Biopolym. Cell. 2001; 17(1):61-69.
http://dx.doi.org/10.7124/bc.00059E
Structure and Function of Biopolymers
Comparative analysis of the tubulin secondary structure
1Niporko A. Yu., 1Blum Ya. B.
  1. Institute of Cell Biology and Genetic Engineering, NAS of Ukraine
    148, Akademika Zabolotnogo Str., Kyiv, Ukraine, 03680

Abstract

The secondary structure of tubulin and FtsZ molecules from evolutionary distant organisms was analyzed. It was revealed that a majority of the secondary structure elements is common for all proteins investigated, but each protein has also unique structure elements. The time stability of molecules secondary structure is clearly different for the tubulin and FtsZ classes. In the case of tubulin we can speak about dynamic metastability of the secondary structure specific for these proteins.
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References

[1] Hyams JS, Lloyd CW. Microtubules. New York: Willey-Liss, 1993.
[2] Fosket DE, Morejohn LC. Structural and functional organization of tubulin. Annu Rev Plant Physiol Plant Mol Biol. 1992;43(1):201–40.
[3] Mandelkow E, Mandelkow EM. Microtubules and microtubule-associated proteins. Curr Opin Cell Biol. 1995;7(1):72-81.
[4] Vallee RB, Sheetz MP. Targeting of motor proteins. Science. 1996;271(5255):1539-44.
[5] Nath JP, Himes RH. Localization of the exchangeable nucleotide binding domain in beta-tubulin. Biochem Biophys Res Commun. 1986;135(3):1135-43.
[6] Carlier MF. Role of nucleotide hydrolysis in the polymerization of actin and tubulin. Cell Biophys. 1988;12:105-17.
[7] de Boer PA, Cook WR, Rothfield LI. Bacterial cell division. Annu Rev Genet. 1990;24:249-74.
[8] Erickson HP. FtsZ, a tubulin homologue in prokaryote cell division. Trends Cell Biol. 1997;7(9):362-7.
[9] Rothfield LI, Justice SS. Bacterial cell division: the cycle of the ring. Cell. 1997;88(5):581-4.
[10] Kuroiwa T, Kuroiwa H, Sakai A, Takahashi H, Toda K, Itoh R. The division apparatus of plastids and mitochondria. Int Rev Cytol. 1998;181:1-41.
[11] Nogales E, Downing KH, Amos LA, L?we J. Tubulin and FtsZ form a distinct family of GTPases. Nat Struct Biol. 1998;5(6):451-8.
[12] Nogales E, Wolf SG, Zhang SX, Downing KH. Preservation of 2-D crystals of tubulin for electron crystallography. J Struct Biol. 1995;115(2):199-208.
[13] Nogales E, Wolf SG, Downing KH. Structure of the alpha beta tubulin dimer by electron crystallography. Nature. 1998;391(6663):199-203.
[14] L?we J, Amos LA. Crystal structure of the bacterial cell-division protein FtsZ. Nature. 1998;391(6663):203-6.
[15] Damaschun G, Damaschun H, Gast K, Zirwer D. Proteins can adopt totally different folded conformations. J Mol Biol. 1999;291(3):715-25.
[16] MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wi?rkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998;102(18):3586-616.
[17] Koehl P, Levitt M. Theory and simulation. Can theory challenge experiment? Curr Opin Struct Biol. 1999;9(2):155-6.
[18] Alm E, Baker D. Matching theory and experiment in protein folding. Curr Opin Struct Biol. 1999;9(2):189-96.
[19] Yemets AI, Blume YaB. Resistance to herbicides with antimicrotubular activity: from natural mutants to transgenic plants. Fiziologiia rasteniy. 1999; 46(6):899-907.
[20] Cronin KE, Hussey PJ, Ray JA, Waldin TR. Herbicide resistant plants. World Intellect Property Org Int Publ. 1993; N WO 93/24637.
[21] Yamamoto E, Zeng L, Baird WV. Alpha-tubulin missense mutations correlate with antimicrotubule drug resistance in Eleusine indica. Plant Cell. 1998;10(2):297-308.
[22] Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 2000;28(1):45-8.
[23] Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25(24):4876-82.
[24] Guex N, Peitsch MC. Molecular modelling of proteins. Immunol News. 1999;6:132-4.
[25] HyperChem release 5.0. Reference manual. Ottawa: Hypercube Inc., 1996. 656 p.
[26] Van der Spoel D, van Buuren AR, Apol E. GROMACS user manual, version 2.0-BIOSON Res. Inst, and Lab. of Biophys. Chem. of Univ. of Groningen. Groningen, 1999.
[27] Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;22(12):2577-637.
[28] Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997;18(15):2714-23.
[29] Amos LA. Focusing-in on microtubules. Curr Opin Struct Biol. 2000;10(2):236-41.