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Biomolecular Concepts

Editor-in-Chief: AVILA, Jesus

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CiteScore 2017: 2.50

SCImago Journal Rank (SJR) 2017: 0.861
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1868-503X
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Volume 1, Issue 5-6

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Dynameomics: protein dynamics and unfolding across fold space

Amanda L. Jonsson
  • Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA
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/ R. Dustin Schaeffer
  • Biomolecular Structure and Design Program, University of Washington, Box 355013, Seattle, WA 98195-5013, USA
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/ Marc W. van der Kamp
  • Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA
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  • De Gruyter OnlineGoogle Scholar
/ Valerie Daggett
  • Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA
  • Biomolecular Structure and Design Program, University of Washington, Box 355013, Seattle, WA 98195-5013, USA
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Published Online: 2011-01-07 | DOI: https://doi.org/10.1515/bmc.2010.032

Abstract

All currently known structures of proteins together define ‘protein fold space’. To increase the general understanding of protein dynamics and protein folding, we selected a set of 807 proteins and protein domains that represent 95% of the currently known autonomous folded domains present in globular proteins. Native state and unfolding simulations of these representatives are now complete and accessible via a novel database containing over 11 000 simulations. Because protein folding is a microscopically reversible process, these simulations effectively sample protein folding across all of protein fold space. Here, we give an overview of how the representative proteins were selected and how the simulations were performed and validated. We then provide examples of different types of analyses that can be performed across our large set of simulations, made possible by the database approach. We further show how the unfolding simulations can be used to compare unfolding of structural elements in isolation and in different structural contexts, using as an example a short, triple stranded β-sheet that forms the WW domain and is present in several larger unrelated proteins.

Keywords: dynameomics; molecular dynamics; protein folding; transition state; WW domain

About the article

Published Online: 2011-01-07

Published in Print: 2010-12-01


Citation Information: BioMolecular Concepts, Volume 1, Issue 5-6, Pages 335–344, ISSN (Online) 1868-503X, ISSN (Print) 1868-5021, DOI: https://doi.org/10.1515/bmc.2010.032.

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