Molecular dynamics simulations of retinoblastoma protein

References

• Almasan, A., Yin, Y., Kelly, R. E., Lee, E. Y., Bradley, A., Li, W., & Wahl, G. M. (1995). Deficiency of retinoblastoma protein leads to inappropriate S-phase entry, activation of E2F-responsive genes, and apoptosis. Proceedings of the National Academy of Sciences of the United States of America, 92, 5436–5440.
   PubMed Web of Science ®Google Scholar
• Bakan, A., Meireles, L. M., & Bahar, I. (2011). ProDy: Protein dynamics inferred from theory and experiments. Bioinformatics, 27(11), 1575–1577.
   PubMed Web of Science ®Google Scholar
• Balog, E. R., Burke, J. R., Hura, G. L., & Rubin, S. M. (2011). Crystal structure of the unliganded retinoblastoma protein pocket domain. Proteins, 79, 2010–2014.
   PubMed Web of Science ®Google Scholar
• Barrientes, S., Cooke, C., & Goodrich, D. W. (2000). Glutamic acid mutagenesis of retinoblastoma protein phosphorylation sites has diverse effects on function. Oncogene, 19, 562–570.
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular-dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684–3690.
   Web of Science ®Google Scholar
• Berman, H. M., Kleywegt, Gerard, J., Nakamura, Haruki, & Markley, John L. (2012). The protein data bank at 40: Reflecting on the past to prepare for the future. Structure, 20(3), 391–396.
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28, 235–242.
   PubMed Web of Science ®Google Scholar
• Brehm, A., Miska, E. A., McCance, D. J., Reid, J. L., Bannister, A. J., & Kouzarides, T. (1998). Retinoblastoma protein recruits histone deacetylase to repress transcription. Nature, 391, 597–600.
   PubMed Web of Science ®Google Scholar
• Brian David Dynlacht, S. F., Jacqueline, A. L., & Harlow, Ed (1994). Differential regulation of E2F transactivation by cyclin/cdk2 complexes. Genes & Development, 8, 1772–1786.
   PubMed Web of Science ®Google Scholar
• Brown, V. D., Phillips, R. A., & Gallie, B. L. (1999). Cumulative effect of phosphorylation of pRB on regulation of E2F Activity. Molecular and Cellular Biology, 19, 3246–3256.
   PubMed Web of Science ®Google Scholar
• Buchkovich, K., Duffy, L. A., & Harlow, E. (1989). The retinoblastoma protein is phosphorylated during specific phases of the cell cycle. Cell, 58, 1097–1105.
   PubMed Web of Science ®Google Scholar
• Burd, C. E., & Sharpless, N. E. (2010). What’s so special about RB? Cancer Cell, 17, 313–314.
   PubMed Web of Science ®Google Scholar
• Chicas, A., Wang, X., Zhang, C., McCurrach, M., Zhao, Z., Mert, O., & Lowe, S. W. (2010). Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence. Cancer Cell, 17, 376–387.
   PubMed Web of Science ®Google Scholar
• Classon, M., Salama, S., Gorka, C., Mulloy, R., Braun, P., & Harlow, E. (2000). Combinatorial roles for pRB, p107, and p130 in E2F-mediated cell cycle control. Proceedings of the National Academy of Sciences of the United States of America, 97, 10820–10825.
   PubMed Web of Science ®Google Scholar
• Cobrinik, D. (2005). Pocket proteins and cell cycle control. Oncogene, 24, 2796–2809.
   PubMed Web of Science ®Google Scholar
• Connolly, M. L. (1983). Analytical molecular surface calculation. Journal of Applied Crystallography, 16, 548–558.
   Web of Science ®Google Scholar
• Dick, F. A., & Dyson, N. J. (2002). Three regions of the pRB pocket domain affect its inactivation by human papillomavirus E7 Proteins. Journal of Virology, 76, 6224–6234.
   PubMed Web of Science ®Google Scholar
• Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24, 1999–2012.
