Please wait a minute...
Chin. Phys. B, 2018, Vol. 27(2): 028704    DOI: 10.1088/1674-1056/27/2/028704
Special Issue: SPECIAL TOPIC — Soft matter and biological physics
SPECIAL TOPIC—Soft matter and biological physics Prev   Next  

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
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.
Keywords:  kinesin      neck linker      water  
Received:  07 September 2017      Revised:  03 November 2017      Accepted manuscript online: 
PACS:  87.16.Nn (Motor proteins (myosin, kinesin dynein))  
  87.10.Tf (Molecular dynamics simulation)  
  87.15.hp (Conformational changes)  
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
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

[1] Lawrence C J, Dawe R K, Christie K R, Cleveland D W, Dawson S C, Endow S A, Goldstein L S, Goodson H V, Hirokawa N, Howard J, Malmberg R L, McIntosh J R, Miki H, Mitchison T J, Okada Y, Reddy A S, Saxton W M, Schliwa M, Scholey J M, Vale R D, Walczak C E and Wordeman L 2004 J. Cell Biol. 167 19
[2] Block S M 2007 Biophys. J. 92 2986
[3] Hirokawa N and Noda Y 2008 Physiol. Rev. 88 1089
[4] Sindelar C V 2011 Biophys. Rev. 3 85
[5] Vale R D and Milligan R A 2000 Science 288 88
[6] Rice S, Lin A W, Safer D, Hart C L, Naber N, Carragher B O, Cain S M, Pechatnikova E, Wilson-Kubalek E M, Whittaker M, Pate E, Cooke R, Taylor E W, Milligan R A and Vale R D 1999 Nature 402 778
[7] Hariharan V and Hancock W 2009 Cell Mol. Bioeng. 2 177
[8] Geng Y Z, Li T, Ji Q and Yan S W 2014 Cell Mol. Bioeng. 7 99
[9] Asenjo A B, Weinberg Y and Sosa H 2006 Nature Structural and Molecular Biology 13 648
[10] Sack S, Mäuller J, Marx A, Thormäahlen M, Mandelkow E M, Brady S T and Mandelkow E 1997 Biochemistry 36 16155
[11] Geng Y Z, Ji Q Liu S X and Yan S W 2014 Chin. Phys. B 23 108701
[12] Hwang W, Lang M J and Karplus M 2008 Structure 16 62
[13] Khalil A S, Appleyard D C, Labno A K, Georges A, Karplus M, Belcher A M, Hwang W and Lang M J 2008 Proc. Natl. Acad. Sci. USA 105 19247
[14] Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kal? e L and Schulten K 2005 J. Comput. Chem. 26 1781
[15] MacKerell A D, Bashford D, Bellott, Dunbrake R L, Evenseck J D, Field M J, Fischer S, Gao J, Guo H, Ha S, Joseph-MaCarthy D, Kuchnir L, Kuczera K, Lau F T K, Mattos C, Michnick S, Ngo T, Nyuyen D T, Prodhom B, Reiher W E, Roux B, Schlenkrich M, Smith J C, Stote R, Straub J, Watanabe M, Wirkiewicz-Kuczera J, Yin D and Karplus M 1998 J. Phys. Chem. 102 3586
[16] Humphrey W, Dalke A and Schulten K 1996 J. Mol. Graphics 14 33
[17] Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W and Klein M L 1983 J. Chem. Phys. 79 926
[18] Huang Y B, Pan Z, Zhang H, An L, Kong D X, and Ji Q 2009 Chin. Phys. Lett. 26 078701
[1] A theoretical study of fragmentation dynamics of water dimer by proton impact
Zhi-Ping Wang(王志萍), Xue-Fen Xu(许雪芬), Feng-Shou Zhang(张丰收), and Xu Wang(王旭). Chin. Phys. B, 2023, 32(3): 033401.
[2] Blue phosphorene/MoSi2N4 van der Waals type-II heterostructure: Highly efficient bifunctional materials for photocatalytics and photovoltaics
Xiaohua Li(李晓华), Baoji Wang(王宝基), and Sanhuang Ke(柯三黄). Chin. Phys. B, 2023, 32(2): 027104.
[3] Theoretical study of M6X2 and M6XX' structure (M = Au, Ag; X,X' = S, Se): Electronic and optical properties, ability of photocatalytic water splitting, and tunable properties under biaxial strain
Jiaqi Li(李嘉琪), Xinlu Cheng(程新路), and Hong Zhang(张红). Chin. Phys. B, 2022, 31(9): 097101.
