title: Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine.
abstract: Each amino acid has its intrinsic propensity for certain local backbone conformations, which can be further modulated by the physicochemical environment and post-translational modifications. In this work, we study the effects of phosphorylation on the intrinsic propensity for different local backbone conformations of serine/threonine by molecular dynamics simulations. We showed that phosphorylation has very different effects on the intrinsic propensity for certain local backbone conformations for the serine and threonine. The phosphorylation of serine increases the propensity of forming polyproline II, whereas that of threonine has the opposite effect. Detailed analysis showed that such different responses to phosphorylation mainly arise from their different perturbations to the backbone hydration and the geometrical constraints by forming side-chain-backbone hydrogen bonds due to phosphorylation. Such an effect of phosphorylation on backbone conformations can be crucial for understanding the molecular mechanism of phosphorylation-regulated protein structures/dynamics and functions.
authors.affiliation: National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China.|Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China.
authors.forename: Erbin
authors.initials: E
authors.lastname: He
authors.affiliation: Department of Mathematics and Physics, Nanjing Institute of Technology, Nanjing, 211167, People's Republic of China.
authors.forename: Guanghui
authors.initials: G
authors.lastname: Yan
authors.affiliation: National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China.|Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China. wangj@nju.edu.cn.|Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China. wangj@nju.edu.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China. wfli@nju.edu.cn.|Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China. wfli@nju.edu.cn.
authors.forename: Wenfei
authors.initials: W
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D010766:Phosphorylation; D011487:Protein Conformation; D012694:Serine / Q000737:chemistry* / Q000378:metabolism; D013912:Threonine / Q000737:chemistry* / Q000378:metabolism
chemical_list: D009842:Oligopeptides; D010455:Peptides; C011083:polyproline; D013912:Threonine; D012694:Serine
keywords: Intrinsic backbone conformation propensity; Molecular dynamics; Phosphorylation; Proteins