References
- Andersen, B. L., Shapiro, C. L., Farrar, W. B., Crespin, T., & Wells-DiGregorio, S. (2005). Psychological responses to cancer recurrence. Cancer, 104(7), 1540–1547. https://doi.org/https://doi.org/10.1002/cncr.21309
- Andersen, H. C. (1980). Molecular dynamics simulations at constant pressure and/or temperature. The Journal of Chemical Physics, 72(4), 2384–2393. https://doi.org/https://doi.org/10.1063/1.439486
- Ascierto, P. A., Kirkwood, J. M., Grob, J.-J., Simeone, E., Grimaldi, A. M., Maio, M., Palmieri, G., Testori, A., Marincola, F. M., & Mozzillo, N. (2012). The role of BRAF V600 mutation in melanoma. Journal of Translational Medicine, 10, 85https://doi.org/https://doi.org/10.1186/1479-5876-10-85
- Babbitt, G. A., Fokoue, E. P., Evans, J. R., Diller, K. I., & Adams, L. E. (2020). DROIDS 3.0-detecting genetic and drug class variant impact on conserved protein binding dynamics. Biophysical Journal, 118(3), 541–551. https://doi.org/https://doi.org/10.1016/j.bpj.2019.12.008
- Babbitt, G. A., Mortensen, J. S., Coppola, E. E., Adams, L. E., & Liao, J. K. (2018). DROIDS 1.20: A GUI-based pipeline for GPU-accelerated comparative protein dynamics . Biophysical Journal, 114(5), 1009–1017. https://doi.org/https://doi.org/10.1016/j.bpj.2018.01.020
- Brown, A.-L., Li, M., Goncearenco, A., & Panchenko, A. R. (2019). Finding driver mutations in cancer: Elucidating the role of background mutational processes. PLoS Computational Biology, 15(4), e1006981https://doi.org/https://doi.org/10.1371/journal.pcbi.1006981
- Bürger, R. (1989). Mutation-selection models in population genetics and evolutionary game theory. In A. B. Kurzhanski & K. Sigmund (Eds.), Evolution and control in biological systems (pp. 75–89). Springer.
- Capra, M., Nuciforo, P. G., Confalonieri, S., Quarto, M., Bianchi, M., Nebuloni, M., Boldorini, R., Pallotti, F., Viale, G., Gishizky, M. L., Draetta, G. F., & Di Fiore, P. P. (2006). Frequent alterations in the expression of serine/threonine kinases in human cancers. Cancer Research, 66(16), 8147–8154. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-05-3489
- Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/https://doi.org/10.1002/jcc.20290
- Cope, N., Novak, B., Candelora, C., Wong, K., Cavallo, M., Gunderwala, A., Liu, Z., Li, Y., & Wang, Z. (2019). Biochemical characterization of full-length oncogenic BRAFV600E together with molecular dynamics simulations provide insight into the activation and inhibition mechanisms of RAF kinases. Chembiochem: A European Journal of Chemical Biology, 20(22), 2850–2861. https://doi.org/https://doi.org/10.1002/cbic.201900266
- 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(12), 10089–10092. https://doi.org/https://doi.org/10.1063/1.464397
- Davies, H., Bignell, G. R., Cox, C., Stephens, P., Edkins, S., Clegg, S., Teague, J., Woffendin, H., Garnett, M. J., Bottomley, W., Davis, N., Dicks, E., Ewing, R., Floyd, Y., Gray, K., Hall, S., Hawes, R., Hughes, J., Kosmidou, V., … Futreal, P. A. (2002). Mutations of the BRAF gene in human cancer. Nature, 417(6892), 949–954. https://doi.org/https://doi.org/10.1038/nature00766
- Durrant, D. E., & Morrison, D. K. (2018). Targeting the Raf kinases in human cancer: The Raf dimer dilemma. British Journal of Cancer, 118(1), 3–8. https://doi.org/https://doi.org/10.1038/bjc.2017.399
- Ewald, P. P. (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annalen Der Physik, 369(3), 253–287. https://doi.org/https://doi.org/10.1002/andp.19213690304
- Fiser, A., Do, R. K., & Sali, A. (2000). Modeling of loops in protein structures. Protein Science, 9(9), 1753–1773. https://doi.org/https://doi.org/10.1110/ps.9.9.1753
- Gatenby, R. A., Zhang, J., & Brown, J. S. (2019). First strike–second strike strategies in metastatic cancer: Lessons from the evolutionary dynamics of extinction. Cancer Research, 79(13), 3174–3177. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-19-0807
- Hartl, D. L. (1977). Mutation-selection balance with stochastic selection. Genetics, 86(3), 687–696.
