Literature DB >> 28483383

Applications of NMR and computational methodologies to study protein dynamics.

Chitra Narayanan1, Khushboo Bafna2, Louise D Roux1, Pratul K Agarwal3, Nicolas Doucet4.   

Abstract

Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Allostery; Chemical shift analysis; Conformational sub-states; Protein dynamics; Quasi anharmonic analysis; Relaxation dispersion

Mesh:

Substances:

Year:  2017        PMID: 28483383      PMCID: PMC5545153          DOI: 10.1016/j.abb.2017.05.002

Source DB:  PubMed          Journal:  Arch Biochem Biophys        ISSN: 0003-9861            Impact factor:   4.013


  96 in total

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2.  A 2D ¹³C-CEST experiment for studying slowly exchanging protein systems using methyl probes: an application to protein folding.

Authors:  Guillaume Bouvignies; Lewis E Kay
Journal:  J Biomol NMR       Date:  2012-06-12       Impact factor: 2.835

Review 3.  Relating protein motion to catalysis.

Authors:  Sharon Hammes-Schiffer; Stephen J Benkovic
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Review 4.  Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings.

Authors:  Guillaume Bouvignies; Phineus R L Markwick; Martin Blackledge
Journal:  Chemphyschem       Date:  2007-09-17       Impact factor: 3.102

5.  From protein sequence to dynamics and disorder with DynaMine.

Authors:  Elisa Cilia; Rita Pancsa; Peter Tompa; Tom Lenaerts; Wim F Vranken
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

6.  Hot spots for allosteric regulation on protein surfaces.

Authors:  Kimberly A Reynolds; Richard N McLaughlin; Rama Ranganathan
Journal:  Cell       Date:  2011-12-23       Impact factor: 41.582

7.  Evidence for flexibility in the function of ribonuclease A.

Authors:  Roger Cole; J Patrick Loria
Journal:  Biochemistry       Date:  2002-05-14       Impact factor: 3.162

8.  A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

Authors:  Gira Bhabha; Jeeyeon Lee; Damian C Ekiert; Jongsik Gam; Ian A Wilson; H Jane Dyson; Stephen J Benkovic; Peter E Wright
Journal:  Science       Date:  2011-04-08       Impact factor: 47.728

9.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

Review 10.  NMR Methods to Study Dynamic Allostery.

Authors:  Sarina Grutsch; Sven Brüschweiler; Martin Tollinger
Journal:  PLoS Comput Biol       Date:  2016-03-10       Impact factor: 4.475

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  9 in total

1.  Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.

Authors:  Sophie Sacquin-Mora
Journal:  J R Soc Interface       Date:  2019-07-10       Impact factor: 4.118

2.  Enhanced spectral density mapping through combined multiple-field deuterium 13CH2D methyl spin relaxation NMR spectroscopy.

Authors:  Andrew Hsu; Paul A O'Brien; Shibani Bhattacharya; Mark Rance; Arthur G Palmer
Journal:  Methods       Date:  2017-12-27       Impact factor: 3.608

3.  Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.

Authors:  Julia Koehler Leman; Andrew R D'Avino; Yash Bhatnagar; Jeffrey J Gray
Journal:  Proteins       Date:  2017-11-08

4.  Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation.

Authors:  Iris N Smith; Jennifer E Dawson; James Krieger; Stetson Thacker; Ivet Bahar; Charis Eng
Journal:  J Chem Inf Model       Date:  2022-08-24       Impact factor: 6.162

Review 5.  Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Authors:  Rebecca J Howard; Vincenzo Carnevale; Lucie Delemotte; Ute A Hellmich; Brad S Rothberg
Journal:  Biochim Biophys Acta Biomembr       Date:  2017-12-16       Impact factor: 4.019

Review 6.  Integrated Computational Approaches and Tools forAllosteric Drug Discovery.

Authors:  Olivier Sheik Amamuddy; Wayde Veldman; Colleen Manyumwa; Afrah Khairallah; Steve Agajanian; Odeyemi Oluyemi; Gennady Verkhivker; Ozlem Tastan Bishop
Journal:  Int J Mol Sci       Date:  2020-01-28       Impact factor: 5.923

Review 7.  Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model.

Authors:  Doo Nam Kim; Karissa Y Sanbonmatsu
Journal:  Biosci Rep       Date:  2017-12-05       Impact factor: 3.840

Review 8.  Combining Experimental Data and Computational Methods for the Non-Computer Specialist.

Authors:  Reinier Cárdenas; Javier Martínez-Seoane; Carlos Amero
Journal:  Molecules       Date:  2020-10-18       Impact factor: 4.411

Review 9.  Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.

Authors:  Gennady M Verkhivker; Steve Agajanian; Guang Hu; Peng Tao
Journal:  Front Mol Biosci       Date:  2020-07-09
  9 in total

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