Minehardt T J, Cooke R, Pate E, Kollman P A
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
Biophys J. 2001 Mar;80(3):1151-68. doi: 10.1016/S0006-3495(01)76092-4.
The switch 1 region of myosin forms a lid over the nucleotide phosphates as part of a structure known as the phosphate-tube. The homologous region in kinesin-family motors is more open, not interacting with the nucleotide. We used molecular dynamics (MD) simulations to examine a possible displacement of switch 1 of the microtubule motor, ncd, from the open conformation to the closed conformation seen in myosin. MD simulations were done of both the open and the closed conformations, with either MgADP or MgATP at the active site. All MD structures were stable at 300 K for 500 ps, implying that the open and closed conformers all represented local minima on a global free energy surface. Free energy calculations indicated that the open structure was energetically favored with MgADP at the active site, suggesting why only the open structure has been captured in crystallographic work. With MgATP, the closed and open structures had roughly equal energies. Simulated annealing MD showed the transformation from the closed phosphate-tube ncd structure to an open configuration. The MD simulations also showed that the coordination of switch 1 to the nucleotide dramatically affected the position of both the bound nucleotide and switch 2 and that a closed phosphate-tube may be necessary for catalysis.
肌球蛋白的开关1区域在被称为磷酸管的结构中形成一个覆盖核苷酸磷酸的盖子。驱动蛋白家族马达中的同源区域更为开放，不与核苷酸相互作用。我们使用分子动力学（MD）模拟来研究微管马达ncd的开关1从开放构象到在肌球蛋白中所见的封闭构象的可能位移。对开放和封闭构象都进行了MD模拟，活性位点处存在MgADP或MgATP。所有MD结构在300 K下稳定500 ps，这意味着开放和封闭构象异构体均代表全局自由能表面上的局部最小值。自由能计算表明，活性位点处存在MgADP时，开放结构在能量上更有利，这解释了为什么在晶体学研究中仅捕获到开放结构。对于MgATP，封闭和开放结构具有大致相等的能量。模拟退火MD显示了从封闭的磷酸管ncd结构到开放构型的转变。MD模拟还表明，开关1与核苷酸的配位极大地影响了结合核苷酸和开关2的位置，并且封闭的磷酸管可能是催化所必需的。
