Interaction forces and interface properties of KIF1A kinesin-αβ tubulin complex assessed by molecular dynamics

Journal of Biomechanics

Volumn 41, Issue 15, 2008, Pages 3196-3201

  Aprodu, Iuliana ^a   Soncini, Monica ^a   Redaelli, Alberto ^a  

^a POLITECNICO DI MILANO   (Italy)

Author keywords

tubulin; Interaction properties; Interface properties; Kinesin; Molecular dynamics

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; KINESIN; PROTEIN KIF1A; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; HYDROLYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION;

BINDING SITES; COMPUTER SIMULATION; KINESIN; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR MOTOR PROTEINS; MOTION; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; STRESS, MECHANICAL; TUBULIN;

EID: 55549115655     PISSN: 00219290     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiomech.2008.08.014     Document Type: Article

References (31)

1. Berry M., McMaster T.J., Corfield A.P., and Miles M.J. Exploring the molecular adhesion of ocular mucins. Biomacromolecules 2 (2001) 498-503
2. Crevel I.M.T.C., Lockhart A., and Cross R.A. Weak and strong states of kinesin and ncd. Journal of Molecular Biology 257 (1996) 66-76
3. Dammer U., Hegner M., Anselmetti D., Wagner P., Dreier M., Huber W., et al. Specific antigen/antibody interactions measured by force microscopy. Biophysical Journal 70 (1996) 2437-2441
4. Deriu M.A., Enemark S., Soncini M., Montevecchi F.M., and Redaelli A. Tubulin: from atomistic structure to supramolecular mechanical properties. Journal of Materials Science 42 (2007) 8864-8872
5. Glaser F., Rosenberg Y., Kessel A., Tal Pupko, and Ben-Tal N. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins: Structure, Function, and Bioinformatics 58 (2005) 610-617
6. Hirokawa N. Kinesin and dynein superfamily proteins and the mechanism of organelle transport. Science 279 (1998) 519-526
7. Hirokawa N., and Takemura R. Molecular motors in neuronal development, intracellular transport and diseases. Current Opinions in Neurobiology 14 (2004) 564-573
8. Howard J. Motor proteins. Mechanics of Motor Proteins and the Cytoskeleton (2001), Sinauer Associates Inc., Sunderland
9. Hubbard, S.J., 1992. Analysis of protein-protein molecular recognition. Ph.D. Thesis, University of London.
10. Jones S., Marin A., and Thornton J.M. Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Engineering 13 (2000) 77-82
11. Kawaguchi K., and Ischiwata S. Nucleotide-dependent single- to double-headed binding of kinesin. Science 291 (2001) 667-669
12. Kikkawa M., Sablin E.P., Okada Y., Yajima H., Fletterick R.J., and Hirokawa N. Switch-based mechanism of kinesin motors. Nature 411 (2001) 439-445
13. Laskowski R.A. SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions. Journal of Molecular Graphics 13 (1995) 323-330
14. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26 (1993) 283-291
15. Lenne P.F., Raae A.J., Altmann S.M., Saraste M., and Horber J.K.H. States and transitions during forced unfolding of a single spectrin repeat. FEBS Letters 476 (2000) 124-128
16. Lorenzo A.C., and Bisch P.M. Analyzing different parameters of steered molecular dynamics for small membrane interacting molecules. Journal of Molecular Graphics and Modelling 24 (2005) 59-71
17. Miki H., Okada Y., and Hirokawa N. Analysis of the kinesin superfamily: insights into structure and function. Trends in Cell Biology 15 (2005) 467-476
18. Nishizaka T., Seo R., Tadakuma H., Kinosita K., and Ishiwata S. Characterization of single actomyosin rigor bonds: load dependenceof lifetime and mechanical properties. Biophysical Journal 79 (2000) 962-974
19. Nitta R., Kikkawa M., Okada Y., and Hirokawa N. KIF1A alternately uses two loops to bind microtubules. Science 305 (2004) 678-683
20. Okada Y., and Hirokawa N. A processive single-headed motor: kinesin superfamily protein KIF1A. Science 283 (1999) 1152-1157
21. Okada Y., and Hirokawa N. Mechanism of the single-headed processivity: diffusional anchoring between the K-loop of kinesin and the C-terminus of tubulin. Proceedings of the National Academy of Science 97 (2000) 640-645
22. Okada Y., Yamazaki H., Sekine A.Y., and Hirokawa N. The neuron-specific kinesin superfamily protein KIF1A is a unique monomeric motor for anterograde axonal transport of synaptic vesicle precursors. Cell 81 (1995) 769-780
23. Okada Y., Higuchi H., and Hirokawa N. Processivity of the single-headed kinesin KIF1A through biased binding to tubulin. Nature 424 (2003) 574-577
24. Robertson K.M., and Tieleman D.P. Orientation and interactions of dipolar molecules during transport through OmpF porin. FEBS Letters 525 1-3 (2002) 53-57
25. Sack S., Kull F.J., and Mandelkow E. Motor proteins of the kinesin family-structures, variations, and nucleotide binding sites. European Journal of Biochemistry 262 (1999) 1-11
26. Soncini M., Vesentini S., Ruffoni D., Orsi M., Deriu M.A., and Redaelli A. Mechanical response and conformational changes of alpha-actinin domains during unfolding: a molecular dynamics study. Biomechanics and Modeling in Mechanobiology 6 (2007) 399-407
27. Tsuda Y., Yasutake H., Ishijima A., and Yanagida T. Torsional rigidity of single actin filaments and actin-actin bond breaking force under torsion measured directly by in vitro micromanipulation. Biophysics 93 (1996) 12937-12942
28. Uemura S., Kawaguchi K., Yajima J., Edamatsu M., Toyoshima Y.Y., and Ishiwata S. Kinesin-microtubule binding depends on both nucleotide state and loading direction. Biophysics 99 (2002) 5977-5981
29. Vinckier A., Gervasoni P., Zaugg F., Ziegler U., Lindner P., Groscurth P., et al. Atomic force microscopy detects changes in the interaction forces between GroEL and substrate proteins. Biophysical Journal 74 (1998) 3256-3263
30. Weisel W.J., Shuman H., and Litnov R.I. Protein-protein unbinding induced by force: single-molecule studies. Current Opinion in Structural Biology 13 (2003) 227-235
31. Xing J., Wriggers W., Jefferson G.M., Stein R., Cheung H.C., and Rosenfeld S.S. Kinesin has three nucleotide-dependent conformations, Implications for strain-dependent release. Journal of Biological Chemistry 275 (2000) 35413-35423