Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein

References

• Adams, J. M., & Cory, S. (1998). The Bcl-2 protein family: Arbiters of cell survival. Science, 281, 1322–1326.10.1126/science.281.5381.1322
   PubMed Web of Science ®Google Scholar
• Adams, J. M., & Cory, S. (2001). Life-or-death decisions by the Bcl-2 protein family. Trends in Biochemical Sciences, 26, 61–66.10.1016/S0968-0004(00)01740-0
   PubMed Web of Science ®Google Scholar
• Adams, J. M., & Cory, S. (2007). The Bcl-2 apoptotic switch in cancer development and therapy. Oncogene, 26, 1324–1337.10.1038/sj.onc.1210220
   PubMed Web of Science ®Google Scholar
• Adams, J. M., & Cory, S. (2007). Bcl-2-regulated apoptosis: mechanism and therapeutic potential. Current Opinion in Immunology, 19, 488–496.10.1016/j.coi.2007.05.004
   PubMed Web of Science ®Google Scholar
• Andersson, Y., Juell, S., & Fodstad, Ø. (2004). Downregulation of the antiapoptotic Mcl-1 protein and apoptosis in Ma-11 breast cancer cells induced by an anti-epidermal growth factor receptor-Pseudomonas exotoxin a immunotoxin. International Journal of Cancer, 112, 475–483.10.1002/(ISSN)1097-0215
   PubMed Web of Science ®Google Scholar
• Boisvert-Adamo, K., Longmate, W., Abel, E. V., & Aplin, A. E. (2009). Mcl-1 is required for melanoma cell resistance to anoikis. Molecular Cancer Research, 7, 549–556.10.1158/1541-7786.MCR-08-0358
   PubMed Web of Science ®Google Scholar
• Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., … Kollman, P. A. (2008). AMBER 10. San Francisco, CA: University of California.
   Google Scholar
• Chen, L., Willis, S. N., Wei, A., Smith, B. J., Fletcher, J. I., Hinds, M. G., … Day, D. C. (2005). Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function. Molecular Cell, 17, 393–403.10.1016/j.molcel.2004.12.030
   PubMed Web of Science ®Google Scholar
• Chetoui, N., Sylla, K., Gagnon-Houde, J. V., Alcaide-Loridan, C., Charron, D., Al-Daccak, R., & Aoudjit, F. (2008). Down-regulation of Mcl-1 by small interfering RNA sensitizes resistant melanoma cells to Fas-mediated apoptosis. Molecular Cancer Research, 6, 42–52.10.1158/1541-7786.MCR-07-0080
   PubMed Web of Science ®Google Scholar
• Clohessy, J. G., Zhuang, J., de Boer, J., Gil-Gómez, G., & Brady, H. J. (2006). Mcl-1 Interacts with Truncated Bid and Inhibits Its Induction of Cytochrome c Release and Its Role in Receptor-mediated Apoptosis. Journal of Biological Chemistry, 281, 5750–5759.
   PubMed Web of Science ®Google Scholar
• Cory, S., Huang, D. C., & Adams, J. M. (2003). The Bcl-2 family: roles in cell survival and oncogenesis. Oncogene, 22, 8590–8607.10.1038/sj.onc.1207102
   PubMed Web of Science ®Google Scholar
• Czabotar, P. E., Lee, E. F., Thompson, G. V., Wardak, A. Z., Fairlie, W. D., & Colman, P. M. (2011). Proteins and Promotes Apoptosis Disrupts Interactions with Pro-survival Mutation to Bax beyond the BH3 Domain. Journal of Biological Chemistry, 286, 7123–7131.10.1074/jbc.M110.161281
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092.10.1063/1.464397
   Web of Science ®Google Scholar
• Derenne, S., Monia, B., Dean, N. M., Taylor, J. K., Rapp, M. J., Harousseau, J. L., … Amiot, M. (2002). Antisense strategy shows that Mcl-1 rather than Bcl-2 or Bcl-x(L) is an essential survival protein of human myeloma cells. Blood, 100, 194–199.10.1182/blood.V100.1.194
   PubMed Web of Science ®Google Scholar
• Ding, Q. Q., He, X. H., Xia, W. Y., Hsu, J. M., Chen, C. T., Li, L. Y., … Yang, M. C. (2007). Myeloid Cell Leukemia-1 inversely correlates with glycogen synthase kinase-3β activity and associates with poor prognosis in human breast cancer. Cancer Research, 67, 4564–4571.10.1158/0008-5472.CAN-06-1788
   PubMed Web of Science ®Google Scholar
• Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G. M., Zhang, W., … Cieplak, 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, 1999–2012.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Fire, E., Gulla, S. V., Grant, R. A., & Keating, A. E. (2010). Mcl-1–Bim complexes accommodate surprising point mutations via minor structural changes. Protein Science, 19, 507–519.
