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Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0001-8354-0253
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2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Article in journal (Refereed) Published
Abstract [en]

Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.

Place, publisher, year, edition, pages
Nature Publishing Group, 2016.
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Biological Sciences
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URN: urn:nbn:se:kth:diva-203924DOI: 10.1038/ncomms12575ISI: 000391870700001Scopus ID: 2-s2.0-84984943375OAI: oai:DiVA.org:kth-203924DiVA: diva2:1083042
Note

QC 20170320

Available from: 2017-03-20 Created: 2017-03-20 Last updated: 2017-11-29Bibliographically approved

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Yoluk, OzgeLindahl, Erik

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Orellana, LauraYoluk, OzgeLindahl, Erik
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Theoretical PhysicsScience for Life Laboratory, SciLifeLabExperimental Biomolecular PhysicsSeRC - Swedish e-Science Research Centre
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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
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  • asciidoc
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