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Origin of the surprising mechanical stability of kinesin’s neck coiled coil

Origin of the surprising mechanical stability of kinesin’s neck coiled coil. JI Qing. 河北工业大学 生物物理研究所. Institute of Biophysics Hebei University of Technology. June 2014, Beijing. 1. Macromolecular dynamics: structure, function and life. Kinesin. molecular motor ATPase.

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Origin of the surprising mechanical stability of kinesin’s neck coiled coil

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  1. Origin of the surprising mechanical stability of kinesin’s neck coiled coil JI Qing 河北工业大学 生物物理研究所 Institute of Biophysics Hebei University of Technology June 2014, Beijing

  2. 1. Macromolecular dynamics: structure, function and life Kinesin molecular motor ATPase One motor head: 350 amino acids ATP hydrolysis: Tight coupling Work in one step: Driving motility in life. R.Vale & R.Milligan, Science, 2000.

  3. 2. Neck coiled coil: Function Kinesin’s mechanochemical cycling needs exquisite inter-head communication and cooperation and gating between the mechanical steps and chemical steps. Neck linker (4 nm) High efficiency — Tight coupling — No futile hydrolysis. 8 nm Inter-head tension is crucial. The neck coiled coil should keep zippered under inter-head tension. Experimantal facts: (1) Tomishige & Vale (JCB, 2000) Cross-linking coiled coil had relatively little effect on motor activity. (2) Tripet and Hodges (JSB, 2002) Substitution of Trp 340, the first hydrophobic core d position residue of the coiled-coil, with an Ala residue resulted in a greater than expected decrease in stability and helicity of the coiled-coil structure. (3) Bornschlögl, Woehlke and Rief (PNAS, 2009) The unconventional N-terminal parts of the neck coiled coil exhibit a surprising mechanical stability. The opening of only 2 N-terminal coiled-coil turns will destabilize the complete neck and lead to unfolding.

  4. 3. Neck coiled coil: Structure The neck domain (residues 339–370,2KIN) a b c d e f g a b c d e f g d A E E W K K K Y E K E K E K ----- W 339 346 370 Heptad : A abcdefg The first heptad B The first two turns A B

  5. Structure of conventional coiled coil Cohen and Parry (Proteins, 1990) The key features of coiled coil are as follows: Fig. 2 Fig. 1 The sequence of neck coiled coil Thormählen, Marx, Sack, and Mandelkow (JSC,1998) Fig. 3

  6. 4. Neck coiled coil: Structure-function relationship 4.1 Mechanical response to stretching forces 50 pN: Stable 100 pN: Partially open and then stable 150 pN: Partially open and then stable 170 pN: Totally open

  7. 4.2 Details of the opening process The first platform: 7.5ns Backbone hydrogen bonds breaking 5.5ns The second platform: 4 ns Peptide planes rotation 第一个台阶：Fig. 3 4 ns 5.5 ns 7.5 ns

  8. The unzippering process is stopped at Y346. Y346 Y346

  9. 4.3 Tyrosine buckle and its mechanical function The buckle structure vdW Radii H 1.2 Å O 1.52 Å N 1.55 Å C 1.7 Å Bondi (JPC,1964) a’ a O’Shea et al. (Science,1991) d d’ Fig 7.Schematic drawing (not to scale) showing differences between positions a and d.

  10. 4.4 The buckle mechanics Constraint force Stretching force In equilibrium: (A + B) Contact force (A)

  11. Nyis balanced by the special hydrophobic pressure. The first two heptads in the neck domain a b c d e f g a b c d e f g Lyotropic liquid crystal A E E W K K K Y E K E K E K 339 342 346 Nx = Fc = Fs Micelle N’y = lN’x = lF’s ph ph Hydrophobic pressure Forces in equilibrium For (A), define In equilibrium: N’y N’ Pmust have an upper limit and so doesFs. Ny N Nx N’x

  12. Conclusion The surprising mechanical stability of the neck coiled coil arises from the cooperation between the special hydrophobic pressure and the steric hindrance of the tyrosine buckle.

  13. 5. Special hydrophobic pressure? Average The average distance between the Cas of the two Y346s is 4.678Å (the shortest).

  14. The mechanical function of the Y-buckle is sensitive to the Ca-Ca distance.

  15. The special arrangement of the neck residues results in the special hydrophobic pressure. a b c d e f g a b c d e f g A E E W K K K Y E K E K E K 339 342 346 (1) W342(A) vs K343(B) (2) KKK (3) …… Average r3 3.777 Å Average l1 (blue) 10.382 Å l2 (red) 11.264 Å l3 (black) 10.379 Å

  16. Conclusion Each detail has a reason.

  17. My students in this work 刘书霞 (Shu-Xia Liu) 吕 刚 (Gang Lü) 柳睿殊 (Rui-Shu Liu) 耿轶钊 (Yi-ZhaoGeng) 张 辉 (Hui Zhang) Acknowledgement 卓益忠（Yin-Zhong Zhuo) 郝柏林（Bo-Lin Hao) 包景东（Jing-Dong Bao) 欧阳钟灿（Zhong-Can Ouyang) 张红雨（Hong-Yu Zhang) 陈润生（Run-Sheng Chen) The National Natural Science Foundation of China，No. 90403007 The National Natural Science Foundation of China，No. 10975044

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