Structural debilitation of mutation G322D associated with MSH2 and their role in triple negative breast cancer

References

• Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., … Yeh, L.-S. L. (2004). UniProt: The Universal Protein knowledgebase. Nucleic Acids Research, 32(suppl_1), D115–D119. doi:10.1093/nar/gkh131
   PubMedGoogle Scholar
• Barlow, D. J., & Thornton, J. M. (1983). Ion-pairs in proteins. Journal of Molecular Biology, 168(4), 867–885. doi:10.1016/S0022-2836(83)80079-5
   PubMed Web of Science ®Google Scholar
• Benkert, P., Künzli, M., & Schwede, T. (2009). QMEAN server for protein model quality estimation. Nucleic Acids Research, 37(suppl_2), W510–W514. doi:10.1093/nar/gkp322
   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(1), 235–242.
   PubMed Web of Science ®Google Scholar
• Bhattacharya, D., Nowotny, J., Cao, R., & Cheng, J. (2016). 3Drefine: an interactive web server for efficient protein structure refinement. Nucleic Acids Research, 44(W1), W406–W409. doi:10.1093/nar/gkw336
   PubMed Web of Science ®Google Scholar
• Chakrabarti, P., & Bhattacharyya, R. (2007). Geometry of nonbonded interactions involving planar groups in proteins. Progress in Biophysics and Molecular Biology, 95(1-3), 83–137. doi:10.1016/j.pbiomolbio.2007.03.016
   PubMed Web of Science ®Google Scholar
• Chakravarty, S., & Varadarajan, R. (1999). Residue depth: A novel parameter for the analysis of protein structure and stability. Structure (London, England: 1993), 7(7), 723–732. doi:10.1016/S0969-2126(99)80097-5
   PubMed Web of Science ®Google Scholar
• Chen, C., Gu, P., Wu, J., Chen, X., Niu, S., Sun, H., … Lei, M. (2017). Structural insights into POT1-TPP1 interaction and POT1 C-terminal mutations in human cancer. Nature Communications, 8, 14929. doi:10.1038/ncomms14929
   PubMed Web of Science ®Google Scholar
• Chen, K., Duan, W., Han, Q., Sun, X., Li, W., Hu, S., … Liu, D. (2019). Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation. Journal of Biomolecular Structure and Dynamics, 37(3), 611–622. doi:10.1080/07391102.2018.1433552
   PubMed Web of Science ®Google Scholar
• Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., … Richardson, D. C. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D Biological Crystallography, 66(1), 12–21. doi:10.1107/S0907444909042073
   PubMed Web of Science ®Google Scholar
• David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Methods in Molecular Biology (Clifton, N.J.), 1084, 193–226. https://doi.org/10.1007/978-1-62703-658-0_11
   PubMedGoogle Scholar
• Debe, D. A., & Goddard, W. A. (1999). First principles prediction of protein folding rates11Edited by F. E. Cohen. Journal of Molecular Biology, 294(3), 619–625. doi:10.1006/jmbi.1999.3278
   PubMed Web of Science ®Google Scholar
• Dyson, H. J., Wright, P. E., & Scheraga, H. A. (2006). The role of hydrophobic interactions in initiation and propagation of protein folding. Proceedings of the National Academy of Sciences of the United States of America, 103(35), 13057–13061. doi:10.1073/pnas.0605504103
   PubMed Web of Science ®Google Scholar
• Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). [20] VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404. https://doi.org/10.1016/S0076-6879(97)77022-8
   PubMed Web of Science ®Google Scholar
• Eswar, N., & Ramakrishnan, C. (2000). Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Engineering, Design and Selection, 13(4), 227–238. doi:10.1093/protein/13.4.227
   Web of Science ®Google Scholar
• Gallivan, J. P., & Dougherty, D. A. (1999). Cation-π interactions in structural biology. Proceedings of the National Academy of Sciences, 96(17), 9459–9464. doi:10.1073/pnas.96.17.9459
   PubMed Web of Science ®Google Scholar
