subject:(Conformation)

Hong Kong University of Science and Technology

1. Ding, Dongbo LIFS. Characterization of human testis specific H2B variants H2Bfw153 and H2BFW175.

Degree: 2016, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-95286 ; https://doi.org/10.14711/thesis-b1736681 ; http://repository.ust.hk/ir/bitstream/1783.1-95286/1/th_redirect.html

► In eukaryotic cells, genomic DNA is wrapped by two copies of histone H2A, H2B, H3 and H4 and formed nucleosome. The histones can be pot-translationally… (more)

▼ In eukaryotic cells, genomic DNA is wrapped by two copies of histone H2A, H2B, H3 and H4 and formed nucleosome. The histones can be pot-translationally modified and replaced during many metabolic processes. Histone dynamics play important roles in transcription regulation, DNA damage repair, development and many other processes. In spermatogenesis, canonical histones can also be replaced by testis specific histone variants. H2BFW is one of the testis specific histone H2B variants and is only present in primates. However, expression of H2BFW was only detectable at mRNA level, while the expression at protein level and the localization of H2BFW and the characteristics of H2BFW nucleosome are still unknown. The histone variants influence the characteristics of nucleosomes, such as configuration, stability, and distribution. To learn the characteristics of H2BFW, we first identified the expression of H2BFW at protein level in both HeLa cells and mature sperm, including H2BFW153 and H2BFW175. They both can form mono-nucleosome in vivo but the cellular distributions are different. The H2BFW153 nucleosome is mainly found in euchromatin and the H2BFW175 nucleosome is mainly distributed in heterochromatin and nuclear matrix fractions. Furthermore, we also compared the difference between the canonical nucleosome and the H2BFW nucleosomes by biochemical stability assay. The results show that the stability of the H2BFW nucleosomes, especially the H2BFW175 nucleosome, are lower than canonical nucleosome. And the N terminal of H2BFW175 is the responsible for this destabilization. Since we know that RNA polymerase II has to transcribe through nucleosomes, we studied the effect of RNA polymerase II transcription in the H2BFW nucleosomes. RNA polymerase II is much easier to go through the H2BFW nucleosomes. Taken together, we identified the expression of H2BFW at protein level, and found that both H2BFW153 and H2BFW175 distribute differently from canonical H2B. Moreover, the stabilities of H2BFW nucleosomes are lower than canonical nucleosome mainly because of longer N terminal tail. Key words: Histone Variants, H2BFW, Nucleosome Stability, Histone Distribution

Subjects/Keywords: Histones ; Conformation

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APA (6^th Edition):

Ding, D. L. (2016). Characterization of human testis specific H2B variants H2Bfw153 and H2BFW175. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-95286 ; https://doi.org/10.14711/thesis-b1736681 ; http://repository.ust.hk/ir/bitstream/1783.1-95286/1/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):

Ding, Dongbo LIFS. “Characterization of human testis specific H2B variants H2Bfw153 and H2BFW175.” 2016. Thesis, Hong Kong University of Science and Technology. Accessed April 13, 2021. http://repository.ust.hk/ir/Record/1783.1-95286 ; https://doi.org/10.14711/thesis-b1736681 ; http://repository.ust.hk/ir/bitstream/1783.1-95286/1/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):

Ding, Dongbo LIFS. “Characterization of human testis specific H2B variants H2Bfw153 and H2BFW175.” 2016. Web. 13 Apr 2021.

Vancouver:

Ding DL. Characterization of human testis specific H2B variants H2Bfw153 and H2BFW175. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2016. [cited 2021 Apr 13]. Available from: http://repository.ust.hk/ir/Record/1783.1-95286 ; https://doi.org/10.14711/thesis-b1736681 ; http://repository.ust.hk/ir/bitstream/1783.1-95286/1/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:

Ding DL. Characterization of human testis specific H2B variants H2Bfw153 and H2BFW175. [Thesis]. Hong Kong University of Science and Technology; 2016. Available from: http://repository.ust.hk/ir/Record/1783.1-95286 ; https://doi.org/10.14711/thesis-b1736681 ; http://repository.ust.hk/ir/bitstream/1783.1-95286/1/th_redirect.html

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

Oregon State University

2. Nirudodhi, Sasidhar N. Hydrogen/deuterium exchange mass spectrometry as a technology platform for studying conformational dynamics in large protein complexes.

Degree: PhD, Chemistry, 2013, Oregon State University

URL: http://hdl.handle.net/1957/44792

► Proteins are essential to all biological systems. Proteins participate in numerous cellular processes by interacting with other proteins, other metabolites and membranes in a dynamic… (more)

▼ Proteins are essential to all biological systems. Proteins participate in numerous cellular processes by interacting with other proteins, other metabolites and membranes in a dynamic environment. Studying the structural and conformational properties of proteins in the solution phase is necessary to understand their protein folding and interaction dynamics. This research project focused on the development and application of hydrogen deuterium exchange mass spectrometry (HDX-MS) technology for studying the conformational dynamics of large multi-subunit protein systems. HDX-MS studies were conducted on representative proteins of two much researched protein families, namely Peroxiredoxins (Prxs) and Cullin Ring Ligases (CRLs). As part of this research we implemented tandem mass spectrometry in the data independent acquisition (MS[supserscript E]) mode for the HDX-MS analysis. We also used ion mobility as a second and orthogonal dimension of separation to overcome the spectral crowdedness. Peroxiredoxins are ubiquitous antioxidant enzymes present in many organisms. Their catalytic activity is regulated by redox dependent oligomerization and their sensitivity to overoxidation is related to the flexibility of the active site loop to undergo partial unfolding. In this research we conducted HDX-MS experiments for determining to what extent the flexibility of the active site loop governs the sensitivity of peroxiredoxins to overoxidation. As example of a robust peroxiredoxin we studied initially the conformational properties of Salmonella typhimurium AhpC wild-type protein by HDX-MS. Subsequently, we conducted comparative HDX-MS analysis on the reduced form of the wild-type protein, and two single point mutants, T77V, and T77I, with the objective to decipher to what extent the stability of the dimer-dimer (A)interface affects the conformational dynamics of the active site loop. Differential HDX-MS results of the wild-type, disulfide reduced wild-type protein have exhibited a decrease in the motility of the active site loop and the C-terminal end of the protein upon disulfide reduction. The Thr77 single point mutation by valine enhanced the dimer-dimer interaction thereby stabilizing the decamer interface and increasing the motility of the active site loop. Whereas, the substitution of T77 by isoleucine increased the motility of the interfacial region which forms the dimer-dimer interface thereby promoting the dissociation of the decamer to dimers. A technically more advanced HDX-MS experimental setup was used to study the exchange-in properties of two robust peroxiredoxins, namely the wild-type StAhpC and the C46S mutant of StAhpC, which mimicks the reduced wild-type StAhpC, in comparison to human Prx2, a peroxiredoxin which is considered as sensitive to overoxidation. When differential deuterium uptake of wild-type StAhpC, C46S mutant StAhpC were compared, increased conformational rigidity was observed in the C46S mutant protein compared to the wild-type Prx. The peptide with highest deuterium incorporation levels in the… Advisors/Committee Members: Maier, Claudia S. (advisor), Ostroverkhova, Oksana (committee member).

Subjects/Keywords: Peroxiredoxins; Proteins – Conformation

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APA (6^th Edition):

Nirudodhi, S. N. (2013). Hydrogen/deuterium exchange mass spectrometry as a technology platform for studying conformational dynamics in large protein complexes. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/44792

Chicago Manual of Style (16^th Edition):

Nirudodhi, Sasidhar N. “Hydrogen/deuterium exchange mass spectrometry as a technology platform for studying conformational dynamics in large protein complexes.” 2013. Doctoral Dissertation, Oregon State University. Accessed April 13, 2021. http://hdl.handle.net/1957/44792.

MLA Handbook (7^th Edition):

Nirudodhi, Sasidhar N. “Hydrogen/deuterium exchange mass spectrometry as a technology platform for studying conformational dynamics in large protein complexes.” 2013. Web. 13 Apr 2021.

Vancouver:

Nirudodhi SN. Hydrogen/deuterium exchange mass spectrometry as a technology platform for studying conformational dynamics in large protein complexes. [Internet] [Doctoral dissertation]. Oregon State University; 2013. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1957/44792.

Council of Science Editors:

Nirudodhi SN. Hydrogen/deuterium exchange mass spectrometry as a technology platform for studying conformational dynamics in large protein complexes. [Doctoral Dissertation]. Oregon State University; 2013. Available from: http://hdl.handle.net/1957/44792

King Abdullah University of Science and Technology

3. Pantoja Angles, Aarón. Conformational Regulation of the Essential Epigenetic Regulator UHRF1.

Degree: Biological and Environmental Sciences and Engineering (BESE) Division, 2018, King Abdullah University of Science and Technology

URL: http://hdl.handle.net/10754/627912

► UHRF1 is an essential epigenetic regulator implicated in the maintenance of DNA methylation. While its functional state has been suggested to be allosterically regulated by… (more)

▼ UHRF1 is an essential epigenetic regulator implicated in the maintenance of DNA methylation. While its functional state has been suggested to be allosterically regulated by phosphatidylinositol 5-phosphate and dependent on purification conditions and tags coupled to the protein, the expression system might have a broader impact on UHRF1s interaction properties. We hypothesized that the translation kinetics defined by the expression host has an impact on the folding process of the protein, which ultimately affects its structure and function. To test this idea, the cDNA of UHRF1 was recoded in order to generate optimized and harmonized sequences that were expected to alter the overall translation speed. Both proteins were expressed in Escherichia coli BL21-DE3 and their interaction profiles with H3K9me3 and unmodified H3 peptides were determined by microscale thermophoresis assays. The dissociation constants were compared by ttests in order to evaluate a possible change in the interaction properties of the optimized and harmonized proteins, compared to non-optimized UHRF1 expressed in E. coli BL21-DE3. While no difference was found for the interaction of optimized UHRF1 with the H3K9me3 peptide, a significant difference was found for its interaction with the unmodified H3 peptide. Moreover, both the interactions of harmonized UHRF1 with H3K9me3 and unmodified H3 peptides were determined to change. For this reason, we concluded that translation kinetics dependent on the expression system impacts the functional state of UHRF1. To further study this phenomenon, we expressed the consensus sequence of UHRF1 in Escherichia coli BL21-Codon Plus-(DE3)-RIL, a bacterial strain that is enriched with arginine, isoleucine, and leucine tRNA isoacceptors. Differences in its interaction profile with histone peptides were found when compared with UHRF1 expressed in Escherichia coli BL21-DE3. Since the major difference between these strains is the abundance of tRNAs, we obtained further findings that support our initial hypothesis. Additionally, the interaction profiles from the consensus UHRF1 protein were determined in the presence of PI5P to get an insight into how this phosphoinositide might impact the final structure and function of UHRF1. MST measurements and limited proteolysis assays led us to the idea of a partially open conformation for the UHRF1 expressed in E. coli BL21-DE3 and E.coli Codon Plus-(DE3)-RIL. Advisors/Committee Members: Fischle, Wolfgang (advisor), Adamo, Antonio (committee member), Mahfouz, Magdy M. (committee member), Jaremko, Lukasz (committee member).

Subjects/Keywords: UHRF1; CONFORMATION; REGULATION

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APA (6^th Edition):

Pantoja Angles, A. (2018). Conformational Regulation of the Essential Epigenetic Regulator UHRF1. (Thesis). King Abdullah University of Science and Technology. Retrieved from http://hdl.handle.net/10754/627912

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):

Pantoja Angles, Aarón. “Conformational Regulation of the Essential Epigenetic Regulator UHRF1.” 2018. Thesis, King Abdullah University of Science and Technology. Accessed April 13, 2021. http://hdl.handle.net/10754/627912.

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

MLA Handbook (7^th Edition):

Pantoja Angles, Aarón. “Conformational Regulation of the Essential Epigenetic Regulator UHRF1.” 2018. Web. 13 Apr 2021.

Vancouver:

Pantoja Angles A. Conformational Regulation of the Essential Epigenetic Regulator UHRF1. [Internet] [Thesis]. King Abdullah University of Science and Technology; 2018. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/10754/627912.

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

Council of Science Editors:

Pantoja Angles A. Conformational Regulation of the Essential Epigenetic Regulator UHRF1. [Thesis]. King Abdullah University of Science and Technology; 2018. Available from: http://hdl.handle.net/10754/627912

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

Durban University of Technology

4. Sharma, Parul. An assessment of the conformational profile of bombesin and its mammalian analogues using computational chemistry methods.

