Jiang Zhongming, Biczysko Malgorzata, Moriarty Nigel W
International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, 99 Shangda Road, 200444, Shanghai, China.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
Proteins. 2018 Mar;86(3):273-278. doi: 10.1002/prot.25451. Epub 2018 Jan 12.
Unusual local arrangements of protein in Ramachandran space are not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. In contrast, quantum chemical computations using small poly-peptide molecular models can predict accurate geometries for any well-defined backbone Ramachandran orientation. For conformations along transition regions-ϕ from -60 to 60°-a very good agreement with representative high-resolution experimental X-ray (≤1.5 Å) protein structures is obtained for both backbone C -N-C angle and the nonbonded O …C distance, while "standard geometry" leads to the "clashing" of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high-energy or unusual regions.
在使用简单谐波几何约束进行蛋白质结构优化或使用分子力学力场进行蛋白质模拟时，标准几何工具无法很好地呈现蛋白质在拉马钱德兰空间中不寻常的局部排列。相比之下，使用小多肽分子模型的量子化学计算可以预测任何明确的主链拉马钱德兰取向的精确几何结构。对于沿过渡区域（-60°至60°的ϕ角）的构象，主链C -N-C角和非键合O…C距离与代表性高分辨率实验X射线（≤1.5 Å）蛋白质结构都有很好的一致性，而“标准几何”会导致O…C原子“碰撞”，Amber FF99SB预测的距离大约大0.15 Å。这些结果证实，量子化学计算为蛋白质局部结构排列的详细分析提供了有价值的支持，为了解较少的高能或异常区域提供了改进或缺失的数据。
