Minehardt T J, Kollman P A, Cooke R, Pate E
Department of Pharmaceutical Chemistry, and Cardiovascular Research Institute, University of California, San Francisco, California, USA.
Biophys J. 2006 Apr 1;90(7):2445-9. doi: 10.1529/biophysj.105.072900. Epub 2006 Jan 20.
The open nucleotide pocket conformation of actin in the profilin:actinCaATP x-ray structure has been hypothesized to be a crucial intermediate for nucleotide exchange in the actin depolymerization/polymerization cycle. The requirement for ancillary modification of actin for crystallization leads to ambiguities in this interpretation, however. We have used molecular dynamics simulations to model the thermodynamic properties of the actin x-ray structure, outside the crystal lattice, in an aqueous environment with profilin removed. Our simulations show that the open-nucleotide-pocket, profilin-free structure is actually unstable, and closes. The coordination of actin to the nucleotide in the molecular-dynamics-derived closed structure is virtually identical to that in the closed profilin:actinSrATP x-ray structure. Thus, there is currently no thermodynamically stable structure representing the open-nucleotide-pocket state of actin.
在肌动蛋白解聚/聚合循环中，丝切蛋白：肌动蛋白CaATP的X射线结构中肌动蛋白的开放核苷酸口袋构象被认为是核苷酸交换的关键中间体。然而，肌动蛋白结晶所需的辅助修饰导致了这种解释的模糊性。我们使用分子动力学模拟来模拟肌动蛋白X射线结构在晶格外、去除丝切蛋白的水性环境中的热力学性质。我们的模拟表明，开放核苷酸口袋、无丝切蛋白的结构实际上是不稳定的，会关闭。分子动力学衍生的封闭结构中肌动蛋白与核苷酸的配位与封闭的丝切蛋白：肌动蛋白SrATP X射线结构中的几乎相同。因此，目前没有代表肌动蛋白开放核苷酸口袋状态的热力学稳定结构。
