A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.

Intrinsically disordered proteins play an important role in cellular signalling, mediated by their interactions with other biomolecules. A key question concerns the nature of their binding mechanism, and whether the bound structure is induced only by proximity to the binding partner. This is difficu...

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Autores principales:	Michael Knott, Robert B Best
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/fd65d11f517f41d3857c0a90b0c1415a
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spelling	oai:doaj.org-article:fd65d11f517f41d3857c0a90b0c1415a2021-11-18T05:51:09ZA preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.1553-734X1553-735810.1371/journal.pcbi.1002605https://doaj.org/article/fd65d11f517f41d3857c0a90b0c1415a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22829760/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Intrinsically disordered proteins play an important role in cellular signalling, mediated by their interactions with other biomolecules. A key question concerns the nature of their binding mechanism, and whether the bound structure is induced only by proximity to the binding partner. This is difficult to answer through experiment alone because of the very heterogeneous nature of the unbound ensemble, and the probable rapid interconversion of the various unbound structures. Here we report the most extensive set of simulations on NCBD to date: we use large-scale replica exchange molecular dynamics to explore the unbound state. An important feature of the study is the use of an atomistic force field that has been parametrised against experimental data for weakly structured peptides, together with an accurate explicit water model. Neither the force field nor the starting conformations are biased towards a particular structure. The regions of NCBD that have high helical propensity in the simulations correspond closely to helices in the 'core' unbound conformation determined by NMR, although no single member of the simulated unbound ensemble closely resembles the core conformation, or either of the two known bound conformations. We have validated the results against NMR spectroscopy and SAXS measurements, obtaining reasonable agreement. The two helices which most stabilise the binding of NCBD with ACTR are formed readily; the third helix, which is less important for binding but is involved in most of the intraprotein contacts of NCBD in the bound conformation, is formed more rarely, and tends not to coexist with the other helices. These results support a mechanism by which NCBD gains the advantages of disorder, while forming binding-competent structures in the unbound state. We obtain support for this mechanism from coarse-grained simulations of NCBD with, and without, its binding partner.Michael KnottRobert B BestPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 7, p e1002605 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Michael Knott Robert B Best A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.
description	Intrinsically disordered proteins play an important role in cellular signalling, mediated by their interactions with other biomolecules. A key question concerns the nature of their binding mechanism, and whether the bound structure is induced only by proximity to the binding partner. This is difficult to answer through experiment alone because of the very heterogeneous nature of the unbound ensemble, and the probable rapid interconversion of the various unbound structures. Here we report the most extensive set of simulations on NCBD to date: we use large-scale replica exchange molecular dynamics to explore the unbound state. An important feature of the study is the use of an atomistic force field that has been parametrised against experimental data for weakly structured peptides, together with an accurate explicit water model. Neither the force field nor the starting conformations are biased towards a particular structure. The regions of NCBD that have high helical propensity in the simulations correspond closely to helices in the 'core' unbound conformation determined by NMR, although no single member of the simulated unbound ensemble closely resembles the core conformation, or either of the two known bound conformations. We have validated the results against NMR spectroscopy and SAXS measurements, obtaining reasonable agreement. The two helices which most stabilise the binding of NCBD with ACTR are formed readily; the third helix, which is less important for binding but is involved in most of the intraprotein contacts of NCBD in the bound conformation, is formed more rarely, and tends not to coexist with the other helices. These results support a mechanism by which NCBD gains the advantages of disorder, while forming binding-competent structures in the unbound state. We obtain support for this mechanism from coarse-grained simulations of NCBD with, and without, its binding partner.
format	article
author	Michael Knott Robert B Best
author_facet	Michael Knott Robert B Best
author_sort	Michael Knott
title	A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.
title_short	A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.
title_full	A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.
title_fullStr	A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.
title_full_unstemmed	A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.
title_sort	preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/fd65d11f517f41d3857c0a90b0c1415a
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A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.

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