subject:(Protein Structure Networks PSNs )

Indian Institute of Science

1. Dighe, Anasuya. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.

Degree: PhD, Faculty of Science, 2019, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/4236

► Molecular recognition between proteins and their associated ligands constitutes ligand-induced protein rewiring thereby enabling the formation of a stable protein-ligand complex. The studies presented in… (more)

▼ Molecular recognition between proteins and their associated ligands constitutes ligand-induced protein rewiring thereby enabling the formation of a stable protein-ligand complex. The studies presented in this thesis address the conformational plasticity inherent to proteins by virtue of which they adapt to diverse ligands and orchestrate complex biological processes like signal transduction, transcription and protein-protein interaction. Adopting network theory based formalisms for understanding protein-ligand associations involve deconstructing the three-dimensional structure of a protein in terms of nodes and edges. With this view, Protein Structure Networks (PSNs) of ligand-bound complexes are studied by considering their side-chain non-covalent interactions. Agonist and antagonist-bound G-Protein Coupled Receptors (GPCRs) are investigated to gain mechanistic insights into allostery and its role in signal transduction. The degree of similarity between PSNs of these complexes is quantified by means of Network Similarity Score (NSS). The physical nature of these networks is inspected by subjecting them to perturbations and major players in maintaining the stability of such networks are identified. Residue-wise groupings (at backbone and side-chain level) are obtained by applying graph spectral methods. All-atom Molecular Dynamics (MD) simulations are carried out to gain a better understanding of protein-ligand binding by analysing conformational ensembles of these complexes. In this scenario, two members from a highly versatile ligand-inducible transcription factor superfamily, i.e., Nuclear Receptors (NR) are studied, that are known to exhibit extremes of ligand binding behavior ranging from promiscuity to specificity. Diverse ligands are known to bind to proteins and the overall nature of their binding site is investigated. In particular, similarities among binding sites of diverse proteins are analysed by using PocketMatch. Percolation of these similarities to regions surrounding the binding site is reported and examples depicting this extended similarity are discussed. Overall, studies presented in this thesis provide a structural perspective into the adaptability of proteins for recognizing diverse ligands and undergoing local or global re-organizations in their framework to regulate complex biological processes. Advisors/Committee Members: Vishveshwara, Saraswathi (advisor), Chandra, Nagasuma (advisor).

Subjects/Keywords: Protein-ligand Interactions; Protein Ligand Interactions; Protein Structure Networks (PSNs); Graph Theory; Protein Side-chain Networks (PScN); Muscarinic Acetylcholine Receptors; Muscarinic Receptor Cmplexes; Protein-Protein Interactions; Pregnane X Receptor; G-Protein Coupled Receptors (GPCRs); Network Similarity Score (NSS); Biochemistry

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APA (6^th Edition):

Dighe, A. (2019). Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/4236

Chicago Manual of Style (16^th Edition):

Dighe, Anasuya. “Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.” 2019. Doctoral Dissertation, Indian Institute of Science. Accessed January 23, 2021. http://etd.iisc.ac.in/handle/2005/4236.

MLA Handbook (7^th Edition):

Dighe, Anasuya. “Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins.” 2019. Web. 23 Jan 2021.

Vancouver:

Dighe A. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2019. [cited 2021 Jan 23]. Available from: http://etd.iisc.ac.in/handle/2005/4236.

Council of Science Editors:

Dighe A. Studies on Dynamic Plasticity of Ligand Binding Sites in Proteins. [Doctoral Dissertation]. Indian Institute of Science; 2019. Available from: http://etd.iisc.ac.in/handle/2005/4236

University of Tennessee – Knoxville

2. foutch, david. Network Analysis of Protein Structure Networks Upon Ligand Binding.

Degree: MS, Life Sciences, 2020, University of Tennessee – Knoxville

URL: https://trace.tennessee.edu/utk_gradthes/5598

► Network analysis is a computational approach used to describe the structure and dynamics of complex systems.Residue-residue contacts that are made over the course of MD… (more)

Subjects/Keywords: Graph theory; protein structure networks; protein dynamic networks; network analysis

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APA (6^th Edition):

foutch, d. (2020). Network Analysis of Protein Structure Networks Upon Ligand Binding. (Thesis). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_gradthes/5598

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):

foutch, david. “Network Analysis of Protein Structure Networks Upon Ligand Binding.” 2020. Thesis, University of Tennessee – Knoxville. Accessed January 23, 2021. https://trace.tennessee.edu/utk_gradthes/5598.

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

MLA Handbook (7^th Edition):

foutch, david. “Network Analysis of Protein Structure Networks Upon Ligand Binding.” 2020. Web. 23 Jan 2021.

Vancouver:

foutch d. Network Analysis of Protein Structure Networks Upon Ligand Binding. [Internet] [Thesis]. University of Tennessee – Knoxville; 2020. [cited 2021 Jan 23]. Available from: https://trace.tennessee.edu/utk_gradthes/5598.

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

Council of Science Editors:

foutch d. Network Analysis of Protein Structure Networks Upon Ligand Binding. [Thesis]. University of Tennessee – Knoxville; 2020. Available from: https://trace.tennessee.edu/utk_gradthes/5598

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

University of California – San Diego

3. Mih, Nathan Da-Wei. Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit.

Degree: Bioinformatics & Systems Bio, 2018, University of California – San Diego

URL: http://www.escholarship.org/uc/item/6523m9mh

► The computational representation of metabolic networks has traditionally abstracted the representation of enzymatic components that catalyze their associated reactions. However, the long history of reductionism… (more)

▼ The computational representation of metabolic networks has traditionally abstracted the representation of enzymatic components that catalyze their associated reactions. However, the long history of reductionism in studying biological components, specifically the three-dimensional structure of proteins, has resulted in a rich knowledgebase of experimental data and computational tools capable of describing atomic-level biochemical interactions and inferring functional consequences. The challenge of integrating such information into large-scale computational models of cells results in the intersection of structural and systems biology. This dissertation aims to explore and address the methodological issues that arise from the integration of these two fields, centered around the creation of a computational framework to answer the question of how best to utilize structural data in genome-scale models of metabolism. I present a software framework, ssbio, and an associated pipeline to simplify the integration process and allow the construction of high-quality genome-scale models with protein structures (GEM-PROs). The framework allows for the rigorous consideration and consolidation of the often repetitive or incomplete data of proteins in 3D space. Next, I explore a deep integration of molecular modeling tools into metabolic models to understand the impact of non-synonymous mutations on protein-ligand interactions within the human erythrocyte. I then show how these models provide utility in a comparative analysis of Escherichia coli and Thermotoga maritima by elucidating the impact of the structural proteome on the temperature dependence of growth, the distribution of protein fold families, and substrate specificity. Finally, I extend this framework to understand if hypothesized adaptations to oxidative stress are reflected in the structural proteomes of multiple strains of E. coli, along with the incorporation of a probabilistic model of oxidative damage based on selected structural features into a model of metabolism and protein synthesis. Overall, these studies represent the utility of a multi-scale approach to understanding how changes to the structural proteome can impact the system they participate in, along with providing the basis for future computational studies in structural systems biology.

Subjects/Keywords: Bioinformatics; metabolic networks; molecular dynamics; protein structure; structural biology; systems biology

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APA (6^th Edition):

Mih, N. D. (2018). Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/6523m9mh

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):

Mih, Nathan Da-Wei. “Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit.” 2018. Thesis, University of California – San Diego. Accessed January 23, 2021. http://www.escholarship.org/uc/item/6523m9mh.

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

MLA Handbook (7^th Edition):

Mih, Nathan Da-Wei. “Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit.” 2018. Web. 23 Jan 2021.

Vancouver:

Mih ND. Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Jan 23]. Available from: http://www.escholarship.org/uc/item/6523m9mh.

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

Council of Science Editors:

Mih ND. Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/6523m9mh

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

Indian Institute of Science

4. Vijayabaskar, M S. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.

Degree: PhD, Faculty of Science, 2013, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/1904

► Proteins orchestrate a number of cellular processes either alone or in concert with other biomolecules like nucleic acids, carbohydrates, and lipids. They exhibit an intrinsic… (more)

Subjects/Keywords: Proteins-DNA Graphs (PDGs); Protein Structures; Protein Side–chain Networks (PScNs); Protein–DNA Graphs (PDGs); Protein Energy Networks (PENs); Dps; Mycobacterium smegmatis; Structure Network Analysis; Protein Structure Networks; GraProStr; Structure Networks; Biochemistry

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APA (6^th Edition):

Vijayabaskar, M. S. (2013). Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1904

Chicago Manual of Style (16^th Edition):

Vijayabaskar, M S. “Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.” 2013. Doctoral Dissertation, Indian Institute of Science. Accessed January 23, 2021. http://etd.iisc.ac.in/handle/2005/1904.

MLA Handbook (7^th Edition):

Vijayabaskar, M S. “Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks.” 2013. Web. 23 Jan 2021.

Vancouver:

Vijayabaskar MS. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2013. [cited 2021 Jan 23]. Available from: http://etd.iisc.ac.in/handle/2005/1904.