[4] Influence of water environment on paint removal and the selection criteria of laser parameters
Li-Jun Zhang(张丽君), Kai-Nan Zhou(周凯南), Guo-Ying Feng(冯国英), Jing-Hua Han(韩敬华),Na Xie(谢娜), and Jing Xiao(肖婧). Chin. Phys. B, 2022, 31(6): 064205.
[5] Acoustic multipath structure in direct zone of deep water and bearing estimation of tow ship noise of towed line array
Zhi-Bin Han(韩志斌), Zhao-Hui Peng (彭朝晖), Jun Song(宋俊), Lei Meng(孟雷), Xiu-Ting Yang(杨秀庭), and Bing Su(苏冰). Chin. Phys. B, 2022, 31(5): 054301.
[6] Nanobubbles produced by hydraulic air compression technique
Xiaodong Yang(杨晓东), Qingfeng Yang(杨庆峰), Limin Zhou(周利民),Lijuan Zhang(张立娟), and Jun Hu(胡钧). Chin. Phys. B, 2022, 31(5): 054702.
[7] Water contact angles on charged surfaces in aerosols
Yu-Tian Shen(申钰田), Ting Lin(林挺), Zhen-Ze Yang(杨镇泽), Yong-Feng Huang(黄永峰), Ji-Yu Xu(徐纪玉), and Sheng Meng(孟胜). Chin. Phys. B, 2022, 31(5): 056801.
[8] Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations
Jian-Gang Wang(王建港), Xiao-Xuan Shi(史晓璇), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业),Hong Chen(陈洪), and Ping Xie(谢平). Chin. Phys. B, 2022, 31(5): 058702.
[9] Characteristics of vapor based on complex networks in China
Ai-Xia Feng(冯爱霞), Qi-Guang Wang(王启光), Shi-Xuan Zhang(张世轩), Takeshi Enomoto(榎本刚), Zhi-Qiang Gong(龚志强), Ying-Ying Hu(胡莹莹), and Guo-Lin Feng(封国林). Chin. Phys. B, 2022, 31(4): 049201.
[10] Quantum watermarking based on threshold segmentation using quantum informational entropy
Jia Luo(罗佳), Ri-Gui Zhou(周日贵), Wen-Wen Hu(胡文文), YaoChong Li(李尧翀), and Gao-Feng Luo(罗高峰). Chin. Phys. B, 2022, 31(4): 040302.
[11] Impact of microsecond-pulsed plasma-activated water on papaya seed germination and seedling growth
Deng-Ke Xi(席登科), Xian-Hui Zhang(张先徽), Si-Ze Yang(杨思泽), Seong Shan Yap(叶尚姗), Kenji Ishikawa(石川健治), Masura Hori (堀勝), and Seong Ling Yap(叶尚凌). Chin. Phys. B, 2022, 31(12): 128201.
[12] A study of cavitation nucleation in pure water using molecular dynamics simulation
Hua Xie(谢华), Yuequn Xu(徐跃群), and Cheng Zhong(钟成). Chin. Phys. B, 2022, 31(11): 114701.
[13] Water adsorption performance of UiO-66 modified by MgCl2 for heat transformation applications
Jia-Li Liu(刘佳丽), Guo-Dong Fu(付国栋), Ping Wu(吴平), Shang Liu(刘尚), Jin-Guang Yang(杨金光), Shi-Ping Zhang(张师平), Li Wang(王立), Min Xu(许闽), and Xiu-Lan Huai(淮秀兰). Chin. Phys. B, 2022, 31(11): 118101.
[14] Parallel optimization of underwater acoustic models: A survey
Zi-jie Zhu(祝子杰), Shu-qing Ma(马树青), Xiao-Qian Zhu(朱小谦), Qiang Lan(蓝强), Sheng-Chun Piao(朴胜春), and Yu-Sheng Cheng(程玉胜). Chin. Phys. B, 2022, 31(10): 104301.
[15] Aperture-averaged scintillation index and fade statistics in weak oceanic turbulence
Hao Wang(王昊), Fu-Zeng Kang(康福增), Xuan Wang(王瑄), Wei Zhao(赵卫), and Shu-Wei Sun(孙枢为). Chin. Phys. B, 2021, 30(6): 064207.
No Suggested Reading articles found!