Bojovschi A., Liu M.S., Sadus R.J.
Swinburne University of Technology, AU
Keywords: ATP, ATP/Mg, data mining, interaction energy, Mg2+ coordination, molecular dynamics, motor proteins
ATP-powered motor proteins are driven by ATP hydrolysis. The conformational dynamics of ATP is functionally crucial for the steady operation of motor proteins. In this paper, we present conformational diversity of the ATP/Mg:ATP and coordinating schemes of Mg2+ in motor proteins. Using molecular dynamics and non-equilibrium molecular dynamics the conformational dynamics of ATP/Mg:ATP are investigated. New possibilities in which Mg2+ coordinates with oxygen atoms from the phosphate group of ATP in motor proteins are presented. The coordinating dynamics is interpreted by means of structural conformations and interaction energy changes. ATP conformations were found to be constrained mostly by inter atomic distances in motor proteins. We have observed that ATP tends to adopt extended conformations in tight pockets of motor proteins such as F1-ATPase and actin while compact structures in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg2+ shows an increase in the flexibility of ATP molecules. The conformational dynamics difference of ATP/Mg:ATP from various motor proteins was quantified by the radius of gyration. The relationship between our simulation results and those obtained by data mining of motor proteins available in Protein Data Bank is considered.
Journal: TechConnect Briefs
Volume: 2, Nanotechnology 2012: Electronics, Devices, Fabrication, MEMS, Fluidics and Computational (Volume 2)
Published: June 18, 2012
Pages: 653 - 656
Industry sector: Advanced Materials & Manufacturing
Topic: Informatics, Modeling & Simulation
ISBN: 978-1-4665-6275-2