Paper Citing NAMD - Abstract
Bojovschi, A.; Liu, Ming S.; Sadus, Richard J.
Conformational dynamics of ATP/Mg:ATP in motor proteins via data mining and molecular simulation
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 075101, AUG 21 2012
The conformational diversity of ATP/Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F-1-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg2+ leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP/Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational diversity of the phosphate group of ATP obtained computationally. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4739308]
