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PLOS ONE  2012 

Are Coiled-Coils of Dimeric Kinesins Unwound during Their Walking on Microtubule?

DOI: 10.1371/journal.pone.0036071

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Abstract:

Dimeric kinesin motor proteins such as homodimeric kinesin-1, homodimeric Ncd and heterodimeric Kar3/Vik1are composed of two head domains which are connected together by a rod-shaped, coiled-coil stalk. Despite the extensive and intensive studies on structures, kinetics, dynamics and walking mechanism of the dimers, whether their coiled-coils are unwound or not during their walking on the microtubule is still an unclear issue. Here, we try to clarify this issue by using molecular dynamics simulations. Our simulation results showed that, for Ncd, a large change in potential of mean force is required to unwind the coiled-coil by only several pairs of residues. For both Ncd and kinesin-1, the force required to initiate the coiled-coil unwinding is larger than that required for unfolding of the single -helix that forms the coiled-coil or is larger than that required to unwind the DNA duplex, which is higher than the unbinding force of the kinesin head from the microtubule in strong microtubule-binding states. Based on these results and the comparison of the sequence between the coiled-coil of Kar3/Vik1 and those of Ncd and kinesin-1, it was deduced that the coiled-coil of the Kar3/Vik1 should also be very stable. Thus, we concluded that the coiled-coils of kinesin-1, Ncd and Kar3/Vik1 are almost impossible to unwind during their walking on the microtubule.

