Literature DB >> 27300592

Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.

Nicola Salvi1, Anton Abyzov1, Martin Blackledge1.   

Abstract

Intrinsically disordered proteins (IDPs) access highly diverse ensembles of conformations in their functional states. Although this conformational plasticity is essential to their function, little is known about the dynamics underlying interconversion between accessible states. Nuclear magnetic resonance (NMR) relaxation rates contain a wealth of information about the time scales and amplitudes of motion in IDPs, but the highly dynamic nature of IDPs complicates their interpretation. We present a novel framework in which a series of molecular dynamics (MD) simulations are used in combination with experimental (15)N relaxation measurements to characterize the ensemble of dynamic processes contributing to the observed rates. By accounting for the distinct dynamic averaging present in the different conformational states sampled by the equilibrium ensemble, we are able to accurately describe both dynamic time scales and local and global conformational sampling. The method is robust, systematically improving agreement with independent experimental relaxation data, irrespective of the actively targeted rates, and suggesting interdependence of motions occurring on time scales varying over 3 orders of magnitude.

Entities:  

Year:  2016        PMID: 27300592     DOI: 10.1021/acs.jpclett.6b00885

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  25 in total

Review 1.  Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding.

Authors:  Jing Yang; Meng Gao; Junwen Xiong; Zhengding Su; Yongqi Huang
Journal:  Protein Sci       Date:  2019-09-04       Impact factor: 6.725

Review 2.  NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes.

Authors:  Kyle W East; Erin Skeens; Jennifer Y Cui; Helen B Belato; Brandon Mitchell; Rohaine Hsu; Victor S Batista; Giulia Palermo; George P Lisi
Journal:  Biophys Rev       Date:  2019-12-14

3.  Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions.

Authors:  Vojtěch Zapletal; Arnošt Mládek; Kateřina Melková; Petr Louša; Erik Nomilner; Zuzana Jaseňáková; Vojtěch Kubáň; Markéta Makovická; Alice Laníková; Lukáš Žídek; Jozef Hritz
Journal:  Biophys J       Date:  2020-02-29       Impact factor: 4.033

Review 4.  Intrinsic protein disorder in oncogenic KRAS signaling.

Authors:  Ruth Nussinov; Hyunbum Jang; Chung-Jung Tsai; Tsung-Jen Liao; Shuai Li; David Fushman; Jian Zhang
Journal:  Cell Mol Life Sci       Date:  2017-06-08       Impact factor: 9.261

Review 5.  Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.

Authors:  Anton Abyzov; Martin Blackledge; Markus Zweckstetter
Journal:  Chem Rev       Date:  2022-02-18       Impact factor: 60.622

Review 6.  Interactions between the Intrinsically Disordered Proteins β-Synuclein and α-Synuclein.

Authors:  Jonathan K Williams; Xue Yang; Jean Baum
Journal:  Proteomics       Date:  2018-09-09       Impact factor: 3.984

7.  Structural Model of the Proline-Rich Domain of Huntingtin Exon-1 Fibrils.

Authors:  Alexander S Falk; José M Bravo-Arredondo; Jobin Varkey; Sayuri Pacheco; Ralf Langen; Ansgar B Siemer
Journal:  Biophys J       Date:  2020-10-20       Impact factor: 4.033

8.  Computational pipeline for estimation of small-molecule T1 relaxation times.

Authors:  Joseph C Wildenberg; Nicholas R Perkons; Gabrielle Pilla; Stephen Kadlecek; Terence P F Gade
Journal:  J Magn Reson       Date:  2020-04-18       Impact factor: 2.229

9.  Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation.

Authors:  Jamie A Macpherson; Alina Theisen; Laura Masino; Louise Fets; Paul C Driscoll; Vesela Encheva; Ambrosius P Snijders; Stephen R Martin; Jens Kleinjung; Perdita E Barran; Franca Fraternali; Dimitrios Anastasiou
Journal:  Elife       Date:  2019-07-02       Impact factor: 8.713

Review 10.  Generating Ensembles of Dynamic Misfolding Proteins.

Authors:  Theodoros K Karamanos; Arnout P Kalverda; Sheena E Radford
Journal:  Front Neurosci       Date:  2022-03-31       Impact factor: 4.677

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