Council of Science Editors:

Vijayabaskar MS. Protein-DNA Graphs And Interaction Energy Based Protein Structure Networks. [Doctoral Dissertation]. Indian Institute of Science; 2013. Available from: http://etd.iisc.ac.in/handle/2005/1904

Indian Institute of Science

5. Bhattacharyya, Moitrayee. Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory.

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

URL: http://etd.iisc.ac.in/handle/2005/2341

► The fidelity of biological processes and reactions, inspite of the widespread diversity, is programmed by highly specific physico-chemical principles. This underlines our basic understanding of… (more)

▼ The fidelity of biological processes and reactions, inspite of the widespread diversity, is programmed by highly specific physico-chemical principles. This underlines our basic understanding of different interesting phenomena of biological relevance, ranging from enzyme specificity to allosteric communication, from selection of fold to structural organization / states of oligomerization, from half-sites-reactivity to reshuffling of the conformational free energy landscape, encompassing the dogma of sequence-structure dynamics-function of macromolecules. The role of striking an optimal balance between rigidity and flexibility in macromolecular 3D structural organisation is yet another concept that needs attention from the functional perspective. Needless to say that the variety of protein structures and conformations naturally leads to the diversity of their function and consequently many other biological functions in general. Classical models of allostery like the ‘MWC model’ or the ‘KNF model’ and the more recently proposed ‘population shift model’ have advanced our understanding of the underlying principles of long range signal transfer in macromolecules. Extensive studies have also reported the importance of the fold selection and 3D structural organisation in the context of macromolecular function. Also ligand induced conformational changes in macromolecules, both subtle and drastic, forms the basis for controlling several biological processes in an ordered manner by re-organizing the free energy landscape. The above mentioned biological phenomena have been observed from several different biochemical and biophysical approaches. Although these processes may often seem independent of each other and are associated with regulation of specialized functions in macromolecules, it is worthwhile to investigate if they share any commonality or interdependence at the detailed atomic level of the 3D structural organisation. So the nagging question is, do these diverse biological processes have a unifying theme, when probed at a level that takes into account even subtle re-orchestrations of the interactions and energetics at the protein/nucleic acid side-chain level. This is a complex problem to address and here we have made attempts to examine this problem using computational tools. Two methods have been extensively applied: Molecular Dynamics (MD) simulations and network theory and related parameters. Network theory has been extensively used in the past in several studies, ranging from analysis of social networks to systems level networks in biology (e.g., metabolic networks) and have also found applications in the varied fields of physics, economics, cartography and psychology. More recently, this concept has been applied to study the intricate details of the structural organisation in proteins, providing a local view of molecular interactions from a global perspective. On the other hand, MD simulations capture the dynamics of interactions and the conformational space associated with a given state (e.g., different… Advisors/Committee Members: Vishveshwara, Saraswathi (advisor).

Subjects/Keywords: Protein Structure; Protein - Non Covalent Interactions; Nucleic Acids- Non Covalent Interactions; Bacterial LuxS Protein; Protein-Ligand Interactions; Protein Structure Networks; Proteins - Conformation; Allosteric Proteins; Energy-Weighted Network Formalism; Proteins - Allosterism; Protein Structure Network (PSN); Protein Structure Graph (PSN); Protein Complex Energy Network (PcEN); Biochemistry

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

APA (6^th Edition):

Bhattacharyya, M. (2014). Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/2341

Chicago Manual of Style (16^th Edition):

Bhattacharyya, Moitrayee. “Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory.” 2014. Doctoral Dissertation, Indian Institute of Science. Accessed January 23, 2021. http://etd.iisc.ac.in/handle/2005/2341.

MLA Handbook (7^th Edition):

Bhattacharyya, Moitrayee. “Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory.” 2014. Web. 23 Jan 2021.

Vancouver:

Bhattacharyya M. Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2014. [cited 2021 Jan 23]. Available from: http://etd.iisc.ac.in/handle/2005/2341.

Council of Science Editors:

Bhattacharyya M. Probing Ligand Induced Perturbations In Protien Structure Networks : Physico-Chemical Insights From MD Simulations And Graph Theory. [Doctoral Dissertation]. Indian Institute of Science; 2014. Available from: http://etd.iisc.ac.in/handle/2005/2341

University of Rochester

6. Yang, Na. Algorithms for affective and ubiquitous sensing systems and for protein structure prediction.

Degree: PhD, 2015, University of Rochester

URL: http://hdl.handle.net/1802/29666

► Rapid development in sensing technologies has facilitated increased design of more affective and ubiquitous sensing environments for humans. Through affective sensing of human emotions and… (more)

▼ Rapid development in sensing technologies has facilitated increased design of more affective and ubiquitous sensing environments for humans. Through affective sensing of human emotions and behaviors, devices can respond accordingly to provide the users with a better human-computer interaction experience. While affective sensing provides electronic devices with a better understanding of humans, ubiquitous sensing provides humans with a better knowledge of their environments. Wireless sensor networks (WSNs) have been proposed for different ubiquitous sensing scenarios over the decades, and in-home monitoring is one of the successful examples that have been widely deployed. Algorithms designed to optimize such in-home sensor networks can also be mapped to other domains. In particular, the problem of optimizing coverage in directional sensor networks can be mapped to the problem of predicting the structure of proteins, an important challenge for bioinformatics research that is needed for effective drug therapy design. In this dissertation, we contribute algorithms to enable affective and ubiquitous sensing systems as well as algorithms to improve protein structure prediction. Accurate acquisition and interpretation of human physical signals are two essential components for affective sensing. In the first part of this dissertation, we develop a speech-based emotion classification system, which uses several one against- all support vector machines with a threshold-based fusion mechanism to combine the individual outputs. A thorough performance evaluation of this system is provided for different test scenarios, including classification using noisy speech samples and samples from real users. Results show that the system achieves a six-emotion decision-level correct classification rate of 80% for an acted dataset with clean speech. Applications for this proposed emotion sensing system range from behavior studies to context-aware electronics design. Fundamental frequency (F0) is one of the speech features used for emotion classification. However, noise is inevitably included during the speech signal’s acquisition. We present a novel noise resilient F0 detection algorithm named BaNa that combines the approaches of harmonic ratios and Cepstrum analysis. We test the performance of the proposed BaNa algorithm using real human speech samples corrupted by different types of noise. Results show that for almost all types of noise and signal-to-noise ratio values investigated, BaNa achieves the lowest Gross Pitch Error rate among all the classic and state-of-the-art algorithms. In the second part of this dissertation, we study the aforementioned in-home monitoring problem, considering energy efficiency for both the monitoring and transmission processes. In particular, we evaluate the performance of different camera and motion sensor placement strategies, and formulate optimization problems to achieve the minimum energy consumption, longest network lifetime, or the lowest monetary cost. In the image…

Subjects/Keywords: Affective computing; Emotion classification; Mood sensing; Protein structure prediction; Ubiquitous computing; Wireless sensor networks

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APA (6^th Edition):

Yang, N. (2015). Algorithms for affective and ubiquitous sensing systems and for protein structure prediction. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/29666

Chicago Manual of Style (16^th Edition):

Yang, Na. “Algorithms for affective and ubiquitous sensing systems and for protein structure prediction.” 2015. Doctoral Dissertation, University of Rochester. Accessed January 23, 2021. http://hdl.handle.net/1802/29666.

MLA Handbook (7^th Edition):

Yang, Na. “Algorithms for affective and ubiquitous sensing systems and for protein structure prediction.” 2015. Web. 23 Jan 2021.

Vancouver:

Yang N. Algorithms for affective and ubiquitous sensing systems and for protein structure prediction. [Internet] [Doctoral dissertation]. University of Rochester; 2015. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1802/29666.

Council of Science Editors:

Yang N. Algorithms for affective and ubiquitous sensing systems and for protein structure prediction. [Doctoral Dissertation]. University of Rochester; 2015. Available from: http://hdl.handle.net/1802/29666

University of South Carolina

7. Cole, Casey Anne. From Cellular to Holistic: Development of Algorithms to Study Human Health and Diseases.

Degree: PhD, Computer Science and Engineering, 2020, University of South Carolina

URL: https://scholarcommons.sc.edu/etd/5804

► The development of theoretical computational methods and their application has become widespread in the world today. In this dissertation, I present my work in… (more)

Subjects/Keywords: Computer Sciences; Artificial Intelligence; Artificial Neural Networks; dynamics; human activity recognition; protein structure; smartwatches

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APA (6^th Edition):

Cole, C. A. (2020). From Cellular to Holistic: Development of Algorithms to Study Human Health and Diseases. (Doctoral Dissertation). University of South Carolina. Retrieved from https://scholarcommons.sc.edu/etd/5804

Chicago Manual of Style (16^th Edition):

Cole, Casey Anne. “From Cellular to Holistic: Development of Algorithms to Study Human Health and Diseases.” 2020. Doctoral Dissertation, University of South Carolina. Accessed January 23, 2021. https://scholarcommons.sc.edu/etd/5804.

MLA Handbook (7^th Edition):

Cole, Casey Anne. “From Cellular to Holistic: Development of Algorithms to Study Human Health and Diseases.” 2020. Web. 23 Jan 2021.

Vancouver:

Cole CA. From Cellular to Holistic: Development of Algorithms to Study Human Health and Diseases. [Internet] [Doctoral dissertation]. University of South Carolina; 2020. [cited 2021 Jan 23]. Available from: https://scholarcommons.sc.edu/etd/5804.

Council of Science Editors:

Cole CA. From Cellular to Holistic: Development of Algorithms to Study Human Health and Diseases. [Doctoral Dissertation]. University of South Carolina; 2020. Available from: https://scholarcommons.sc.edu/etd/5804

Indian Institute of Science

8. Brinda, K V. Protein Structure Networks : Implications To Protein Stabiltiy And Protein-Protein Interactions.

Degree: PhD, Faculty of Science, 2011, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/1504

Subjects/Keywords: Protein Networks; Protein-Protein Interactions; Protein Stability; Protein Structures; Protein Folding; Protein Functions; Protein Structure Analysis; Protein Structure Graphs; Protein Structure Networks; Homodimeric Protein Interfaces; Lectins; Graph Spectral Method; Structure Graphs; Biochemistry

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

APA (6^th Edition):

Brinda, K. V. (2011). Protein Structure Networks : Implications To Protein Stabiltiy And Protein-Protein Interactions. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/1504

Chicago Manual of Style (16^th Edition):

Brinda, K V. “Protein Structure Networks : Implications To Protein Stabiltiy And Protein-Protein Interactions.” 2011. Doctoral Dissertation, Indian Institute of Science. Accessed January 23, 2021. http://etd.iisc.ac.in/handle/2005/1504.

MLA Handbook (7^th Edition):

Brinda, K V. “Protein Structure Networks : Implications To Protein Stabiltiy And Protein-Protein Interactions.” 2011. Web. 23 Jan 2021.