- Hatzivassiliou, G., Song, K., Yen, I., Brandhuber, B. J., Anderson, D. J., Alvarado, R., Ludlam, M. J. C., Stokoe, D., Gloor, S. L., Vigers, G., Morales, T., Aliagas, I., Liu, B., Sideris, S., Hoeflich, K. P., Jaiswal, B. S., Seshagiri, S., Koeppen, H., Belvin, M., Friedman, L. S., & Malek, S. (2010). RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth. Nature, 464(7287), 431–435. https://doi.org/https://doi.org/10.1038/nature08833
- Henzler-Wildman, K. A., Lei, M., Thai, V., Kerns, S. J., Karplus, M., & Kern, D. (2007). A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature, 450(7171), 913–916. https://doi.org/https://doi.org/10.1038/nature06407
- Janz, N. K., Li, Y., Zikmund-Fisher, B. J., Jagsi, R., Kurian, A. W., An, L. C., McLeod, M. C., Lee, K. L., Katz, S. J., & Hawley, S. T. (2017). The Impact of Doctor-Patient Communication on patients' perceptions of their risk of breast cancer recurrence. Breast Cancer Research and Treatment, 161(3), 525–535. https://doi.org/https://doi.org/10.1007/s10549-016-4076-5
- 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. https://doi.org/https://doi.org/10.1063/1.445869
- Karoulia, Z., Wu, Y., Ahmed, T. A., Xin, Q., Bollard, J., Krepler, C., Wu, X., Zhang, C., Bollag, G., Herlyn, M., Fagin, J. A., Lujambio, A., Gavathiotis, E., & Poulikakos, P. I. (2016). An Integrated Model of RAF Inhibitor Action Predicts Inhibitor Activity against Oncogenic BRAF Signaling. Cancer Cell, 30(3), 485–498. https://doi.org/https://doi.org/10.1016/j.ccell.2016.06.024
- Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. https://doi.org/https://doi.org/10.1093/molbev/msw054
- Liu, T., Wang, Z., Guo, P., & Ding, N. (2019). Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: Molecular implications for the selectivity difference between type-I and type-II inhibitors. European Biophysics Journal: EBJ, 48(1), 73–82. https://doi.org/https://doi.org/10.1007/s00249-018-1334-y
- Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/https://doi.org/10.1021/acs.jctc.5b00255
- Montagut, C., & Settleman, J. (2009). Targeting the RAF-MEK-ERK pathway in cancer therapy. Cancer Letters, 283(2), 125–134. https://doi.org/https://doi.org/10.1016/j.canlet.2009.01.022
- Moretti, S., De Falco, V., Tamburrino, A., Barbi, F., Tavano, M., Avenia, N., Santeusanio, F., Santoro, M., Macchiarulo, A., & Puxeddu, E. (2009). Insights into the molecular function of the inactivating mutations of B-Raf involving the DFG motif. Biochimica et Biophysica Acta, 1793(11), 1634–1645. https://doi.org/https://doi.org/10.1016/j.bbamcr.2009.09.001
- Nunney, L. (2003). The population genetics of multistage carcinogenesis. Proceedings Biological Sciences, 270(1520), 1183–1191. https://doi.org/https://doi.org/10.1098/rspb.2003.2351
- 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. https://doi.org/https://doi.org/10.1002/jcc.20084
- Pierce, L. C. T., Salomon-Ferrer, R., Augusto, F., de Oliveira, C., McCammon, J. A., & Walker, R. C. (2012). Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. Journal of Chemical Theory and Computation, 8(9), 2997–3002. https://doi.org/https://doi.org/10.1021/ct300284c
- Poulikakos, P. I., Zhang, C., Bollag, G., Shokat, K. M., & Rosen, N. (2010). RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF. Nature, 464(7287), 427–430. https://doi.org/https://doi.org/10.1038/nature08902
