ABSTRACT
Purpose
To explore possible ways in which yew tree tubulin is naturally resistant to paclitaxel. While the yew produces a potent cytotoxin, paclitaxel, it is immune to paclitaxel’s cytotoxic action.
Methods
Tubulin sequence data for plant species were obtained from Alberta 1000 Plants Initiative. Sequences were assembled with Trinity de novo assembly program and tubulin identified. Homology modeling using MODELLER software was done to generate structures for yew tubulin. Molecular dynamics simulations and molecular mechanics Poisson–Boltzmann calculations were performed with the Amber package to determine binding affinity of paclitaxel to yew tubulin. ClustalW2 program and PHYLIP package were used to perform phylogenetic analysis on plant tubulin sequences.
Results
We specifically analyzed several important regions in tubulin structure: the high-affinity paclitaxel binding site, as well as the intermediate binding site and microtubule nanopores. Our analysis indicates that the high-affinity binding site contains several substitutions compared to human tubulin, all of which reduce the binding energy of paclitaxel.
Conclusions
The yew has achieved a significant reduction of paclitaxel’s affinity for its tubulin by utilizing several specific residue changes in the binding pocket for paclitaxel.
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Abbreviations
- 1KP:
-
1000 plants initiative
- BLAST:
-
basic local alignment search tool
- MD:
-
molecular dynamics
- MM-PBSA:
-
molecular mechanics Poisson–Boltzmann surface area
- MT:
-
microtubule
- NDGA:
-
nordihydroguaiaretic acid
- ORF:
-
open reading frames
- PDB:
-
protein data bank
- PTX:
-
paclitaxel
- RMSD:
-
root mean square deviation
REFERENCES
Cragg GML, Kingston DGI, Newman DJ. Anticancer agents from natural products. 2nd ed. Boca Raton: CRC; 2011.
The Alberta 1000 Plants Initiative (Alberta Advanced Education and Technology, Musea Ventures, BGI-Shenzhen, Alberta iCORE, to Wong GKS). Available from: http://www.onekp.com/.
Wani MC, Taylor HL, Wall ME, Coggon P, McPhail AT. Plant antitumor agents. VI. The isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifolia. J Am Chem Soc. 1971;93(9):2325–7.
Schiff PB, Horwitz SB. Taxol stabilizes microtubules in mouse fibroblast cells. Proc Natl Acad Sci U S A. 1980;77(3):1561–5.
VanBuren V, Odde DJ, Cassimeris L. Estimates of lateral and longitudinal bond energies within the microtubule lattice. Proc Natl Acad Sci U S A. 2002;99(9):6035–40.
Xiao H, Verdier-Pinard P, Fernandez-Fuentes N, Burd B, Angeletti R, Fiser A, et al. Insights into the mechanism of microtubule stabilization by Taxol. Proc Natl Acad Sci U S A. 2006;103(27):10166–73.
Löwe J, Li H, Downing KH, Nogales E. Refined Structure of alpha beta-tubulin at 3.5 A resolution. J Mol Biol. 2001;313(5):1045–57.
Nogales E, Wolf SG, Downing KH. Structure of the alpha beta tubulin dimer by electron crystallography. Nature. 1998;391(6663):199–203.
Huzil JT, Ludueña RF, Tuszynski J. Comparative modelling of human β tubulin isotypes and implications for drug binding. Nanotechology. 2006;17(4):S90–S100.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2012;40:D48–53.
Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000;16(6):276–7.
The UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012;40:D71–5.
Ludueña RF, Banerjee A. The isotypes of tubulin. In: Fojo T, editor. The role of microtubules in cell biology, neurobiology, and oncology. Totowa: Humana; 2008. p. 123–75.
Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EE, Brice MD, Rodgers JR, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977;112(3):535–42.
Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, Duke RE, et al. AMBER 9. San Francisco: University of California; 2006.
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006;65(3):712–25.
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26(16):1781–802.
Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, et al. NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys. 1999;151(1):283–312.
Freedman H, Huzil JT, Luchko T, Ludueña RF, Tuszynski JA. Identification and characterization of an intermediate taxol binding site within microtubule nanopores and a mechanism for tubulin isotype binding selectivity. J Chem Inf Model. 2009;49(2):424–36.