   PubMed Web of Science ®Google Scholar
• Fleischer, B., Schulze-Bergkamen, H., Cchuchmann, M., Weber, A., Biesterfeld, S., Muller, M., … Galle, P. R. (2006). Mcl-1 is an anti-apoptotic factor for human hepatocellular carcinoma. International Journal of Oncology, 28, 25–32.
   PubMed Web of Science ®Google Scholar
• Gohlke, H., Kiel, C., & Case, D. A. (2003). Insights into Protein–Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras–Raf and Ras–RalGDS Complexes. Journal of Molecular Biology, 330, 891–913.10.1016/S0022-2836(03)00610-7
   PubMed Web of Science ®Google Scholar
• Green, D. R., & Reed, J. C. (1998). Mitochondria and apoptosis. Science, 281, 1309–1312.10.1126/science.281.5381.1309
   PubMed Web of Science ®Google Scholar
• Han, J., Goldstein, L. A., Hou, W., & Rabinowich, H. (2007). Regulation of Mitochondrial Apoptotic Events by p53-mediated Disruption of Complexes between Antiapoptotic Bcl-2 Members and Bim. Journal of Biological Chemistry, 282, 16223–16231.10.1074/jbc.M611186200
   PubMed Web of Science ®Google Scholar
• Hou, T. J., McLaughlin, W., Lu, B., Chen, K., & Wang, W. (2006). Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. Journal of Proteome Research, 5, 32–43.10.1021/pr0502267
   PubMed Web of Science ®Google Scholar
• Hou, T., Wang, J., Zhang, W., Wang, W., & Xu, X. (2006). Recent advances in computational prediction of drug absorption and permeability in drug discovery. Current Medicinal Chemistry, 13, 2653–2667.
   PubMed Web of Science ®Google Scholar
• Hussain, S. R., Cheney, C. M., Johnson, A. J., Lin, T. S., Grever, M. R., Caligiuri, M. A., … Byrd, J. C. (2007). Targeting Mcl-1 for the therapy of cancer. Clinical Cancer Research, 13, 2144–2150.10.1158/1078-0432.CCR-06-2294
   PubMed Web of Science ®Google Scholar
• Itoh, T., Itoh, A., & Pleasure, D. (2003). Bcl-2-related protein family gene expression during oligodendroglial differentiation. Journal of Neurochemistry, 85, 1500–1512.10.1046/j.1471-4159.2003.01795.x
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L. (1982). Revised TIPS for Simulations of Liquid Water and Aqueous Solutions. The Journal of Chemical Physics, 77, 4156–4163.10.1063/1.444325
   Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of Simple Potential Functions for Simulating Liquid Water. The Journal of Chemical Physics, 79, 926–935.10.1063/1.445869
   Web of Science ®Google Scholar
• Kelekar, A., & Thompson, C. B. (1998). Bcl-2-family proteins: the role of the BH3 domain in apoptosis. Trends in Cell Biology, 8, 324–330.10.1016/S0962-8924(98)01321-X
   PubMed Web of Science ®Google Scholar
• Konopleva, M., Contractor, R., Tsao, T., Samudio, I., Ruvolo, P. P., Kitada, S., … Zhai, M. (2006). Mechanisms of apoptosis sensitivity and resistance to the BH3 mimetic ABT-737 in acute myeloid leukemia. Cancer Cell, 10, 375–388.10.1016/j.ccr.2006.10.006
   PubMed Web of Science ®Google Scholar
• Koshy, C., Parthiban, M., & Sowdhamini, R. (2010). 100ns Molecular Dynamics Simulations to study intramolecular conformational changes in Bax. Journal of Biomolecular Structure and Dynamics, 28, 71–83.10.1080/07391102.2010.10507344
   PubMed Web of Science ®Google Scholar
• Krajewshi, S., Bodurg, S., Krajewshi, M., Shabaik, A., Gascoyne, R., Berean, K., & Reed, J. C. (1995). Immunohistochemical determination of in vivo distribution of Bax, a dominant inhibitor of Bcl-2. The American Journal of Pathology, 146, 1219–1309.