Degree: 2011, Durban University of Technology

URL: http://hdl.handle.net/10321/729

►

Submitted in fulfillment of the requirements of the Degree of Doctor of Technology: Chemistry, Durban University of Technology, 2011.

Understanding the dynamics and mechanism of… (more)

▼

Submitted in fulfillment of the requirements of the Degree of Doctor of Technology: Chemistry, Durban University of Technology, 2011.

Understanding the dynamics and mechanism of protein folding continues to be one of the central problems in molecular biology. Peptide folding experiments characterize the dynamics and molecular mechanisms of the early events of protein folding. However, generally the highly flexible nature of peptides makes their bioactive conformation assessment reasonably difficult as peptides fold at very fast rates experimentally, requiring probing on the nanosecond time resolution. On the other hand, determining the bioactive conformation of biological peptides is a requirement for the design of peptidomimetics in computer-aided drug design. Peptides offer a unique opportunity to bridge the gap between theoretical and experimental understanding of protein folding. Therefore, the present work focuses on the exploration of the conformational space of biologically active neuropeptides with the aim of characterizing their conformational profile. Specifically, bombesin, neuromedin B (NMB) and neuromedin C (NMC), have been chosen for the current investigations. These peptides are widely distributed in the gastrointestinal tract, spinal cord and brain, and are known to elicit various physiological effects, including inhibition of feeding, smooth muscle contraction, exocrine and endocrine secretions, thermoregulation, blood pressure and sucrose regulations and cell growth. These peptides act as a growth factor in a wide range of tumours including carcinomas of the pancreas, stomach, breast, prostate, and colon. This work is intended to get some insight into the performance of different procedures used to explore the configurational space to provide an adequate atomic description of these systems. Different methodological studies involving utilization of molecular dynamics (MD), multicanonical replica exchange molecular dynamics (REMD) and simulate annealing (SA) are undertaken to explore the folding characteristics and thermodynamics of these neuropeptides. MD and REMD calculations on bombesin peptide have revealed its dual conformational behaviour never discovered before and is described in chapter 3. These results explain the known structure-activity studies and open the door to the understanding of the affinity of this peptide to two different receptors: BB1 and BB2. In the case of NMC, REMD calculations are carried out in explicit and implicit solvents, using the Generalized Born (GB) surface area, and are then complemented with two additional MD simulations performed using Langevin and Berendsen thermostats. The results obtained clearly reveal that REMD, performed under explicit solvent conditions, is more efficient and samples preferentially folded conformations with a higher content of  and γ turns. Moreover, these results show good agreement with the experimental results supporting the role of two -turns for its biological action, as reported in the …

Advisors/Committee Members: Bisetty, Krishna.

Subjects/Keywords: Peptides – Conformation; Bombesin – Conformation; Chemistry – Data processing; Protein folding; Proteins – Conformation

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APA (6^th Edition):

Sharma, P. (2011). An assessment of the conformational profile of bombesin and its mammalian analogues using computational chemistry methods. (Thesis). Durban University of Technology. Retrieved from http://hdl.handle.net/10321/729

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):

Sharma, Parul. “An assessment of the conformational profile of bombesin and its mammalian analogues using computational chemistry methods.” 2011. Thesis, Durban University of Technology. Accessed April 13, 2021. http://hdl.handle.net/10321/729.

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

MLA Handbook (7^th Edition):

Sharma, Parul. “An assessment of the conformational profile of bombesin and its mammalian analogues using computational chemistry methods.” 2011. Web. 13 Apr 2021.

Vancouver:

Sharma P. An assessment of the conformational profile of bombesin and its mammalian analogues using computational chemistry methods. [Internet] [Thesis]. Durban University of Technology; 2011. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/10321/729.

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

Council of Science Editors:

Sharma P. An assessment of the conformational profile of bombesin and its mammalian analogues using computational chemistry methods. [Thesis]. Durban University of Technology; 2011. Available from: http://hdl.handle.net/10321/729

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

University of Alberta

5. Manafiazar,Ghader. Investigation of Residual Feed Intake in Dairy Cows.

Degree: PhD, Department of Agricultural, Food, and Nutritional Science, 2013, University of Alberta

URL: https://era.library.ualberta.ca/files/5712m710t

► This thesis research was aimed to develop a residual feed intake (RFI) prediction equation in dairy cattle while accounting for the animals’ multifunctional lactation non-linear… (more)

▼ This thesis research was aimed to develop a residual feed intake (RFI) prediction equation in dairy cattle while accounting for the animals’ multifunctional lactation non-linear energy requirements profiles. The possibility of shortening RFI test period and finding indicator traits for RFI selection were also investigated. A total of 281 first-lactation dairy cows at the Dairy Research and Technology Center of the University of Alberta from June 2007 through October 2012 were used. Individual daily feed intakes, repeated measurements of monthly body weight, and body condition scores of these animals were recorded from 5 to 305 days-in-milk. Milk production and milk composition data were extracted from the Dairy Herd Improvement Program, and their first type classification data was retrieved from the Canadian Dairy Network. To reduce the test period in a lactation, the acquired data from whole lactation (5 to 305 DIM) was subdivided equally into three shortened periods, early, mid, and late stage of lactation. RFI prediction equations were developed for the whole and each of the shortened periods. Each animal, based on its predicted RFI value, was assigned to high (RFI> 0.5 SD) medium (RFI= ± 0.5 SD) or low (RFI< 0.5 SD) RFI classes within each of the test period. Compared with whole lactation, numbers of the animals’ remaining in the same RFI class within any of the shortened test periods were determined to study the consistency of RFI prediction. Moreover, genetic and phenotypic correlations between conformation traits and RFI were estimated to investigate the possibility to use these conformation traits as indicator traits for RFI selection. The results showed that RFI could be predicted in whole, early, mid and late lactation with R-square of 0.68, 0.47, 0.49, and 0.79, respectively. Compared with the whole lactation, most of the animals (65.5%) remained in the same RFI classes in mid stage, so mid RFI prediction could be considered as the best representative of whole RFI in compare with early and late periods. Moreover, combinations of eight conformation traits could be used as indicator traits for RFI selection, since they had high genetic correlation with whole lactation RFI.

Subjects/Keywords: Conformation; RFI; Dairy; Efficiency; Feed

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APA (6^th Edition):

Manafiazar,Ghader. (2013). Investigation of Residual Feed Intake in Dairy Cows. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/5712m710t

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

Manafiazar,Ghader. “Investigation of Residual Feed Intake in Dairy Cows.” 2013. Doctoral Dissertation, University of Alberta. Accessed April 13, 2021. https://era.library.ualberta.ca/files/5712m710t.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

Manafiazar,Ghader. “Investigation of Residual Feed Intake in Dairy Cows.” 2013. Web. 13 Apr 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

Manafiazar,Ghader. Investigation of Residual Feed Intake in Dairy Cows. [Internet] [Doctoral dissertation]. University of Alberta; 2013. [cited 2021 Apr 13]. Available from: https://era.library.ualberta.ca/files/5712m710t.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

Manafiazar,Ghader. Investigation of Residual Feed Intake in Dairy Cows. [Doctoral Dissertation]. University of Alberta; 2013. Available from: https://era.library.ualberta.ca/files/5712m710t

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

University of Manchester

6. Le Bailly, Bryden. Controlling macromolecular conformation for the nanoscale transmission of information.

Degree: 2015, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:266282

► Helical oligomers made up of the achiral amino acid Aib (2-aminoisobutyric acid) have great potential in relaying stereochemical information over nanometre distances by control of… (more)

Subjects/Keywords: helix; conformation; stereochemical information

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

APA (6^th Edition):

Le Bailly, B. (2015). Controlling macromolecular conformation for the nanoscale transmission of information. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:266282

Chicago Manual of Style (16^th Edition):

Le Bailly, Bryden. “Controlling macromolecular conformation for the nanoscale transmission of information.” 2015. Doctoral Dissertation, University of Manchester. Accessed April 13, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:266282.

MLA Handbook (7^th Edition):

Le Bailly, Bryden. “Controlling macromolecular conformation for the nanoscale transmission of information.” 2015. Web. 13 Apr 2021.

Vancouver:

Le Bailly B. Controlling macromolecular conformation for the nanoscale transmission of information. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2021 Apr 13]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:266282.

Council of Science Editors:

Le Bailly B. Controlling macromolecular conformation for the nanoscale transmission of information. [Doctoral Dissertation]. University of Manchester; 2015. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:266282

Texas A&M University

7. Reddy Chinnaswamy, Sreedhar. De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase.

Degree: PhD, Biochemistry, 2011, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-2010-05-7816

► Hepatitis C Virus (HCV) is a positive-strand RNA virus that has infected more than 3% of the world population. Chronic infections by the virus lead… (more)

▼ Hepatitis C Virus (HCV) is a positive-strand RNA virus that has infected more than 3% of the world population. Chronic infections by the virus lead to cirrhosis and hepatocellular carcinoma. HCV is currently the leading cause for liver transplantation in the US. The nonstructural protein NS5B of HCV is the RNA-dependent RNA polymerase (RdRp) that replicates the viral RNA on host derived membranous structures. Structurally NS5B has the characteristic fingers, thumb and palm domains seen in all polymerase proteins. However, extensive interactions between the fingers and thumb domains completely encircle the active site of NS5B as seen in solved X-ray diffraction crystal structures. These interactions are primarily mediated by a short (35 residues) flexible loop called the Delta 1 loop. NS5B produced from heterologous systems can initiate RNA synthesis by a de novo initiation mechanism from 3?ends of RNA templates or can also extend from 3'ends of primers that are annealed stably to a template RNA in biochemical assays. The closed conformation of NS5B as per X-ray crystal structures can only accommodate a ssRNA but not a dsRNA, hence necessitating a conformational change between de novo initiation and elongation. The details of these conformational changes are not known and will prove to be important to design potent polymerase inhibitors. The study performed for this dissertation focused on the conformational requirements of NS5B during de novo initiation and primer extension (or elongation). Biochemical assays utilizing template RNAs that can lead to both de novo initiation and primer extension products were utilized, and a systematic mutational analysis of the template channel of the RdRp was performed. Mutants W397A and H428A were identified that showed only primer extension but no de novo initiation. Structural analysis of NS5B suggested that these residues were important contact points in the Delta 1 loop and thumb domain interactions. A deletion mutant, m26-30 with a five amino acid deletion at the apex of the Delta 1 loop also failed in de novo initiation but not primer extension reactions. Biophysical and gel shift assays showed that m26-30 was in a more open conformation than the WT enzyme. Furthermore, oligomerization of NS5B was demonstrated and its role in RNA synthesis was examined. It was found that the de novo initiation competent conformation of NS5B is maintained by oligomeric contacts between individual subunits, likely by stabilizing the Delta 1 loop and thumb domain interactions. Mutations disrupting the Delta 1 loop and thumb domain interactions as well as those in the allosteric GTP binding site induced conformational changes in the protein partially explaining the defect in de novo initiation activity in enzymes carrying those mutations. These results not only contribute to the overall mechanism of RNA synthesis in viral RdRps but also open new avenues for developing HCV polymerase inhibitors. Advisors/Committee Members: Kao, Cheng C. (advisor), Young, Ryland F. (advisor), Leibowitz, Julian L. (committee member), Scholtz, Martin J. (committee member).

Subjects/Keywords: HCV; RdRp; Polymerase; Conformation; Oligomerization

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

APA (6^th Edition):

Reddy Chinnaswamy, S. (2011). De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2010-05-7816

Chicago Manual of Style (16^th Edition):

Reddy Chinnaswamy, Sreedhar. “De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase.” 2011. Doctoral Dissertation, Texas A&M University. Accessed April 13, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-2010-05-7816.

MLA Handbook (7^th Edition):

Reddy Chinnaswamy, Sreedhar. “De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase.” 2011. Web. 13 Apr 2021.

Vancouver:

Reddy Chinnaswamy S. De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase. [Internet] [Doctoral dissertation]. Texas A&M University; 2011. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2010-05-7816.

