Dynameomics: Protein dynamics and unfolding across fold space

Amanda L. Jonsson, R. Dustin Schaeffer, Marc W. Van Der Kamp, Valerie Daggett

Research output: Contribution to journalReview article

1 Citation (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)335-344
Number of pages10
JournalBiomolecular Concepts
Volume1
Issue number5-6
DOIs
StatePublished - Jan 1 2010

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Protein Unfolding
Protein folding
Protein Folding
Proteins
Databases

Keywords

  • dynameomics
  • molecular dynamics
  • protein folding
  • transition state
  • WW domain

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Cellular and Molecular Neuroscience

Cite this

Dynameomics : Protein dynamics and unfolding across fold space. / Jonsson, Amanda L.; Schaeffer, R. Dustin; Van Der Kamp, Marc W.; Daggett, Valerie.

In: Biomolecular Concepts, Vol. 1, No. 5-6, 01.01.2010, p. 335-344.

Research output: Contribution to journalReview article

Jonsson, Amanda L. ; Schaeffer, R. Dustin ; Van Der Kamp, Marc W. ; Daggett, Valerie. / Dynameomics : Protein dynamics and unfolding across fold space. In: Biomolecular Concepts. 2010 ; Vol. 1, No. 5-6. pp. 335-344.
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