   Google Scholar
• Lama, D., & Sankararamakrishnan, R. (2008). Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: Comparative molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics, 73, 492–514.10.1002/prot.22075
   PubMed Web of Science ®Google Scholar
• Li, D., Han, J. G., Chen, H., Li, L., Zhao, R. N., Liu, G., & Duan, Y. (2012). Insights into the structural function of the complex o fHIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations. Journal of Molecular Modeling, 18, 1841–1854.10.1007/s00894-011-1205-2
   PubMed Web of Science ®Google Scholar
• Li, L., Li, D., Chen, H., & Han, J. G. (2013). Studies on the binding modes of Lassa nucleoprotein complexed with m7GpppG and dTTP by molecular dynamic simulations and free energy calculations. Journal of Biomolecular Structure and Dynamics, 31, 299–315.
   PubMed Web of Science ®Google Scholar
• Li, T., Froeyen, M., & Herdewijn, P. (2008). Computational alanine scanning and free energy decomposition for E-coli type I signal peptidase with lipopeptide inhibitor complex. Journal of Molecular Graphics and Modelling, 26, 813–823.10.1016/j.jmgm.2007.04.007
   PubMed Web of Science ®Google Scholar
• Liu, X. Q., Dai, S. D., Zhu, Y. N., Marrack, P., & Kappler, J. W. (2003). The structure of a Bcl-xL/Bim fragment complex: implications for Bim function. Immunity, 19, 341–352.10.1016/S1074-7613(03)00234-6
   PubMed Web of Science ®Google Scholar
• Luo, C., Xu, L., Zheng, S., Luo, X., Shen, J., Jiang, H., … Zhou, M. (2005). Computational analysis of molecular basis of 1:1 interactions of NRG-1β wild-type and variants with ErbB3 and ErbB4. Proteins: Structure, Function, and Bioinformatics, 59, 742–756.10.1002/prot.20443
   PubMed Web of Science ®Google Scholar
• Massova, I., & Kollman, P. A. (1999). Computational Alanine Scanning To Probe Protein-Protein Interactions: A Novel Approach To Evaluate Binding Free Energies. Journal of the American Chemical Society, 121, 8133–8143.10.1021/ja990935j
   Web of Science ®Google Scholar
• Miyamoto, S., & Kollman, P. A. (1992). Settle—An analytical version of the Shake and Rattle algorithm for rigid water models. Journal of Computational Chemistry, 13, 952–962.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Molina, J. M., & Hill, A. (2007). Darunavir (TMC114): a new HIV-1 protease inhibitor. Expert Opinion on Pharmacotherapy. Expert Opinion on Pharmacotherapy, 8, 1951–1964.10.1517/eop.2007.8.issue-12
   PubMed Web of Science ®Google Scholar
• Nguyen, M., Marcellus, R. C., Roulston, A., Watson, M., Serfass, L., Murthy Madiraju, S. R., … Viallet, G. C. (2007). Small molecule obatoclax (GX15–070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis. Proceedings of the National Academy of Sciences, 104, 19512–19517.10.1073/pnas.0709443104
   PubMed Web of Science ®Google Scholar
• Oltval, Z. N., Milliman, C. L., & Korsmeyer, S. J. (1993). Bcl-2 heterodimerizes in vivo with a conserved homolog, Bax, that accelerates programmed cell death. Cell, 74, 609–619.10.1016/0092-8674(93)90509-O
   PubMed Web of Science ®Google Scholar
• Paoluzzi, L., Gonen, M., Gardner, J. R., Mastrella, J., Yang, D., Holmlund, J., … Leopold, O. A. (2008). Targeting Bcl-2 family members with the BH3 mimetic AT-101 markedly enhances the therapeutic effects of chemotherapeutic agents in in vitro and in vivo models of B-cell lymphoma. Blood, 111, 5350–5358.10.1182/blood-2007-12-129833
   PubMed Web of Science ®Google Scholar
• Parikh, N., Koshy, C., Dhayabaran, V., Perumalsamy, L. R., Sowdhamini, R., & Sarin, A. (2007). The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL. BMC Cell Biology, 23, 8–16.