- Rezaei Adariani, S., Buchholzer, M., Akbarzadeh, M., Nakhaei-Rad, S., Dvorsky, R., & Ahmadian, M. R. (2018). Structural snapshots of RAF kinase interactions. Biochemical Society Transactions, 46(6), 1393–1406. https://doi.org/https://doi.org/10.1042/BST20170528
- Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/https://doi.org/10.1021/ct400341p
- Roskoski, R. (2010). RAF protein-serine/threonine kinases: Structure and regulation. Biochemical and Biophysical Research Communications, 399(3), 313–317. https://doi.org/https://doi.org/10.1016/j.bbrc.2010.07.092
- Sali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234(3), 779–815. https://doi.org/https://doi.org/10.1006/jmbi.1993.1626
- Salomon-Ferrer, R., Götz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh ewald. Journal of Chemical Theory and Computation, 9(9), 3878–3888. https://doi.org/https://doi.org/10.1021/ct400314y
- Tang, H.-C., & Chen, Y.-C. (2015). Insight into molecular dynamics simulation of BRAF(V600E) and potent novel inhibitors for malignant melanoma. International Journal of Nanomedicine, 10, 3131–3146. https://doi.org/https://doi.org/10.2147/IJN.S80150
- Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/https://doi.org/10.1002/jcc.21334
- Villanueva, J., Vultur, A., & Herlyn, M. (2011). Resistance to BRAF inhibitors: Unraveling mechanisms and future treatment options. Cancer Research, 71(23), 7137–7140. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-11-1243
- Wagner, A. H., Walsh, B., Mayfield, G., Tamborero, D., Sonkin, D., Krysiak, K., Pons, J. D., Duren, R. P., Gao, J., McMurry, J., Patterson, S., Fitz, C. D. V., Sezerman, O. U., Warner, J. L., Rieke, D. T., Aittokallio, T., Cerami, E., Ritter, D., Schriml, L. M., … Consortium, V. I., For, C. (2018). A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants. BioRxiv, 366856. https://doi.org/https://doi.org/10.1101/366856
- Wan, P. T. C., Garnett, M. J., Roe, S. M., Lee, S., Niculescu-Duvaz, D., Good, V. M., Jones, C. M., Marshall, C. J., Springer, C. J., Barford, D., Marais, R., & Project, C. G., (2004). Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell, 116(6), 855–867. https://doi.org/https://doi.org/10.1016/S0092-8674(04)00215-6
- Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling, 25(2), 247–260. https://doi.org/https://doi.org/10.1016/j.jmgm.2005.12.005
- Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/https://doi.org/10.1002/jcc.20035
- Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54, 5.6.1–5.6.37. https://doi.org/https://doi.org/10.1002/cpbi.3
- Yang, H.-C., Thornton, L. M., Shapiro, C. L., & Andersen, B. L. (2008). Surviving recurrence: Psychological and quality-of-life recovery. Cancer, 112(5), 1178–1187. https://doi.org/https://doi.org/10.1002/cncr.23272
- Zhang, C., Spevak, W., Zhang, Y., Burton, E. A., Ma, Y., Habets, G., Zhang, J., Lin, J., Ewing, T., Matusow, B., Tsang, G., Marimuthu, A., Cho, H., Wu, G., Wang, W., Fong, D., Nguyen, H., Shi, S., Womack, P., … Bollag, G. (2015). RAF inhibitors that evade paradoxical MAPK pathway activation. Nature, 526(7574), 583–586. https://doi.org/https://doi.org/10.1038/nature14982
- Zhang, J., Cunningham, J. J., Brown, J. S., & Gatenby, R. A. (2017). Integrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancer. Nature Communications, 8(1), 1816 https://doi.org/https://doi.org/10.1038/s41467-017-01968-5