Literature DB >> 21388216

Nuclear magnetic resonance provides a quantitative description of protein conformational flexibility on physiologically important time scales.

Loïc Salmon1, Guillaume Bouvignies, Phineus Markwick, Martin Blackledge.   

Abstract

A complete description of biomolecular activity requires an understanding of the nature and the role of protein conformational dynamics. In recent years, novel nuclear magnetic resonance-based techniques that provide hitherto inaccessible detail concerning biomolecular motions occurring on physiologically important time scales have emerged. Residual dipolar couplings (RDCs) provide precise information about time- and ensemble-averaged structural and dynamic processes with correlation times up to the millisecond and thereby encode key information for understanding biological activity. In this review, we present the application of two very different approaches to the quantitative description of protein motion using RDCs. The first is purely analytical, describing backbone dynamics in terms of diffusive motions of each peptide plane, using extensive statistical analysis to validate the proposed dynamic modes. The second is based on restraint-free accelerated molecular dynamics simulation, providing statistically sampled free energy-weighted ensembles that describe conformational fluctuations occurring on time scales from pico- to milliseconds, at atomic resolution. Remarkably, the results from these two approaches converge closely in terms of distribution and absolute amplitude of motions, suggesting that this kind of combination of analytical and numerical models is now capable of providing a unified description of protein conformational dynamics in solution.

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Year:  2011        PMID: 21388216     DOI: 10.1021/bi200177v

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  21 in total

1.  Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results.

Authors:  Enrique Marcos; Pau Mestres; Ramon Crehuet
Journal:  Biophys J       Date:  2011-12-07       Impact factor: 4.033

2.  An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation.

Authors:  Denise Steiner; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2012-06-16       Impact factor: 1.733

3.  On the calculation of ³Jαβ-coupling constants for side chains in proteins.

Authors:  Denise Steiner; Jane R Allison; Andreas P Eichenberger; Wilfred F van Gunsteren
Journal:  J Biomol NMR       Date:  2012-06-20       Impact factor: 2.835

4.  The Exact NOE as an Alternative in Ensemble Structure Determination.

Authors:  Beat Vögeli; Simon Olsson; Peter Güntert; Roland Riek
Journal:  Biophys J       Date:  2016-01-05       Impact factor: 4.033

Review 5.  Characterizing weak protein-protein complexes by NMR residual dipolar couplings.

Authors:  Malene Ringkjøbing Jensen; Jose-Luis Ortega-Roldan; Loïc Salmon; Nico van Nuland; Martin Blackledge
Journal:  Eur Biophys J       Date:  2011-06-28       Impact factor: 1.733

6.  Protein dynamics: whispering within.

Authors:  Rafael Brüschweiler
Journal:  Nat Chem       Date:  2011-08-23       Impact factor: 24.427

7.  The dynamic structure of thrombin in solution.

Authors:  Brian Fuglestad; Paul M Gasper; Marco Tonelli; J Andrew McCammon; Phineus R L Markwick; Elizabeth A Komives
Journal:  Biophys J       Date:  2012-07-03       Impact factor: 4.033

Review 8.  Applications of NMR and computational methodologies to study protein dynamics.

Authors:  Chitra Narayanan; Khushboo Bafna; Louise D Roux; Pratul K Agarwal; Nicolas Doucet
Journal:  Arch Biochem Biophys       Date:  2017-05-05       Impact factor: 4.013

9.  Simultaneous detection of intra- and inter-molecular paramagnetic relaxation enhancements in protein complexes.

Authors:  Cristina Olivieri; Manu Veliparambil Subrahmanian; Youlin Xia; Jonggul Kim; Fernando Porcelli; Gianluigi Veglia
Journal:  J Biomol NMR       Date:  2018-02-02       Impact factor: 2.835

10.  A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.

Authors:  Loïc Salmon; Gavin Bascom; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2013-03-28       Impact factor: 15.419

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