Primary Structure Effects on Peptide Group Hydrogen Exchange
TLDR
The results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo‐ and polypeptides.Abstract:
The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest-neighbor blocking and inductive effects was tested in oligo- and polypeptides and, surprisingly, confirmed. Reference rates for alanine-containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured oligo- and polypeptides. The application of this approach to protein studies is discussed.read more
Citations
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Journal ArticleDOI
Solution dynamics of the trp repressor : a study of amide proton exchange by t1 relaxation
TL;DR: The implication of these findings is that the "open" state of the two-state model in the DNA-binding region is not completely open and has an intrinsic exchange rate different from that of a random coil peptide.
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Hydrogen exchange and ligand binding: ligand-dependent and ligand-independent protection in the Src SH3 domain.
David Wildes,Susan Marqusee +1 more
TL;DR: The results demonstrate that the slowing of hydrogen exchange induced by ligand interactions should be interpreted with caution, and more extensive experiments are required to correlate changes in hydrogen exchange with changes in structure or internal dynamics.
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Absence of stable intermediates on the folding pathway of barnase.
Jiro Takei,Rui-Ai Chu,Yawen Bai +2 more
TL;DR: Doubts are cast on the previous conclusions on the nature of the early folding state in barnase and these results should have important implications in understanding the early fold events of barnases and other proteins in general.
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Role of Enthalpy–Entropy Compensation Interactions in Determining the Conformational Propensities of Amino Acid Residues in Unfolded Peptides.
TL;DR: The enthalpy-entropy compensation discovered as well as the iso-equilbrium and thermodynamics obtained for each amino acid residue provide a new and informative way of identifying the determinants of amino acid propensities in unfolded and disordered states.
Journal ArticleDOI
Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis.
In-Hee Park,John D. Venable,Caitlin Steckler,Susan E. Cellitti,Scott A. Lesley,Scott A. Lesley,Glen Spraggon,Ansgar Brock +7 more
TL;DR: A transferable and scalable MD based HX prediction approach based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated and it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD.
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