   PubMed Web of Science ®Google Scholar
• Dyson, N., Howley, P. M., Munger, K., & Harlow, E. (1989). The human papilloma virus-16 E7 oncoprotein is able to bind to the retinoblastoma gene product. Science, 243, 934–937.
   PubMed Web of Science ®Google Scholar
• Fahraeus, R., Paramio, J. M., Ball, K. L., Lain, S., & Lane, D. P. (1996). Inhibition of pRb phosphorylation and cell-cycle progression by 20-residue peptide derived from p16CDKN2/INK4A. Current Biology, 6, 84–91.
   PubMed Web of Science ®Google Scholar
• Fang, S. C., De los Reyes, C., & Umen, J. G. (2006). Cell size checkpoint control by the retinoblastoma tumor suppressor pathway. PLoS Genetics, 2(e167), 1565–1579.
   Google Scholar
• Felsani, A., Mileo, A. M., & Paggi, M. G. (2006). Retinoblastoma family proteins as key targets of the small DNA virus oncoproteins. Oncogene, 25, 5277–5285.
   PubMed Web of Science ®Google Scholar
• Frolov, M. V., & Dyson, N. J. (2004). Molecular mechanisms of E2F-dependent activation and pRB-mediated repression. Journal of Cell Science, 117, 2173–2181.
   PubMed Web of Science ®Google Scholar
• Frienser, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749.
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein−ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196.
   PubMed Web of Science ®Google Scholar
• Garrett, M. D. (2001). Cell cycle control and cancer. Current Science, 81, 515–522.
   Web of Science ®Google Scholar
• Guo, C. P., Liu, K. W., Luo, H. B., Chen, H. B., Zheng, Y., Sun, S. N., Zhang, Q., & Huang, L. (2011). Potent anti-tumor effect generated by a novel human papillomavirus (HPV) Antagonist peptide reactivating the pRb/E2F pathway. PLoS ONE, 6, e17734.
   PubMed Web of Science ®Google Scholar
• Hamel, P. A., Gill, R. M., Phillips, R. A., & Gallie, B. L. (1992). Transcriptional repression of the E2-containing promoters EII, c-myc, and RB1 by the product of the RB1 gene. Molecular and Cellular Biology, 12, 3431–3438.
   PubMed Web of Science ®Google Scholar
• Hartigan, J. A., & Wong, M. A. (1979). A k-means clustering algorithm. Applied Statistics, 28, 100–108.
   Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51, 69–82.
   PubMed Web of Science ®Google Scholar
• Hubbard, S. J., & Thornton, J. M. (1993). NACCESS. London: Department of Biochemistry and Molecular Biology University College.
   Google Scholar
• Hurford, R. K., Jr, Cobrinik, D., Lee, M. H., & Dyson, N. (1997). PRB and p107/p130 are required for the regulated expression of different sets of E2F responsive genes. Genes & Development, 11, 1447–1463.
   PubMed Web of Science ®Google Scholar
• Ianari, A., Natale, T., Calo, E., Ferretti, E., Alesse, E., Screpanti, I., Haigis, K., Gulino, A., & Lees, J. A. (2009). Proapoptotic function of the retinoblastoma tumor suppressor protein. Cancer Cell, 15, 184–194.
   PubMed Web of Science ®Google Scholar
• Jones, R. E., Wegrzyn, R. J., Patrick, D. R., Balishin, N. L., Vuocolo, G. A., Riemen, M. W., Defeo-Jones, D., Garsky, V. M., Heimbrook, D. C., & Oliff, A. (1990). Identification of HPV-16 E7 peptides that are potent antagonists of E7 binding to the retinoblastoma suppressor protein. Journal of Biological Chemistry, 265, 12782–12785.
   PubMed Web of Science ®Google Scholar
• Kim, H. Y., Ahn, B. Y., & Cho, Y. (2001). Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen. EMBO Journal, 20, 295–304.
