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
Anabaena apoflavodoxin hydrogen exchange: on the stable exchange core of the alpha/beta(21345) flavodoxin-like family.
Grant M. Langdon,M. Angeles Jiménez,Carlos G. Genzor,Susana Maldonado,Javier Sancho,Manuel Rico +5 more
TL;DR: The backbone internal dynamics of the apoflavodoxin from Anabaena is analyzed here by the hydrogen exchange method and it is of interest that a cluster of a few structurally equivalent residues in the central β‐strands and in helix 5 is common to the cores.
Journal ArticleDOI
Contributions of chemical and diffusive exchange to T1ρ dispersion.
TL;DR: Simulations and measurements show that single‐ and double‐inflection points in R1ρ dispersion profiles were observed, respectively, in simulations of slow diffusive exchange alone and when combined with rapid chemical exchange, which are consistent with the combined effects of slow diffusion and rapid −OH exchange processes.
Journal ArticleDOI
Computational method allowing Hydrogen-Deuterium Exchange Mass Spectrometry at single amide Resolution.
Chris Gessner,Wieland Steinchen,Sabrina Bédard,John J. Skinner,Virgil L. Woods,Thomas J. Walsh,Gert Bange,Dennis Pantazatos +7 more
TL;DR: A method for extracting information beyond that needed for defining protein stability at single amide resolution from an HDX dataset to generate a HDXMS protein stability fingerprint is presented.
Journal ArticleDOI
Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase
Victoria A. Roberts,Michael E. Pique,Simon Hsu,Sheng Li,Geir Slupphaug,Robert P. Rambo,Jonathan W. Jamison,Tong Liu,Jun H. Lee,John A. Tainer,Lynn F. Ten Eyck,Virgil L. Woods +11 more
TL;DR: A new approach is presented that can use longer DNA substrates and reveal new protein–DNA interactions even in extensively studied systems, and combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS).
Book ChapterDOI
Structural information on proteins from circular dichroism spectroscopy possibilities and limitations.
TL;DR: This chapter gives a general survey of the application of circular dichroism (CD) spectroscopy for structural studies of proteins and the less well-known vibrational CD will be discussed.
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