Vancouver:

Brinda KV. Protein Structure Networks : Implications To Protein Stabiltiy And Protein-Protein Interactions. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2011. [cited 2021 Jan 23]. Available from: http://etd.iisc.ac.in/handle/2005/1504.

Council of Science Editors:

Brinda KV. Protein Structure Networks : Implications To Protein Stabiltiy And Protein-Protein Interactions. [Doctoral Dissertation]. Indian Institute of Science; 2011. Available from: http://etd.iisc.ac.in/handle/2005/1504

Queens University

9. 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 January 23, 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. 23 Jan 2021.

Vancouver:

Wathen B. Sequence and Structure Based Protein Folding Studies With Implications . [Internet] [Thesis]. Queens University; 2011. [cited 2021 Jan 23]. 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

Queens University

10. Ahmed, Hazem Radwan A. Pattern Discovery in Protein Structures and Interaction Networks .

Degree: Computing, 2014, Queens University

URL: http://hdl.handle.net/1974/12051

► Pattern discovery in protein structures is a fundamental task in computational biology, with important applications in protein structure prediction, profiling and alignment. We propose a… (more)

▼ Pattern discovery in protein structures is a fundamental task in computational biology, with important applications in protein structure prediction, profiling and alignment. We propose a novel approach for pattern discovery in protein structures using Particle Swarm-based flying windows over potentially promising regions of the search space. Using a heuristic search, based on Particle Swarm Optimization (PSO) is, however, easily trapped in local optima due to the sparse nature of the problem search space. Thus, we introduce a novel fitness-based stagnation detection technique that effectively and efficiently restarts the search process to escape potential local optima. The proposed fitness-based method significantly outperforms the commonly-used distance-based method when tested on eight classical and advanced (shifted/rotated) benchmark functions, as well as on two other applications for proteomic pattern matching and discovery. The main idea is to make use of the already-calculated fitness values of swarm particles, instead of their pairwise distance values, to predict an imminent stagnation situation. That is, the proposed fitness-based method does not require any computational overhead of repeatedly calculating pairwise distances between all particles at each iteration. Moreover, the fitness-based method is less dependent on the problem search space, compared with the distance-based method. The proposed pattern discovery algorithms are first applied to protein contact maps, which are the 2D compact representation of protein structures. Then, they are extended to work on actual protein 3D structures and interaction networks, offering a novel and low-cost approach to protein structure classification and interaction prediction. Concerning protein structure classification, the proposed PSO-based approach correctly distinguishes between the positive and negative examples in two protein datasets over 50 trials. As for protein interaction prediction, the proposed approach works effectively on complex, mostly sparse protein interaction networks, and predicts high-confidence protein-protein interactions — validated by more than one computational and experimental source — through knowledge transfer between topologically-similar interaction patterns of close proximity. Such encouraging results demonstrate that pattern discovery in protein structures and interaction networks are promising new applications of the fast-growing and far-reaching PSO algorithms, which is the main argument of this thesis.

Subjects/Keywords: 3D Structural Motif Matching ; Protein Structure Classification ; Protein Structure Alignment ; Protein Interaction Networks ; Protein-Protein Interaction Prediction ; Multi-Start Particle Swarm Optimization ; Fitness-based Agile Restart ; Efficient Stagnation Detection ; Proteomic Pattern Matching and Discovery ; Protein Contact Maps

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APA (6^th Edition):

Ahmed, H. R. A. (2014). Pattern Discovery in Protein Structures and Interaction Networks . (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/12051

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):

Ahmed, Hazem Radwan A. “Pattern Discovery in Protein Structures and Interaction Networks .” 2014. Thesis, Queens University. Accessed January 23, 2021. http://hdl.handle.net/1974/12051.

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

MLA Handbook (7^th Edition):

Ahmed, Hazem Radwan A. “Pattern Discovery in Protein Structures and Interaction Networks .” 2014. Web. 23 Jan 2021.

Vancouver:

Ahmed HRA. Pattern Discovery in Protein Structures and Interaction Networks . [Internet] [Thesis]. Queens University; 2014. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1974/12051.

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

Council of Science Editors:

Ahmed HRA. Pattern Discovery in Protein Structures and Interaction Networks . [Thesis]. Queens University; 2014. Available from: http://hdl.handle.net/1974/12051

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

11. Cottat, Maximilien. Optimisation de nanostructures plasmoniques pour la détection et la caractérisation structurelle des protéines par Diffusion Raman Exaltée de Surface : Optimization of plasmonics nanostructures for detection and characterization of proteins structure by Surface Enhanced Raman Scattering.

Degree: Docteur es, Physique, 2014, Paris 13

URL: http://www.theses.fr/2014PA132049

►

Les protéines jouent un rôle important dans les cellules, via leur activité enzymatique et les interactions qu’elles mettent en jeu. Ces fonctions sont principalement basées… (more)

▼

Les protéines jouent un rôle important dans les cellules, via leur activité enzymatique et les interactions qu’elles mettent en jeu. Ces fonctions sont principalement basées sur la structure des protéines. Afin de détecter leur présence, et de caractériser leur structure, nous nous sommes appuyés sur les propriétés optiques des nanostructures. La résonance des plasmons de surface localisés (RPSL), ainsi que la diffusion Raman exaltée de surface(DRES), nous ont permis de détecter différentes protéines. Une optimisation des nanostructures nous a également permis de concevoir un biocapteur basé sur la DRES, qui soit sensible, reproductible et spécifique. En effet, la détection spécifique d’un biomarqueur pathologique, la protéine Manganèse Super Oxide Dismutase (MnSOD), a été réalisée grâce à l’utilisation de nanostructures optimisées et fonctionnalisées avec un aptamère (séquence ADN). Avec ce système, nous avons démontré la détection de la MnSOD à des concentrations physiologiques dans des fluides corporels comme le sérum et la salive. Enfin, l’étude de la structure de la protéine Spleen Tyrosine kinase (Syk), par DRES, nous a permis de mettre en évidence un réarrangement structurale de Syk lors de sa phosphorylation. Une étude complémentaire par Western Blot montre que son activité kinase est dépendante de son état de phosphorylation indiquant que la structure et l’activité de Syk sont liées. L’ensemble de ces travaux contribue à une meilleure connaissance de l’interface entre la physique et la biologie.

Proteins play an important role in cells via their enzymatic activity and the irinteractions. Their functions are mainly based on the protein structure. In order to detect their presence and to characterize their structure, we used optical properties of nanostructures. The localized surface plasmon resonance (LSPR), as well as the surface enhanced Raman scattering (SERS), allowed us to detect various proteins. We also optimized nanostructures to build a sensitive, reproducible and specific biosensor based on SERS. Indeed, specific detection of one pathological biomarker, the Manganese Super Oxide Dismutase (MnSOD) protein, was investigated by using optically optimized and aptamer-functionalized nanostructures. Using this system, we were able to detect the MnSOD at physiological concentration in body fluids, such as serum and saliva. Finally, the structural study of the Spleen Tyrosine kinase (Syk) protein by SERS, allowed us to demonstrate that its structure varied with its phosphorylation levels. A complementary Western Blot analysis showed that the Syk kinase activity depended also on its phosphorylation state, meaning that the structure and the activity of Syk were linked. Altogether, these data contributed to a better understanding of the interface between physics and biology.

Advisors/Committee Members: Lamy de la Chapelle, Marc (thesis director), Le Roy, Christine (thesis director), Lidgi, Nathalie (thesis director).

Subjects/Keywords: Protéines / structure; Protein / structure

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APA (6^th Edition):

Cottat, M. (2014). Optimisation de nanostructures plasmoniques pour la détection et la caractérisation structurelle des protéines par Diffusion Raman Exaltée de Surface : Optimization of plasmonics nanostructures for detection and characterization of proteins structure by Surface Enhanced Raman Scattering. (Doctoral Dissertation). Paris 13. Retrieved from http://www.theses.fr/2014PA132049

Chicago Manual of Style (16^th Edition):

Cottat, Maximilien. “Optimisation de nanostructures plasmoniques pour la détection et la caractérisation structurelle des protéines par Diffusion Raman Exaltée de Surface : Optimization of plasmonics nanostructures for detection and characterization of proteins structure by Surface Enhanced Raman Scattering.” 2014. Doctoral Dissertation, Paris 13. Accessed January 23, 2021. http://www.theses.fr/2014PA132049.

MLA Handbook (7^th Edition):

Cottat, Maximilien. “Optimisation de nanostructures plasmoniques pour la détection et la caractérisation structurelle des protéines par Diffusion Raman Exaltée de Surface : Optimization of plasmonics nanostructures for detection and characterization of proteins structure by Surface Enhanced Raman Scattering.” 2014. Web. 23 Jan 2021.

Vancouver:

Cottat M. Optimisation de nanostructures plasmoniques pour la détection et la caractérisation structurelle des protéines par Diffusion Raman Exaltée de Surface : Optimization of plasmonics nanostructures for detection and characterization of proteins structure by Surface Enhanced Raman Scattering. [Internet] [Doctoral dissertation]. Paris 13; 2014. [cited 2021 Jan 23]. Available from: http://www.theses.fr/2014PA132049.

Council of Science Editors:

Cottat M. Optimisation de nanostructures plasmoniques pour la détection et la caractérisation structurelle des protéines par Diffusion Raman Exaltée de Surface : Optimization of plasmonics nanostructures for detection and characterization of proteins structure by Surface Enhanced Raman Scattering. [Doctoral Dissertation]. Paris 13; 2014. Available from: http://www.theses.fr/2014PA132049

12. 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 January 23, 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. 23 Jan 2021.