• Goldhirsch, A., Ingle, J. N., Gelber, R. D., Coates, A. S., Thürlimann, B., & Senn, H.-J. (2009). Thresholds for therapies: Highlights of the St Gallen International Expert Consensus on the primary therapy of early breast cancer 2009. Annals of Oncology: Official Journal of the European Society for Medical Oncology, 20(8), 1319–1329. doi:10.1093/annonc/mdp322
   PubMed Web of Science ®Google Scholar
• Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling. ELECTROPHORESIS, 18(15), 2714–2723. doi:10.1002/elps.1150181505
   PubMed Web of Science ®Google Scholar
• Hamosh, A., Scott, A. F., Amberger, J. S., Bocchini, C. A., & McKusick, V. A. (2005). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research, 33(Database issue), D514–D517. doi:10.1093/nar/gki033
   PubMed Web of Science ®Google Scholar
• Hsieh, P., & Yamane, K. (2008). DNA mismatch repair: Molecular mechanism, cancer, and ageing. Mechanisms of Ageing and Development, 129(7-8), 391–407. doi:10.1016/j.mad.2008.02.012
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. 27–28. doi:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Iaccarino, I., Marra, G., Palombo, F., & Jiricny, J. (1998). hMSH2 and hMSH6 play distinct roles in mismatch binding and contribute differently to the ATPase activity of hMutSalpha. The EMBO Journal, 17(9), 2677–2686. doi:10.1093/emboj/17.9.2677
   PubMed Web of Science ®Google Scholar
• Irshad, S., Ellis, P., & Tutt, A. (2011). Molecular heterogeneity of triple-negative breast cancer and its clinical implications. Current Opinion in Oncology, 23(6), 566. doi:10.1097/CCO.0b013e32834bf8ae
   PubMed Web of Science ®Google Scholar
• Jiricny, J. (2006). The multifaceted mismatch-repair system. Nature Reviews Molecular Cell Biology, 7(5), 335–346. doi:10.1038/nrm1907
   PubMed Web of Science ®Google Scholar
• John, E. M., Hines, L. M., Phipps, A. I., Koo, J., Longacre, T. A., Ingles, S. A., … Wu, A. H. (2018). Reproductive history, breast-feeding and risk of triple negative breast cancer: The Breast Cancer Etiology in Minorities (BEM) study. International Journal of Cancer, 142(11), 2273–2285. doi:10.1002/ijc.31258
   PubMed Web of Science ®Google Scholar
• Kumar, A., Srivastava, G., Negi, A. S., & Sharma, A. (2019). Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β. Journal of Biomolecular Structure and Dynamics, 37(2), 275–290. doi:10.1080/07391102.2018.1426043
   PubMed Web of Science ®Google Scholar
• Lambrughi, M., Papaleo, E., Testa, L., Brocca, S., De Gioia, L., & Grandori, R. (2012). Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation. Frontiers in Physiology, 3, 435. https://doi.org/10.3389/fphys.2012.00435
   PubMed Web of Science ®Google Scholar
• Landrum, M. J., Lee, J. M., Riley, G. R., Jang, W., Rubinstein, W. S., Church, D. M., & Maglott, D. R. (2014). ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research, 42(D1), D980–D985. doi:10.1093/nar/gkt1113
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. doi:10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Li, X., Yang, J., Peng, L., Sahin, A. A., Huo, L., Ward, K. C., … Meisel, J. L. (2017). Triple-negative breast cancer has worse overall survival and cause-specific survival than non-triple-negative breast cancer. Breast Cancer Research and Treatment, 161(2), 279–287. doi:10.1007/s10549-016-4059-6
   PubMed Web of Science ®Google Scholar
• Lord, C. J., & Ashworth, A. (2012). The DNA Damage Response and Cancer Therapy. Nature, 481, 7381. doi:10.1038/nature10760
   Google Scholar
• Martin, S. A., McCabe, N., Mullarkey, M., Cummins, R., Burgess, D. J., Nakabeppu, Y., … Ashworth, A. (2010). DNA polymerases as potential therapeutic targets for cancers deficient in the DNA mismatch repair proteins MSH2 or MLH1. Cancer Cell, 17(3), 235–248. doi:10.1016/j.ccr.2009.12.046
