The focus of this thesis work was to shed more light on those interactions relevant for Gcn2 regulation. Firstly, we have identified that the Yih1 mediated interactions occur at distinct cellular locations within the cell, supporting the idea that spatially restricted cellular interactions controlled Gcn2 function. Using in vitro studies we have identified the regions on eEF1A that are involved in Gcn2 and Yih1 binding. The distinct binding sites for both proteins on eEF1A led to further investigations on how the dynamics of these interactions involving eEF1A might affect Gcn2 function. Together with unpublished observations by E Sattlegger and B Castilho, a function for the Yih1 ancient domain in interacting with eEF1A has been identified. Finally, the mechanisms by which Actin might control Gcn2 function were studied. In this regard, we have identified the Yih1-Actin interaction as one of the key PPIs involved in the crosstalk between the cytoskeleton and Gcn2 regulation. Together, the findings presented in this thesis, support the hypothesis that Gcn2 activity is spatiotemporally controlled by dynamic PPIs that occur at specific time at particular locations.

Subjects/Keywords: Protein interactions; Protein synthesis; Actin

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APA (6^th Edition):

Ramesh, R. (2016). Unraveling the dynamics of protein-protein interactions in the Gcn2 signal transduction pathway : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics, Massey University, Albany, New Zealand . (Thesis). Massey University. Retrieved from http://hdl.handle.net/10179/10003

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ramesh, Rashmi. “Unraveling the dynamics of protein-protein interactions in the Gcn2 signal transduction pathway : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics, Massey University, Albany, New Zealand .” 2016. Thesis, Massey University. Accessed April 11, 2021. http://hdl.handle.net/10179/10003.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ramesh, Rashmi. “Unraveling the dynamics of protein-protein interactions in the Gcn2 signal transduction pathway : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics, Massey University, Albany, New Zealand .” 2016. Web. 11 Apr 2021.

Vancouver:

Ramesh R. Unraveling the dynamics of protein-protein interactions in the Gcn2 signal transduction pathway : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics, Massey University, Albany, New Zealand . [Internet] [Thesis]. Massey University; 2016. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/10179/10003.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ramesh R. Unraveling the dynamics of protein-protein interactions in the Gcn2 signal transduction pathway : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics, Massey University, Albany, New Zealand . [Thesis]. Massey University; 2016. Available from: http://hdl.handle.net/10179/10003

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Massey University

28. Prescott, Hayley Dawn. Identification of potential Gcn2 regulating proteins.

Degree: MS, Genetics, 2016, Massey University

URL: http://hdl.handle.net/10179/10014

► The viability of any organism relies greatly on their ability to adapt their metabolic processes in response to environmental stimuli. Proteins are essential for almost… (more)

▼ The viability of any organism relies greatly on their ability to adapt their metabolic processes in response to environmental stimuli. Proteins are essential for almost every intracellular biological process. Proteins are composed of amino acid precursors and the levels of amino acids within the cell available for protein synthesis requires careful monitoring. Amino acid conservation needs to be initiated in response to declining availability. Under conditions of amino acid deprivation, cessation of non-essential protein synthesis and activation of amino acid biosynthetic pathways is initiated. This regulatory mechanism is referred to as the General Amino Acid Control (GAAC) pathway. General control non-derepressible 2 (Gcn2) is a fundamental constituent of the GAAC response pathway. Gcn2 senses a decline in amino acid availability and initiates the stress response by phosphorylating the alpha subunit of eukaryotic translation initiation factor 2 (eIF2a). The phosphorylation of eIF2a triggers a sequence of events resulting in increased translation of the transcriptional activator Gcn4, which subsequently induces selective expression of genes necessary for de novo amino acid synthesis. The activation and activity of Gcn2 is moderated by inhibitory and facilitative protein interactions. Published large scale purification studies identified many novel Gcn2 binding partners, some of which may function in Gcn2 regulation. However known Gcn2 regulators were absent from these datasets indicating that they were incomplete. This work aimed to identify and screen potential Gcn2 binding partners for those that regulate Gcn2 activity. Analysis identified 135 proteins that were potentially in complex with Gcn2. Of those, Sse1, Chs5, Ncl1, Tir4 and Npr1 were subsequently identified as potential Gcn2 regulators. For the purpose of comprehensively identifying novel Gcn2 binding proteins, a protocol was successfully optimised to enable Gcn2 affinity purification under conditions that would be specifically conducive for the maintenance of bonds between Gcn2 and its interaction partners. In this method, Gcn2 was overexpressed in cells to drive weak and/or transient interactions, and the usage of formaldehyde to crosslink interactions and further stabilise them was explored. This method will enable the future compilation of a comprehensive Gcn2 interactome.

