Journal of Computer-Aided Molecular Design

, Volume 8, Issue 4, pp 367–388

Nucleotide-binding properties of adenylate kinase from Escherichia coli: A molecular dynamics study in aqueous and vacuum environments


  • Petra Kern
    • Department of PharmacyETH
  • Roger M. Brunne
    • Department of Physical ChemistryETH-Hönggerberg
  • Gerd Folkers
    • Department of PharmacyETH
Research Papers

DOI: 10.1007/BF00125373

Cite this article as:
Kern, P., Brunne, R.M. & Folkers, G. J Computer-Aided Mol Des (1994) 8: 367. doi:10.1007/BF00125373


The complex of adenylate kinase with its transition-state inhibitor has been studied by molecular dynamics simulations in water and in vacuum environments with the GROMOS force field over a period of 300 ps. The adenylate kinase, a member of the nucleotide-binding protein family, was exemplarily chosen for the inspection of the nucleotide-binding properties in the active site. The ligand binding and the domain movements have been studied in detail over the simulation period and compared with the crystal structure. Secondary structure transitions and domain closures defined those parts of the structure which are involved in an induced-fit movement of the enzyme. The presence of more stable hydrogen bonds on the substrate side leads to the assumption that substrate binding is more specific than cosubstrate binding. Reliable results were achieved only if water was explicitly included in the simulation.

Key words

GROMOSDomain movementPhosphate transfer
Download to read the full article text

Copyright information

© ESCOM Science Publishers B.V 1994