   PubMed Web of Science ®Google Scholar
• Mersin, H., Yildirim, E., Berberoglu, U., & Gülben, K. (2008). The prognostic importance of triple negative breast carcinoma. Breast (Edinburgh, Scotland), 17(4), 341–346. doi:10.1016/j.breast.2007.11.031
   PubMed Web of Science ®Google Scholar
• Muthu, K., Panneerselvam, M., Jayaraman, M., Topno, N. S., Das, A. A., & Ramadas, K. (2012). Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies. Journal of Molecular Modeling, 18(11), 4865–4884. doi:10.1007/s00894-012-1489-x
   PubMed Web of Science ®Google Scholar
• Newman, L. A., Reis-Filho, J. S., Morrow, M., Carey, L. A., & King, T. A. (2015). The 2014 Society of Surgical Oncology Susan G. Komen for the Cure Symposium: Triple-negative breast cancer. Annals of Surgical Oncology, 22(3), 874–882. doi:10.1245/s10434-014-4279-0
   PubMed Web of Science ®Google Scholar
• Podo, F., Buydens, L. M. C., Degani, H., Hilhorst, R., Klipp, E., Gribbestad, I. S., … Børresen-Dale, A.-L. (2010). Triple-negative breast cancer: Present challenges and new perspectives. Molecular Oncology, 4(3), 209–229. doi:10.1016/j.molonc.2010.04.006
   PubMed Web of Science ®Google Scholar
• Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854. doi:10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Raghuraman, P., Jesu Jaya Sudan, R., Lesitha Jeeva Kumari, J., & Sudandiradoss, C. (2017a). Casting the critical regions in nucleotide binding oligomerization domain 2 protein: A signature mediated structural dynamics approach. Journal of Biomolecular Structure & Dynamics, 35(15), 1–19. https://doi.org/10.1080/07391102.2016.1254116
   PubMed Web of Science ®Google Scholar
• Raghuraman, P., Jesu Jaya Sudan, R., Lesitha Jeeva Kumari, J., & Sudandiradoss, C. (2017). Systematic prioritization of functional hotspot in RIG-1 domains using pattern based conventional molecular dynamic simulation. Life Sciences, 184, 58–70. doi:10.1016/j.lfs.2017.07.011
   PubMed Web of Science ®Google Scholar
• Raghuraman, P., & Sudandiradoss, C. (2018). R516Q mutation in Melanoma differentiation-associated protein 5 (MDA5) and its pathogenic role towards rare Singleton-Merten syndrome; a signature associated molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 37(3), 1–16. https://doi.org/10.1080/07391102.2018.1439770
   PubMed Web of Science ®Google Scholar
• Rakha, E. A., Reis-Filho, J. S., Baehner, F., Dabbs, D. J., Decker, T., Eusebi, V., … Ellis, I. O. (2010). Breast cancer prognostic classification in the molecular era: the role of histological grade. Breast Cancer Research, 12(4), 207. doi:10.1186/bcr2607
   Google Scholar
• Ramireddy, S., Raghuraman, P., Khandelwal, P., Abraham, J., & Sudandiradoss, C. (2018). A molecular simulation analysis of vitamin D targets interleukin 13 (IL13) as an alternative to mometasone in asthma. 3 Biotech, 8(8), 373. https://doi.org/10.1007/s13205-018-1394-9
   PubMedGoogle Scholar
• Roberts, M. E., Jackson, S. A., Susswein, L. R., Zeinomar, N., Ma, X., Marshall, M. L., … Chung, W. K. (2018). MSH6 and PMS2 germ-line pathogenic variants implicated in Lynch syndrome are associated with breast cancer. Genetics in Medicine: Official Journal of the American College of Medical Genetics, 20(10), 1167–1174. doi:10.1038/gim.2017.254
   Web of Science ®Google Scholar
• Smolarz, B., Makowska, M., Samulak, D., Michalska, M. M., & Romanowicz, H. (2015). Gly322Asp and Asn127Ser single nucleotide polymorphisms (SNPs) of hMSH2 mismatch repair gene and the risk of triple-negative breast cancer in Polish women. Familial Cancer, 14(1), 81–88. doi:10.1007/s10689-014-9746-z
   PubMed Web of Science ®Google Scholar