Council of Science Editors:

Reddy Chinnaswamy S. De Novo Initiated RNA Synthesis by the Hepatitis C Virus RNA-dependent RNA Polymerase. [Doctoral Dissertation]. Texas A&M University; 2011. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2010-05-7816

Texas A&M University

8. Tuvilla, Mavreen Rose. Enzymatic Digestion in Aqueous-Organic Solvents: A Mass Spectrometry-Based Approach in Monitoring Protein Conformation Changes.

Degree: MS, Chemistry, 2013, Texas A&M University

URL: http://hdl.handle.net/1969.1/149503

► The three dimensional structure of a protein is important for its function. When misfolded, a protein may be rendered inactive or adapt a conformation that… (more)

▼ The three dimensional structure of a protein is important for its function. When misfolded, a protein may be rendered inactive or adapt a conformation that could be toxic. Studying protein folding requires an understanding of protein conformation. Traditionally, protein conformation has been studied using x-ray crystallography and nuclear magnetic resonance (NMR). X-ray crystallography is limited in the analysis of crystallized proteins and is computationally intensive. NMR deals with proteins in solution but reports only an average of conformation and the technique severely suffers from spectral overlapping due to the thousands of resonances of the protein. More recently, mass spectrometry has been employed not only to elucidate primary structures but also gather information on the three-dimensional conformation of proteins. In this study, a mass spectrometric-based approach is used to study the changes in conformation of cytochrome c and the green fluorescent protein when subjected to aqueous-organic solvent systems. The technique involved trypsin digestion and generation of peptide mass maps. For cytochrome c, the experiments were done with ethanol, methanol and acetonitrile to gain insights on naturation and denaturation. An apparent solvent effect to the rate of digestion and propensity for missed cleavages attributed to weakening of hydrophobic interactions and strengthening of intramolecular hydrogen bonding was observed. For the green fluorescent protein, sulfolane, a known supercharging agent, was used to gain insights on the effect of supercharging to protein conformation. Addition of 2.0% sulfolane shifted the charge state envelope of the protein towards lower m/z while adding lower amounts of sulfolane enhanced lower charge states while broadening the charge state envelope. The time course study showed different patterns of digestion dependent on solvent conditions implying changes in conformation. Furthermore, absorbance and fluorescence measurements suggested that addition of sulfolane protects the fluorophore from quenching. The activity of trypsin is not affected by addition of low amounts of sulfolane. Advisors/Committee Members: Russell, David H (advisor), Liu, Wenshe (committee member), Capareda, Sergio (committee member).

Subjects/Keywords: Mass Spectrometry; Protein Conformation

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

APA (6^th Edition):

Tuvilla, M. R. (2013). Enzymatic Digestion in Aqueous-Organic Solvents: A Mass Spectrometry-Based Approach in Monitoring Protein Conformation Changes. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/149503

Chicago Manual of Style (16^th Edition):

Tuvilla, Mavreen Rose. “Enzymatic Digestion in Aqueous-Organic Solvents: A Mass Spectrometry-Based Approach in Monitoring Protein Conformation Changes.” 2013. Masters Thesis, Texas A&M University. Accessed April 13, 2021. http://hdl.handle.net/1969.1/149503.

MLA Handbook (7^th Edition):

Tuvilla, Mavreen Rose. “Enzymatic Digestion in Aqueous-Organic Solvents: A Mass Spectrometry-Based Approach in Monitoring Protein Conformation Changes.” 2013. Web. 13 Apr 2021.

Vancouver:

Tuvilla MR. Enzymatic Digestion in Aqueous-Organic Solvents: A Mass Spectrometry-Based Approach in Monitoring Protein Conformation Changes. [Internet] [Masters thesis]. Texas A&M University; 2013. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1969.1/149503.

Council of Science Editors:

Tuvilla MR. Enzymatic Digestion in Aqueous-Organic Solvents: A Mass Spectrometry-Based Approach in Monitoring Protein Conformation Changes. [Masters Thesis]. Texas A&M University; 2013. Available from: http://hdl.handle.net/1969.1/149503

Université Laval

9. Bussières, Sylvain. Étude de l'activité enzymatique, de la structure secondaire et de la liaison membranaire de la lécithine : rétinol acyltransférase.

Degree: 2011, Université Laval

URL: http://hdl.handle.net/20.500.11794/23136

► La lécithine:rétinol acyltransferase (LRAT) est une enzyme de l'épithélium pigmentaire rétinien (EPR) qui joue un rôle essentiel dans le cycle visuel des rétinoïdes au niveau… (more)

▼ La lécithine:rétinol acyltransferase (LRAT) est une enzyme de l'épithélium pigmentaire rétinien (EPR) qui joue un rôle essentiel dans le cycle visuel des rétinoïdes au niveau de l'estérification du rétinol tout-trans en rétinyl ester tout-trans. Plusieurs travaux de caractérisation de cette protéine ont été publiés depuis les 20 dernières années, mais ce n'est que depuis 2003 qu'il est possible d'utiliser une forme tronquée et purifiée de la LRAT qui correspond à sa portion cytosolique (tLRAT) (Bok et al. 2003). Bien que plusieurs mécanismes biochimiques aient été approfondis avec la tLRAT purifiée, très peu d'investigations à propos de sa structure et de son interaction membranaire ont été publiées jusqu'à maintenant. De plus, même si les paramètres enzymatiques de la tLRAT ont été étudiés par différents groupes de recherche, ces travaux ont été effectués avec un protocole expérimental indadéquat conduisant à des niveaux d'activité non-reproductibles d'un article à l'autre. Nous avons donc produit la tLRAT afin d'étudier en profondeur sa structure secondaire, son interaction membranaire et son activité enzymatique. En élaborant un nouveau protocole de recherche pour étudier l'activité enzymatique de la tLRAT, nous avons pu obtenir des niveaux d'activité très élevés et reproductibles. Par surcroît, les méthodes de spectroscopie infrarouge (IR) dichroïsme circulaire électronique et vibrationnel ont permis de déterminer que la tLRAT était constituée d'une structure secondaire majoritairement en hélice alpha. Ensuite, la spectroscopie de réflexion-absorption par modulation de polarisation en IR (PM-IRRAS) a permis de déterminer que la tLRAT interagissait fortement et hydrolysait des monocouches de phospholipides. L'interaction entre la tLRAT et différents types de lipides retrouvés dans les membranes de l'EPR a également été caractérisée avec la méthode des monocouches de Langmuir par la détermination de la pression d'insertion maximale (PIM). Cette méthode a permis de déterminer que la tLRAT s'adsorbait spontanément aux monocouches de lipides à des pressions de surface au-delà la pression latérale des membranes biologiques. Les deux segments hydrophobes en N- et C-terminal de la LRAT qui n'ont pas été surexprimés dans la tLRAT ont été synthétisés afin de les étudier en PM-IRRAS. Ces expériences ont permis de démontrer qu'ils interagissaient fortement avec les monocouches de lipide et qu'ils adoptaient une structure en hélice alpha. Enfin, le mutant S175R responsable de la rétinite pigmentaire a été produit afin de comprendre les impacts moléculaires de cette mutation. La méthode des monocouches de Langmuir et le dichroïsme circulaire ont permis de démontrer que son interaction membranaire et sa structure secondaire n'étaient pas modifiés en comparaison à la forme sauvage de la tLRAT. Cependant, comme son activité enzymatique est absente, il a été conclu que l'entrée du substrat dans le site actif devait être compromise par la mutation de la serine en arginine. Advisors/Committee Members: Salesse, Christian.

Subjects/Keywords: Acyltransférases; Protéines – Structure; Protéines – Conformation

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

APA (6^th Edition):

Bussières, S. (2011). Étude de l'activité enzymatique, de la structure secondaire et de la liaison membranaire de la lécithine : rétinol acyltransférase. (Thesis). Université Laval. Retrieved from http://hdl.handle.net/20.500.11794/23136

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):

Bussières, Sylvain. “Étude de l'activité enzymatique, de la structure secondaire et de la liaison membranaire de la lécithine : rétinol acyltransférase.” 2011. Thesis, Université Laval. Accessed April 13, 2021. http://hdl.handle.net/20.500.11794/23136.

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

MLA Handbook (7^th Edition):

Bussières, Sylvain. “Étude de l'activité enzymatique, de la structure secondaire et de la liaison membranaire de la lécithine : rétinol acyltransférase.” 2011. Web. 13 Apr 2021.

Vancouver:

Bussières S. Étude de l'activité enzymatique, de la structure secondaire et de la liaison membranaire de la lécithine : rétinol acyltransférase. [Internet] [Thesis]. Université Laval; 2011. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/20.500.11794/23136.

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

Council of Science Editors:

Bussières S. Étude de l'activité enzymatique, de la structure secondaire et de la liaison membranaire de la lécithine : rétinol acyltransférase. [Thesis]. Université Laval; 2011. Available from: http://hdl.handle.net/20.500.11794/23136

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

10. Martins, Ramon Silva. Numerical simulation of turbulent viscoelastic fluid flows : flow classification and preservation of positive-definiteness of the conformation tensor : Simulation numérique d’écoulements turbulents de fluides visco-élastiques classification d’écoulements et préservation de la positivité du tenseur de conformation.

Degree: Docteur es, Mécanique, Énergétique et Sciences des matériaux, 2016, Université Lille I – Sciences et Technologies

URL: http://www.theses.fr/2016LIL10127

►

Le but de ce travail est de fournir une amélioration de la connaissance sur le phénomène de la réduction de la traînée induite par polymère… (more)

▼

Le but de ce travail est de fournir une amélioration de la connaissance sur le phénomène de la réduction de la traînée induite par polymère en considérant certains aspects de sa simulation numérique et les changements qui se produisent dans la cinématique de l’écoulement. Dans un premier temps, les transformations du type racine carrée et kernel racine-k pour le tenseur de conformation du modèle FENE-P ont été implémentées afin d’assurer la positivité du tenseur de conformation. Cependant, ces approches divergent en raison du caractère non-borné du tenseur de conformation. Cette contrainte n’a pas été respectée, même avec l’inclusion de diffusion artificielle. L’effet d’amortissement de la diffusion artificielle a permis d’assurer la stabilité numérique, mais il aboutit à une réduction de la traînée relative de 22% à 42% plus faible que prévue par les approches standards. Dans un second temps, les modes hyperboliques, paraboliques et elliptiques des écoulements turbulents viscoélastiques ont été évalués en utilisant de différents critères de classification d’écoulements. Certains avantages concernant les critères objectifs ont été discutés. On a observé que les domaines hyperboliques contribuent de manière significative à la cinématique de l’écoulement. Enfin, on a observé une tendance des domaines elliptiques et hyperboliques à devenir paraboliques et que cette tendance augmente avec l’élasticité.

The purpose of this work is to provide an enhancement of the knowledge about the polymer-induced drag reduction phenomenon by considering some aspects of its numerical simulation and the changes that occur in the flow kinematics. In the first part, the square root and kernel root-k formulations for the conformation tensor in the FENE-P model were implemented and showed to preserve the positiveness of the conformation tensor. However, they led to numerical divergence due to the loss of boundedness of the conformation tensor. This constraint was violated even with the inclusion of artificial diffusion. The damping effect of artificial diffusion helped to ensure numerical stability, but led to relative drag reduction from 22% to 42% lower than expected from traditional methods. In the second part, the hyperbolic, parabolic and elliptic modes of turbulent viscoelastic flows were evaluated by means of different flow classification criteria. Some advantages of considering objective criteria were discussed. It was shown that the hyperbolic domains significantly contribute to the flow kinematics. Finally, a tendency of both elliptic and hyperbolic domains to become parabolic was observed and found to increase with the elasticity.

Advisors/Committee Members: Thais, Laurent (thesis director), Mompean, Gilmar (thesis director).

Subjects/Keywords: Tenseur de conformation; 532.052 7

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APA (6^th Edition):

Martins, R. S. (2016). Numerical simulation of turbulent viscoelastic fluid flows : flow classification and preservation of positive-definiteness of the conformation tensor : Simulation numérique d’écoulements turbulents de fluides visco-élastiques classification d’écoulements et préservation de la positivité du tenseur de conformation. (Doctoral Dissertation). Université Lille I – Sciences et Technologies. Retrieved from http://www.theses.fr/2016LIL10127

Chicago Manual of Style (16^th Edition):

Martins, Ramon Silva. “Numerical simulation of turbulent viscoelastic fluid flows : flow classification and preservation of positive-definiteness of the conformation tensor : Simulation numérique d’écoulements turbulents de fluides visco-élastiques classification d’écoulements et préservation de la positivité du tenseur de conformation.” 2016. Doctoral Dissertation, Université Lille I – Sciences et Technologies. Accessed April 13, 2021. http://www.theses.fr/2016LIL10127.

