Tian Ye, Schwieters Charles D, Opella Stanley J, Marassi Francesca M
Sanford-Burnham-Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, MD, 20892-5624, USA.
J Biomol NMR. 2017 Jan;67(1):35-49. doi: 10.1007/s10858-016-0082-5. Epub 2016 Dec 29.
Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision, and conformation, and that structure refinement can be obtained by short relaxation with EEFx to obtain improvements in these key metrics. These developments broaden the range of biomolecular structures that can be calculated with high fidelity from NMR restraints.
通过核磁共振（NMR）确定蛋白质结构具有独特的能力，能够在与体内环境和条件极为相似的情况下非常精确地测量结构限制因素。例如，固态NMR方法的进展使得在不含去污剂的脂质双层中确定膜蛋白结构，以及通过沉降制备的大型可溶性蛋白的结构成为可能，同时溶液NMR方法的并行进展和不含去污剂的脂质纳米盘的优化正在迅速突破可溶性蛋白和膜蛋白尺寸极限的边界。然而，这些实验优势在结构计算过程中部分被浪费了，因为常用的力场纯粹是排斥性的，并且忽略了溶剂化、范德华力和静电能。在这里，我们描述了一种新的力场以及更新的能量函数，用于在广泛使用的Xplor - NIH程序中结合EEFx隐式溶剂化、静电和范德华伦纳德 - 琼斯力进行蛋白质结构计算。新的力场主要基于CHARMM22，便于对更广泛的生物分子进行计算。新的EEFx能量函数已被重写以实现OpenMP并行性，并进行了优化以提高计算效率。它同时实现了溶剂化、静电和范德华能量项，从而确保对完整的非键合能量列表进行更一致和高效的计算。相关Python模块的更新允许对相互作用能和相关参数进行详细分析。新的力场和能量函数适用于可溶性蛋白和膜蛋白，包括那些带有辅因子或工程化标签的蛋白，并且在实验限制因素较少的情况下非常有效。对一组五个可溶性蛋白和五个膜蛋白进行NMR约束计算所得到的结果表明，使用EEFx计算得到的结构在准确性、精度和构象方面有显著改进，并且通过使用EEFx进行短时间弛豫可以实现结构优化，从而在这些关键指标上得到改善。这些进展拓宽了可以从NMR约束中以高保真度计算的生物分子结构的范围。
