Dynameomics: Mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

David A C Beck, Amanda L. Jonsson, R. Dustin Schaeffer, Kathryn A. Scott, Ryan Day, Rudesh D. Toofanny, Darwin O V Alonso, Valerie Daggett

Research output: Contribution to journalArticle

53 Scopus citations

Abstract

The goal of Dynameomics is to perform atomistic molecular dynamics (MD) simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways. Here we present 188-fold representatives and their native state simulations and analyses. These 188 targets represent 67% of all the structures in the Protein Data Bank. The behavior of several specific targets is highlighted to illustrate general properties in the full dataset and to demonstrate the role of MD in understanding protein function and stability. As an example of what can be learned from mining the Dynameomics database, we identified a protein fold with heightened localized dynamics. In one member of this fold family, the motion affects the exposure of its phosphorylation site and acts as an entropy sink to offset another portion of the protein that is relatively immobile in order to present a consistent interface for protein docking. In another member of this family, a polymorphism in the highly mobile region leads to a host of disease phenotypes. We have constructed a web site to provide access to a novel hybrid relational/multidimensional database (described in the succeeding two papers) to view and interrogate simulations of the top 30 targets: http://www.dynameomics. org. The Dynameomics database, currently the largest collection of protein simulations and protein structures in the world, should also be useful for determining the rules governing protein folding and kinetic stability, which should aid in deciphering genomic information and for protein engineering and design.

Original languageEnglish (US)
Pages (from-to)353-368
Number of pages16
JournalProtein Engineering, Design and Selection
Volume21
Issue number6
DOIs
StatePublished - Jun 1 2008

Keywords

  • Database
  • Dynameomics
  • Molecular dynamics
  • Protein dynamics
  • Protein folds

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Biochemistry
  • Molecular Biology

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