MLA Handbook (7^th Edition):

Martins, Ramon Silva. “Numerical simulation of turbulent viscoelastic fluid flows : flow classification and preservation of positive-definiteness of the conformation tensor : Simulation numérique d’écoulements turbulents de fluides visco-élastiques classification d’écoulements et préservation de la positivité du tenseur de conformation.” 2016. Web. 13 Apr 2021.

Vancouver:

Martins RS. Numerical simulation of turbulent viscoelastic fluid flows : flow classification and preservation of positive-definiteness of the conformation tensor : Simulation numérique d’écoulements turbulents de fluides visco-élastiques classification d’écoulements et préservation de la positivité du tenseur de conformation. [Internet] [Doctoral dissertation]. Université Lille I – Sciences et Technologies; 2016. [cited 2021 Apr 13]. Available from: http://www.theses.fr/2016LIL10127.

Council of Science Editors:

Martins RS. Numerical simulation of turbulent viscoelastic fluid flows : flow classification and preservation of positive-definiteness of the conformation tensor : Simulation numérique d’écoulements turbulents de fluides visco-élastiques classification d’écoulements et préservation de la positivité du tenseur de conformation. [Doctoral Dissertation]. Université Lille I – Sciences et Technologies; 2016. Available from: http://www.theses.fr/2016LIL10127

Oregon State University

11. Zhou, Guangwen. Stabilization of Z-DNA by demethylation of thymine bases : a crystallization and thermo-dynamic study of d(m⁵CGUAm⁵CG).

Degree: PhD, Biochemistry and Biophysics, 1991, Oregon State University

URL: http://hdl.handle.net/1957/37229

Subjects/Keywords: DNA – Conformation

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APA (6^th Edition):

Zhou, G. (1991). Stabilization of Z-DNA by demethylation of thymine bases : a crystallization and thermo-dynamic study of d(m⁵CGUAm⁵CG). (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/37229

Chicago Manual of Style (16^th Edition):

Zhou, Guangwen. “Stabilization of Z-DNA by demethylation of thymine bases : a crystallization and thermo-dynamic study of d(m⁵CGUAm⁵CG).” 1991. Doctoral Dissertation, Oregon State University. Accessed April 13, 2021. http://hdl.handle.net/1957/37229.

MLA Handbook (7^th Edition):

Zhou, Guangwen. “Stabilization of Z-DNA by demethylation of thymine bases : a crystallization and thermo-dynamic study of d(m⁵CGUAm⁵CG).” 1991. Web. 13 Apr 2021.

Vancouver:

Zhou G. Stabilization of Z-DNA by demethylation of thymine bases : a crystallization and thermo-dynamic study of d(m⁵CGUAm⁵CG). [Internet] [Doctoral dissertation]. Oregon State University; 1991. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1957/37229.

Council of Science Editors:

Zhou G. Stabilization of Z-DNA by demethylation of thymine bases : a crystallization and thermo-dynamic study of d(m⁵CGUAm⁵CG). [Doctoral Dissertation]. Oregon State University; 1991. Available from: http://hdl.handle.net/1957/37229

University of Manchester

12. Le Bailly, Bryden. Controlling macromolecular conformation for the nanoscale transmission of information.

Degree: PhD, 2015, University of Manchester

URL: https://www.research.manchester.ac.uk/portal/en/theses/controlling-macromolecular-conformation-for-the-nanoscale-transmission-of-information(883d33a1-643b-48c5-bb21-fec8c0a06b4a).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.689551

► Helical oligomers made up of the achiral amino acid Aib (2-aminoisobutyric acid) have great potential in relaying stereochemical information over nanometre distances by control of… (more)

Subjects/Keywords: 547; helix; conformation; stereochemical information

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APA (6^th Edition):

Le Bailly, B. (2015). Controlling macromolecular conformation for the nanoscale transmission of information. (Doctoral Dissertation). University of Manchester. Retrieved from https://www.research.manchester.ac.uk/portal/en/theses/controlling-macromolecular-conformation-for-the-nanoscale-transmission-of-information(883d33a1-643b-48c5-bb21-fec8c0a06b4a).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.689551

Chicago Manual of Style (16^th Edition):

Le Bailly, Bryden. “Controlling macromolecular conformation for the nanoscale transmission of information.” 2015. Doctoral Dissertation, University of Manchester. Accessed April 13, 2021. https://www.research.manchester.ac.uk/portal/en/theses/controlling-macromolecular-conformation-for-the-nanoscale-transmission-of-information(883d33a1-643b-48c5-bb21-fec8c0a06b4a).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.689551.

MLA Handbook (7^th Edition):

Le Bailly, Bryden. “Controlling macromolecular conformation for the nanoscale transmission of information.” 2015. Web. 13 Apr 2021.

Vancouver:

Le Bailly B. Controlling macromolecular conformation for the nanoscale transmission of information. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2021 Apr 13]. Available from: https://www.research.manchester.ac.uk/portal/en/theses/controlling-macromolecular-conformation-for-the-nanoscale-transmission-of-information(883d33a1-643b-48c5-bb21-fec8c0a06b4a).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.689551.

Council of Science Editors:

Le Bailly B. Controlling macromolecular conformation for the nanoscale transmission of information. [Doctoral Dissertation]. University of Manchester; 2015. Available from: https://www.research.manchester.ac.uk/portal/en/theses/controlling-macromolecular-conformation-for-the-nanoscale-transmission-of-information(883d33a1-643b-48c5-bb21-fec8c0a06b4a).html ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.689551

Université de Sherbrooke

13. Jeandenans, Catherine. L'analyse des populations de conformations peptidiques hypersurfaces conformationnelles de molécules complexes.

Degree: 1996, Université de Sherbrooke

URL: http://savoirs.usherbrooke.ca/handle/11143/4946

► Dans le cadre de la mécanique moléculaire, nous somme capables de générer des échantillons représentatifs de toutes les conformations accessibles aux molécules complexes et flexibles… (more)

▼ Dans le cadre de la mécanique moléculaire, nous somme capables de générer des échantillons représentatifs de toutes les conformations accessibles aux molécules complexes et flexibles que sont les peptides. La diversité de conformations possibles conduit à des échantillons qui, pour être représentatifs, doivent comporter plusieurs centaines voire des milliers de conformations. Nous proposons d'utiliser les méthodes d'analyses de données pour l'étude de ces échantillons. Ces méthodes sont très largement appliquées aujourd'hui dans de très nombreux domaines et en particulier en chimie où la sophistication croissante des appareils de mesure et de calcul conduit à traiter des quantités massives de données. L'abondance des données devient un obstacle au traitement direct et masque les relations existant entre ces données. L'utilisation des méthodes d'analyse des données permet d'ordonnancer l'ensemble des données en dégageant les structures qui les caractérisent. Ces méthodes ont été appliquées sur des échantillons de conformations de trois peptides de taille croissante, le dernier présentant une diversité conformationnelle maximum. Les échantillons ont été générés par le programme PEPSEA précédemment développé au laboratoire. Nous présentons les résultats obtenus par les méthodes d'analyse de données adaptées au traitement de nos échantillons. Les performances de ces méthodes sont attestées par comparaison des résultats obtenus avec les études expérimentales disponibles. Les résultats obtenus montrent que les méthodes d'analyse de données sont particulièrement utiles dans le traitement de gros échantillons de conformation nécessaires pour traduire la flexibilité conformationnelle extrême des peptides. Ces résultats sont particulièrement intéressants quand il s'agit d'expliquer les relations structure-activité pour les peptides biologiquement actifs ainsi que nous le montrons avec le dernier peptide étudié. [Résumé abrégé par UMI]. Advisors/Committee Members: [non identifié] (advisor).

Subjects/Keywords: Peptides; Conformation

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APA (6^th Edition):

Jeandenans, C. (1996). L'analyse des populations de conformations peptidiques hypersurfaces conformationnelles de molécules complexes. (Doctoral Dissertation). Université de Sherbrooke. Retrieved from http://savoirs.usherbrooke.ca/handle/11143/4946

Chicago Manual of Style (16^th Edition):

Jeandenans, Catherine. “L'analyse des populations de conformations peptidiques hypersurfaces conformationnelles de molécules complexes.” 1996. Doctoral Dissertation, Université de Sherbrooke. Accessed April 13, 2021. http://savoirs.usherbrooke.ca/handle/11143/4946.

MLA Handbook (7^th Edition):

Jeandenans, Catherine. “L'analyse des populations de conformations peptidiques hypersurfaces conformationnelles de molécules complexes.” 1996. Web. 13 Apr 2021.

Vancouver:

Jeandenans C. L'analyse des populations de conformations peptidiques hypersurfaces conformationnelles de molécules complexes. [Internet] [Doctoral dissertation]. Université de Sherbrooke; 1996. [cited 2021 Apr 13]. Available from: http://savoirs.usherbrooke.ca/handle/11143/4946.

Council of Science Editors:

Jeandenans C. L'analyse des populations de conformations peptidiques hypersurfaces conformationnelles de molécules complexes. [Doctoral Dissertation]. Université de Sherbrooke; 1996. Available from: http://savoirs.usherbrooke.ca/handle/11143/4946

University of Melbourne

14. İrtegün, Sevgi. Tracking open and closed conformations of c-Src in the cell using fluorescent biosensors.

Degree: 2012, University of Melbourne

URL: http://hdl.handle.net/11343/37585

► c-Src, a member of Src-family tyrosine kinases, is critical to a diverse array of signalling pathways driving many fundamental processes. Aberrant c-Src activity is involved… (more)

▼ c-Src, a member of Src-family tyrosine kinases, is critical to a diverse array of signalling pathways driving many fundamental processes. Aberrant c-Src activity is involved in the development and progression of human cancers. c-Src has “open” active and “closed” inactive conformations that are structurally well understood; however, how conformational change occurs in cells and how it is connected to regulatory mechanisms remain unclear. In this thesis, a tetracysteine-based biosensor of c-Src conformation was developed for studying the regulation of c-Src activity in cells and for the screening of c-Src-specific inhibitors and activators. The biosensor was developed by engineering a tetracysteine (TC) sequence into the SH2 domain that only binds to the biarsenical dyes (ReAsH or FIAsH) in the open conformation and tagging the C-terminus of protein by Emerald fluorescent protein for tracking c-Src localization. Conformational selectivity of the biosensor was screened using constitutively open and closed c-Src variants. The biosensor specifically bound the red-fluorescent ReAsH only in the open conformation. Differential ReAsH reactivity of the sensor was validated in the truncated c-Src forms, corresponding to crystallographic structures of open and closed c-Src. In addition, the behaviour of the sensor was assessed in the full length c-Src. The biosensor was found to be more open than wild-type c-Src. While the TC mutations did not affect subcellular localization, the activity of the sensor was increased compared to wild-type c-Src. Further investigation revealed that the TC mutations did not influence on the secondary structure of the SH2 domain, but the mutations had reduced the affinity of the SH2 domain to the C-tail. A flow cytometry-based approach was employed to quantitate the conformation of the sensor. The biosensor appeared to be intermediate between the open and closed conformations. The conformational read out from the biosensor could be modulated by modifiers of c-Src activity. Over expression of Csk, c-Src inactivator, and binding of both PP2 and PP1, small-molecules SFKs selective inhibitor, shifted the conformational equilibrium towards the closed state, while binding of SI1, a small-molecule SFKs selective inhibitor, shifted the conformational equilibrium towards the open state. Autophosphorylation levels of Tyr-416, commonly used as an indicator of c-Src activity, did not correlate with open or closed status at high expression levels, as closed c-Src was substantially phosphorylated at Tyr-416. However, c-Src dependent phosphorylation of STAT3 appeared to be a good indicator of c-Src activity towards substrates and conformational status. Taken together, the results in this thesis suggest that this biosensor of c-Src conformation is a valuable new tool to differentiate regulatory effects on c-Src conformation in live cells, which will make it useful in studies of…

Subjects/Keywords: c-Src; conformation; biosensor

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

APA (6^th Edition):

İrtegün, S. (2012). Tracking open and closed conformations of c-Src in the cell using fluorescent biosensors. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/37585

Chicago Manual of Style (16^th Edition):

İrtegün, Sevgi. “Tracking open and closed conformations of c-Src in the cell using fluorescent biosensors.” 2012. Doctoral Dissertation, University of Melbourne. Accessed April 13, 2021. http://hdl.handle.net/11343/37585.