   PubMed Web of Science ®Google Scholar
• Knudsen, E. S., & Wang, J. Y. (1997). Dual mechanisms for the inhibition of E2F binding to RB by cyclin-dependent kinase-mediated RB phosphorylation. Molecular and Cellular Biology, 17, 5771–5783.
   PubMed Web of Science ®Google Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S. H., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897.
   PubMed Web of Science ®Google Scholar
• Lee, C., Chang, J. H., Lee, H. S., & Cho, Y. (2002). Structural basis for the recognition of the E2F transactivation domain by the retinoblastoma tumor suppressor. Genes & Development, 16, 3199–3212.
   PubMed Web of Science ®Google Scholar
• Lee, C., & Cho, Y. (2002). Interactions of SB40 large T antigen and other viral proteins with retinoblastoma tumour suppressor. Reviews in Medical Virology, 12, 81–92.
   PubMed Web of Science ®Google Scholar
• Lee, J. O., Russo, A. A., & Pavletich, N. P. (1998). Structure of the retinoblastoma tumour-suppressor pocket domain bound to a peptide from HPV E7. Nature, 391, 859–865.
   PubMed Web of Science ®Google Scholar
• Liu, X., Clements, A., Zhao, K., & Marmorstein, R. (2006). Structure of the human papillomavirus E7 oncoprotein and its mechanism for inactivation of the retinoblastoma tumor suppressor. Journal of Biological Chemistry, 281, 578–586.
   PubMed Web of Science ®Google Scholar
• Liu, X., & Marmorstein, R. (2007). Structure of the retinoblastoma protein bound to adenovirus E1A reveals the molecular basis for viral oncoprotein inactivation of a rumor suppressor. Genes & Development, 21, 2711–2716.
   PubMed Web of Science ®Google Scholar
• Ludlow, J. W., DeCaprio, J. A., Huang, C. M., Lee, W. H., Paucha, E., & Livingston, D. M. (1989). SV40 large T antigen binds preferentially to an underphosphorylated member of the retinoblastoma susceptibility gene product family. Cell, 56, 57–65.
   PubMed Web of Science ®Google Scholar
• Lundberg, A. S., & Weinberg, R. A. (1998). Functional inactivation of the retinoblastoma protein requires sequential modification by at least two distinct cyclin-cdk complexes. Molecular and Cellular Biology, 18, 753–761.
   PubMed Web of Science ®Google Scholar
• Luo, R. X., Postigo, A. A., & Dean, D. C. (1998). Rb interacts with histone deacetylase to repress transcription. Cell, 92, 463–473.
   PubMed Web of Science ®Google Scholar
• McDonald, I. K., & Thornton, J. M. (1994). Satisfying hydrogen bonding potential in proteins. Journal of Molecular Biology, 238, 777–793.
   PubMed Web of Science ®Google Scholar
• Michael, F., John, K., Charles, L., & Brooks, I. I. I. (2004). MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology. Journal of Molecular Graphics and Modeling, 22, 377–395.
   PubMed Web of Science ®Google Scholar
• Noble, M. E., Endicott, J. A., Brown, N. R., & Johnson, L. N. (1997). The cyclin box fold: Protein recognition in cell-cycle and transcription control. Trends in Biochemical Sciences, 22, 482–487.
   PubMed Web of Science ®Google Scholar
• Pahel, G., Aulabaugh, A., Short, S. A., Barnes, J. A., Painter, G. R., Ray, P., & Phelps, W. C. (1993). Structural and functional characterization of the HPV16 E7 protein expressed in bacteria. Journal of Biological Chemistry, 268, 26018–26025.
   PubMed Web of Science ®Google Scholar
• Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., De Bolt, S., III, Ferguson, D., Seibel, G., & Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91, 1–41.
   Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera – A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25, 1605–1612.
   PubMed Web of Science ®Google Scholar
• Ponder, J. W., & Case, D. A. (2003). Force fields for protein simulations. Advances in Protein Chemistry, 66, 27–85.