Vancouver:

Muley VY. Improved computational prediction and analysis of protein - protein interaction networks. [Internet] [Thesis]. Manipal University; 2012. [cited 2021 Jan 23]. 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 Waterloo

13. Cui, Xuefeng. Finding Similar Protein Structures Efficiently and Effectively.

Degree: 2014, University of Waterloo

URL: http://hdl.handle.net/10012/8349

► To assess the similarities and the differences among protein structures, a variety of structure alignment algorithms and programs have been designed and implemented. We introduce… (more)

▼ To assess the similarities and the differences among protein structures, a variety of structure alignment algorithms and programs have been designed and implemented. We introduce a low-resolution approach and a high-resolution approach to evaluate the similarities among protein structures. Our results show that both the low-resolution approach and the high-resolution approach outperform state-of-the-art methods. For the low-resolution approach, we eliminate false positives through the comparison of both local similarity and remote similarity with little compromise in speed. Two kinds of contact libraries (ContactLib) are introduced to fingerprint protein structures effectively and efficiently. Each contact group from the contact library consists of one local or two remote fragments and is represented by a concise vector. These vectors are then indexed and used to calculate a new combined hit-rate score to identify similar protein structures effectively and efficiently. We tested our ContactLibs on the high-quality protein structure subset of SCOP30, which contains 3,297 protein structures. For each protein structure of the subset, we retrieved its neighbor protein structures from the rest of the subset. The best area under the ROC curve, archived by a ContactLib, is as high as 0.960. This is a significant improvement over 0.747, the best result achieved by the state-of-the-art method, FragBag. For the high-resolution approach, our PROtein STructure Alignment method (PROSTA) relies on and verifies the fact that the optimal protein structure alignment always contains a small subset of aligned residue pairs, called a seed, such that the rotation and translation (ROTRAN), which minimizes the RMSD of the seed, yields both the optimal ROTRAN and the optimal alignment score. Thus, ROTRANs minimizing the RMSDs of small subsets of residues are sampled, and global alignments are calculated directly from the sampled ROTRANs. Moreover, our method incorporates remote information and filters similar ROTRANs (or alignments) by clustering, rather than by an exhaustive method, to overcome the computational inefficiency. Our high-resolution protein structure alignment method, when applied to optimizing the TM-score and the GDT-TS score, produces a significantly better result than state-of-the-art protein structure alignment methods. Specifically, if the highest TM-score found by TM-align is lower than 0.6 and the highest TM-score found by one of the tested methods is higher than 0.5, our alignment method tends to discover better protein structure alignments with (up to 0.21) higher TM-scores. In such cases, TM-align fails to find TM-scores higher than 0.5 with a probability of 42%; however, our alignment method fails the same task with a probability of only 2%. In addition, existing protein structure alignment scoring functions focus on atom coordinate similarity alone and simply ignore other important similarities, such as sequence similarity. Our scoring function has the capacity…

Subjects/Keywords: Bioinformatics; Protein Structure Retrieval; Protein Structure Alignment

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

APA (6^th Edition):

Cui, X. (2014). Finding Similar Protein Structures Efficiently and Effectively. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/8349

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):

Cui, Xuefeng. “Finding Similar Protein Structures Efficiently and Effectively.” 2014. Thesis, University of Waterloo. Accessed January 23, 2021. http://hdl.handle.net/10012/8349.

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

MLA Handbook (7^th Edition):

Cui, Xuefeng. “Finding Similar Protein Structures Efficiently and Effectively.” 2014. Web. 23 Jan 2021.

Vancouver:

Cui X. Finding Similar Protein Structures Efficiently and Effectively. [Internet] [Thesis]. University of Waterloo; 2014. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10012/8349.

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

Council of Science Editors:

Cui X. Finding Similar Protein Structures Efficiently and Effectively. [Thesis]. University of Waterloo; 2014. Available from: http://hdl.handle.net/10012/8349

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

Rice University

14. Cheng, Yushao. Template-based Protein Structure Prediction and its Applications.

Degree: PhD, Engineering, 2013, Rice University

URL: http://hdl.handle.net/1911/76475

► Protein structure prediction, also called protein folding, is one of the most significant and challenging research areas in computational biophysics and structural bioinformatics. With the… (more)

▼ Protein structure prediction, also called protein folding, is one of the most significant and challenging research areas in computational biophysics and structural bioinformatics. With the rapid growth of PDB database, template-based modeling such as homology modeling and threading has become a popular method in protein structure prediction. However, it is still hard to detect good templates when the sequence identity is below 30%. In chapter 1, a profile-profile alignment method is proposed. It uses evolutionary and structural profiles to detect homologs, and a z-score-based method to rank templates. The performance of this method in the critical assessment of protein structure prediction experiments (CASP) was reported. In chapter 2, p53 mutations are studied as an application of protein structure prediction. The TP53 gene encodes a tumor suppressor protein called p53, and p53 mutations occur in about half of human cancers. Experimental studies showed that p53 cancer mutants can be reactivated by mutations on other sites. Machine learning technologies were used in this research. Multiple classifiers were built to predict whether a p53 mutant (single-point or multiple-point) would be transcriptionally active or not, based on features extracted from amino acid sequences and structures. The mutant structures were modeled using template-based protein structure prediction. Theses features were selected and analyzed using different feature selection methods, and classifiers were built under different learning settings, such as supervised learning and semi-supervised learning. The performances of these classifiers were analyzed and compared. Besides the study of single proteins, protein complexes in yeast are studied in chapter 3. Multiple classifiers were built to predict whether several given proteins can form a protein complex, based on features generated from amino acid sequences and protein-protein interaction network. Theses features were selected and analyzed using different feature selection methods. Also, these classifiers were built under different learning settings, such as supervised learning and active learning. The performances of these classifiers were analyzed and compared. Advisors/Committee Members: Ma, Jianpeng (advisor), Diehl, Michael R. (committee member), Tao, Yizhi Jane (committee member).

Subjects/Keywords: Protein structure prediction

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

APA (6^th Edition):

Cheng, Y. (2013). Template-based Protein Structure Prediction and its Applications. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/76475

Chicago Manual of Style (16^th Edition):

Cheng, Yushao. “Template-based Protein Structure Prediction and its Applications.” 2013. Doctoral Dissertation, Rice University. Accessed January 23, 2021. http://hdl.handle.net/1911/76475.

MLA Handbook (7^th Edition):

Cheng, Yushao. “Template-based Protein Structure Prediction and its Applications.” 2013. Web. 23 Jan 2021.

Vancouver:

Cheng Y. Template-based Protein Structure Prediction and its Applications. [Internet] [Doctoral dissertation]. Rice University; 2013. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1911/76475.

Council of Science Editors:

Cheng Y. Template-based Protein Structure Prediction and its Applications. [Doctoral Dissertation]. Rice University; 2013. Available from: http://hdl.handle.net/1911/76475

15. Gravina, Lucia Concetta. Imunohistochemical profile of the neuroblasts of the peripheral sympathetic nervous system and human neuroblastoma of childhood.

Degree: 2014, Università degli Studi di Catania

URL: http://hdl.handle.net/10761/1537

► ABSTRACT I focused on the analysis of a protein involved in the development of the peripheral nervous system: the Wilms tumor1 (WT1). My thesis is… (more)

▼ ABSTRACT I focused on the analysis of a protein involved in the development of the peripheral nervous system: the Wilms tumor1 (WT1). My thesis is divided into two experimental phases: I) spatio-temporal distribution of WT1 during human embryonic development, II) expression and functional roles of WT1 during development of the peripheral sympathetic nervous system and gastrointestinal tract. The Wilms tumor (WT1) gene and its protein product are known to exhibit a dynamic expression profile during development and in the adult organism. Apart from a nuclear expression observed in the urogenital system, its precise localization in other developing human tissues is still largely unknown. Accordingly, the aim of this study was to investigate immunohistochemically the temporal and spatial distribution of WT1 in epithelial and mesenchymal developing human tissues from gestational weeks 7 24. For this purpose we used antibodies against the N-terminal of WT1. As might be expected, WT1 nuclear expression was observed in mesonephric/metanephric glomeruli, metanephric blastema, celomderived membranes (pleura, peritoneum, serosal surfaces) and sex cords. With regard to mesenchymal tissues, a similar nuclear staining was also obtained in the mesenchyme surrounding Müllerian and Wolffian ducts, as well as in the submesothelial mesenchymal cells of all celomatic-derived membranes. The most striking finding was the detection of strong WT1 cytoplasmic immunostaining in developing skeletal and cardiac muscle cells and endothelial cells. The tissue-specific expression of WT1, together with its different nuclear/cytoplasmic localization, both suggest that WT1 protein may have shuttling properties, acting as a protein with complex regulator activity in transcriptional/translation processes during human ontogenesis. The reported cytoplasmic expression of WT1 in human rhabdomyosarcomas and in many vascular tumors strongly suggests an oncofetal expression of this protein. Although not specific, WT1 cytoplasmic expression can be used as a marker of skeletal muscle and endothelial differentiation in an appropriate morphological context. Developmental expression of Wilms tumor gene (WT1) and protein is crucial for cell proliferation, apoptosis, differentiation and cytoskeletal architecture regulation. More recently, it has been suggested a potential role of WT1 in the development of neural tissue and in neurodegenerative disorders. We have investigated immunohistochemically the developmentally regulated expression and distribution of WT1 in human fetal (from the 8th to the 28th week gestational age) peripheral sympathetic nervous system (PSNS) and gastro-enteric nervous system (GENS). Interestingly WT1 expression was restricted to the cytoplasm of sympathetic neuroblasts, while it progressively disappeared with advancing morphologic differentiation of these cells along both ganglionic and chromaffin cell lineages. In adult tissues, both ganglion and chromaffin cells lacked any WT1 expression. These findings show that WT1 is a reliable…

Subjects/Keywords: Area 06 - Scienze mediche; WT1, developing, PSNS

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APA (6^th Edition):

Gravina, L. C. (2014). Imunohistochemical profile of the neuroblasts of the peripheral sympathetic nervous system and human neuroblastoma of childhood. (Thesis). Università degli Studi di Catania. Retrieved from http://hdl.handle.net/10761/1537

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):

Gravina, Lucia Concetta. “Imunohistochemical profile of the neuroblasts of the peripheral sympathetic nervous system and human neuroblastoma of childhood.” 2014. Thesis, Università degli Studi di Catania. Accessed January 23, 2021. http://hdl.handle.net/10761/1537.