MLA Handbook (7^th Edition):

İrtegün, Sevgi. “Tracking open and closed conformations of c-Src in the cell using fluorescent biosensors.” 2012. Web. 13 Apr 2021.

Vancouver:

İrtegün S. Tracking open and closed conformations of c-Src in the cell using fluorescent biosensors. [Internet] [Doctoral dissertation]. University of Melbourne; 2012. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/11343/37585.

Council of Science Editors:

İrtegün S. Tracking open and closed conformations of c-Src in the cell using fluorescent biosensors. [Doctoral Dissertation]. University of Melbourne; 2012. Available from: http://hdl.handle.net/11343/37585

University of New South Wales

15. Khoury, Amanda. Untangling Mechanisms of the Architectural Protein CTCF.

Degree: Clinical School - St Vincent's Hospital, 2018, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/60391 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51997/SOURCE02?view=true

► The three-dimensional structure of chromatin regulates gene expression by facilitating contacts between promoters and regulatory elements, demarcating regions of activity and repression and compartmentalising the… (more)

Subjects/Keywords: CTCF; Three-dimensional chromatin conformation

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APA (6^th Edition):

Khoury, A. (2018). Untangling Mechanisms of the Architectural Protein CTCF. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/60391 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51997/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Khoury, Amanda. “Untangling Mechanisms of the Architectural Protein CTCF.” 2018. Doctoral Dissertation, University of New South Wales. Accessed April 13, 2021. http://handle.unsw.edu.au/1959.4/60391 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51997/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Khoury, Amanda. “Untangling Mechanisms of the Architectural Protein CTCF.” 2018. Web. 13 Apr 2021.

Vancouver:

Khoury A. Untangling Mechanisms of the Architectural Protein CTCF. [Internet] [Doctoral dissertation]. University of New South Wales; 2018. [cited 2021 Apr 13]. Available from: http://handle.unsw.edu.au/1959.4/60391 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51997/SOURCE02?view=true.

Council of Science Editors:

Khoury A. Untangling Mechanisms of the Architectural Protein CTCF. [Doctoral Dissertation]. University of New South Wales; 2018. Available from: http://handle.unsw.edu.au/1959.4/60391 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51997/SOURCE02?view=true

NSYSU

16. Fu, Ji-Qian. The Configuration and Conformation of Nature poetryââA Case Study of Wang Wei and William Wordsworth.

Degree: Master, Chinese Literature, 2017, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0614117-144917

► Configuration and conformation are two concepts of Chemistry, the former is similar to meaning of the grammatical structure in linguistics; the latter is to molecular… (more)

Subjects/Keywords: Wang Wei; William Wordsworth; Linguistic; Conformation; Configuration

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APA (6^th Edition):

Fu, J. (2017). The Configuration and Conformation of Nature poetryââA Case Study of Wang Wei and William Wordsworth. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0614117-144917

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):

Fu, Ji-Qian. “The Configuration and Conformation of Nature poetryââA Case Study of Wang Wei and William Wordsworth.” 2017. Thesis, NSYSU. Accessed April 13, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0614117-144917.

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

MLA Handbook (7^th Edition):

Fu, Ji-Qian. “The Configuration and Conformation of Nature poetryââA Case Study of Wang Wei and William Wordsworth.” 2017. Web. 13 Apr 2021.

Vancouver:

Fu J. The Configuration and Conformation of Nature poetryââA Case Study of Wang Wei and William Wordsworth. [Internet] [Thesis]. NSYSU; 2017. [cited 2021 Apr 13]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0614117-144917.

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

Council of Science Editors:

Fu J. The Configuration and Conformation of Nature poetryââA Case Study of Wang Wei and William Wordsworth. [Thesis]. NSYSU; 2017. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0614117-144917

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

University of Rochester

17. Aytenfisu, Asaminew H. Applying and improving the amber RNA force field.

Degree: PhD, 2016, University of Rochester

URL: http://hdl.handle.net/1802/30943

► RNA was believed to act as an information carrier between genes (DNA) and proteins in cells. However, RNA is now known to play a central… (more)

▼ RNA was believed to act as an information carrier between genes (DNA) and proteins in cells. However, RNA is now known to play a central role in many cellular functions. RNA can act as reaction catalyst, assist in peptide bond formation and regulate gene expression. In addition, RNA is also an important drug target. Molecular mechanics and molecular dynamics calculations can provide significant insight about the behavior of RNA in solution. </br> The aim of my work is to model RNA dynamics and conformational change, refine and understand experimental results, test the force fields on small RNA molecules and identify problems and perform revisions of force field parameters. In the first work, umbrella sampling was used to model conformational preference of tandem GA base pairs. A modification to the standard Amber ff10 force field, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088-2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil, was needed. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson-Crick / Watson-Crick A-G) or sheared (trans Hoogsteen / sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The free energy calculations allow direct comparison between simulation and experiment, and provide a benchmark for force fields. The results showed the importance of broadening the set of RNA molecules used to test force field performance. </br> Then in the second work in collaboration with the Wedekind lab, molecular dynamic simulations were performed using the Amber force field to gain insight into the dynamics of the class II preQ1 riboswitch [Nat. Chem. Biol. 2013, 9, 353-355]. Four simulations were run each with and without the ligand present. In the presence of ligand, all four of the simulations demonstrated rearranged base pairs at the 3´ end, consistent with expected base pairing from comparative sequence analysis [RNA 2008, 14, 685-695]. In the absence of ligand, three of the simulations demonstrated similar changes in base pairing at the ligand binding site. </br> In the final work, a new method is described for improving the backbone dihedral parameters of the Amber RNA force field by fitting to energies from quantum chemistry calculations using linear regression. To validate the new parameter sets, umbrella sampling was used to determine potentials of mean force (PMF) along the dihedral angles in explicit solvent, and then compared to the population of conformations observed in the protein data bank. Molecular dynamics simulations were also performed on a set of hairpin loops, duplexes and tetramers. Results from both umbrella sampling and molecular dynamics show improved performance as compared to the standard Amber force field.

Subjects/Keywords: Amber; Conformation; Riboswitchs; RNA; Simulations; Tetramers

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APA (6^th Edition):

Aytenfisu, A. H. (2016). Applying and improving the amber RNA force field. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/30943

Chicago Manual of Style (16^th Edition):

Aytenfisu, Asaminew H. “Applying and improving the amber RNA force field.” 2016. Doctoral Dissertation, University of Rochester. Accessed April 13, 2021. http://hdl.handle.net/1802/30943.

MLA Handbook (7^th Edition):

Aytenfisu, Asaminew H. “Applying and improving the amber RNA force field.” 2016. Web. 13 Apr 2021.

Vancouver:

Aytenfisu AH. Applying and improving the amber RNA force field. [Internet] [Doctoral dissertation]. University of Rochester; 2016. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1802/30943.

Council of Science Editors:

Aytenfisu AH. Applying and improving the amber RNA force field. [Doctoral Dissertation]. University of Rochester; 2016. Available from: http://hdl.handle.net/1802/30943

University of Manchester

18. Back, Kevin Richard. The Crystallisation of Conformationally Flexible Molecules.

Degree: 2012, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:159063

►

Crystallising large, flexible molecules, which are becoming more common in pharmaceutical development, often presents significant challenges for chemists and particle scientists. These difficulties are sometimes… (more)

▼

Crystallising large, flexible molecules, which are becoming more common in pharmaceutical development, often presents significant challenges for chemists and particle scientists. These difficulties are sometimes attributed to the flexibility of the molecule, and the existence of multiple conformers in solution. Structurally related impurities, frequently present when crystallising these materials, can also impact on growth and habit, and both these aspects are considered in this thesis. This work considers two pharmaceutical compounds, a relatively small but nonetheless flexible molecule, ethenzamide, and a precursor of Amprenavir, a much larger molecule. Both compounds typically grow as thin needles in a wide variety of solvents, and effort was required to grow suitable crystals for structure determination. Ethenzamide has an unusual structure, the amide group being out-of-plane relative to the ring, while in all known co-crystals of the compound, including three new co-crystal structures determined in this work, it has a planar structure with an intramolecular hydrogen bond not seen in the single component crystal. Theoretical structure generation calculations suggest a second polymorph with a planar conformation may exist, though a screen has not found any further solid phases. ab initio work suggests the planar conformation is the stable arrangement in vacuo. Several structures for the Amprenavir intermediate have been determined, as an ethanol solvate, a methanol solvate and a hydrate. A phase diagram has been measured in the industrial solvent mix, and the nucleation and growth properties of this molecule, both pure and in the presence of several structurally related impurities, have been measured. The Cambridge Structural Database has been searched for similar structures, and conformational searches have been carried out for both molecules, using vacuum phase ab initio energy calculations. Infrared spectroscopy has been used to investigate solution phase structure. These theoretical and practical studies will try to relate conformational properties to crystallisation behaviour.

CD-ROM containing electronic appendices, including large datasets from conformational searches and crystal structure data.

None

Advisors/Committee Members: Davey, Roger.

Subjects/Keywords: Crystallisation; Pharmaceuticals; Conformation; Impurities; Nucleation; Crystal Growth

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

APA (6^th Edition):

Back, K. R. (2012). The Crystallisation of Conformationally Flexible Molecules. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:159063

Chicago Manual of Style (16^th Edition):

Back, Kevin Richard. “The Crystallisation of Conformationally Flexible Molecules.” 2012. Doctoral Dissertation, University of Manchester. Accessed April 13, 2021. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:159063.

MLA Handbook (7^th Edition):

Back, Kevin Richard. “The Crystallisation of Conformationally Flexible Molecules.” 2012. Web. 13 Apr 2021.

Vancouver:

Back KR. The Crystallisation of Conformationally Flexible Molecules. [Internet] [Doctoral dissertation]. University of Manchester; 2012. [cited 2021 Apr 13]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:159063.

Council of Science Editors:

Back KR. The Crystallisation of Conformationally Flexible Molecules. [Doctoral Dissertation]. University of Manchester; 2012. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:159063

Colorado State University

19. Vollmar, Kaycee. Survey of the prevalence of conformational defects in feedlot receiving cattle in the United States.

Degree: MS(M.S.), Animal Sciences, 2016, Colorado State University

URL: http://hdl.handle.net/10217/173532

► A survey was conducted on large beef cattle feedlots in Colorado and Texas between March and July 2015, to assess the current status of conformational… (more)

▼ A survey was conducted on large beef cattle feedlots in Colorado and Texas between March and July 2015, to assess the current status of conformational defects in U.S. fed steers and heifers. The objectives were to: 1) determine the prevalence of conformational defects in feedlot receiving cattle in a population across multiple regions within the United States; and 2) increase industry awareness of the structural problems found in the current cattle population to help ultimately improve a practical selection focus. Conformational traits of front and rear claw, front and rear feet angles, rear leg side view, and rear leg hind view were evaluated on a scale of 1-9 with scores 4-6 serving as the most desirable. Overall soundness was evaluated from 0-100 with 66-100 serving as optimal soundness. A new scoring tool was developed and added to assess conformational problems in cattle shoulder and hip structure. Data from 2,886 head of feedlot cattle was used to evaluate the frequency of these conformational defects. Phenotypic evaluation revealed the highest prevalence of conformational issues in the shoulder, hip, and rear leg covering multiple relationships with demographic characteristics. Of the entire sample, 49.97% had a less than ideal shoulder structure, 53.33% had a less than ideal hip structure, and 29.97% displayed a less than ideal hock structure when viewed from the side. Heavier weight cattle showed a significantly higher (P<0.0001) prevalence of front claw scissor type abnormalities (7-9) and an increase (P<0.0001) in impaired mobility scores (group 2). Northern cattle exhibited a significant (P<0.0001) increase in front claw defects of scissor claw type abnormalities (7-9). Lastly, Bos Indicus cattle displayed a higher prevalence (P<0.0001) of round hip structures (7-9) and an increase (P<0.0001) of impaired mobility scores (group 2). The remaining traits had significantly higher proportions in the desirable (normal) group, and thus, the industry has shown positive developments in rear claw set and front and rear feet angles. Additionally, 85.85% of our total sample demonstrated overall comprehensive soundness scores for sound and flexible mobility (group 3). These findings will be useful to the beef industry in creating a benchmark for the conformational status of the current cattle herd to ultimately improve skeletal structure for improved welfare and performance in feedlot cattle. Advisors/Committee Members: Grandin, Temple (advisor), Edwards-Callaway, Lily (committee member), Engle, Terry (committee member), Ogden, Brenda (committee member), Woerner, Dale (committee member).