Subjects/Keywords: Proteins; Synthesis; Protein-protein interactions

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Prescott, H. D. (2016). Identification of potential Gcn2 regulating proteins. (Masters Thesis). Massey University. Retrieved from http://hdl.handle.net/10179/10014

Chicago Manual of Style (16^th Edition):

Prescott, Hayley Dawn. “Identification of potential Gcn2 regulating proteins.” 2016. Masters Thesis, Massey University. Accessed April 11, 2021. http://hdl.handle.net/10179/10014.

MLA Handbook (7^th Edition):

Prescott, Hayley Dawn. “Identification of potential Gcn2 regulating proteins.” 2016. Web. 11 Apr 2021.

Vancouver:

Prescott HD. Identification of potential Gcn2 regulating proteins. [Internet] [Masters thesis]. Massey University; 2016. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/10179/10014.

Council of Science Editors:

Prescott HD. Identification of potential Gcn2 regulating proteins. [Masters Thesis]. Massey University; 2016. Available from: http://hdl.handle.net/10179/10014

University of Texas – Austin

29. Laber, Joshua Ryan. The effects of protein-protein interactions on in vitro and in vivo behavior of protein solutions.

Degree: PhD, Chemical Engineering, 2017, University of Texas – Austin

URL: http://hdl.handle.net/2152/72727

► Protein-based therapeutics such as monoclonal antibodies (mAbs) and related fragments are increasingly attractive modalities to treat a variety of diseases due to the ability to… (more)

▼ Protein-based therapeutics such as monoclonal antibodies (mAbs) and related fragments are increasingly attractive modalities to treat a variety of diseases due to the ability to engineer their biochemical and biophysical properties, streamlined manufacturing processes, minimal toxicity, and low immunogenicity/low risk of adverse side effects. Research in the methods used to deliver these treatments are limited when compared to small molecule drugs, as it is difficult to administer proteins orally and the high concentrations required for subcutaneous delivery are associated with high viscosities precluding syringe injection. Therefore, most protein therapeutics are delivered intravenously over long periods of time (>30 min) at dilute concentrations under medical supervision. Subcutaneous self-administration is a major objective in the field as it is expected to increase patient accessibility and compliance in addition to reducing pain and cost. Two common approaches under active investigation are 1) engineering the primary amino acid sequence for such traits as increased solubility and aggregation resistance, as well as 2) optimizing solution parameters for reduced viscosity via addition of excipients or optimizing manufacturing parameters. These approaches are unable to achieve stable protein solutions at concentrations sufficient for self-administration due to the dominant role of attractive forces at high concentration where even single amino acid mutations can drastically alter solution properties and thus solution optimization becomes protein-specific in nature. My overarching goals for this document are to systematically determine the dominant effects of protein-specific properties on this protein delivery technology in vitro and in vivo. Specifically, (1) investigate the role of protein-protein interactions on protein solution properties, and (2) investigate the effect of protein therapeutics can have on the immune system in vivo. Advisors/Committee Members: Maynard, Jennifer Anne, 1974- (advisor), Georgiou, George (committee member), Ehrlich, Lauren I.R. (committee member), Truskett, Thomas M. (committee member), Johnston, Keith P. (committee member).