References

[1]  Scholey JM (1996) Kinesin-II, a membrane traffic motor in axons, axonemes, and spindles. J Cell Biol 133: 1–4.
[2]  Hirokawa N (1998) Kinesin and dynein superfamily proteins and the mechanism of organelle transport. Science 279: 519–526.
[3]  Yang JT, Laymon RA, Goldstein LS (1989) A three-domain structure of kinesin heavy chain revealed by DNA sequence and microtubule binding analyses. Cell 56: 879–889.
[4]  Vale RD (2003) The molecular motor toolbox for intracellular transport. Cell 112: 467–480.
[5]  Hua W, Chung J, Gelles J (2002) Distinguishing inchworm and hand-over-hand processive kinesin movement by neck rotation measurements. Science 295: 844–848.
[6]  Asbury CL, Fehr AN, Block SM (2003) Kinesin moves by an asymmetric hand-over-hand mechanism. Science 302: 2130–2134.
[7]  Kaseda K, Higuchi H, Hirose K (2003) Alternate fast and slow stepping of a heterodimeric kinesin molecule. Nat Cell Biol 5: 1079–1082.
[8]  Yildiz A, Tomishige M, Vale RD, Selvin PR (2004) Kinesin walks hand-over-hand. Science 303: 676–678.
[9]  Rice S, Lin AW, Safer D, Hart CL, Naber N, et al. (1999) A structural change in the kinesin motor protein that drives motility. Nature 402: 778–784.
[10]  Wade RH, Kozielski F (2000) Structural links to kinesin directionality and movement. Nat Struct Biol 7: 456–460.
[11]  Miyazono Y, Hayashi M, Karagiannis P, Harada Y, Tadakuma H (2010) Strain through the neck linker ensures processive runs: a DNA-kinesin hybrid nanomachine study. EMBO J 29: 93–106.
[12]  Shastry S, Hancock WO (2010) Neck linker length determines the degree of processivity in kinesin-1 and kinesin-2 motors. Curr Biol 20: 939–943.
[13]  Hwang W, Lang MJ, Karplus M (2008) Force generation in kinesin hinges on cover-neck bundle formation. Structure 16: 62–71.
[14]  Vale RD, Milligan RA (2000) The way things move: looking under the hood of molecular motor proteins. Science 288: 88–95.
[15]  Xie P (2010) Mechanism of processive movement of monomeric and dimeric kinesin molecules. Int J Biol Sci 6: 665–674.
[16]  Kutys ML, Fricks J, Hancock WO (2010) Monte Carlo analysis of neck linker extension in kinesin molecular motors. PLoS Comput Biol 6: e1000980.
[17]  Howard J (1996) The movement of kinesin along microtubules. Annu Rev Physiol 58: 703–729.
[18]  Walker RA, Salmon ED, Endow SA (1990) The Drosophila claret segregation protein is a minus-end directed motor molecule. Nature 347: 780–782.
[19]  Endow SA, Kang SJ, Satterwhite LL, Rose MD, Skeen VP, et al. (1994) Yeast Kar3 is a minus-end microtubule motor protein that destabilizes microtubules preferentially at the minus ends. EMBO J 13: 2708–2713.
[20]  Sablin EP, Kull FJ, Cooke R, Vale RD, Fletterick RJ (1996) Crystal structure of the motor domain of the kinesin-related motor ncd. Nature 380: 555–559.
[21]  Sablin EP, Case RB, Dai SC, Hart CL, Ruby A, et al. (1998) Direction determination in the minus-end-directed kinesin motor ncd. Nature 395: 813–816.
[22]  Sosa H, Dias DP, Hoenger A, Whittaker M, Wilson-Kubalek E, et al. (1997) A model for the microtubule-Ncd motor protein complex obtained by cryo-electron microscopy and image analysis. Cell 90: 217–224.
[23]  Hirose K, Cross RA, Amos LA (1998) Nucleotide-dependent structural changes in dimeric NCD molecules complexed to microtubules. J Mol Biol 278: 389–400.
[24]  Wendt TG, Volkmann N, Skiniotis G, Goldie KN, Muller J, et al. (2002) Microscopic evidence for a minus-end-directed power stroke in the kinesin motor ncd. EMBO Journal 21: 5969–5978.
[25]  Endres NF, Yoshioka C, Milligan RA, Vale RD (2006) A lever-arm rotation drives motility of the minus-end-directed kinesin Ncd. Nature 439: 875–878.
[26]  Kozielski F, De Bonis S, Burmeister WP, Cohen-Addad C, Wade RH (1999) The crystal structure of the minus-end-directed microtubule motor protein ncd reveals variable dimer conformations. Structure 7: 1407–1416.
[27]  Yun M, Bronner CE, Park CG, Cha SS, Park HW, et al. (2003) Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein, Ncd. EMBO J 22: 5382–5389.
[28]  Cross RA (2010) Kinesin-14: the roots of reversal. BMC Biol 8: 107.
[29]  Heuston E, Bronner CE, Kull FJ, Endow SA (2010) A kinesin motor in a force-producing conformation. BMC Struct Biol 10: 19.
[30]  Page BD, Satterwhite LL, Rose MD, Snyder M (1994) Localization of the Kar3 kinesin heavy chain-related protein requires the Cik1 interacting protein. J Cell Biol 124: 507–519.
