Molecular dynamics simulation reveals structural and thermodynamic features of kinase activation by cancer mutations within the epidermal growth factor receptor

Journal of Computational Chemistry

Volumn 32, Issue 13, 2011, Pages 2843-2852

  Wan, Shunzhou ^a   Coveney, Peter V ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

cancer mutation; epidermal growth factor receptor; free energy landscape; molecular dynamics simulation; protein activation

Indexed keywords

CANCER MUTATION; EPIDERMAL GROWTH FACTOR RECEPTORS; FREE ENERGY LANDSCAPE; MOLECULAR DYNAMICS SIMULATION; PROTEIN ACTIVATION;

AMINO ACIDS; BINDING ENERGY; BIOLOGICAL ORGANS; CELL GROWTH; CHEMICAL ACTIVATION; DISEASES; ENZYMES; FREE ENERGY; GROWTH KINETICS; MOLECULAR MECHANICS; PEPTIDES;

MOLECULAR DYNAMICS;

EPIDERMAL GROWTH FACTOR RECEPTOR;

ARTICLE; CHEMISTRY; ENZYME ACTIVATION; ENZYMOLOGY; GENETICS; HUMAN; LUNG TUMOR; MOLECULAR DYNAMICS; MUTATION; POINT MUTATION; PROTEIN CONFORMATION; THERMODYNAMICS;

ENZYME ACTIVATION; HUMANS; LUNG NEOPLASMS; MOLECULAR DYNAMICS SIMULATION; MUTATION; POINT MUTATION; PROTEIN CONFORMATION; RECEPTOR, EPIDERMAL GROWTH FACTOR; THERMODYNAMICS;

EID: 79960642090     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21866     Document Type: Article

References (26)

1. S. V. Sharma, D. W. Bell, J. Settleman, D. A. Haber, Nat Rev Cancer 2007, 7, 169.
2. R. S. Herbst, D. M. Shin, Cancer 2002, 94, 1593.
3. J. M. Zhang, P. L. Yang, N. S. Gray, Nat Rev Cancer 2009, 9, 28.
4. R. Y. Patel, R. J. Doerksen, J Proteome Res 2010, 9, 4433.
5. X. W. Zhang, J. Gureasko, K. Shen, P. A. Cole, J. Kuriyan, Cell 2006, 125, 1137.
6. O. M. Fischer, S. Hart, A. Gschwind, A. Ullrich, Biochem Soc Trans 2003, 31, 1203.
7. A. Kumar, E. T. Petri, B. Halmos, T. J. Boggon, J Clin Oncol 2008, 26, 1742.
8. M. Landau, N. Ben Tal, Biochim Biophys Acta-Rev Cancer 2008, 1785, 12.
9. C. H. Yun, K. E. Mengwasser, A. V. Toms, M. S. Woo, H. Greulich, K. K. Wong, M. Meyerson, M. J. Eck, Proc Nat Acad Sci USA 2008, 105, 2070.
10. S. Wan, P. V. Coveney, J R Soc Interface (published online before print, 2011), doi: 10.1098/rsif.2010.0609.
11. C. H. Yun, T. J. Boggon, Y. Q. Li, M. S. Woo, H. Greulich, M. Meyerson, M. J. Eck, Cancer Cell 2007, 11, 217.
12. A. Papakyriakou, D. Vourloumis, F. Tzortzatou-Stathopoulou, M. Karpusas, Protein Struct Funct Bioinf 2009, 76, 375.
13. A. Dixit, G. M. Verkhivker, PLoS Comput Biol 2009, 5, e1000487.
14. B. J. Grant, A. A. Gorfe, J. A. McCammon, PLoS Comput Biol 2009, 5, e1000325.
15. A. Fiser, A. Sali, Bioinformatics 2003, 19, 2500.
16. S. K. Sadiq, D. Wright, S. J. Watson, S. J. Zasada, I. Stoica, P. V. Coveney, J Chem Inf Model 2008, 48, 1909.
17. Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. M. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. M. Wang, P. Kollman, J Comput Chem 2003, 24, 1999.
18. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J Chem Phys 1983, 79, 926.
19. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, J Comput Chem 2005, 26, 1781.
20. W. Humphrey, A. Dalke, K. Schulten, J Mol Graph 1996, 14, 33.
21. S. K. Sadiq, S. Wan, P. V. Coveney, Biochemistry 2007, 46, 14865.
22. D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, R. J. Woods, J Comput Chem 2005, 26, 1668.
23. N. Vajpai, A. Strauss, G. Fendrich, S. W. Cowan-Jacob, P. W. Manley, S. Grzesiek, W. Jahnke, J Biol Chem 2008, 283, 18292.
24. Y. B. Shan, M. A. Seeliger, M. P. Eastwood, F. Frank, H. F. Xu, M. O. Jensen, R. O. Dror, J. Kuriyan, D. E. Shaw, Proc Nat Acad Sci USA 2009, 106, 139.
25. D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, C. Young, B. Batson, K. J. Bowers, J. C. Chao, M. P. Eastwood, J. Gagliardo, J. P. Grossman, C. R. Ho, D. J. Ierardi, I. Kolossvary, J. L. Klepeis, T. Layman, C. Mcleavey, M. A. Moraes, R. Mueller, E. C. Priest, Y. B. Shan, J. Spengler, M. Theobald, B. Towles, S. C. Wang, Commun ACM 2008, 51, 91.
26. K. Marias, D. Dionysiou, V. Sakkalis, N. Graf, R. M. Bohle, P. V. Coveney, S. Wan, A. Folarin, P. Büchler, M. Reyes, G. Clapworthy, E. Liu, J. Sabczynski, T. Bily, A. Roniotis, M. Tsiknakis, E. Kolokotroni, S. Giatili, C. Veith, E. Messe, H. Stenzhorn, Yoo-Jin Kim, S. Zasada, A. N. Haidar, C. May, S. Bauer, T. Wang, Y. Zhao, M. Karasek, R. Grewer, A. Franz, G. Stamatakos, Interface Focus 2011, 1, 450.