Homology modeling of tubulin: Influence predictions for microtubule's biophysical properties

European Biophysics Journal

Volumn 36, Issue 1, 2006, Pages 35-43

  Carpenter, Eric J ^a   Huzil, J Torin ^a   Ludueña, Richard F ^b   Tuszynski, Jack A ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b Mays Cancer Center at UT Health San Antonio   (United States)

Author keywords

Comparative homology modeling; Dipole; Isotype; Microtubule; Tubulin

Indexed keywords

ALPHA TUBULIN; BETA TUBULIN; SOLVENT;

ARTICLE; BIOPHYSICS; CONFORMATION; DIPOLE; ELECTRICITY; MICROTUBULE; PREDICTION; SEQUENCE HOMOLOGY; SURFACE PROPERTY;

BIOPHYSICS; DATABASES, PROTEIN; ELECTROSTATICS; HUMANS; IONS; KINETICS; MICROTUBULE PROTEINS; MICROTUBULES; MODELS, STATISTICAL; MOLECULAR CONFORMATION; SOFTWARE; SOLVENTS; TUBULIN;

EID: 33750934118     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-006-0088-0     Document Type: Article

References (44)

1. Aldaz H et al (2005) Insights into microtubule nucleation from the crystal structure of human gamma-tubulin. Nature 435:523-527
2. Baker N et al (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037-10041
3. Berman HM et al (2000) The protein data bank. Nucleic Acids Res 28:235-242
4. Boeckmann B et al (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31:365-370
5. Chothia C, Lesk A (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826
6. Connolly M (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709-713
7. Gigant B et al (2000) The 4 A X-ray structure of a tubulin: stathmin-like domain complex. Cell 102:809-816
8. Gigant B et al (2005) Structural basis for the regulation of tubulin by vinblastine. Nature 435:519-522
9. Higgins D, Sharp P (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244
10. Hooft RW et al (1996) Errors in protein structures. Nature 381:272
11. Hoogland C et al (2004) SWISS-2DPAGE, ten years later. Proteomics 4:2352-2356
12. Horio T, Hotani H (1986) Visualization of the dynamic instability of individual microtubules by dark-field microscopy. Nature 321:605-607
13. Hyams JS, Stebbings H (1979) The mechanism of microtubule associated cytoplasmic transport. Isolation and preliminary characterisation of a microtubule transport system. Cell Tissue Res 196:103-116
14. Inclan Y, Nogales E (2001) Structural models for the self-assembly and microtubule interactions of gamma-, delta-and epsilon-tubulin. J Cell Sci 114:413-422
15. Jordan M, Wilson L (2004) Mary Ann Jordan, Leslie Wilson. Nat Rev Cancer 4:253-265
16. Kikkawa M et al (2001) Switch-based mechanism of kinesin motors. Nature 411:439-445
17. Kirschner M, Schulze E (1986) Morphogenesis and the control of microtubule dynamics in cells. J Cell Sci Suppl 5:293-310
18. Laskowski RA et al (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291
19. Li H et al (2002) Microtubule structure at 8 A resolution. Structure (Camb) 10:1317-1328
20. Lindahl E, Hess B, Van Der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Mod 7:306-317
21. Lowe J et al (2001) Refined structure of alpha beta-tubulin at 3.5 A resolution. J Mol Biol 313:1045-1057
22. Lu Q, Luduena R (1994) In vitro analysis of microtubule assembly of isotypically pure tubulin dimers. Intrinsic differences in the assembly properties of alpha beta II, alpha beta III, and alpha beta IV tubulin dimers in the absence of microtubule-associated proteins. J Biol Chem 269:2041-2047
23. Luduena R (1998) Multiple forms of tubulin: different gene products and covalent modifications. Int Rev Cytol 178:207-275
24. Mandelkow E, Mandelkow E (1992) Microtubule oscillations. Cell Motil Cytoskeleton 22:235-244
25. Margolis R, Wilson L (1981) Microtubule treadmills - possible molecular machinery. Nature 293:705-711
26. Melki R et al (1989) Cold depolymerization of microtubules to double rings: geometric stabilization of assemblies. Biochemistry 28:9143-9152
27. Minoura I, Muto E (2006) Dielectric measurements of individual microtubles using the electroorientation method. Biophys J 90:3739-3748
28. Mitchison T, Kirschner M (1984) Dynamic instability of microtubule growth. Nature 312:237-242
29. Nettles J et al (2004) The binding mode of epothilone A on alpha, beta-tubulin by electron crystallography. Science 305:866-869
30. Nogales E, Wolf S, Downing K (1998) Structure of the alpha beta tubulin dimer by electron crystallography. Nature 391:199-203
31. Oakley B et al (1990) Gamma-tubulin is a component of the spindle pole body that is essential for microtubule function in Aspergillus nidulans. Cell 61:1289-1301
32. Panda D et al (1994) Microtubule dynamics in vitro are regulated by the tubulin isotype composition. Proc Natl Acad Sci USA 91:11358-11362
33. Pichichero M, Avers C (1973) The evolution of cellular movement in eukaryotes: the role of microfilaments and microtubules. Subcell Biochem 2:97-105
34. Ravelli R et al (2004) Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Nature 428:198-202
35. Roach MC et al (1998) Preparation of a monoclonal antibody specific for the class I isotype of beta-tubulin: the beta isotypes of tubulin differ in their cellular distributions within human tissues. Cell Motil Cytoskeleton 39:273-285
36. Sanchez R, Sali A (2000) Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol 143:97-129
37. Schlieper D et al (2005) Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer. Proc Natl Acad Sci USA 102:9170-9175
38. Schoutens JE (2005) Dipole' dipole interactions in microtubules. J Biol Phys 31:35-55
39. Schuessler HA et al (2003) Surface plasmon resonance study of the actin-myosin sarcomeric complex and tubulin dimers. J Mod Optics 50:2381-2391
40. Sept D, Baker NA, Mccammon J (2003) The physical basis of microtubule structure and stability. Protein Sci 12:2257-2261
41. Stracke R et al (2002) Analysis of the migration behaviour of single microtubules in electric fields. Biochem Biophys Res Commun 293:602-609
42. van Gunsteren WF (1996) Biomolecular simulation: the GROMOS96 manual and user guide. Hochschulverlag AG an der ETH Zurich, Zurich
43. Walker R, Pryer NK, Salmon E (1991) Dilution of individual microtubules observed in real time in vitro: evidence that cap size is small and independent of elongation rate. J Cell Biol 114:73-81
44. Westermann S et al (2006) The Dam1 kinetochore ring complex moves processively on depolymerizing microtubule ends. Nature 440:565-569