References
- Acoca, S., Cui, Q., Shore, G. C., & Purisima, E. O. (2011). Molecular dynamics study of small molecule inhibitors of the Bcl-2 family. Proteins, 79(9), 2624–2636. doi: 10.1002/prot.23083
- Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Bioinformatics, 17(4), 412–425. doi: 10.1002/prot.340170408
- Andersen, O. J., Risor, M. W., Poulsen, E. C., Nielsen, N. C., Miao, Y., Enghild, J. J., & Schiott, B. (2017). Reactive center loop insertion in alpha-1-antitrypsin captured by accelerated molecular dynamics simulation. Biochemistry, 56(4), 634–646. doi: 10.1021/acs.biochem.6b00839
- Antignani, A., & Youle, R. J. (2006). How do Bax and Bak lead to permeabilization of the outer mitochondrial membrane? Current Opinion in Cell Biology, 18(6), 685–689. doi: 10.1016/j.ceb.2006.10.004
- Bakan, A., Meireles, L. M., & Bahar, I. (2011). ProDy: Protein dynamics inferred from theory and experiments. Bioinformatics, 27(11), 1575–1577. doi: 10.1093/bioinformatics/btr168
- Binkowski, T. A., Naghibzadeh, S., & Liang, J. (2003). CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Research, 31(13), 3352–3355.
- Bruncko, M., Oost, T. K., Belli, B. A., Ding, H., Joseph, M. K., Kunzer, A., … Elmore, S. W. (2007). Studies leading to potent, dual inhibitors of Bcl-2 and Bcl-xL. Journal of Medicinal Chemistry, 50(4), 641–662. doi: 10.1021/jm061152t
- Case, D. A., Betz, R. M., Cerutti, D. S., Cheatham, T., Darden, T., Duke, R. E., & Kollman, P. A. (2016). AMBER 2016. San Francisco, CA: University of California.
- Czabotar, P. E., Westphal, D., Dewson, G., Ma, S., Hockings, C., Fairlie, W. D., … Colman, P. M. (2013). Bax crystal structures reveal how BH3 domains activate Bax and nucleate its oligomerization to induce apoptosis. Cell, 152(3), 519–531. doi: 10.1016/j.cell.2012.12.031
- Delbridge, A. R., Grabow, S., Strasser, A., & Vaux, D. L. (2016). Thirty years of BCL-2: Translating cell death discoveries into novel cancer therapies. Nature Reviews Cancer, 16(2), 99–109. doi: 10.1038/nrc.2015.17
- Deng, X., Gao, F., & May, W. S. (2009). Protein phosphatase 2A inactivates Bcl2’s antiapoptotic function by dephosphorylation and up-regulation of Bcl2-p53 binding. Blood, 113(2), 422–428. doi: 10.1182/blood-2008-06-165134
- Do, H., & Troisi, A. (2015). Developing accurate molecular mechanics force fields for conjugated molecular systems. Physical Chemistry Chemical Physics, 17(38), 25123–25132. doi: 10.1039/c5cp04328j
- Elmore, S. (2007). Apoptosis: a review of programmed cell death. Toxicologic Pathology, 35(4), 495–516. doi: 10.1080/01926230701320337
- Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2016). Gaussian 16 Rev. B.01. Wallingford, CT: Gaussian 09 Rev. A.02.
- Gibson, C. J., & Davids, M. S. (2015). BCL-2 antagonism to target the intrinsic mitochondrial pathway of apoptosis. Clinical Cancer Research, 21(22), 5021–5029. doi: 10.1158/1078-0432.ccr-15-0364
- Hamelberg, D., Mongan, J., & McCammon, J. A. (2004). Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. The Journal of Chemical Physics, 120(24), 11919–11929. doi: 10.1063/1.1755656
- Han, B., Park, D., Li, R., Xie, M., Owonikoko, T. K., Zhang, G., … Deng, X. (2015). Small-molecule Bcl2 BH4 antagonist for lung cancer therapy. Cancer Cell, 27(6), 852–863. doi: 10.1016/j.ccell.2015.04.010
- Hardwick, J. M., & Soane, L. (2013). Multiple functions of BCL-2 family proteins. Cold Spring Harbor Perspectives Biology, 5(2), 152–158. doi: 10.1101/cshperspect.a008722
- Hou, T., Zhang, W., Case, D. A., & Wang, W. (2008). Characterization of domain-peptide interaction interface: A case study on the amphiphysin-1 SH3 domain. Journal of Molecular Biology, 376(4), 1201–1214. doi: 10.1016/j.jmb.2007.12.054
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38, 27–38.