[31]  Manning BD, Barrett JG, Wallace JA, Granok H, Snyder M (1999) Differential regulation of the Kar3p kinesin-related protein by two associated proteins, Cik1p and Vik1p. J Cell Biol 144: 1219–1233.
[32]  Barrett JG, Manning BD, Snyder M (2000) The Kar3p kinesin-related protein forms a novel heterodimeric structure with its associated protein Cik1p. Mol Biol Cell 11: 2373–2385.
[33]  Manning BD, Snyder M (2000) Drivers and passengers wanted! the role of kinesin-associated proteins. Trends Cell Biol 10: 281–289.
[34]  Chu HM, Yun M, Anderson DE, Sage H, Park HW, et al. (2005) Kar3 interaction with Cik1 alters motor structure and function. EMBO J 24: 3214–3223.
[35]  Sproul LR, Anderson DJ, Mackey AT, Saunders WS, Gilbert SP (2005) Cik1 targets the minus-end kinesin depolymerase kar3 to microtubule plus ends. Curr Biol 15: 1420–1427.
[36]  Allingham J, Sproul L, Rayment I, Gilbert S (2007) Vik1 Modulates Microtubule-Kar3 Interactions through a Motor Domain that Lacks an Active Site. Cell 128: 1161–1172.
[37]  Gulick AM, Song H, Endow SA, Rayment I (1998) X-ray crystal structure of the yeast Kar3 motor domain complexed with Mg.ADP to 2.3 A resolution. Biochemistry 37: 1769–1776.
[38]  Woehlke G, Schliwa M (2007) Kinesin Kar3 and Vik1 Go Head to Head. Cell 128: 1033–1034.
[39]  Xie P, Dou SX, Wang PY (2007) Limping of homodimeric kinesin motors. J Mol Biol 366: 976–985.
[40]  Hou R, Wang Z (2010) A coordinated molecular ‘fishing’ mechanism in heterodimeric kinesin. Physical Biology 7: 036003.
[41]  Cai D, Hoppe AD, Swanson JA, Verhey KJ (2007) Kinesin-1 structural organization and conformational changes revealed by FRET stoichiometry in live cells. J Cell Biol 176: 51–63.
[42]  Evans E, Ritchie K (1997) Dynamic strength of molecular adhesion bonds. Biophys J 72: 1541–1555.
[43]  Rief M, Pascual J, Saraste M, Gaub HE (1999) Single molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundles. J Mol Biol 286: 553–561.
[44]  Paci E, Karplus M (2000) Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc Natl Acad Sci U S A 97: 6521–6526.
[45]  Essevaz-Roulet B, Bockelmann U, Heslot F (1997) Mechanical separation of the complementary strands of DNA. Proc Natl Acad Sci U S A 94: 11935–11940.
[46]  Uemura S, Kawaguchi K, Yajima J, Edamatsu M, Toyoshima YY, et al. (2002) Kinesin-microtubule binding depends on both nucleotide state and loading direction. Proc Natl Acad Sci U S A 99: 5977–5981.
[47]  Bornschlogl T, Woehlke G, Rief M (2009) Single molecule mechanics of the kinesin neck. Proc Natl Acad Sci U S A 106: 6992–6997.
[48]  Tomishige M, Vale RD (2000) Controlling kinesin by reversible disulfide cross-linking. Identifying the motility-producing conformational change. J Cell Biol 151: 1081–1092.
[49]  Mason JM, Arndt KM (2004) Coiled coil domains: stability, specificity, and biological implications. Chembiochem 5: 170–176.
[50]  Thormahlen M, Marx A, Sack S, Mandelkow E (1998) The coiled-coil helix in the neck of kinesin. J Struct Biol 122: 30–41.
[51]  Tripet B, Hodges RS (2002) Helix capping interactions stabilize the N-terminus of the kinesin neck coiled-coil. J Struct Biol 137: 220–235.
[52]  Ito M, Morii H, Shimizu T, Tanokura M (2006) Coiled coil in the stalk region of ncd motor protein is nonlocally sustained. Biochemistry 45: 3315–3324.
[53]  Hackney DD (1994) Evidence for alternating head catalysis by kinesin during microtubule-stimulated ATP hydrolysis. Proc Natl Acad Sci U S A 91: 6865–6869.
[54]  Alonso MC, Drummond DR, Kain S, Hoeng J, Amos L, et al. (2007) An ATP gate controls tubulin binding by the tethered head of kinesin-1. Science 316: 120–123.
[55]  Xie P (2008) Stepping behavior of two-headed kinesin motors. Biochim Biophys Acta 1777: 1195–1202.
[56]  Altman D, Sweeney HL, Spudich JA (2004) The mechanism of myosin VI translocation and its load-induced anchoring. Cell 116: 737–749.
[57]  Xie P, Dou SX, Wang PY (2006) A hand-over-hand diffusing model for myosin-VI molecular motors. Biophys Chem 122: 90–100.
[58]  Kozielski F (1997) The Crystal Structure of Dimeric Kinesin and Implications for Microtubule-Dependent Motility. Cell 91:
[59]  Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules .1. The Method. Journal of Computational Chemistry 13: 1011–1021.
[60]  Bartels C (2000) Analyzing biased Monte Carlo and molecular dynamics simulations. Chemical Physics Letters 331: 446–454.

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