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

MLA Handbook (7^th Edition):

Gravina, Lucia Concetta. “Imunohistochemical profile of the neuroblasts of the peripheral sympathetic nervous system and human neuroblastoma of childhood.” 2014. Web. 23 Jan 2021.

Vancouver:

Gravina LC. Imunohistochemical profile of the neuroblasts of the peripheral sympathetic nervous system and human neuroblastoma of childhood. [Internet] [Thesis]. Università degli Studi di Catania; 2014. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10761/1537.

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

Council of Science Editors:

Gravina LC. Imunohistochemical profile of the neuroblasts of the peripheral sympathetic nervous system and human neuroblastoma of childhood. [Thesis]. Università degli Studi di Catania; 2014. Available from: http://hdl.handle.net/10761/1537

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

University of Georgia

16. Buchner, John Michael. Structural and functional analysis of a novel recombinase.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/24839

► The DNA site-specific invertase Piv catalyzes the inversion of a 2.1 kb segment in Moraxella lacunata and Moraxella bovis altering the expression of type 4… (more)

▼ The DNA site-specific invertase Piv catalyzes the inversion of a 2.1 kb segment in Moraxella lacunata and Moraxella bovis altering the expression of type 4 pilin genes in two phases. The switch is a biphasic system, alternating between expression the tfpI and tfpQ pilin genes. In M. lacunata this switch is an on/off phase variation. Outside but adjacent to the invertible region, piv encodes the DNA invertase (Piv) that interacts with invL and invR as the loci of recombination. Other sites of Piv DNA binding have been observed, and one, sub1, has been characterized. Piv does not have homology with the traditional site-specific tyrosine or serine recombinases. Instead, Piv has homology to the transposases of the IS110/IS492 family of insertion elements. Modeling of Piv revealed three structures of interest: 1) the ribonuclease H-like fold, a catalytic domain associated with DDE-motif transposases, retroviral integrases, and RuvC Holliday junction resolvases, 2) a potential leucine zipper that could be the site of protein dimerization, 3) a predicted helix-hairpin-helix (HhH) DNA binding motif, best studied in RuvA, a protein that binds Holliday junctions in a non sequence-specific manner. We determined that four acidic residues that are conserved among Piv and the recombinases of the IS110/IS492 family of recombinases are required for catalysis of inversion and comprise a DEDD motif in Piv like that of RuvC. There was no requirement for the predicted leucine zipper in our in vivo inversion system. We also mutated residues that are conserved in a consensus HhH sequence and observed that they are required for DNA inversion and may play a role in binding to Holliday junctions in vitro. Through electrophoretic mobility shift assays, we observed an affinity of Piv for Holliday junctions and branched DNA substrates containing mismatched DNA. This leads us to our hypothesis: Piv is unique among enzymes in that it is a site-specific invertase that catalyzes recombination through hydrolysis and transesterification, like the DDE-motif transposases, and generates a Holliday junction intermediate that is resolved by Piv with a pair of hydrolysis reactions, like RuvC.

Subjects/Keywords: Predicted Structure; Protein Structure; Tertiary Structure

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APA (6^th Edition):

Buchner, J. M. (2014). Structural and functional analysis of a novel recombinase. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/24839

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):

Buchner, John Michael. “Structural and functional analysis of a novel recombinase.” 2014. Thesis, University of Georgia. Accessed January 23, 2021. http://hdl.handle.net/10724/24839.

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

MLA Handbook (7^th Edition):

Buchner, John Michael. “Structural and functional analysis of a novel recombinase.” 2014. Web. 23 Jan 2021.

Vancouver:

Buchner JM. Structural and functional analysis of a novel recombinase. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10724/24839.

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

Council of Science Editors:

Buchner JM. Structural and functional analysis of a novel recombinase. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/24839

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

Indian Institute of Science

17. 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 January 23, 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. 23 Jan 2021.

Vancouver:

Swapna LS. Structural And Evolutionary Studies On Protein-Protein Interactions. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2014. [cited 2021 Jan 23]. 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

Indian Institute of Science

18. Gadiyaram, Vasundhara. Graph Spectral Methods for Analysis of Protein Structures.

Degree: PhD, Faculty of Science, 2019, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/4280

► Network representation of protein structures is an information-rich mode of examining protein structure, dynamics and its interactions with biomolecules. Graph spectral methods are extremely useful… (more)

Subjects/Keywords: Protein Structure Networks (PSN); Spectral Theory; Protein Structure Models; Spectral Graph Theory; G-Protein Coupled Receptors; Graph Spectral Method; Correspondence Score (CRS); Eigenvalue-Weighted Cosine Score (EWCS); Eigenvalue-Weighted Cosine Score (EWCS); Network Similarity Score (NSS); Mathematics

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APA (6^th Edition):

Gadiyaram, V. (2019). Graph Spectral Methods for Analysis of Protein Structures. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/4280

Chicago Manual of Style (16^th Edition):

Gadiyaram, Vasundhara. “Graph Spectral Methods for Analysis of Protein Structures.” 2019. Doctoral Dissertation, Indian Institute of Science. Accessed January 23, 2021. http://etd.iisc.ac.in/handle/2005/4280.

MLA Handbook (7^th Edition):

Gadiyaram, Vasundhara. “Graph Spectral Methods for Analysis of Protein Structures.” 2019. Web. 23 Jan 2021.

Vancouver:

Gadiyaram V. Graph Spectral Methods for Analysis of Protein Structures. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2019. [cited 2021 Jan 23]. Available from: http://etd.iisc.ac.in/handle/2005/4280.

Council of Science Editors:

Gadiyaram V. Graph Spectral Methods for Analysis of Protein Structures. [Doctoral Dissertation]. Indian Institute of Science; 2019. Available from: http://etd.iisc.ac.in/handle/2005/4280

Wayne State University

19. Holcomb, Joshua. Structural Basis Of Membrane Protein Scaffolding And Signaling In Human Disease.

Degree: PhD, Biochemistry and Molecular Biology, 2017, Wayne State University

URL: https://digitalcommons.wayne.edu/oa_dissertations/1809

► Protein structural elucidation by means of X-ray crystallography is a powerful approach for both insight into a proteins biophysical properties and function. To date… (more)

▼ Protein structural elucidation by means of X-ray crystallography is a powerful approach for both insight into a proteins biophysical properties and function. To date X-ray crystallography remains the gold standard in high resolution structural determination and serves as the basis for rational drug design for the purpose of combating a number of human diseases. Such an approach also allows for the exploitation of how various proteins interact with their substrates providing a molecular basis for their physiological function. In this dissertation, using X-ray crystallographic analysis along with other biophysical characterization methods, we seek to understand the mechanistic foundation for which scaffolding proteins such as NHERF1 and NHERF2 interact with their substrates in which leads to a wide variety of critical cellular events. Additionally, we attempt elucidate the structure and function of a recently identified membrane protein, NgBR, with hopes to understand the molecular basis in which it influences the activation of the infamous oncoprotein Ras. Protein scaffolding is a term that denotes the coming together of two or more proteins in which results in the formation of macromolecular complexes. Such events are known to regulate several cellular processes including membrane protein recycling, protein stabilization, cell to cell adhesion, and regulation of signaling pathways. There are several families of scaffolding proteins with one of the most known to be the PDZ domain containing family. Two proteins within this family, NHERF1 and NHERF2, contain two PDZ domains in which are responsible for a variety of signaling events. The second PDZ domain of NHERF1 has been shown to complex with chemokine receptor CXCR2 and mediate the formation of the CXCR2-NHERF1-PLCβ2 complex. This complex formation has been shown to be influential in chemokine induced neutrophil migration and infiltration in regions of inflammation leading to the exacerbation of a variety of inflammatory diseases. Additionally, the first PDZ domain of NHERF2 has been shown to mediate the scaffolding of the CFTR-NHERF2-LAP2 complex which has been shown to inhibit CFTR activity by the LPA2 mediated inhibition of adenylate cyclase. Furthermore, disruption of this complex has been shown to be enough to augment CFTR activity in vivo. And thus, the determining the molecular basis by means both NHERF1 and NHERF2 scaffolding with its respective targets could lead to therapeutic targeting in a variety of human diseases. In this dissertation, we solved the co-crystal complexes between both NHERF1 PDZ2 with the C-terminal peptide of CXCR2 in addition to solving the co- crystal complex between NHERF2 PDZ1 with the C-terminal LPA2 peptide. Both structures reveal an expected mode of PDZ binding to their respective substrates with various ligand specific interactions. However, both structures also reveal unexpected findings which may unveil additional therapeutic strategies other than targeting the PDZ substrate binding site. … Advisors/Committee Members: Zhe Yang, Jian-Ping Jin.

Subjects/Keywords: protein scaffolding; protein structure; Biogeochemistry; Biophysics

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

APA (6^th Edition):

Holcomb, J. (2017). Structural Basis Of Membrane Protein Scaffolding And Signaling In Human Disease. (Doctoral Dissertation). Wayne State University. Retrieved from https://digitalcommons.wayne.edu/oa_dissertations/1809

Chicago Manual of Style (16^th Edition):

Holcomb, Joshua. “Structural Basis Of Membrane Protein Scaffolding And Signaling In Human Disease.” 2017. Doctoral Dissertation, Wayne State University. Accessed January 23, 2021. https://digitalcommons.wayne.edu/oa_dissertations/1809.

MLA Handbook (7^th Edition):

Holcomb, Joshua. “Structural Basis Of Membrane Protein Scaffolding And Signaling In Human Disease.” 2017. Web. 23 Jan 2021.

Vancouver:

Holcomb J. Structural Basis Of Membrane Protein Scaffolding And Signaling In Human Disease. [Internet] [Doctoral dissertation]. Wayne State University; 2017. [cited 2021 Jan 23]. Available from: https://digitalcommons.wayne.edu/oa_dissertations/1809.

