Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case.
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.
Elamrani
S
S
W.M. Keck Center for Computational Biology, Department of Chemistry, University of Houston, Texas 77204-5641, USA.
Berry
M B
MB
Phillips
G N
GN
McCammon
J A
JA
D000249:Adenosine Monophosphate / Q000737:chemistry / Q000378:metabolism; D000263:Adenylate Kinase / Q000737:chemistry* / Q000378:metabolism*; D000266:Adenylyl Imidodiphosphate / Q000737:chemistry; D000465:Algorithms; D003198:Computer Simulation; D004926:Escherichia coli / Q000201:enzymology; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012984:Software
D000266:Adenylyl Imidodiphosphate; D000249:Adenosine Monophosphate; D000263:Adenylate Kinase