Paper Citing NAMD - Abstract
Bojovschi, A.; Liu, Ming S.; Sadus, Richard J.
Mg2+ coordinating dynamics in Mg:ATP fueled motor proteins
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 115102, MAR 21 2014
The coordination of Mg2+ with the triphosphate group of adenosine triphosphate (ATP) in motor proteins is investigated using data mining and molecular dynamics. The possible coordination structures available from crystal data for actin, myosin, RNA polymerase, DNA polymerase, DNA helicase, and F-1-ATPase are verified and investigated further by molecular dynamics. Coordination states are evaluated using structural analysis and quantified by radial distribution functions, coordination numbers, and pair interaction energy calculations. The results reveal a diverse range of both transitory and stable coordination arrangements between Mg2+ and ATP. The two most stable coordinating states occur when Mg2+ coordinates two or three oxygens from the triphosphate group of ATP. Evidence for five-site coordination is also reported involving water in addition to the triphosphate group. The stable states correspond to a pair interaction energy of either similar to-2750 kJ/mol or -3500 kJ/mol. The role of water molecules in the hydration shell surrounding Mg2+ is also reported. (C) 2014 AIP Publishing LLC.