Council of Science Editors:

Holcomb J. Structural Basis Of Membrane Protein Scaffolding And Signaling In Human Disease. [Doctoral Dissertation]. Wayne State University; 2017. Available from: https://digitalcommons.wayne.edu/oa_dissertations/1809

Massey University

20. Saraswat, Mayank. In search of novel folds : protein evolution via non-homologous recombination.

Degree: PhD, Biochemistry, 2014, Massey University

URL: http://hdl.handle.net/10179/5979

► The emergence of proteins from short peptides or subdomains, facilitated by the duplication and fusion of the minigenes encoding them, is believed to have played… (more)

▼ The emergence of proteins from short peptides or subdomains, facilitated by the duplication and fusion of the minigenes encoding them, is believed to have played a role in the origin of life. In this study it was hypothesised that new domains or basic elements of protein structure, may result from nonhomologous recombination of the genes coding for smaller subdomains. The hypothesis was tested by randomly recombining two distantly related (βα)8-barrel proteins: Escherichia coli phosphoribosylanthranilate isomerase (PRAI), and β subunit of voltage dependent K+ channels (Kvβ2) from Rattus norvegicus. The aim was to identify new, folded structures, which may or may not be (βα)8-barrels. Incremental truncation (ITCHY), a method for fragmenting and randomly recombining genes, was used to mimic in vivo non-homologous recombination and to create a library of chimeric variants. Clones from the library were selected for right reading frame and solubility (foldability) of the recombined chimeras, using the pSALect selection system. Out of the six clones identified as soluble by pSALect, only one (P25K86) was found to be actually soluble. The protein, P25K86, was found to form oligomers and on treatment with a reducing agent, β-mercaptoethanol the multimeric state disappeared. The protein has three cysteines and one of the cysteines (Cys56) was found to mediate in the bond formation, thus giving a dimeric state. An engineered version of P25K86 that has the Cys56 replaced by serine was expressed as a monomer and additionally it was found to be ! iv! more stable. As the pSALect folding selection system reported false positives, i.e. only one of the six chimeras was actually soluble, it was concluded that the in vivo solubility selection system was leaky. A series of experiments were conducted so as to improve pSALect that led to the creation of pFoldM – a more stringent selection system, discussed in chapter 4. Comparing the newer improved version with the old, two more interesting chimeras were discovered. A total of 240,000 non-homologous recombination events were created in vitro and three soluble chimeras (evolutionary solutions) were found. Data from circular dichroism spectroscopy (CD) combined with heteronuclear single quantum coherence (HSQC) spectra suggest that the proteins, P24K89 and P25K86, are present in a molten globule state. ITCHY, as a means of mimicking the subdomain assembly model, was applied in vitro. The discovery of two interesting chimeras (P25K86 and P24K89) using highthroughput engineering experiments widens the possibilities of exploring the protein structure space, and perhaps offers close encounters with these never born proteins that may be trapped in an ensemble of fluctuating (structured and unstructured) states.

Subjects/Keywords: Protein evolution; Protein structure; Genetic recombination

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

APA (6^th Edition):

Saraswat, M. (2014). In search of novel folds : protein evolution via non-homologous recombination. (Doctoral Dissertation). Massey University. Retrieved from http://hdl.handle.net/10179/5979

Chicago Manual of Style (16^th Edition):

Saraswat, Mayank. “In search of novel folds : protein evolution via non-homologous recombination.” 2014. Doctoral Dissertation, Massey University. Accessed January 23, 2021. http://hdl.handle.net/10179/5979.

MLA Handbook (7^th Edition):

Saraswat, Mayank. “In search of novel folds : protein evolution via non-homologous recombination.” 2014. Web. 23 Jan 2021.

Vancouver:

Saraswat M. In search of novel folds : protein evolution via non-homologous recombination. [Internet] [Doctoral dissertation]. Massey University; 2014. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10179/5979.

Council of Science Editors:

Saraswat M. In search of novel folds : protein evolution via non-homologous recombination. [Doctoral Dissertation]. Massey University; 2014. Available from: http://hdl.handle.net/10179/5979

University of Cambridge

21. Perron, Umberto. The Influence of Structural Constraints on Protein Evolution.

Degree: PhD, 2020, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/311064

► Few mathematical models of sequence evolution incorporate parameters describingprotein structure, despite its high conservation, essential functional role and the increasingavailability of structural data. The primary… (more)

▼ Few mathematical models of sequence evolution incorporate parameters describingprotein structure, despite its high conservation, essential functional role and the increasingavailability of structural data. The primary goal of my PhD project was to create astructurally aware amino acid substitution model in which proteins are represented usingan expanded alphabet that relays both amino acid identity and structural information.Each character in this alphabet specifies an amino acid as well as information aboutthe rotamer configuration of its side chain: the discrete geometric pattern of permittedside chain atomic positions, as defined by the dihedral angles between covalently linkedatoms. I generated a 55-state “Dayhoff-like” substitution model (RAM55) by assigningrotamer states in 79,558 structures (∼50%of all PDBe entries) and identifying substitu-tions between closely related sequences. RAM55’s rotamer state exchange patterns clearlyshow that the evolutionary properties of amino acids depend strongly upon side chain ge-ometry. Exploiting knowledge of these patterns assists in phylogenetic analyses: I showthat RAM55 performs as well as or better than traditional 20-state models on simulatedand empirical data for divergence time estimation, tree inference, side chain configurationprediction and ancestral sequence reconstruction.Further, encoding observed characters in an alignment as ambiguous representations ofcharacters in a larger state-space allows the application of RAM55 to 20-state amino aciddata for which structures are not known. Adding structural information to as few as12.5%of the sequences in an amino acid alignment results in excellent ancestral reconstructionperformance compared to a benchmark that considers the full rotamer state information.This strategy significantly expands the applicability of RAM55 to real-world scenarioswhere structure might only be available for some of the sequences of interest.Thus, not only is rotamer configuration a valuable source of information for phylo-genetic studies, but modelling the concomitant evolution of sequence and structure mayhave important implications for understanding protein folding and function.

Subjects/Keywords: protein; evolution; protein structure; phylogenetics; modelling

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

APA (6^th Edition):

Perron, U. (2020). The Influence of Structural Constraints on Protein Evolution. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/311064

Chicago Manual of Style (16^th Edition):

Perron, Umberto. “The Influence of Structural Constraints on Protein Evolution.” 2020. Doctoral Dissertation, University of Cambridge. Accessed January 23, 2021. https://www.repository.cam.ac.uk/handle/1810/311064.

MLA Handbook (7^th Edition):

Perron, Umberto. “The Influence of Structural Constraints on Protein Evolution.” 2020. Web. 23 Jan 2021.

Vancouver:

Perron U. The Influence of Structural Constraints on Protein Evolution. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Jan 23]. Available from: https://www.repository.cam.ac.uk/handle/1810/311064.

Council of Science Editors:

Perron U. The Influence of Structural Constraints on Protein Evolution. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://www.repository.cam.ac.uk/handle/1810/311064

University of Cambridge

22. Perron, Umberto. The influence of structural constraints on protein evolution.

Degree: PhD, 2020, University of Cambridge

URL: https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131

► Few mathematical models of sequence evolution incorporate parameters describing protein structure, despite its high conservation, essential functional role and the increasing availability of structural data.… (more)

▼ Few mathematical models of sequence evolution incorporate parameters describing protein structure, despite its high conservation, essential functional role and the increasing availability of structural data. The primary goal of my PhD project was to create a structurally aware amino acid substitution model in which proteins are represented using an expanded alphabet that relays both amino acid identity and structural information. Each character in this alphabet specifies an amino acid as well as information about the rotamer configuration of its side chain: the discrete geometric pattern of permitted side chain atomic positions, as defined by the dihedral angles between covalently linked atoms. I generated a 55-state “Dayhoff-like” substitution model (RAM55) by assigning rotamer states in 79,558 structures (∼50%of all PDBe entries) and identifying substitutions between closely related sequences. RAM55’s rotamer state exchange patterns clearly show that the evolutionary properties of amino acids depend strongly upon side chain geometry. Exploiting knowledge of these patterns assists in phylogenetic analyses: I show that RAM55 performs as well as, or better than, traditional 20-state models on simulated and empirical data for divergence time estimation, tree inference, side chain configuration prediction and ancestral sequence reconstruction. Further, encoding observed characters in an alignment as ambiguous representations of characters in a larger state-space allows the application of RAM55 to 20-state amino acid data for which structures are not known. Adding structural information to as few as 12.5% of the sequences in an amino acid alignment results in excellent ancestral reconstruction performance compared to a benchmark that considers the full rotamer state information. This strategy significantly expands the applicability of RAM55 to real-world scenarios where structure might only be available for some of the sequences of interest. Thus, not only is rotamer configuration a valuable source of information for phylo-genetic studies, but modelling the concomitant evolution of sequence and structure may have important implications for understanding protein folding and function.

Subjects/Keywords: protein; evolution; protein structure; phylogenetics; modelling

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

APA (6^th Edition):

Perron, U. (2020). The influence of structural constraints on protein evolution. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131

Chicago Manual of Style (16^th Edition):

Perron, Umberto. “The influence of structural constraints on protein evolution.” 2020. Doctoral Dissertation, University of Cambridge. Accessed January 23, 2021. https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131.

MLA Handbook (7^th Edition):

Perron, Umberto. “The influence of structural constraints on protein evolution.” 2020. Web. 23 Jan 2021.

Vancouver:

Perron U. The influence of structural constraints on protein evolution. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Jan 23]. Available from: https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131.