Subjects/Keywords: conformation; feedlot; beef cattle; survey; defects

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APA (6^th Edition):

Vollmar, K. (2016). Survey of the prevalence of conformational defects in feedlot receiving cattle in the United States. (Masters Thesis). Colorado State University. Retrieved from http://hdl.handle.net/10217/173532

Chicago Manual of Style (16^th Edition):

Vollmar, Kaycee. “Survey of the prevalence of conformational defects in feedlot receiving cattle in the United States.” 2016. Masters Thesis, Colorado State University. Accessed April 13, 2021. http://hdl.handle.net/10217/173532.

MLA Handbook (7^th Edition):

Vollmar, Kaycee. “Survey of the prevalence of conformational defects in feedlot receiving cattle in the United States.” 2016. Web. 13 Apr 2021.

Vancouver:

Vollmar K. Survey of the prevalence of conformational defects in feedlot receiving cattle in the United States. [Internet] [Masters thesis]. Colorado State University; 2016. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/10217/173532.

Council of Science Editors:

Vollmar K. Survey of the prevalence of conformational defects in feedlot receiving cattle in the United States. [Masters Thesis]. Colorado State University; 2016. Available from: http://hdl.handle.net/10217/173532

Vanderbilt University

20. Chandra, Aroop. The application of new methods to the synthesis of constrained proline derivatives, (+)-serratezomine A, and hapalindoles A, G, I, and K.

Degree: PhD, Chemistry, 2011, Vanderbilt University

URL: http://hdl.handle.net/1803/11611

► The development of new chemical methods to tackle synthetic challenges is presented in this dissertation. Application of these methods has led to the completion of… (more)

▼ The development of new chemical methods to tackle synthetic challenges is presented in this dissertation. Application of these methods has led to the completion of the following projects: The first total synthesis of the Lycopodium alkaloid (+)-serratezomine A, a strong acetyl-choline esterase inhibitor. Key aspects of the synthesis include (a) the first deployment of free-radical-mediated vinyl amination (an intramolecular alkyne aminostannation) in a complex target synthesis, (b) the use of a â-stannyl enamine as the lynchpin for convergent assembly of the natural product backbone, (c) the use of an oxidative allylation promoted by cerium(IV) (CAN) to establish the all-carbon quaternary chiral center with the proper configuration, and (d) an intramolecular substitution reaction to form the sensitive bridging lactone. Overall, 15 steps (longest linear sequence) are required to prepare the natural product from commercially available starting materials, and assembly of the contiguous array of six stereocenters is accomplished with high stereocontrol. The first total synthesis of marine indole alkaloids hapalindoles K and A, and a formal synthesis of hapalindole G. In so doing, use of (a) a two-fold electrophilic aromatic substitution (EAS) reaction between indole and á-methyl tiglic acid chloride, (b) a demanding intermolecular [4+2] cycloaddition, and (c) a late stage Ritter reaction provided the needed convergency and functional group installation to deliver each target in 15 steps or less. An examination of the effects of proline analogs, indoline and azaindoline amino acids, on prolyl N-terminal cis-trans amide isomer population. A series of di, tri, and tetrapeptides containing indoline amino acids with or without a nitrogen mutation at C7 were synthesized, utilizing a free-radical-mediated aryl amination (an intramolecular aryl aminostannation), and evaluated. Because of A1,3-strain between the fused aromatic group (indoline) and prolyl N-terminal residue in unmutated indoline amino acids, the cis-amide bond geometry about the L-Ind fragment was able to be favored. However, all the peptides incorporating the N7Ind mutations resulted in exclusive formation of the trans-rotamer about the Phe-N7Ind amide bond. This conformation preference for N7Ind containing peptides was due to an unfavorable lone-pair/lone-pair repulsion between the preceding carbonyl oxygen and azaindoline nitrogen in the s-cis conformation. The subtle, yet predictable control that these proline frameworks provides at this stage may lead to a more effective chemical tool and ultimately, more effective therapeutics. Advisors/Committee Members: Ned A. Porter (committee member), Gary A. Sulikowski (committee member), Lawrence J. Marnett (committee member), Dr. Jeffrey N. Johnston (Committee Chair).

Subjects/Keywords: (+)-serratezomine A; alkaloids; peptide conformation; hapalindole; ambiguine

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APA (6^th Edition):

Chandra, A. (2011). The application of new methods to the synthesis of constrained proline derivatives, (+)-serratezomine A, and hapalindoles A, G, I, and K. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/11611

Chicago Manual of Style (16^th Edition):

Chandra, Aroop. “The application of new methods to the synthesis of constrained proline derivatives, (+)-serratezomine A, and hapalindoles A, G, I, and K.” 2011. Doctoral Dissertation, Vanderbilt University. Accessed April 13, 2021. http://hdl.handle.net/1803/11611.

MLA Handbook (7^th Edition):

Chandra, Aroop. “The application of new methods to the synthesis of constrained proline derivatives, (+)-serratezomine A, and hapalindoles A, G, I, and K.” 2011. Web. 13 Apr 2021.

Vancouver:

Chandra A. The application of new methods to the synthesis of constrained proline derivatives, (+)-serratezomine A, and hapalindoles A, G, I, and K. [Internet] [Doctoral dissertation]. Vanderbilt University; 2011. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1803/11611.

Council of Science Editors:

Chandra A. The application of new methods to the synthesis of constrained proline derivatives, (+)-serratezomine A, and hapalindoles A, G, I, and K. [Doctoral Dissertation]. Vanderbilt University; 2011. Available from: http://hdl.handle.net/1803/11611

Texas A&M University

21. Zhao, Qinliang. Conformation and electronic configuration of complexes with multiple dimetal units.

Degree: PhD, Chemistry, 2009, Texas A&M University

URL: http://hdl.handle.net/1969.1/ETD-TAMU-1441

► By using the building blocks Mo2(DAniF)3(O2CCH3) (DAniF = N,N'-di-panisylformamidinate) and [Mo2(cis-DAniF)2(NCCH3)4](BF4)2, a series of complexes with multiple dimolybdenum units, bridged by a variety of linkers… (more)

▼ By using the building blocks Mo2(DAniF)3(O2CCH3) (DAniF = N,N'-di-panisylformamidinate) and [Mo2(cis-DAniF)2(NCCH3)4](BF4)2, a series of complexes with multiple dimolybdenum units, bridged by a variety of linkers and having various oxidation states, has been synthesized and studied by various physical and chemical methods. The isomeric neutral diamidate-bridged molecules, α– and β– (DAniF)3Mo2(ArN(O)CC(O)NAr)Mo2(DAniF)3 (Ar = p-anisyl), have been oxidized to give the PF6 salts of the four cations α1+, α2+, β1+, β2+; all four structures together with supporting evidence show that in α1+ and α2+ the unpaired electrons are localized while in β1+ and β2+ they are delocalized in the time scale of these experiments. It is also found that a hydroxide bridged complex having a [Mo2](µ-OH)2[Mo2] core undergoes a oxidative deprotomation, both in solution and in crystals, to a compound with a [Mo2](µ-O)2[Mo2] core. A probable key intermediate with one OH and one O bridge has also been characterized. One electron oxidation of the tetrabridged compounds [Mo2(cis-DAniF)2]2(µ-X)4, where X is a halogen atom (Cl, Br, I), produces a decrease of about 0.24 Å in the separation between the midpoints of the multiply bonded dimolybdenum units. DFT calculations suggest partial bond formation during the oxidation, which is consistent with NIR, EPR and electrochemical measurements. Additionally, a pair of isomeric cyclic triads containing three [Mo2(cis-DAniF)2]2+ units, bridged by six fluoride anions, have been synthesized and crystallographically characterized. The symmetry of the α isomer is C2v because the three [Mo2] units are oriented in two orthogonal directions while that of the other isomer is D3h because the three [Mo2] units are parallel. No direct interconversion between isomers has been detected by heating or irradiation of solutions but oxidation of the α isomer first generates an α+ species that changes to β+. Finally, reaction of [Mo2(cis-DAniF)2(NCCH3)4](BF4)2 and Bun 4NBH4 in ether gives [Mo2(cis-DAniF)2]2(µ-H)4 (14), a compound whose Mo4H4 core may be described as an elongated tetrahedron in which the four H atoms are along the four long edges and the Mo2 units along the short edges. Advisors/Committee Members: Darensbourg, Marcetta Y. (advisor), Murillo, Carlos A. (advisor), Simanek, Eric E. (committee member), Summers, Max D. (committee member).

Subjects/Keywords: conformation; electronic configuration

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APA (6^th Edition):

Zhao, Q. (2009). Conformation and electronic configuration of complexes with multiple dimetal units. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-1441

Chicago Manual of Style (16^th Edition):

Zhao, Qinliang. “Conformation and electronic configuration of complexes with multiple dimetal units.” 2009. Doctoral Dissertation, Texas A&M University. Accessed April 13, 2021. http://hdl.handle.net/1969.1/ETD-TAMU-1441.

MLA Handbook (7^th Edition):

Zhao, Qinliang. “Conformation and electronic configuration of complexes with multiple dimetal units.” 2009. Web. 13 Apr 2021.

Vancouver:

Zhao Q. Conformation and electronic configuration of complexes with multiple dimetal units. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1441.

Council of Science Editors:

Zhao Q. Conformation and electronic configuration of complexes with multiple dimetal units. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1441

22. Hendrickx, Johann. Développement méthodologique pour l'étude des phénomènes d'interaction protéine-glucide : Methodologic developments for studies of protein-carbohydrate interaction phenomena.

Degree: Docteur es, Bio-informatique structurale, 2019, Nantes

URL: http://www.theses.fr/2019NANT1023

►

Un ensemble de méthodes permettant d'étudier in silico des interactions protéine-glucide, primordiales dans de nombreux processus biologiques, sont proposées dans cette étude. En s'appuyant sur… (more)

▼

Un ensemble de méthodes permettant d'étudier in silico des interactions protéine-glucide, primordiales dans de nombreux processus biologiques, sont proposées dans cette étude. En s'appuyant sur des informations fournies par la bio-cristallographie, il est devenu possible d'étudier à grande échelle les modalités d'interaction existantes entre ces deux entités moléculaires. Une étude statistique complète fut donc réalisée afin de déterminer aussi bien les tendances générales que les cas extrêmes observés dans les complexes protéine glucide. Les caractéristiques des interactions protéine glucide sont ainsi décrites, en particulier les liaisons hydrogène (LH) et le rôle des molécules d'eau. Un programme d'identification des LH et de reconstitution de leur(s) réseau(x) hypothétique(s) a été développé. Il comprend entre autres l'ajout putatif des hydrogènes, dans le cas où ils sont absents de la structure, notamment sur les groupes hydroxyles et les molécules d'eau. Une stratégie originale pour positionner de manière putative des molécules d'eau sur les sites de reconnaissance protéiques est également décrite. Cette stratégie a pour prétention de permettre le développement d'un protocole d'amarragemoléculaire protéine-glucide, les glucides et les molécules d'eau partageant sensiblement le même réseau de LH. Suite aux nombreuses anomalies décelées dans la PDB au niveau des glucides, une méthode d'identification et de vérification des structures 3D des glucides est également décrite. Elle a permis de limiter les bruits statistiques de cette étude. Environ 280 monosaccharides sous forme furanique et pyranique ont ainsi été référencés. La flexibilité intrinsèque des glucides a également amené à une étude approfondie de la conformation des glucides observée dans les structurescristallographiques.

A set of methods to study in silico protein carbohydrate interactions, which are essential in many biological processes, are proposed in this study. Based on crystallographic data, it has become possible to study on a large scale the existing interaction modalities between the two molecular entities. A complete statistical study has thus been carried out to determine both the general trends and extreme cases observed in protein-carbohydrate complexes. The characteristics of protein-carbohydrate interactions are thus reported, in particular hydrogen bonds (HB) and the role of water molecules. A program to identify the HBs and reconstitute their hypothetical network(s) is being developed. This includes, in particular, the putative addition of hydrogens, if they are absent from the structure, especially on hydroxyl groups and water molecules. An original strategy for putatively positioning water molecules at protein recognition sites is also described. This strategy aims to allow the development of a protein-carbohydrate molecular docking protocol, as carbohydrates and water molecules share essentially the same HB network. As a result of the many carbohydrate anomalies detected in PDB, a method for identifying and verifying 3D…

Advisors/Committee Members: Sanejouand, Yves-Henri (thesis director), Tran, Huu Vinh (thesis director).