• Sridharan, U., Ragunathan, P., Spellerberg, B., & Ponnuraj, K. (2019). Molecular dynamics simulation of metal free structure of Lmb, a laminin-binding adhesin of Streptococcus agalactiae: metal removal and its structural implications. Journal of Biomolecular Structure and Dynamics, 37(3), 714–725. doi:10.1080/07391102.2018.1438923
   PubMed Web of Science ®Google Scholar
• Srinivasan, E., & Rajasekaran, R. (2017). Computational investigation of the human SOD1 mutant, Cys146Arg, that directs familial amyotrophic lateral sclerosis. Molecular Biosystems, 13(8), 1495–1503. doi:10.1039/C7MB00106A
   PubMedGoogle Scholar
• Srinivasan, E., & Rajasekaran, R. (2018). Comparative binding of kaempferol and kaempferide on inhibiting the aggregate formation of mutant (G85R) SOD1 protein in familial amyotrophic lateral sclerosis: A quantum chemical and molecular mechanics study. BioFactors, 44(5), 431–442. doi:10.1002/biof.1441
   PubMed Web of Science ®Google Scholar
• Srinivasan, E., & Rajasekaran, R. (2018b). Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein. Journal of Computer-Aided Molecular Design, 32(12), 1347–1361. doi:10.1007/s10822-018-0175-1
   PubMed Web of Science ®Google Scholar
• Srinivasan, E., & Rajasekaran, R. (2019). Effect of β-cyclodextrin-EGCG complexion against aggregated a-synuclein through density functional theory and discrete molecular dynamics. Chemical Physics Letters, 717, 38–46. doi:10.1016/j.cplett.2018.12.042
   Web of Science ®Google Scholar
• Stenson, P. D., Mort, M., Ball, E. V., Shaw, K., Phillips, A. D., & Cooper, D. N. (2014). The Human Gene Mutation Database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics, 133(1), 1–9. doi:10.1007/s00439-013-1358-4
   PubMed Web of Science ®Google Scholar
• Tan, D. S. P., Marchió, C., Jones, R. L., Savage, K., Smith, I. E., Dowsett, M., & Reis-Filho, J. S. (2008). Triple negative breast cancer: Molecular profiling and prognostic impact in adjuvant anthracycline-treated patients. Breast Cancer Research and Treatment, 111(1), 27–44. doi:10.1007/s10549-007-9756-8
   PubMed Web of Science ®Google Scholar
• Tina, K. G., Bhadra, R., & Srinivasan, N. (2007). PIC: Protein Interactions Calculator. Nucleic Acids Research, 35(Web Server)suppl_2), W473–W476. doi:10.1093/nar/gkm423
   PubMed Web of Science ®Google Scholar
• Wallner, B., & Elofsson, A. (2003). Can correct protein models be identified? Protein Science, 12(5), 1073–1086. doi:10.1110/ps.0236803
   PubMed Web of Science ®Google Scholar
• Wen, Y. H., Brogi, E., Zeng, Z., Akram, M., Catalano, J., Paty, P. B., … Shia, J. (2012). DNA mismatch repair deficiency in breast carcinoma: A pilot study of triple-negative and non-triple-negative tumors. The American Journal of Surgical Pathology, 36(11), 1700–1708. doi:10.1097/PAS.0b013e3182627787
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server)SUPPL.2), W407–W410. doi:10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Yip, Y. L., Famiglietti, M., Gos, A., Duek, P. D., David, F. P. A., Gateau, A., & Bairoch, A. (2008). Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Human Mutation, 29(3), 361–366. doi:10.1002/humu.20671
   PubMed Web of Science ®Google Scholar
• Yu, W., Clyne, M., Khoury, M. J., & Gwinn, M. (2010). Phenopedia and Genopedia: Disease-centered and gene-centered views of the evolving knowledge of human genetic associations. Bioinformatics, 26(1), 145–146. doi:10.1093/bioinformatics/btp618
   PubMed Web of Science ®Google Scholar
• Zarei, M., Nezafat, N., Rahbar, M. R., Negahdaripour, M., Sabetian, S., Morowvat, M. H., & Ghasemi, Y. (2019). Decreasing the immunogenicity of arginine deiminase enzyme via structure‐based computational analysis. Journal of Biomolecular Structure and Dynamics, 37(2), 523–536. doi:10.1080/07391102.2018.1431151
   PubMed Web of Science ®Google Scholar