Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case

Proteins. 1996 May;25(1):79-88. doi: 10.1002/(SICI)1097-0134(199605)25:1<79::AID-PROT6>3.0.CO;2-F.

Abstract

The weighted masses molecular dynamics (WMMD) technique is applied to the protein adenylate kinase. A novel set of restraints has been developed to allow the use of this technique with proteins. The WMMD simulation is successful in predicting the flexibility of the two mobile domains of the protein. The end product of the simulation is similar to the known open and AMP bound forms of the enzyme. The biological relevance of the restraints used and potential methods of improving the technique are discussed.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Monophosphate / chemistry
  • Adenosine Monophosphate / metabolism
  • Adenylate Kinase / chemistry*
  • Adenylate Kinase / metabolism*
  • Adenylyl Imidodiphosphate / chemistry
  • Algorithms
  • Computer Simulation
  • Escherichia coli / enzymology
  • Models, Molecular
  • Protein Conformation*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Software

Substances

  • Adenylyl Imidodiphosphate
  • Adenosine Monophosphate
  • Adenylate Kinase