- 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(2), 926–935. doi: 10.1063/1.445869
- Kalenkiewicz, A., Grant, B. J., & Yang, C. Y. (2015). Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics. Biology (Basel), 4(2), 344–366. doi: 10.3390/biology4020344
- Kerr, J. F., Wyllie, A. H., & Currie, A. R. (1972). Apoptosis: A basic biological phenomenon with wide-ranging implications in tissue kinetics. British Journal of Cancer, 26(4), 239–257.
- Kolluri, S. K., Zhu, X., Zhou, X., Lin, B., Chen, Y., Sun, K., … Zhang, X. K. (2008). A short Nur77-derived peptide converts Bcl-2 from a protector to a killer. Cancer Cell, 14(4), 285–298. doi: 10.1016/j.ccr.2008.09.002
- Koshy, C., Parthiban, M., & Sowdhamini, R. (2010). 100 ns molecular dynamics simulations to study intramolecular conformational changes in Bax. Journal of Biomolecular Structure and Dynamics, 28(1), 71–83. doi: 10.1080/07391102.2010.10507344
- Ku, B., Liang, C., Jung, J. U., & Oh, B. H. (2011). Evidence that inhibition of BAX activation by BCL-2 involves its tight and preferential interaction with the BH3 domain of BAX. Cell Research, 21(4), 627–641. doi: 10.1038/cr.2010.149
- Li, Y., Sun, J., Li, D., & Lin, J. (2016). Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor. Physical Chemistry Chemical Physics, 18(18), 12642–12650. doi: 10.1039/c6cp00798h
- Liu, Z., Wild, C., Ding, Y., Ye, N., Chen, H., Wold, E. A., & Zhou, J. (2016). BH4 domain of Bcl-2 as a novel target for cancer therapy. Drug Discovery Today, 21(6), 989–996. doi: 10.1016/j.drudis.2015.11.008
- Lopez, J., & Tait, S. W. (2015). Mitochondrial apoptosis: Killing cancer using the enemy within. British Journal of Cancer, 112(6), 957–962. doi: 10.1038/bjc.2015.85
- Markwick, P. R., & McCammon, J. A. (2011). Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Physical Chemistry Chemical Physics, 13(45), 20053–20065. doi: 10.1039/c1cp22100k
- Miao, Y., Feixas, F., Eun, C., & McCammon, J. A. (2015). Accelerated molecular dynamics simulations of protein folding. Journal of Computational Chemistry, 36(20), 1536–1549. doi: 10.1002/jcc.23964
- Miles, J. A., Yeo, D. J., Rowell, P., Rodriguez-Marin, S., Pask, C. M., Warriner, S. L., … Wilson, A. J. (2016). Hydrocarbon constrained peptides – Understanding preorganisation and binding affinity. Chemical Science, 7(6), 3694–3702. doi: 10.1039/C5SC04048E
- Moldoveanu, T., Follis, A. V., Kriwacki, R. W., & Green, D. R. (2014). Many players in BCL-2 family affairs. Trends in Biochemistry Sciences, 39(3), 101–111. doi: 10.1016/j.tibs.2013.12.006
- Moldoveanu, T., Grace, C. R., Llambi, F., Nourse, A., Fitzgerald, P., Gehring, K., … Green, D. R. (2013). BID-induced structural changes in BAK promote apoptosis. Nature Structural and Molecular Biology, 20(5), 589–597. doi: 10.1038/nsmb.2563
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi: 10.1002/jcc.21256
- Ola, M. S., Nawaz, M., & Ahsan, H. (2011). Role of Bcl-2 family proteins and caspases in the regulation of apoptosis. Molecular and Cellular Biochemistry, 351(1–2), 41–58. doi: 10.1007/s11010-010-0709-x
- Oltersdorf, T., Elmore, S. W., Shoemaker, A. R., Armstrong, R. C., Augeri, D. J., Belli, B. A., … Rosenberg, S. H. (2005). An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature, 435(7042), 677–681. doi: 10.1038/nature03579
