Protection-against-water-attack determined difference between strengths of backbone hydrogen bonds in kinesin＇s neck zipper region  

作　　者：覃静宇 耿轶钊 吕刚 纪青 方海平 

机构地区：[1]Division of Interracial Water and Key Laboratory of Interfhcial Physics and Technology,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China [2]University of Chinese Academy of Sciences, Beijing 100049, China [3]Institute of Biophysics, hebei Universily of Technology, Tianjin 300401, China [4]School of Science, Hebei University of Technology, Tianjin 300401, China [5]Mathematical and Physical Science School, North China Electric Power University, Baoding 071003, China [6]State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1O0190, China

出　　处：《Chinese Physics B》2018年第2期80-87,共8页中国物理B（英文版）

基　　金：Project supported by the National Natural Science Foundation of China(Grant No.11605038);the Open Project Program of State Key Laboratory of Theoretical Physics,Institute of Theoretical Physics,Chinese Academy of Sciences,China(Grant No.Y5KF211CJ1)

摘　　要：Docking of the kinesin＇s neck linker （NL） to the motor domain is the key force-generation process of the kinesin. In this process, NL＇sβ10 portion forms four backbone hydrogen bonds （HBs） with the motor domain. These backbone hydrogen bonds show big differences in their effective strength. The origins of these strength differences are still unclear. Using molecular dynamics method, we investigate the stability of the backbone HBs in explicit water environment. We find that the strength differences of these backbone HBs mainly arise from their relationships with water molecules which are controlled by arranging the surrounding residue sidechains. The arrangement of the residues in the C-terminal part of /310 results in the existence of the water-attack channels around the backbone HBs in this region. Along these channels the water molecules can directly attack the backbone HBs and make these HBs relatively weak. In contrast, the backbone HB at the N-terminus ofβ 10 is protected by the surrounding hydrophobic and hydrophilic residues which cooperate positively with the central backbone HB and make this HB highly strong. The intimate relationship between the effective strength of protein backbone HB and water revealed here should be considered when performing mechanical analysis for protein conformational changes.Docking of the kinesin＇s neck linker （NL） to the motor domain is the key force-generation process of the kinesin. In this process, NL＇sβ10 portion forms four backbone hydrogen bonds （HBs） with the motor domain. These backbone hydrogen bonds show big differences in their effective strength. The origins of these strength differences are still unclear. Using molecular dynamics method, we investigate the stability of the backbone HBs in explicit water environment. We find that the strength differences of these backbone HBs mainly arise from their relationships with water molecules which are controlled by arranging the surrounding residue sidechains. The arrangement of the residues in the C-terminal part of /310 results in the existence of the water-attack channels around the backbone HBs in this region. Along these channels the water molecules can directly attack the backbone HBs and make these HBs relatively weak. In contrast, the backbone HB at the N-terminus ofβ 10 is protected by the surrounding hydrophobic and hydrophilic residues which cooperate positively with the central backbone HB and make this HB highly strong. The intimate relationship between the effective strength of protein backbone HB and water revealed here should be considered when performing mechanical analysis for protein conformational changes.

关 键 词：KINESIN neck linker water 

分 类 号：Q51[生物学—生物化学]