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
Equilibrium Unfolding Thermodynamics of β2-Microglobulin Analyzed through Native-State H/D Exchange
Enrico Rennella,Alessandra Corazza,Federico Fogolari,Paolo Viglino,Sofia Giorgetti,Monica Stoppini,Vittorio Bellotti,Gennaro Esposito +7 more
TL;DR: The exchange rates for the amide hydrogens of beta(2)-microglobulin, the protein responsible for dialysis-related amyloidosis, were measured under native conditions at different temperatures and indicates the presence of mixed EX1- and EX2-limit mechanisms.
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Structural features of interferon‐γ aggregation revealed by hydrogen exchange
TL;DR: Results show that helix C, which forms the hydrophobic core of the IFN‐γ dimer, is highly protected from HX under native conditions, is more stable in GdnHCl than the rest of the protein and remains intact in both GDNHCl‐ and KSCN‐induced aggregates.
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Eukaryotic class 1 translation termination factor eRF1--the NMR structure and dynamics of the middle domain involved in triggering ribosome-dependent peptidyl-tRNA hydrolysis.
Elena V. Ivanova,Peter M. Kolosov,Berry Birdsall,Geoff Kelly,Annalisa Pastore,Lev L. Kisselev,Vladimir I. Polshakov +6 more
TL;DR: The protein backbone dynamics, studied using 15N relaxation experiments, showed that the GGQ loop is the most flexible part of the middle domain, which could be a determinant of the functional activity of the eukaryotic class’1 polypeptide chain release factor.
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Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery.
TL;DR: A quantitative analysis of accelerated molecular dynamics simulations that provides impressive agreement with peptide-length HDXMS data is presented and reveals that the simulation analysis can distinguish the subtle differences in exchange due to mutation.
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Insights into the Dynamic Structural Properties of a Lanthipeptide Synthetase using Hydrogen-Deuterium Exchange Mass Spectrometry.
TL;DR: The first comprehensive application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) to study the biophysical properties of a RiPP biosynthetic enzyme is reported, highlighting the broad utility of the HDX- MS platform for revealing importantBiophysical properties and enzyme structural dynamics that likely play a widespread role in Ri PP biosynthesis.
References
More filters
Journal ArticleDOI
MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy
Ad Bax,Donald G. Davis +1 more
TL;DR: In this article, a new mixing scheme based on the MLEV-16 composite pulse decoupling cycle (II) was proposed, which is less sensitive to pulse imperfections and provides net magnetization transfer over a substantial bandwidth with only limited rf power.
Journal ArticleDOI
Coherence transfer by isotropic mixing: Application to proton correlation spectroscopy
Journal ArticleDOI
Use of glass electrodes to measure acidities in deuterium oxide1,2
Paul K. Glasoe,F. A. Long +1 more
TL;DR: In this article, a pH meter reading in D/sub 2/O solutions was 0-40 pH unit lower than in H/sub O solutions, attributed to the glass electrode.
Journal ArticleDOI
Dithiothreitol, a New Protective Reagent for SH Groups*
TL;DR: Strominger, J. L. H. (1960), Instruction Manual and Handbook, Beckman/Spinco Model 120 Amino Acid Analyzer, Palo Alto, California,Beckman Instruments Inc., Spinco Division.
Journal ArticleDOI
A two-dimensional nuclear overhauser enhancement (2d noe) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules
TL;DR: The 2D NOE experiment has the principal advantage that it avoids detrimental effects arising from the limited selectivity of preirradiation in crowded spectral regions, and yields with a single instrument setting a complete network of NOE's between all the protons in the macromolecule.
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