- Perez, H. L., Banfi, P., Bertrand, J., Cai, Z. W., Grebinski, J. W., Kim, K., … Borzilleri, R. M. (2012). Identification of a phenylacylsulfonamide series of dual Bcl-2/Bcl-xL antagonists. Bioorganic and Medicinal Chemistry Letters, 22(12), 3946–3950. doi: 10.1016/j.bmcl.2012.04.103
- Petros, A. M., Medek, A., Nettesheim, D. G., Kim, D. H., Yoon, H. S., Swift, K., … Fesik, S. W. (2001). Solution structure of the antiapoptotic protein bcl-2. Proceedings of the National Academy of Sciences of the United States of America, 98(6), 3012–3017. doi: 10.1073/pnas.041619798
- 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(13), 1605–1612. doi: 10.1002/jcc.20084
- Pierce, B. G., Wiehe, K., Hwang, H., Kim, B. H., Vreven, T., & Weng, Z. (2014). ZDOCK server: Interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics, 30(12), 1771–1773. doi: 10.1093/bioinformatics/btu097
- Raghav, P. K., Verma, Y. K., & Gangenahalli, G. U. (2012). Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain. Journal of Molecular Modeling, 18(5), 1885–1906. doi: 10.1007/s00894-011-1201-6
- Rajan, S., Choi, M., Baek, K., & Yoon, H. S. (2015). Bh3 induced conformational changes in Bcl-Xl revealed by crystal structure and comparative analysis. Proteins, 83(7), 1262–1272. doi: 10.1002/prot.24816
- Rastelli, G., Del Rio, A., Degliesposti, G., & Sgobba, M. (2010). Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. Journal of Computational Chemistry, 31(4), 797–810. doi: 10.1002/jcc.21372
- Schrodinger, LLC. (2015). The PyMOL Molecular Graphics System, Version 1.8. New York, NY: Author.
- Shamas-Din, A., Kale, J., Leber, B., & Andrews, D. W. (2013). Mechanisms of action of Bcl-2 family proteins. Cold Spring Harbor Perspectives Biology, 5(4), a008714. doi: 10.1101/cshperspect.a008714
- 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(6), 2312–2334. doi: 10.1021/ct700119m
- Sun, H., Li, Y., Shen, M., Tian, S., Xu, L., Pan, P., … Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Physical Chemistry Chemical Physics, 16(40), 22035–22045. doi: 10.1039/c4cp03179b
- Sun, H., Li, Y., Tian, S., Xu, L., & Hou, T. (2014). Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Physical Chemistry Chemical Physics, 16(31), 16719–16729. doi: 10.1039/c4cp01388c
- Thomas, S., Quinn, B. A., Das, S. K., Dash, R., Emdad, L., Dasgupta, S., … Fisher, P. B. (2013). Targeting the Bcl-2 family for cancer therapy. Expert Opinion on Therapeutic Targets, 17(1), 61–75. doi: 10.1517/14728222.2013.733001
- Toure, B. B., Miller-Moslin, K., Yusuff, N., Perez, L., Dore, M., Joud, C., … Visser, M. (2013). The role of the acidity of N-heteroaryl sulfonamides as inhibitors of bcl-2 family protein-protein interactions. ACS Medicinal Chemistry Letters, 4(2), 186–190. doi: 10.1021/ml300321d
- Vela, L., & Marzo, I. (2015). Bcl-2 family of proteins as drug targets for cancer chemotherapy: The long way of BH3 mimetics from bench to bedside. Current Opinion in Pharmacology, 23, 74–81. doi: 10.1016/j.coph.2015.05.014
- Willis, S. N., Fletcher, J. I., Kaufmann, T., van Delft, M. F., Chen, L., Czabotar, P. E., … Huang, D. C. (2007). Apoptosis initiated when BH3 ligands engage multiple Bcl-2 homologs, not Bax or Bak. Science, 315(5813), 856–859. doi: 10.1126/science.1133289