Zhang Oufan, Naik Shubhankar A, Liu Zi Hao, Forman-Kay Julie, Head-Gordon Teresa
Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.
Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.
ArXiv. 2024 May 6:arXiv:2405.03120v1.
Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered proteins (IDPs). However much of protein function is modulated beyond the translated sequence through thFiguree introduction of post-translational modifications (PTMs). In this work we have provided a curated set of side chain rotamers for the most common PTMs derived from the RCSB PDB database, including phosphorylated, methylated, and acetylated sidechains. Our rotamer libraries improve upon existing methods such as SIDEpro and Rosetta in predicting the experimental structures for PTMs in folded proteins. In addition, we showcase our PTM libraries in full use by generating ensembles with the Monte Carlo Side Chain Entropy (MCSCE) for folded proteins, and combining MCSCE with the Local Disordered Region Sampling algorithms within IDPConformerGenerator for proteins with intrinsically disordered regions.
蛋白质常见氨基酸的侧链旋转异构体文库对于确定折叠蛋白结构以及生成内在无序蛋白（IDP）集合很有用。然而，蛋白质的许多功能是通过引入翻译后修饰（PTM）在翻译序列之外进行调节的。在这项工作中，我们从RCSB PDB数据库中提供了一组经过整理的、针对最常见PTM的侧链旋转异构体，包括磷酸化、甲基化和乙酰化侧链。我们的旋转异构体文库在预测折叠蛋白中PTM的实验结构方面比现有方法（如SIDEpro和Rosetta）有所改进。此外，我们通过使用蒙特卡罗侧链熵（MCSCE）为折叠蛋白生成集合，并将MCSCE与IDPConformerGenerator中的局部无序区域采样算法相结合，用于具有内在无序区域的蛋白质，充分展示了我们的PTM文库。