Subjects/Keywords: Bio-cristallographie; Bio-informatique structurale; Conformation moléculaire

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APA (6^th Edition):

Hendrickx, J. (2019). Développement méthodologique pour l'étude des phénomènes d'interaction protéine-glucide : Methodologic developments for studies of protein-carbohydrate interaction phenomena. (Doctoral Dissertation). Nantes. Retrieved from http://www.theses.fr/2019NANT1023

Chicago Manual of Style (16^th Edition):

Hendrickx, Johann. “Développement méthodologique pour l'étude des phénomènes d'interaction protéine-glucide : Methodologic developments for studies of protein-carbohydrate interaction phenomena.” 2019. Doctoral Dissertation, Nantes. Accessed April 13, 2021. http://www.theses.fr/2019NANT1023.

MLA Handbook (7^th Edition):

Hendrickx, Johann. “Développement méthodologique pour l'étude des phénomènes d'interaction protéine-glucide : Methodologic developments for studies of protein-carbohydrate interaction phenomena.” 2019. Web. 13 Apr 2021.

Vancouver:

Hendrickx J. Développement méthodologique pour l'étude des phénomènes d'interaction protéine-glucide : Methodologic developments for studies of protein-carbohydrate interaction phenomena. [Internet] [Doctoral dissertation]. Nantes; 2019. [cited 2021 Apr 13]. Available from: http://www.theses.fr/2019NANT1023.

Council of Science Editors:

Hendrickx J. Développement méthodologique pour l'étude des phénomènes d'interaction protéine-glucide : Methodologic developments for studies of protein-carbohydrate interaction phenomena. [Doctoral Dissertation]. Nantes; 2019. Available from: http://www.theses.fr/2019NANT1023

University of Vermont

23. Egri, Shawn Bruce. THE ROLE OF PROTEIN STRUCTURE CONFORMATIONAL CHANGE IN SECONDARY FUNCTIONS OF THREONYL-tRNA SYNTHETASE.

Degree: Biochemistry, 2015, University of Vermont

URL: https://scholarworks.uvm.edu/castheses/7

► Traditionally, threonyl-tRNA synthetase (ThrRS) has been studied for its canonical function of aminoacylation. Recently, however, the enzyme has been identified as a potent angiogenic… (more)

Subjects/Keywords: Synthetase; Enzyme; Conformation; Inhibitor; Fluorescence; Aminoacylation

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APA (6^th Edition):

Egri, S. B. (2015). THE ROLE OF PROTEIN STRUCTURE CONFORMATIONAL CHANGE IN SECONDARY FUNCTIONS OF THREONYL-tRNA SYNTHETASE. (Thesis). University of Vermont. Retrieved from https://scholarworks.uvm.edu/castheses/7

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):

Egri, Shawn Bruce. “THE ROLE OF PROTEIN STRUCTURE CONFORMATIONAL CHANGE IN SECONDARY FUNCTIONS OF THREONYL-tRNA SYNTHETASE.” 2015. Thesis, University of Vermont. Accessed April 13, 2021. https://scholarworks.uvm.edu/castheses/7.

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

MLA Handbook (7^th Edition):

Egri, Shawn Bruce. “THE ROLE OF PROTEIN STRUCTURE CONFORMATIONAL CHANGE IN SECONDARY FUNCTIONS OF THREONYL-tRNA SYNTHETASE.” 2015. Web. 13 Apr 2021.

Vancouver:

Egri SB. THE ROLE OF PROTEIN STRUCTURE CONFORMATIONAL CHANGE IN SECONDARY FUNCTIONS OF THREONYL-tRNA SYNTHETASE. [Internet] [Thesis]. University of Vermont; 2015. [cited 2021 Apr 13]. Available from: https://scholarworks.uvm.edu/castheses/7.

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

Council of Science Editors:

Egri SB. THE ROLE OF PROTEIN STRUCTURE CONFORMATIONAL CHANGE IN SECONDARY FUNCTIONS OF THREONYL-tRNA SYNTHETASE. [Thesis]. University of Vermont; 2015. Available from: https://scholarworks.uvm.edu/castheses/7

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

24. Tezcan, Hasan Gokhan. A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation.

Degree: MSin Electrical and Computer Engineering (M.S.E.C.E.), Electrical & Computer Engineering, 2010, U of Massachusetts : Masters

URL: http://scholarworks.umass.edu/theses/482

► In this thesis we develop a molecular modeling toolkit that models the conformation space of proteins and allows easy prototyping of algorithms on the conformation… (more)

Subjects/Keywords: proteins; free energy; conformation space; graphical models

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APA (6^th Edition):

Tezcan, H. G. (2010). A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation. (Masters Thesis). U of Massachusetts : Masters. Retrieved from http://scholarworks.umass.edu/theses/482

Chicago Manual of Style (16^th Edition):

Tezcan, Hasan Gokhan. “A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation.” 2010. Masters Thesis, U of Massachusetts : Masters. Accessed April 13, 2021. http://scholarworks.umass.edu/theses/482.

MLA Handbook (7^th Edition):

Tezcan, Hasan Gokhan. “A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation.” 2010. Web. 13 Apr 2021.

Vancouver:

Tezcan HG. A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation. [Internet] [Masters thesis]. U of Massachusetts : Masters; 2010. [cited 2021 Apr 13]. Available from: http://scholarworks.umass.edu/theses/482.

Council of Science Editors:

Tezcan HG. A Molecular Modeling Toolkit with Applications to Efficient Free Energy Computation. [Masters Thesis]. U of Massachusetts : Masters; 2010. Available from: http://scholarworks.umass.edu/theses/482

University of Cambridge

25. Mielczarek, Olga. Spatial organisation of the immunoglobulin heavy chain locus and inter-chromosomal gene networks driving B cell development.

Degree: PhD, 2018, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/273740

► B lymphocytes produce a wide array of antibodies to recognize a countless number of antigens. This highly diverse repertoire is produced during B cell development… (more)

▼ B lymphocytes produce a wide array of antibodies to recognize a countless number of antigens. This highly diverse repertoire is produced during B cell development in the bone marrow from the immunoglobulin heavy chain (Igh) and light chain (Igk and Igl) loci. The mouse Igh is a large (~3Mb) multigene locus that contains 195 variable (V), 10 diversity (D) and 4 joining (J) genes that undergo developmentally regulated V(D)J recombination to produce the variable region of the antibody. Gene expression depends on spatial organisation of chromatin. To ensure that all V genes have a chance to recombine, they are brought into physical proximity to the D-J region by locus contraction and DNA looping. Not all V genes recombine with equal frequencies and we aim to investigate how dynamic changes in 3D structure of the Igh locus facilitate V(D)J recombination. Chromosome conformation capture techniques have revolutionised studies of genome conformation. I have applied a novel form of enriched Hi-C to study both intra-locus (cis) and genome-wide (trans) interactions of the immunoglobulin loci in pro-B and pre-B cells. This method provides a higher resolution than Hi-C and is less biased than 4C and 5C. I have mapped all cis interactions within the Igh locus to produce a comprehensive view of the structure of the locus prior to recombination. This approach has shown that the 3’ superanchor (3’CBEs) and the Intergenic Control Region 1 (IGCR1) containing CTCF sites are the two most interacting regions in the locus making long-range contacts with all V genes. A second major conformational feature is that the distal V genes form a large tightly looped domain forming the centre of mass of the locus to which the 3’CBEs and IGCR1 loop. Thanks to a collaboration on polymer modelling, 5000 single conformations were simulated based on the ensemble Hi-C data. This showed that every structure is different, supporting a model of dynamic and flexible organisation of the locus rather than hierarchical subdomains therein. Moreover, there is only a slight trend for V genes interacting more often with the D-J region to have higher recombination scores, supporting an ‘equal opportunity for all’ model in which participation of V genes in V(D)J recombination is not constrained by linear genomic distance from the DJ region. Nevertheless, CTCF binding level does contribute to V gene recombination frequency. I have also discovered that Igh and Igk loci participate in a highly specialised network of genome-wide (trans) interactions involving genes encoding B cell-specific factors essential for activation and maintenance of B cell identity, including Pax5, Foxo1, Ebf1, and Runx1. I have validated these by 3D DNA FISH and found that at the pro-B cell stage the Igh is involved in many trans interactions, whereas Igk does not make any contacts. In contrast, Igk gains numerous trans interactions at the pre-B cell stage, many of which overlap with the interactions Igh participates in at both developmental stages. Together, these findings reveal a complex…

Subjects/Keywords: B cell development; chromosome conformation; Igh locus

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APA (6^th Edition):

Mielczarek, O. (2018). Spatial organisation of the immunoglobulin heavy chain locus and inter-chromosomal gene networks driving B cell development. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/273740

Chicago Manual of Style (16^th Edition):

Mielczarek, Olga. “Spatial organisation of the immunoglobulin heavy chain locus and inter-chromosomal gene networks driving B cell development.” 2018. Doctoral Dissertation, University of Cambridge. Accessed April 13, 2021. https://www.repository.cam.ac.uk/handle/1810/273740.

MLA Handbook (7^th Edition):

Mielczarek, Olga. “Spatial organisation of the immunoglobulin heavy chain locus and inter-chromosomal gene networks driving B cell development.” 2018. Web. 13 Apr 2021.

Vancouver:

Mielczarek O. Spatial organisation of the immunoglobulin heavy chain locus and inter-chromosomal gene networks driving B cell development. [Internet] [Doctoral dissertation]. University of Cambridge; 2018. [cited 2021 Apr 13]. Available from: https://www.repository.cam.ac.uk/handle/1810/273740.

Council of Science Editors:

Mielczarek O. Spatial organisation of the immunoglobulin heavy chain locus and inter-chromosomal gene networks driving B cell development. [Doctoral Dissertation]. University of Cambridge; 2018. Available from: https://www.repository.cam.ac.uk/handle/1810/273740

University of Missouri – Columbia

26. Wang, Zheng. Revealing the conformation and properties of human genome, protein molecules and protein domain co-occurrence network.

Degree: 2012, University of Missouri – Columbia

URL: http://hdl.handle.net/10355/36742

► Deoxyribonucleic acid, or DNA, encodes genetic instructions for the functionalities of organisms. For human beings, 23 pairs of chromosomes, containing DNA strands, form a globule… (more)

Subjects/Keywords: chromosomal conformation; chromosomal proximity; protein tertiary structures

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APA (6^th Edition):

Wang, Z. (2012). Revealing the conformation and properties of human genome, protein molecules and protein domain co-occurrence network. (Thesis). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/36742

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

Chicago Manual of Style (16^th Edition):

Wang, Zheng. “Revealing the conformation and properties of human genome, protein molecules and protein domain co-occurrence network.” 2012. Thesis, University of Missouri – Columbia. Accessed April 13, 2021. http://hdl.handle.net/10355/36742.

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

MLA Handbook (7^th Edition):

Wang, Zheng. “Revealing the conformation and properties of human genome, protein molecules and protein domain co-occurrence network.” 2012. Web. 13 Apr 2021.

Vancouver:

Wang Z. Revealing the conformation and properties of human genome, protein molecules and protein domain co-occurrence network. [Internet] [Thesis]. University of Missouri – Columbia; 2012. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/10355/36742.

