Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 19 of 19 for “"solvent accessibility"”.
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Fast learning optimized prediction methodology for protein secondary structure prediction, relative solvent accessibility prediction and phosphorylation prediction
… gains. Other research areas include Relative Solvent Accessibility (RSA) predictions and predictions of phosphorylation sites, which is one of the Post-Translational Modification (PTM) sites in proteins.</p> <p>Protein secondary structures and other features of proteins are predicted …
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Statistical physics and biological information : hydrophobicity patterns in protein design and differential motif finding in DNA
(cont.) is dictated by the solvent accessibility of structures. The distinct intrinsic tendencies of sequence and structure profiles are most pronounced at long periods, where sequence hydrophobicity fluctuates less, while solvent accessibility fluctuates more than average. Correlations between the …
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Improving Structural Features Prediction in Protein Structure Modeling
… as secondary structures, disulfide bonds, and solvent accessibility is a critical intermediate step stone to obtain correct three-dimensional models ultimately.</p> <p>In this dissertation, we report a set of approaches for improving the accuracy of structural features prediction in protein …
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From Solution Into the Gas Phase: Studying Protein Hydrogen Exchange and Electrospray Ionization Using Molecular Dynamics Simulation
… often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting …
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Probing Isoforms of the Prion Protein through Tyrosine Nitration
… in which Tyr residues undergo a change in solvent accessibility, which may be due to a conformational change in that region or to inter-subunit packing.
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Probing Isoforms of the Prion Protein through Tyrosine Nitration
… in which Tyr residues undergo a change in solvent accessibility, which may be due to a conformational change in that region or to inter-subunit packing.
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Probing Structural Differences of Recombinant Prion Isoforms Using Fluorescence Spectroscopy
… two misfolded isoforms of prion, PrPb and PrPF. Solvent accessibilities of the six tryptophan residues were probed among the three isoforms using various tryptophan fluorescence techniques. For all six mutants, solvent accessibility was shown to decrease following conversion to the misfolded …
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Probing Structural Differences of Recombinant Prion Isoforms Using Fluorescence Spectroscopy
… two misfolded isoforms of prion, PrPb and PrPF. Solvent accessibilities of the six tryptophan residues were probed among the three isoforms using various tryptophan fluorescence techniques. For all six mutants, solvent accessibility was shown to decrease following conversion to the misfolded …
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Understanding the Molecular Level Interactions of Cancer Inhibitor Imatinib with Human Fibroblast Growth Factor-1
… to hFGF-1 and enhances its thermal stability and solvent accessibility. In addition, biacore analysis was carried out to determine the binding affinity of imatinib to hFGF-1.</p>
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Localized methods for protein interaction prediction
… uses a profile of secondary structure and solvent accessibility predictions with residue contact maps to guide and constrain alignments. Using a decision tree classifier and low-throughput experimental data for training, it combines information inferred from statistical interaction …
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The reaction kinetics and three-dimensional architecture of a catalytic RNA
… radical probing, which provided a measure of the solvent accessibility at each position in the RNA backbone. In collaboration with another group, these data were used to model the tertiary architecture of the ligase in three dimensions. Finally, the predictive value of the model was.tested and …
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Structure, dynamics, and interactions of Angiotensin family of peptides with functional implications.
… side-chain packing and marked increase of Phe8 solvent accessibility upon AngI truncation to AngII. Our combined approach of experiment and extensive computer simulation thus yields new information on the conformational dynamics of the angiotensins, helping provide insight into the structural …
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Computer simulation of titration behavior in proteins
… multiple site titration theory based on solvent accessibility is proposed, and it is shown that this model results in improved agreement of calculated pK$\rm\sb{a}$ values with experiment when a low protein interior dielectric constant is used. The techniques developed are applied to two …
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Structural and Functional Studies of the Human Saposin Proteins
… They function in part to increase the solvent accessibility of these SLs to specific acid hydrolases by two proposed modes of action. In the solubilizer model, saposins extract SLs into soluble saposin-lipid complexes, and in the liftase model, the saposins reorganize lipids within …
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Mass spectrometric indentification of formaldehyde-induced modifications of peptides and proteins under in vivo protein cross-linking conditions
… are reactive to formaldehyde and that residue accessibility appears to play a role in reactivity. How applicable these findings are to formaldehyde cross-linking studies done under in vivo conditions (10-20 min incubations) is unclear. The chemistry of formaldehyde cross-linking was therefore …
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Development and Application of 19F NMR of Proteins
… Paramagnetic effects from dissolved oxygen, solvent isotope shifts from deuterium oxide, and 1H-19F NOEs were each sufficient in establishing relative solvent exposure, while the combination of effects from oxygen and deuterium oxide were able to delineate local hydrophobicity and solvent …
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The Advancement of Mass Spectrometry-based Hydroxyl Radical Protein Footprinting: Application of Novel Analysis Methods to Model Proteins and Apolipoprotein E
… reactivity of hydroxyl radicals to stably modify solvent accessible residues non-specifically in a microsecond. The extent of *OH labeling at sites assays their solvent accessibility. We have corroborated the predicted profoundly short timescale of labeling empirically, by FPOP-labeling three …
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Engineering the future of Hybrid Materials with Coarse-Grained Molecular Dynamics
… of factors such as glycan density in enhancing solvent accessibility, which directly impacts binding affinities and bioactivity. In parallel, CG model development efforts are directed at physically representing lipid bilayer systems, facilitating the simulation of cellular interfaces and hybrid …
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Molecular Level Interaction of Human Fibroblast Growth Factor-1 (hFGF-1) With Phloridzin
… performed to assess the thermal stability and solvent accessibility of hFGF-1 in the presence of phloridzin respectively. It was found from interaction studies that hFGF-1 in the presence of phloridzin shown increased thermal stability and increased resistance against trypsin digestion. In …