Subjects/Keywords: Protein-protein interactions; Aggregation; Viscosity

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Laber, J. R. (2017). The effects of protein-protein interactions on in vitro and in vivo behavior of protein solutions. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/72727

Chicago Manual of Style (16^th Edition):

Laber, Joshua Ryan. “The effects of protein-protein interactions on in vitro and in vivo behavior of protein solutions.” 2017. Doctoral Dissertation, University of Texas – Austin. Accessed April 11, 2021. http://hdl.handle.net/2152/72727.

MLA Handbook (7^th Edition):

Laber, Joshua Ryan. “The effects of protein-protein interactions on in vitro and in vivo behavior of protein solutions.” 2017. Web. 11 Apr 2021.

Vancouver:

Laber JR. The effects of protein-protein interactions on in vitro and in vivo behavior of protein solutions. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2017. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/2152/72727.

Council of Science Editors:

Laber JR. The effects of protein-protein interactions on in vitro and in vivo behavior of protein solutions. [Doctoral Dissertation]. University of Texas – Austin; 2017. Available from: http://hdl.handle.net/2152/72727

University of Texas – Austin

30. Jackson, Eleisha Lynnette. Protein design, modeling, and the evolution of proteins.

Degree: PhD, Ecology, evolution, and behavior, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/45939

► Proteins are crucial players in the functional processes that allow for cellular life. Changes in the sequences of proteins have consequences for how these proteins… (more)

▼ Proteins are crucial players in the functional processes that allow for cellular life. Changes in the sequences of proteins have consequences for how these proteins function. Therefore, the study of how proteins change over time has been a central question in the field of evolutionary biology. As our understanding of how proteins function and change increases, we are not only able to test our hypotheses but we are also able to design and model new proteins, which is the ultimate test of our knowledge of how proteins function. Using the information from our protein modeling attempts, we can learn more about how natural proteins function and change over time. In this dissertation, I used protein modeling techniques to understand protein evolution. In Chapter 2, I assessed how closely designed proteins recapitulate observed patterns in natural proteins. I have found that designing proteins with a flexible-backbone protocol results in site variability that more closely mimics what is seen in natural proteins. In addition, I have also found that, in designed proteins, hydrophobic residues are often underrepresented in the core of the protein. These results suggest that our scoring functions and/or backbone sampling methods could be further improved. In Chapter 3, I used protein design to predict site-wise evolutionary rates in proteins. I found that protein design is a poor predictor of evolutionary rate, explaining only approximately 7% of the variation in rate across sites in enzymes. In Chapter 4, I used protein design and homology modeling to predict tolerance to deletions in enhanced green fluorescent protein. I also compared these predictions to predictions made using other structural properties including solvent accessibility, local packing density and secondary structure. I found that when combining computational scores from modeled structures along with other structural properties (i.e., local packing density, solvent accessibility and secondary structure) as predictors, I was largely able predict whether or not a given deletion would result in a functional protein product. Finally, in Chapter 5, I developed a computational pipeline to assess binding affinity in protein-protein interactions. I used this pipeline to recapitulate patterns of Machupo virus entry across various species. Taken together, the work presented in this dissertation has given us insight into which structural constraints affect protein evolution. Advisors/Committee Members: Wilke, C. (Claus) (advisor), Moran, Nancy (committee member), Hofmann, Hans (committee member), Sullivan, Christopher (committee member), Ellington, Andrew (committee member).

Subjects/Keywords: Protein evolution; Protein design

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Jackson, E. L. (2016). Protein design, modeling, and the evolution of proteins. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/45939

Chicago Manual of Style (16^th Edition):

Jackson, Eleisha Lynnette. “Protein design, modeling, and the evolution of proteins.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed April 11, 2021. http://hdl.handle.net/2152/45939.

MLA Handbook (7^th Edition):

Jackson, Eleisha Lynnette. “Protein design, modeling, and the evolution of proteins.” 2016. Web. 11 Apr 2021.

Vancouver:

Jackson EL. Protein design, modeling, and the evolution of proteins. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Apr 11]. Available from: http://hdl.handle.net/2152/45939.

Council of Science Editors:

Jackson EL. Protein design, modeling, and the evolution of proteins. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/45939

Open Access Theses and Dissertations