Literature DB >> 35129612

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins.

F Emil Thomasen1, Kresten Lindorff-Larsen.   

Abstract

Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic weights. Determining conformational ensembles usually involves the integration of biophysical experiments and computational models. In this review, we discuss current approaches to determine conformational ensembles of IDPs and multidomain proteins, including the choice of biophysical experiments, computational models used to sample protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest future directions for research in the field.
© 2022 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Entities:  

Keywords:  conformational ensemble; molecular dynamics; protein structure

Mesh:

Substances:

Year:  2022        PMID: 35129612     DOI: 10.1042/BST20210499

Source DB:  PubMed          Journal:  Biochem Soc Trans        ISSN: 0300-5127            Impact factor:   5.407


  4 in total

Review 1.  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

2.  IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States.

Authors:  João M C Teixeira; Zi Hao Liu; Ashley Namini; Jie Li; Robert M Vernon; Mickaël Krzeminski; Alaa A Shamandy; Oufan Zhang; Mojtaba Haghighatlari; Lei Yu; Teresa Head-Gordon; Julie D Forman-Kay
Journal:  J Phys Chem A       Date:  2022-08-28       Impact factor: 2.944

3.  Characterisation of HOIP RBR E3 ligase conformational dynamics using integrative modelling.

Authors:  Marius Kausas; Diego Esposito; Katrin Rittinger; Franca Fraternali
Journal:  Sci Rep       Date:  2022-09-08       Impact factor: 4.996

4.  Ligand-induced shifts in conformational ensembles that describe transcriptional activation.

Authors:  Sabab Hasan Khan; Sean M Braet; Stephen John Koehler; Elizabeth Elacqua; Ganesh Srinivasan Anand; C Denise Okafor
Journal:  Elife       Date:  2022-10-12       Impact factor: 8.713

  4 in total

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