   Google Scholar
• Pastor, R. W., Brooks, B. R., & Szabo, A. (1988). An analysis of the accuracy of Langevin and molecular dynamics algorithms. Molecular Physics, 65, 1409.10.1080/00268978800101881
   Web of Science ®Google Scholar
• Petros, A. M., Nettesheim, D. G., Wang, Y., Olejniczak, E. T., Meadows, R. P., Mack, J., … Matayoshi, S. F. (2000). Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies. Protein Science, 9, 2528–2534.10.1017/S096183680000331X
   PubMed Web of Science ®Google Scholar
• Petros, A. M., Olejniczak, E. T., & Fesik, S. W. (2004). Structural biology of the Bcl-2 family of proteins. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research, 1644, 83–94.10.1016/j.bbamcr.2003.08.012
   PubMed Web of Science ®Google Scholar
• Sattler, M., Liang, H., Nettesheim, D. G., Meadows, R. P., Harlan, J. E., Eberstadt, M., … Fesik, S. F. (1997). Structure of Bcl-XL-Bak peptide complex: Recognition between regulators of apoptosis. Science, 275, 983–986.10.1126/science.275.5302.983
   PubMed Web of Science ®Google Scholar
• Shimazu, T., Degenhardt, K., Nur-E-Kamal, A., Zhang, J., Yoshida, T., Zhang, Y., … White, M. (2007). NBK/BIK Antagonizes MCL-1 and BCL-X L and Activates BAK-mediated Apoptosis in Response to Protein Synthesis Inhibition. Genes & Development, 21, 929–941.10.1101/gad.1522007
   PubMed Web of Science ®Google Scholar
• Skommer, J., Wlodkowic, D., & Deptala, A. (2007). Larger than life: Mitochondria and the Bcl-2 family. Leukemia Research, 31, 277–286.10.1016/j.leukres.2006.06.027
   PubMed Web of Science ®Google Scholar
• Spierings, D., McStay, G., Saleh, M., Bender, C., Chipuk, J., Maurer, U., & Green, D. R. (2005). Connected to death: the (unexpurgated) mitochondrial pathway of apoptosis. Science, 310, 66–67.10.1126/science.1117105
   PubMed Web of Science ®Google Scholar
• Stewart, M. L., Fire, E., Keating, A. E., & Walensky, L. D. (2010). The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitize. Nature Chemical Biology, 6, 595–601.10.1038/nchembio.391
   PubMed Web of Science ®Google Scholar
• Tsui, V., & Case, D. A. (2000). Theory and applications of the generalized born solvation model in macromolecular simulations. Biopolymers, 56, 275–291.10.1002/(ISSN)1097-0282
   PubMed Web of Science ®Google Scholar
• Vivek, M., Dilraj, L., & Ramasubbu, S. (2013). Relationship between helix stability and binding affinities: molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent. Journal of Biomolecular Structure & Dynamics, 31, 65–77.
   PubMed Web of Science ®Google Scholar
• Wei, S. H., Dong, K., Lin, F., Wang, X., Li, B., Shen, J. J., … Wang, H. Z. (2008). Inducing apoptosis and enhancing chemosensitivity to gemcitabine via RNA interference targeting Mcl-1 gene in pancreatic carcinoma cell. Cancer Chemotherapy and Pharmacology, 62, 1055–1064.10.1007/s00280-008-0697-7
   PubMed Web of Science ®Google Scholar
• Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20, 217–230.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Willis, S. N., Chen, L., Dewson, G., Wei, A., Nail, E., Fletcher, J. I., … Huang, D. C. (2005). Pro-apoptotic Bak is sequestered by Mc1-1 and Bcl-xL, but not Bcl-2, until displaced by BH3-only proteins. Genes & Development, 19, 1294–1305.10.1101/gad.1304105
   PubMed Web of Science ®Google Scholar
• Xu, Y., & Wang, R. (2006). A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method. Proteins: Structure, Function, and Bioinformatics, 64, 1058–1068.10.1002/prot.21044
   PubMed Web of Science ®Google Scholar
• Zhang, B., Gojo, I., & Fenton, R. G. (2002). Myeloid cell factor-1 is a critical survival factor for multiple myeloma. Blood, 99, 1885–1893.10.1182/blood.V99.6.1885
   PubMed Web of Science ®Google Scholar
• Zhuang, L., Lee, C. S., Scolyer, R. A., McCarthy, S. W., Zhang, X. D., Thompson, J. F., & Hersey, P. (2007). Mcl-1, Bcl-XL and Stat3 expression are associated with progression of melanoma whereas Bcl-2, AP-2 and MITF levels decrease during progression of melanoma. Modern Pathology, 20, 416–426.10.1038/modpathol.3800750
   PubMed Web of Science ®Google Scholar