Council of Science Editors:

Perron U. The influence of structural constraints on protein evolution. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://doi.org/10.17863/CAM.58154 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.818131

University of Arizona

23. Kumirov, Vlad K. Mechanisms and Consequences of Evolving a New Protein Fold .

Degree: 2016, University of Arizona

URL: http://hdl.handle.net/10150/605218

► The ability of mutations to change the fold of a protein provides evolutionary pathways to new structures. To study hypothetical pathways for protein fold evolution,… (more)

Subjects/Keywords: protein fold transformation; protein nmr spectroscopy; protein structure; Chemistry; protein evolution

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APA (6^th Edition):

Kumirov, V. K. (2016). Mechanisms and Consequences of Evolving a New Protein Fold . (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/605218

Chicago Manual of Style (16^th Edition):

Kumirov, Vlad K. “Mechanisms and Consequences of Evolving a New Protein Fold .” 2016. Doctoral Dissertation, University of Arizona. Accessed January 23, 2021. http://hdl.handle.net/10150/605218.

MLA Handbook (7^th Edition):

Kumirov, Vlad K. “Mechanisms and Consequences of Evolving a New Protein Fold .” 2016. Web. 23 Jan 2021.

Vancouver:

Kumirov VK. Mechanisms and Consequences of Evolving a New Protein Fold . [Internet] [Doctoral dissertation]. University of Arizona; 2016. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10150/605218.

Council of Science Editors:

Kumirov VK. Mechanisms and Consequences of Evolving a New Protein Fold . [Doctoral Dissertation]. University of Arizona; 2016. Available from: http://hdl.handle.net/10150/605218

Oregon State University

24. Berkholz, Donald S. Modeling protein structure at atomic resolution.

Degree: PhD, Biochemistry and Biophysics, 2009, Oregon State University

URL: http://hdl.handle.net/1957/12475

► This thesis includes three studies involving different aspects of modeling protein structure. The first study illustrates the levels of insight available from atomic-resolution protein structures.… (more)

▼ This thesis includes three studies involving different aspects of modeling protein structure. The first study illustrates the levels of insight available from atomic-resolution protein structures. The second study derives general trends of protein geometry from atomic-resolution structures and shows their implications for modeling. The third study creates a model of a protein and uses it to derive new biological insights. In the first study, a series of structures were analyzed from human glutathione reductase, a biomedically relevant enzyme. Newly accessible at atomic resolution is structural evidence showing the catalytic importance of active-site compression, which additionally causes distortions from standard geometry that further enhance catalytic power. Another aspect of geometry visible at atomic resolution is the remarkably ideal positioning of atoms for catalysis. The stereoelectronic control displayed by compression and geometric preorganization provides insight into the origins of catalytic power. The second study builds upon quantum-mechanics calculations and empirical analyses of protein structure from the 1990s that showed the concept of a single ideal value for backbone geometry was wrong. Here, a nonredundant set of protein structures at atomic resolution is probed to better define the dependence of backbone geometry upon the conformation of the backbone torsion angles Φ and Ψ. The set was taken from the Protein Geometry Database created here (http://pgd.science.oregonstate.edu/). The trends seen make structural sense and lay the groundwork for a paradigm shift in the concept of ideal geometry. A conformation-dependent library accounting for these trends has the potential to improve modeling accuracy. In the third study, a model of the tumor-suppressor merlin is created and used to gain new understanding of merlin's function. Merlin is the only known cytoskeletal tumor suppressor, and loss of functional merlin results in neurofibromatosis 2, characterized by nervous-system tumors, cataracts, and skin tumors. Clear errors were evident in available automatically created models, driving the need for a reliable structure. Merlin and its homologs have distinct functions, so the differences between them were probed, suggesting critical functional clusters. A new technique developed here for discovering gains and losses of function should be generally applicable to any two protein subfamilies with distinct functions. Advisors/Committee Members: Karplus, P. Andrew (advisor), Beckman, Joseph S (committee member).

Subjects/Keywords: protein structure; Proteins – Structure – Mathematical models

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

APA (6^th Edition):

Berkholz, D. S. (2009). Modeling protein structure at atomic resolution. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/12475

Chicago Manual of Style (16^th Edition):

Berkholz, Donald S. “Modeling protein structure at atomic resolution.” 2009. Doctoral Dissertation, Oregon State University. Accessed January 23, 2021. http://hdl.handle.net/1957/12475.

MLA Handbook (7^th Edition):

Berkholz, Donald S. “Modeling protein structure at atomic resolution.” 2009. Web. 23 Jan 2021.

Vancouver:

Berkholz DS. Modeling protein structure at atomic resolution. [Internet] [Doctoral dissertation]. Oregon State University; 2009. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1957/12475.

Council of Science Editors:

Berkholz DS. Modeling protein structure at atomic resolution. [Doctoral Dissertation]. Oregon State University; 2009. Available from: http://hdl.handle.net/1957/12475

25. Veyron, Simon. Structure et fonction des toxines bactériennes à domaine FIC : Structural and Biochemical studies of bacterial FIC toxins.

Degree: Docteur es, Biochimie et biologie structurale, 2017, Université Paris-Saclay (ComUE)

URL: http://www.theses.fr/2017SACLS452

► Les protéines à domaine FIC (Filamentation induced by cAMP) sont très répandues chez les bactéries où elles catalysent l’ajout d’une modification post-traductionnelle contenant un phosphate… (more)

▼ Les protéines à domaine FIC (Filamentation induced by cAMP) sont très répandues chez les bactéries où elles catalysent l’ajout d’une modification post-traductionnelle contenant un phosphate à une protéine cible, en utilisant différents co-substrats comme l’ATP. Certaines de ces protéines sont des toxines sécrétées par des pathogènes humains, mais la fonction de la plupart d’entre elles reste mystérieuse. Plus d’une dizaine de structures de protéines FIC ont été déterminées récemment, qui ont permis d’élucider leur mécanisme catalytique. L’une des sous-familles de protéines FIC possède un glutamate dans leur site catalytique, dont il a été proposé qu’il aurait une fonction auto-inhibitrice pour la fixation de l’ATP. Durant ma thèse, j’ai étudié la structure et les mécanismes de régulation de deux familles de protéines FIC : les protéines FIC à glutamate inhibiteur, et la toxine AnkX de la bactérie pathogène Legionella pneumophila.La première étude s’est intéressée à la protéine FIC de la bactérie pathogène Enterococcus faecalis (EfFIC), qui fait partie de la sous-famille des protéines FIC possédant un glutamate inhibiteur. J’ai résolu plusieurs structures cristallographique d’EfFIC, qui ont permis de caractériser son site catalytique et comment elle fixe l’AMP et l’ADP. En utilisant une propriété fréquemment observée d’auto-AMPylation (modification par l’AMP), j’ai montré au moyen d’ATP radioactif qu’EfFIC possède une activité basale d’auto-AMPylation, et j’ai identifié une nouvelle activité de dé-AMPylation. En m’inspirant des métaux observés dans mes structures cristallographiques, j’ai montré que l’alternance entre les activités d’AMPylation et de de-AMPylation dépend de la nature du métal fixé dans le site actif et de la présence du glutamate. Ce glutamate régulateur est également présent chez une protéine humaine, HYPE, qui possède une double activité d’AMPylation et dé-AMPylation d’ une chaperone du réticulum endoplasmique. Par un test de fluorescence, j’ai enfin montré que l’activité de HYPE était elle aussi régulée par les métaux comme celle de EfFIC. Ces résultats suggèrent un nouveau modèle de régulation partagé par des protéines FIC de la bactérie à l’homme.La seconde étude a porté sur la toxine AnkX de Legionella pneumophila, qui modifie les petites protéines G de la famille de Rab Rab1 et Rab35 (régulatrices du trafic cellulaire) par une molécule de phosphocholine (PC). En utilisant des liposomes de composition contrôlée, j’ai montré qu’AnkX interagit avec les membranes, et j’ai identifié par mutagenèse son domaine d’interaction avec les membranes. Au moyen de petites GTPases Rab ancrées artificiellement à la surface de liposomes par une queue 6his remplaçant le lipide naturel, j’ai montré que l’activité d’AnkX est stimulée par la présence de membranes. Des résultats préliminaires suggérent que Rab35 est un meilleur substrat que Rab1a, ce qui pourrait renseigner sur la fonction et le compartiment cellulaire où se trouve la toxine. J’ai ensuite mené une étude structurale d’AnkX par diffusion des rayons X… Advisors/Committee Members: Cherfils, Jacqueline (thesis director).

Subjects/Keywords: Structure; Toxine; Fonction; Structure; Pathogen; Protein

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APA (6^th Edition):

Veyron, S. (2017). Structure et fonction des toxines bactériennes à domaine FIC : Structural and Biochemical studies of bacterial FIC toxins. (Doctoral Dissertation). Université Paris-Saclay (ComUE). Retrieved from http://www.theses.fr/2017SACLS452

Chicago Manual of Style (16^th Edition):

Veyron, Simon. “Structure et fonction des toxines bactériennes à domaine FIC : Structural and Biochemical studies of bacterial FIC toxins.” 2017. Doctoral Dissertation, Université Paris-Saclay (ComUE). Accessed January 23, 2021. http://www.theses.fr/2017SACLS452.

MLA Handbook (7^th Edition):

Veyron, Simon. “Structure et fonction des toxines bactériennes à domaine FIC : Structural and Biochemical studies of bacterial FIC toxins.” 2017. Web. 23 Jan 2021.

Vancouver:

Veyron S. Structure et fonction des toxines bactériennes à domaine FIC : Structural and Biochemical studies of bacterial FIC toxins. [Internet] [Doctoral dissertation]. Université Paris-Saclay (ComUE); 2017. [cited 2021 Jan 23]. Available from: http://www.theses.fr/2017SACLS452.

Council of Science Editors:

Veyron S. Structure et fonction des toxines bactériennes à domaine FIC : Structural and Biochemical studies of bacterial FIC toxins. [Doctoral Dissertation]. Université Paris-Saclay (ComUE); 2017. Available from: http://www.theses.fr/2017SACLS452

NSYSU

26. Chen, Chun-jen. A New Fitness Function for Evaluating the Quality of Predicted Protein Structures.

Degree: Master, Computer Science and Engineering, 2010, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0902110-103900

► For understanding the function of a protein, the protein structure plays an important role. The prediction of protein structure from its primary sequence has significant… (more)

Subjects/Keywords: prediction; tertiary structure; protein

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

APA (6^th Edition):

Chen, C. (2010). A New Fitness Function for Evaluating the Quality of Predicted Protein Structures. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0902110-103900

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, Chun-jen. “A New Fitness Function for Evaluating the Quality of Predicted Protein Structures.” 2010. Thesis, NSYSU. Accessed January 23, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0902110-103900.

