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Special Issue:
SPECIAL TOPIC — Soft matter and biological physics
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| SPECIAL TOPIC—Soft matter and biological physics |
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Protection-against-water-attack determined difference between strengths of backbone hydrogen bonds in kinesin's neck zipper region |
| Jing-Yu Qin(覃静宇)1,2, Yi-Zhao Geng(耿轶钊)3,4, Gang Lü(吕刚)5, Qing Ji(纪青)3,4,6, Hai-Ping Fang(方海平)1 |
1. Division of Interfacial Water and Key Laboratory of Interfacial 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 University 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 100190, China |
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Abstract 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's β 10 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 β 10 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 of β 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.
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Received: 07 September 2017
Revised: 03 November 2017
Accepted manuscript online:
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PACS:
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87.16.Nn
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(Motor proteins (myosin, kinesin dynein))
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87.10.Tf
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(Molecular dynamics simulation)
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87.15.hp
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(Conformational changes)
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| Fund: Project supported by the National Natural Science Foundation of China (Grant No. 11605038) and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5KF211CJ1). |
Corresponding Authors:
Qing Ji, Hai-Ping Fang
E-mail: jiqingch@hebut.edu.cn;fanghaiping@sinap.ac.cn
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| About author: 87.16.Nn; 87.10.Tf; 87.15.hp |
Cite this article:
Jing-Yu Qin(覃静宇), Yi-Zhao Geng(耿轶钊), Gang Lü(吕刚), Qing Ji(纪青), Hai-Ping Fang(方海平) Protection-against-water-attack determined difference between strengths of backbone hydrogen bonds in kinesin's neck zipper region 2018 Chin. Phys. B 27 028704
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