   PubMedGoogle Scholar
• Poznic, M. (2009). Retinoblastoma protein: A central processing unit. Journal of Bioscience, 34, 305–312.
   PubMed Web of Science ®Google Scholar
• Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.
   Web of Science ®Google Scholar
• Sali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234, 779–815.
   PubMed Web of Science ®Google Scholar
• Sellers, W. R., Novitch, B. G., Miyake, S., Heith, A., Otterson, G. A., Kaye, F. J., Lassar, A. B., & Kaelin, W. G., Jr (1997). Stable binding to E2F is not required for the retinoblastoma protein to activate transcription, promote differentiation and suppress tumor cell growth. Genes & Development, 12, 95–106.
   Web of Science ®Google Scholar
• Shao, J., Tanner, S. W., Thompson, N., & Cheatham, T. E. (2007). Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. Journal of Chemical Theory and Computation, 3, 2312–2334.
   PubMed Web of Science ®Google Scholar
• Sherr, C. J. (1996). Cancer cell cycles. Science, 274, 1672–1677.
   PubMed Web of Science ®Google Scholar
• Singh, M., Krajewski, M., Mikolajka, A., & Holak, T. A. (2005). Molecular determinants for the complex formation between the retinoblastoma protein and LxCxE sequences. Journal of Biological Chemistry, 280, 37868–37876.
   PubMed Web of Science ®Google Scholar
• Stengel, K. R., Thangavel, C., Solomon, D. A., Angus, S. P., Zheng, Y., & Knudsen, E. S. (2009). Retinoblastoma/p107/p130 POCKET proteins. Journal of Biological Chemistry, 284, 19265–19271.
   PubMed Web of Science ®Google Scholar
• Sun, A., Bagella, L., Tutton, S., Romano, G., & Giordano, A. (2007). From G0 to S Phase: A view of the roles played by the retinoblastoma (Rb) family members in the Rb-E2F pathway. Journal of Cellular Biochemistry, 102, 1400–1404.
   PubMed Web of Science ®Google Scholar
• Thomas W., & Colin K., (2008). http://www.gnuplot.info/.
   Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8, 127–134.
   PubMedGoogle Scholar
• Wang, W., Donini, O., Reyes, C. M., & Kollman, P. A. (2001). Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein–ligand, protein–protein, and protein–nucleic acid noncovalent interactions. Annual Review of Biophysics and Biomolecular Structure, 30, 211–243.
   PubMedGoogle Scholar
• Wang, J.M., Hou, T.J., & Xu, X.J. (2006). Recent advances in free energy calculations with a combination of molecular mechanics and continuum models. Current Computer-Aided Drug Design, 2(3), 287–306.
   Google Scholar
• Weintraub, S. J., Chow, K. N., Luo, R. X., Zhang, S. H., He, S., & Dean, D. C. (1995). Mechanism of active transcriptional repression by the retinoblastoma protein. Nature, 375, 812–815.
   PubMed Web of Science ®Google Scholar
• Whyte, P., Buchkovich, K. J., Horowitz, J. M., Friend, S. H., Raybuck, M., Weinberg, R. A., & Harlow, E. (1988). Association between an oncogene and an anti-oncogene: The adenovirus E1A proteins bind to the retinoblastoma gene product. Nature, 334, 124–129.
   PubMed Web of Science ®Google Scholar
• Wong, S., & Weber, J. D. (2007). Deacetylation of the retinoblastoma tumour suppressor protein by SIRT1. Biochemical Journal, 407, 451–460.
   PubMed Web of Science ®Google Scholar
• Xiao, B., Spencer, J., Clements, A., Ali-Khan, N., Mittnacht, S., Broceno, C., Burghammer, M., Perrakis, A., Marmorstein, R., & Gamblin, S. J. (2003). Crystal structure of the retinoblastoma tumor suppressor protein bound to E2F and the molecular basis of its regulation. Proceedings of the National Academy of Sciences of the United States of America, 100, 2363–2368.
   PubMed Web of Science ®Google Scholar