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, Chun-jen. “A New Fitness Function for Evaluating the Quality of Predicted Protein Structures.” 2010. Web. 23 Jan 2021.

Vancouver:

Chen C. A New Fitness Function for Evaluating the Quality of Predicted Protein Structures. [Internet] [Thesis]. NSYSU; 2010. [cited 2021 Jan 23]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0902110-103900.

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

Council of Science Editors:

Chen C. A New Fitness Function for Evaluating the Quality of Predicted Protein Structures. [Thesis]. NSYSU; 2010. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0902110-103900

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

University of Alberta

27. Lee, Brian L. An NMR-based approach to the structural and functional investigation of the Na+/H+ exchanger NHE1.

Degree: PhD, Department of Biochemistry, 2013, University of Alberta

URL: https://era.library.ualberta.ca/files/h415pb712

► The Na+/H+ exchanger isoform 1 (NHE1) is the predominant isoform in mammalian cells, and regulates intracellular pH and ion concentrations. NHE1 also interacts with numerous… (more)

▼ The Na+/H+ exchanger isoform 1 (NHE1) is the predominant isoform in mammalian cells, and regulates intracellular pH and ion concentrations. NHE1 also interacts with numerous proteins and signalling pathways. Consequently, it has been found to influence cell volume, growth, differentiation, and motility, and has roles in heart disease and cancer. While a wealth of biochemical and physiological data is available on NHE1, little is known about its structure or mechanism of function. In this thesis, a "divide and conquer" approach was used to study the structure and function of NHE1. The structures of individual transmembrane (TM) segments were determined using nuclear magnetic resonance (NMR) spectroscopy, and the function of the TM segments in the full protein were investigated using site-directed mutagenesis in cultured cells. We first examined the structures and functions of the second (EL 2) and fourth (EL 4) extracellular loops of NHE1. Both loops contained functionally important residues, however, EL 2 was found to be structured by NMR while EL 4 was unstructured. Next, we investigated two critical TM segments in NHE1, TM VI and TM XI, as well as TM IV of sod2, a yeast Na+/H+ exchanger. These TM segments were found to have unusual structures consisting of a N- and C-terminal alpha-helix, with an extended segment in between, and the structures correlated well with the functional data. We also looked at larger regions of NHE1 using NMR to examine the TM – TM interactions in the protein, starting with a structure of a two-TM segment of NHE1, TM VI – VII. We also present preliminary NMR experiments on two three-TM segments, TM V – VII and TM X – XII, as well as full-length Escherichia coli NhaA. Overall, the "divide and conquer" approach has allowed us to successfully examine the structures and functions of single-TM segments of NHE1. Furthermore, studies on multi-TM segments and NhaA suggest that we may be able to assemble the structure of NHE1 from its segments or even study the complete protein by NMR spectroscopy.

Subjects/Keywords: NHE1; membrane protein; structure; NMR

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

APA (6^th Edition):

Lee, B. L. (2013). An NMR-based approach to the structural and functional investigation of the Na+/H+ exchanger NHE1. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/h415pb712

Chicago Manual of Style (16^th Edition):

Lee, Brian L. “An NMR-based approach to the structural and functional investigation of the Na+/H+ exchanger NHE1.” 2013. Doctoral Dissertation, University of Alberta. Accessed January 23, 2021. https://era.library.ualberta.ca/files/h415pb712.

MLA Handbook (7^th Edition):

Lee, Brian L. “An NMR-based approach to the structural and functional investigation of the Na+/H+ exchanger NHE1.” 2013. Web. 23 Jan 2021.

Vancouver:

Lee BL. An NMR-based approach to the structural and functional investigation of the Na+/H+ exchanger NHE1. [Internet] [Doctoral dissertation]. University of Alberta; 2013. [cited 2021 Jan 23]. Available from: https://era.library.ualberta.ca/files/h415pb712.

Council of Science Editors:

Lee BL. An NMR-based approach to the structural and functional investigation of the Na+/H+ exchanger NHE1. [Doctoral Dissertation]. University of Alberta; 2013. Available from: https://era.library.ualberta.ca/files/h415pb712

University of Waterloo

28. Holtby, Daniel James. Loop Modeling in Proteins Using a Database Approach with Multi-Dimensional Scaling.

Degree: 2013, University of Waterloo

URL: http://hdl.handle.net/10012/7935

► Modeling loops is an often necessary step in protein structure and function determination, even with experimental X-ray and NMR data. It is well known to… (more)

Subjects/Keywords: loop modeling; protein structure

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

APA (6^th Edition):

Holtby, D. J. (2013). Loop Modeling in Proteins Using a Database Approach with Multi-Dimensional Scaling. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/7935

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):

Holtby, Daniel James. “Loop Modeling in Proteins Using a Database Approach with Multi-Dimensional Scaling.” 2013. Thesis, University of Waterloo. Accessed January 23, 2021. http://hdl.handle.net/10012/7935.

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

MLA Handbook (7^th Edition):

Holtby, Daniel James. “Loop Modeling in Proteins Using a Database Approach with Multi-Dimensional Scaling.” 2013. Web. 23 Jan 2021.

Vancouver:

Holtby DJ. Loop Modeling in Proteins Using a Database Approach with Multi-Dimensional Scaling. [Internet] [Thesis]. University of Waterloo; 2013. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/10012/7935.

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

Council of Science Editors:

Holtby DJ. Loop Modeling in Proteins Using a Database Approach with Multi-Dimensional Scaling. [Thesis]. University of Waterloo; 2013. Available from: http://hdl.handle.net/10012/7935

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

University of Toronto

29. Taylor, Matthew Wade. Expression and Structural Studies of Nucleic Acid Binding Cytidine Deaminases.

Degree: 2016, University of Toronto

URL: http://hdl.handle.net/1807/76196

►

Activation Induced Deaminase (AID) and the APOBEC3 proteins are nucleic acid cytidine deaminases (CDs) which play critical roles the immune system. These proteins bind both… (more)

Subjects/Keywords: Crystallography; Deaminase; Protein Structure; 0487

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

APA (6^th Edition):

Taylor, M. W. (2016). Expression and Structural Studies of Nucleic Acid Binding Cytidine Deaminases. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/76196

Chicago Manual of Style (16^th Edition):

Taylor, Matthew Wade. “Expression and Structural Studies of Nucleic Acid Binding Cytidine Deaminases.” 2016. Masters Thesis, University of Toronto. Accessed January 23, 2021. http://hdl.handle.net/1807/76196.

MLA Handbook (7^th Edition):

Taylor, Matthew Wade. “Expression and Structural Studies of Nucleic Acid Binding Cytidine Deaminases.” 2016. Web. 23 Jan 2021.

Vancouver:

Taylor MW. Expression and Structural Studies of Nucleic Acid Binding Cytidine Deaminases. [Internet] [Masters thesis]. University of Toronto; 2016. [cited 2021 Jan 23]. Available from: http://hdl.handle.net/1807/76196.

Council of Science Editors:

Taylor MW. Expression and Structural Studies of Nucleic Acid Binding Cytidine Deaminases. [Masters Thesis]. University of Toronto; 2016. Available from: http://hdl.handle.net/1807/76196

Hong Kong University of Science and Technology

30. Li, Youjun. Complex structure of crumbs cytoplasmic tail with moesin FERM domain reveals a novel FERM-binding mode.

Degree: 2012, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-73408 ; https://doi.org/10.14711/thesis-b1190245 ; http://repository.ust.hk/ir/bitstream/1783.1-73408/1/th_redirect.html

► The apical transmembrane protein Crumbs is a determinant of apical-basal cell polarity. The short cytoplasmic domain of Crumbs, containing two highly conserved motifs, a PSD95/Discs-large/ZO1… (more)

Subjects/Keywords: Membrane proteins ; Structure ; Protein binding

Record Details Similar Records Cite « Share

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

APA (6^th Edition):

Li, Y. (2012). Complex structure of crumbs cytoplasmic tail with moesin FERM domain reveals a novel FERM-binding mode. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-73408 ; https://doi.org/10.14711/thesis-b1190245 ; http://repository.ust.hk/ir/bitstream/1783.1-73408/1/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):

Li, Youjun. “Complex structure of crumbs cytoplasmic tail with moesin FERM domain reveals a novel FERM-binding mode.” 2012. Thesis, Hong Kong University of Science and Technology. Accessed January 23, 2021. http://repository.ust.hk/ir/Record/1783.1-73408 ; https://doi.org/10.14711/thesis-b1190245 ; http://repository.ust.hk/ir/bitstream/1783.1-73408/1/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):

Li, Youjun. “Complex structure of crumbs cytoplasmic tail with moesin FERM domain reveals a novel FERM-binding mode.” 2012. Web. 23 Jan 2021.

Vancouver:

Li Y. Complex structure of crumbs cytoplasmic tail with moesin FERM domain reveals a novel FERM-binding mode. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2012. [cited 2021 Jan 23]. Available from: http://repository.ust.hk/ir/Record/1783.1-73408 ; https://doi.org/10.14711/thesis-b1190245 ; http://repository.ust.hk/ir/bitstream/1783.1-73408/1/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:

Li Y. Complex structure of crumbs cytoplasmic tail with moesin FERM domain reveals a novel FERM-binding mode. [Thesis]. Hong Kong University of Science and Technology; 2012. Available from: http://repository.ust.hk/ir/Record/1783.1-73408 ; https://doi.org/10.14711/thesis-b1190245 ; http://repository.ust.hk/ir/bitstream/1783.1-73408/1/th_redirect.html

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

Open Access Theses and Dissertations