DeLano W. PyMOL Release 0.99. Palo Alto: DeLano Scientific LLC; 2002.
Li H, DeRosier DJ, Nicholson WV, Nogales E, Downing KH. Microtubule structure at 8 A resolution. Strucr. 2002;10:1317–28.
Sali A, Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol. 1993;234(3):779–815.
Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst. 1993;26(2):283–91.
Sept D, Baker NA, McCammon JA. The physical basis of microtubule structure and stability. Protein Sci. 2003;12(10):2257–61.
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157–74.
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 2007;35:W522–5.
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004;32:W665–7.
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res. 2000;33(12):889–97.
Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, Duke RE, et al. AMBER 10. San Francisco: University of California; 2008.
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A. 2001;98(18):10037–41.
Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, et al. ClustalW and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–8.
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992;8(3):275–82.
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–25.
Felsenstein J. PHYLIP—phylogeny inference package (version 3.2). Cladistics. 1989;5:164–6.
Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007;23(1):127–8.
Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39:W475–8.
Nakamura M, Nakazawa J, Usui T, Osada H, Kono Y, Takatsuki A. Nordihydroguaiaretic acid, of a new family of microtubule-stabilizing agents, shows effects differentiated from paclitaxel. Biosci Biotechnol Biochem. 2003;67(1):151–7.
Díaz JF, Valpuesta JM, Chacón P, Diakun G, Andreu JM. Changes in microtubule protofilament number induced by Taxol binding to an easily accessible site. Internal microtubule dynamics. J Biol Chem. 1998;273(50):33803–10.
Ross JL, Fygenson DK. Mobility of taxol in microtubule bundles. Biophys J. 2003;84(6):3959–67.
Buey RM, Calvo E, Barasoain I, Pineda O, Edler MC, Matesanz R, et al. Cyclostreptin binds covalently to microtubule pores and lumenal taxoid binding sites. Nat Chem Biol. 2007;3(2):117–25.
Díaz JF, Barasoain I, Souto AA, Amat-Guerri F, Andreu JM. Macromolecular accessibility of fluorescent taxoids bound at a paclitaxel binding site in the microtubule surface. J Biol Chem. 2005;280(5):3928–37.
Díaz JF, Barasoain I, Andreu JM. Fast kinetics of Taxol binding to microtubules. Effects of solution variables and microtubule-associated proteins. J Biol Chem. 2003;278(10):8407–19.
Mitra A, Sept D. Taxol allosterically alters the dynamics of the tubulin dimer and increases the flexibility of microtubules. Biophys J. 2008;95(7):3252–8.
Hari M, Loganzo F, Annable T, Tan X, Musto S, Morilla DB, et al. Paclitaxel-resistant cells have a mutation in the paclitaxel-binding region of beta-tubulin (Asp26Glu) and less stable microtubules. Mol Cancer Ther. 2006;5(2):270–8.
Verrills NM, Flemming CL, Liu M, Ivery MT, Cobon GS, Norris MD, et al. Microtubule alterations and mutations induced by desoxyepothilone B: implications for drug-target interactions. Chem Biol. 2003;10(7):597–607.
Ludueña RF. Multiple forms of tubulin: different gene products and covalent modifications. Int Rev Cytol. 1998;178:207–75.
ACKNOWLEDGMENTS AND DISCLOSURES
J.A.T. acknowledges support for this research from the Alberta Cancer Foundation, Alberta Advanced Education and Technology, the Allard Foundation, the Canadian Breast Cancer Foundation, and the National Sciences and Engineering Research Council of Canada (NSERC Canada). T.J.A.C. acknowledges funding support for this research from NSERC Canada. G.K.S.W. acknowledges Alberta Advanced Education and Technology, Genome Alberta, Alberta Innovates Tech Futures iCORE, Musea Ventures, and BGI-Shenzhen for the funding of the Alberta 1000 Plants Initiative.
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Tuszynski, J.A., Craddock, T.J.A., Mane, J.Y. et al. Modeling the Yew Tree Tubulin and a Comparison of its Interaction with Paclitaxel to Human Tubulin. Pharm Res 29, 3007–3021 (2012). https://doi.org/10.1007/s11095-012-0829-y
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DOI: https://doi.org/10.1007/s11095-012-0829-y