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

Council of Science Editors:

Wang Z. Revealing the conformation and properties of human genome, protein molecules and protein domain co-occurrence network. [Thesis]. University of Missouri – Columbia; 2012. Available from: http://hdl.handle.net/10355/36742

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

University of Minnesota

27. Jena, Sampreeti. Effect of the Thermodynamic and Physical State of the Freeze-Concentrate on Protein Stability.

Degree: PhD, Mechanical Engineering, 2017, University of Minnesota

URL: http://hdl.handle.net/11299/201180

► In this dissertation research, specific interactions (excipient-excipient, excipient/protein-ice, protein-excipient) governing protein conformational stability and crystallization behavior of excipients in the freeze concentrate, were explored. Furthermore,… (more)

▼ In this dissertation research, specific interactions (excipient-excipient, excipient/protein-ice, protein-excipient) governing protein conformational stability and crystallization behavior of excipients in the freeze concentrate, were explored. Furthermore, the effects of formulation composition (type and mole fractions of excipients in the formulation) on afore-mentioned interactions, during freeze-thaw and freeze-drying of protein formulations, was investigated. Concentration dependent effects of excipients including the bulking agent, lyo/cryo-protectant and surfactant on the nucleation and growth of crystalline phases in the freeze concentrate were characterized and quantified. Changes in the secondary and tertiary conformations of model proteins (such as Bovine Serum Albumin and Immunoglobulin) due to crystallization of excipients, were determined as a function of formulation composition during freeze-thaw and freeze-drying. Infrared (IR) Spectroscopy was used to detect onset of crystallization the bulking agent and lyo/cryo-protectant. X-Ray Diffractometry (XRD) was used to characterize the polymorphic form of crystalline phases. Far UV circular Dichroism (CD) was used to characterize secondary conformation of protein in thawed and reconstituted (freeze-dried) formulations. IR Spectroscopy was used to characterize secondary conformation of protein in frozen and freeze-dried formulations. A bulking agent – lyo/cryo-protectant – protein system, a typical freeze-drying formulation, was chosen for characterization of frozen and freeze-dried formulations. It was observed that high concentrations of non-crystallizing components such as the protein and lyo/cryo-protectant (usually a disaccharide such as trehalose) inhibited crystallization of the (otherwise readily crystallizing) bulking agent (such as mannitol) and vice versa. At low concentrations, surfactants such as Polysorbate 20, prevented growth of crystalline phases due to amphiphilic interface coverage, but when their concentrations exceeded the critical micelle concentration (CMC), they enhanced degree of crystallinity in the formulation. Structural unfolding of the protein was detected upon crystallization of the lyo/cryo-protectant and micelle formation (when surfactant concentration exceeded CMC). Detection of protein aggregates in reconstituted solutions, confirmed that unfolding induced during freezing, thawing and drying processes, did not reverse upon reconstitution. Presence of ice surfaces and other crystalline interfaces (such as those introduced by the bulking agent) significantly contributed to protein degradation. In our model system, thawing induced stresses such as recrystallization were found to be more detrimental than the stresses induced by freezing and desiccation and hence, freeze-drying yielded better structural recovery of the protein than freeze-thaw in our model system. Secondary relaxations arising from the flexible polar groups on the protein surface (millisecond time scales) and dynamic ring flips of the monosaccharide units…

Subjects/Keywords: conformation; crystallization; excipient; formulation; protein; stabilization

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APA (6^th Edition):

Jena, S. (2017). Effect of the Thermodynamic and Physical State of the Freeze-Concentrate on Protein Stability. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/201180

Chicago Manual of Style (16^th Edition):

Jena, Sampreeti. “Effect of the Thermodynamic and Physical State of the Freeze-Concentrate on Protein Stability.” 2017. Doctoral Dissertation, University of Minnesota. Accessed April 13, 2021. http://hdl.handle.net/11299/201180.

MLA Handbook (7^th Edition):

Jena, Sampreeti. “Effect of the Thermodynamic and Physical State of the Freeze-Concentrate on Protein Stability.” 2017. Web. 13 Apr 2021.

Vancouver:

Jena S. Effect of the Thermodynamic and Physical State of the Freeze-Concentrate on Protein Stability. [Internet] [Doctoral dissertation]. University of Minnesota; 2017. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/11299/201180.

Council of Science Editors:

Jena S. Effect of the Thermodynamic and Physical State of the Freeze-Concentrate on Protein Stability. [Doctoral Dissertation]. University of Minnesota; 2017. Available from: http://hdl.handle.net/11299/201180

Texas Tech University

28. Thomas, Susan Tansey. Rules of helix termination by the c-capping box: calorimetric and spectroscopic studies.

Degree: Chemistry, 1999, Texas Tech University

URL: http://hdl.handle.net/2346/10929

► Interest in increasing the reliability of protein structural prediction has focused attention on exploring mechanisms of stabilization of helical domains by comparing the helical forming… (more)

▼ Interest in increasing the reliability of protein structural prediction has focused attention on exploring mechanisms of stabilization of helical domains by comparing the helical forming potential of each amino acid residue at different positions in the a-helix. To achieve this, detailed knowledge of thermodynamic information of protein stability with different sequences and under different solvent conditions is required and must be combined with information about the structural properties of these proteins. Using differential scanning calorimetry, circular dichroism, and fluorescence and NMR spectroscopy combined with site directed mutagenisis and chemical modifications of selected positions on the protein sequence, we studied several model systems. The ionic composition of a protein's environment is very important for its function and stability. At this time there is no common understanding of the role neutral salts play in the stabilization and destabilization of proteins. In order to address this, we studied the effects of neutral salts on the stability of the ubiquitin molecule. We found that the stability of the ubiquitin molecule increases with an increase in the concentration of electrolytes. This increase correlates with anion concentration rather than with an increase in ionic strength. This strongly suggests that the stabilizing effect occurs via specific bhiding of anions. We found an interesting interpretation of this. GdmHCl, a well known protein denaturant, can have dual actions on ubiquitin, the classical denaturant effect from the Gdm+ and a stabilizing effect from the CI. We also have complete thermodynamic analysis of more than 50 single and double, natural and non-natural amino acid substitutions at positions C-cap and C4-C" in the C-capping box of the a-helix in the ubiquitin molecule. We found that all of these variants of ubiquitin have perturbed thermodynamics of folding. From this we have generated a propensity scale of amino acid residue substitutions at the C-cap position In substitutions at positions C4 and C there were several cases in which we observed changes in the enthalpy and heat capacity of unfolding. A decrease in the enthalpy of unfolding and an increase in the heat capacity change upon unfolding is corroborated by the observation of partial cold denaturation of some of the hydrophobic variants of ubiquitin.

Subjects/Keywords: Ubiquitin; Proteins – Conformation

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APA (6^th Edition):

Thomas, S. T. (1999). Rules of helix termination by the c-capping box: calorimetric and spectroscopic studies. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/10929

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):

Thomas, Susan Tansey. “Rules of helix termination by the c-capping box: calorimetric and spectroscopic studies.” 1999. Thesis, Texas Tech University. Accessed April 13, 2021. http://hdl.handle.net/2346/10929.

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

MLA Handbook (7^th Edition):

Thomas, Susan Tansey. “Rules of helix termination by the c-capping box: calorimetric and spectroscopic studies.” 1999. Web. 13 Apr 2021.

Vancouver:

Thomas ST. Rules of helix termination by the c-capping box: calorimetric and spectroscopic studies. [Internet] [Thesis]. Texas Tech University; 1999. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/2346/10929.

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

Council of Science Editors:

Thomas ST. Rules of helix termination by the c-capping box: calorimetric and spectroscopic studies. [Thesis]. Texas Tech University; 1999. Available from: http://hdl.handle.net/2346/10929

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

University of Edinburgh

29. Moore, Benjamin Luke. Unravelling higher order chromatin organisation through statistical analysis.

Degree: PhD, 2016, University of Edinburgh

URL: http://hdl.handle.net/1842/22906

► Recent technological advances underpinned by high throughput sequencing have given new insights into the three-dimensional structure of mammalian genomes. Chromatin conformation assays have been the… (more)

▼ Recent technological advances underpinned by high throughput sequencing have given new insights into the three-dimensional structure of mammalian genomes. Chromatin conformation assays have been the critical development in this area, particularly the Hi-C method which ascertains genome-wide patterns of intra and inter-chromosomal contacts. However many open questions remain concerning the functional relevance of such higher order structure, the extent to which it varies, and how it relates to other features of the genomic and epigenomic landscape. Current knowledge of nuclear architecture describes a hierarchical organisation ranging from small loops between individual loci, to megabase-sized self-interacting topological domains (TADs), encompassed within large multimegabase chromosome compartments. In parallel with the discovery of these strata, the ENCODE project has generated vast amounts of data through ChIP-seq, RNA-seq and other assays applied to a wide variety of cell types, forming a comprehensive bioinformatics resource. In this work we combine Hi-C datasets describing physical genomic contacts with a large and diverse array of chromatin features derived at a much finer scale in the same mammalian cell types. These features include levels of bound transcription factors, histone modifications and expression data. These data are then integrated in a statistically rigorous way, through a predictive modelling framework from the machine learning field. These studies were extended, within a collaborative project, to encompass a dataset of matched Hi-C and expression data collected over a murine neural differentiation timecourse. We compare higher order chromatin organisation across a variety of human cell types and find pervasive conservation of chromatin organisation at multiple scales. We also identify structurally variable regions between cell types, that are rich in active enhancers and contain loci of known cell-type specific function. We show that broad aspects of higher order chromatin organisation, such as nuclear compartment domains, can be accurately predicted in a variety of human cell types, using models based upon underlying chromatin features. We dissect these quantitative models and find them to be generalisable to novel cell types, presumably reflecting fundamental biological rules linking compartments with key activating and repressive signals. These models describe the strong interconnectedness between locus-level patterns of local histone modifications and bound factors, on the order of hundreds or thousands of basepairs, with much broader compartmentalisation of large, multi-megabase chromosomal regions. Finally, boundary regions are investigated in terms of chromatin features and co-localisation with other known nuclear structures, such as association with the nuclear lamina. We find boundary complexity to vary between cell types and link TAD aggregations to previously described lamina-associated domains, as well as exploring the concept of meta-boundaries that span multiple levels of…

Subjects/Keywords: 572.8; bioinformatics; chromosome conformation; machine learning

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

APA (6^th Edition):

Moore, B. L. (2016). Unravelling higher order chromatin organisation through statistical analysis. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/22906

Chicago Manual of Style (16^th Edition):

Moore, Benjamin Luke. “Unravelling higher order chromatin organisation through statistical analysis.” 2016. Doctoral Dissertation, University of Edinburgh. Accessed April 13, 2021. http://hdl.handle.net/1842/22906.

MLA Handbook (7^th Edition):

Moore, Benjamin Luke. “Unravelling higher order chromatin organisation through statistical analysis.” 2016. Web. 13 Apr 2021.

Vancouver:

Moore BL. Unravelling higher order chromatin organisation through statistical analysis. [Internet] [Doctoral dissertation]. University of Edinburgh; 2016. [cited 2021 Apr 13]. Available from: http://hdl.handle.net/1842/22906.

Council of Science Editors:

Moore BL. Unravelling higher order chromatin organisation through statistical analysis. [Doctoral Dissertation]. University of Edinburgh; 2016. Available from: http://hdl.handle.net/1842/22906

Louisiana State University

30. Sepehri, Aliasghar. Innovative Monte Carlo Methods for Sampling Molecular Conformations.

Degree: PhD, Physical Chemistry, 2018, Louisiana State University

URL: https://digitalcommons.lsu.edu/gradschool_dissertations/4201

► Sampling molecular conformations is an important step in evaluating physical, mechanical, hydrodynamic, and optical properties of flexible molecules especially polymers. One powerful method for… (more)

Subjects/Keywords: Monte Carlo; Molecular Conformation; Molecular Simulation

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

APA (6^th Edition):

Sepehri, A. (2018). Innovative Monte Carlo Methods for Sampling Molecular Conformations. (Doctoral Dissertation). Louisiana State University. Retrieved from https://digitalcommons.lsu.edu/gradschool_dissertations/4201

Chicago Manual of Style (16^th Edition):

Sepehri, Aliasghar. “Innovative Monte Carlo Methods for Sampling Molecular Conformations.” 2018. Doctoral Dissertation, Louisiana State University. Accessed April 13, 2021. https://digitalcommons.lsu.edu/gradschool_dissertations/4201.

MLA Handbook (7^th Edition):

Sepehri, Aliasghar. “Innovative Monte Carlo Methods for Sampling Molecular Conformations.” 2018. Web. 13 Apr 2021.

Vancouver:

Sepehri A. Innovative Monte Carlo Methods for Sampling Molecular Conformations. [Internet] [Doctoral dissertation]. Louisiana State University; 2018. [cited 2021 Apr 13]. Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/4201.

Council of Science Editors:

Sepehri A. Innovative Monte Carlo Methods for Sampling Molecular Conformations. [Doctoral Dissertation]. Louisiana State University; 2018. Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/4201

Open Access Theses and Dissertations