Li Da-Wei, Brüschweiler Rafael
Campus Chemical Instrument Center and Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.
Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32306, United States.
J Chem Theory Comput. 2014 Apr 8;10(4):1781-7. doi: 10.1021/ct4010646.
A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_φψ(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better than the original NMR structures as is demonstrated for four protein systems. Moreover, for all proteins studied here the simulations spontaneously approach the X-ray crystal structures, thereby improving the effective resolution of the initial structural models.
本文提出了一种用于处理核磁共振（NMR）蛋白质结构的稳健方案，该方案使这些结构适用于长时间尺度的稳定分子动力学（MD）模拟。该方案将NMR结构嵌入到最近开发的ff99SB_φψ(g24;CS)分子力学力场的天然低能区域。从这些结构开始的长时间MD轨迹显示出与质子-质子核Overhauser效应数据具有良好的一致性，并且如四个蛋白质系统所证明的那样，它们比原始NMR结构能更好地重现NMR化学位移数据。此外，对于本文研究的所有蛋白质，模拟会自发地趋近于X射线晶体结构，从而提高了初始结构模型的有效分辨率。
