An Empirical Correlation between Amide Deuterium Isotope Effects on13CαChemical Shifts and Protein Backbone Conformation

1997 ◽  
Vol 119 (34) ◽  
pp. 8070-8075 ◽  
Author(s):  
Marcel Ottiger ◽  
Ad Bax
Keyword(s):  
Isotope Effects ◽  
Empirical Correlation ◽  
Protein Backbone ◽  
Backbone Conformation ◽  
Deuterium Isotope Effects ◽  
Protein Backbone Conformation

scholarly journals Knowledge-based prediction of protein backbone conformation using a structural alphabet

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0186215 ◽  
Author(s):  
Iyanar Vetrivel ◽  
Swapnil Mahajan ◽  
Manoj Tyagi ◽  
Lionel Hoffmann ◽  
Yves-Henri Sanejouand ◽  
...  
Keyword(s):  
Protein Backbone ◽  
Structural Alphabet ◽  
Knowledge Based ◽  
Backbone Conformation ◽  
Protein Backbone Conformation

Prediction of protein backbone conformation based on seven structure assignments

1991 ◽  
Vol 221 (3) ◽  
pp. 961-979 ◽  
Author(s):  
Marianne J. Rooman ◽  
Jean-Pierre A. Kocher ◽  
Shoshana J. Wodak
Keyword(s):  
Protein Backbone ◽  
Backbone Conformation ◽  
Protein Backbone Conformation

scholarly journals Investigation of the impact of PTMs on the protein backbone conformation

Amino Acids ◽  
2019 ◽  
Vol 51 (7) ◽  
pp. 1065-1079 ◽  
Author(s):  
Pierrick Craveur ◽  
Tarun J. Narwani ◽  
Joseph Rebehmed ◽  
Alexandre G. de Brevern
Keyword(s):  
Protein Backbone ◽  
Backbone Conformation ◽  
The Impact ◽  
Protein Backbone Conformation

scholarly journals A new default restraint library for the protein backbone inPhenix: a conformation-dependent geometry goes mainstream

2016 ◽  
Vol 72 (1) ◽  
pp. 176-179 ◽  
Author(s):  
Nigel W. Moriarty ◽  
Dale E. Tronrud ◽  
Paul D. Adams ◽  
P. Andrew Karplus
Keyword(s):  
Protein Structure ◽  
Protein Data Bank ◽  
Transition Period ◽  
Structure Refinement ◽  
Data Bank ◽  
Protein Backbone ◽  
Protein Structure Refinement ◽  
Fundamental Part ◽  
Backbone Conformation ◽  
Protein Backbone Conformation

Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.

Mechanism of hydration and isomerisation of 4-ethylidene-2,6-di-tert-butyl-2,5-cyclohexadien-1-one. Kinetics, acid-base catalysis and solvent deuterium isotope effects

1979 ◽  
Vol 44 (1) ◽  
pp. 110-122 ◽  
Author(s):  
Jiří Velek ◽  
Bohumír Koutek ◽  
Milan Souček
Keyword(s):  
Aqueous Medium ◽  
Rate Equation ◽  
Kinetic Data ◽  
Isotope Effects ◽  
Base Catalysis ◽  
Quinone Methide ◽  
Reaction Products ◽  
Acid Base ◽  
Deuterium Isotope Effects ◽  
Hydroxybenzyl Alcohol

Competitive hydration and isomerisation of the quinone methide I at 25 °C in an aqueous medium in the region of pH 2.4-13.0 was studied spectrophotometrically. The only reaction products in the studied range of pH are 4-hydroxybenzyl alcohol (II) and 4-hydroxystyrene (III). The form of the overall rate equation corresponds to a general acid-base catalysis. The mechanism of both reactions for three markedly separated pH regions is discussed on the basis of kinetic data and solvent deuterium effect.

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