Exploring the cause of the inhibitor 4AX attaching to binding site disrupting protein tyrosine phosphatase 4A1 trimerization by molecular dynamic simulation

References

• Abdolmaleki, A., Ghasemi, F., & Ghasemi, J. B. (2017). Computer-aided drug design to explore cyclodextrin therapeutics and biomedical applications. Chemical Biology & Drug Design, 89(2), 257–268. doi: 10.1111/cbdd.12825
   PubMed Web of Science ®Google Scholar
• Alvarez, H. A., McCarthy, A. N., & Grigera, J. R. (2012). A molecular dynamics approach to ligand–receptor interaction in the aspirin-human serum albumin complex. Journal of Biophysics, 2012, 1. doi: 10.1155/2012/642745
   Google Scholar
• Amadei, A., Linssen, A. B., de Groot, B. L., van Aalten, D. M., & Berendsen, H. J. (1996). An efficient method for sampling the essential subspace of proteins. Journal of Biomolecular Structure and Dynamics, 13(4), 615–625. doi: 10.1080/07391102.1996.10508874
   PubMed Web of Science ®Google Scholar
• Amitai, G., Shemesh, A., Sitbon, E., Shklar, M., Netanely, D., Venger, I., & Pietrokovski, S. (2004). Network analysis of protein structures identifies functional residues. Journal of Molecular Biology, 344(4), 1135–1146. doi: 10.1016/j.jmb.2004.10.055
   PubMed Web of Science ®Google Scholar
• Bai, Y., Yu, Z.-H., Liu, S., Zhang, L., Zhang, R.-Y., Zeng, L.-F., … Zhang, Z.-Y. (2016). Novel anticancer agents based on targeting the trimer interface of the PRL phosphatase. Cancer Research, 76(16), 4805–4815. doi: 10.1158/0008-5472.CAN-15-2323
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., & Hayward, S. (2000). Collective protein dynamics in relation to function. Current Opinion in Structural Biology, 10(2), 165–169.
   PubMed Web of Science ®Google Scholar
• Bhattacharyya, M., & Vishveshwara, S. (2010). Elucidation of the conformational free energy landscape in H. pylori LuxS and its implications to catalysis. BMC Structural Biology, 10(1), 27. doi: 10.1186/1472-6807-10-27
   PubMedGoogle Scholar
• Bosch, F. X., Ribes, J., Diaz, M., & Cleries, R. (2004). Primary liver cancer: Worldwide incidence and trends. Gastroenterology, 127(5), S5–S16. doi: 10.1053/j.gastro.2004.09.011
   PubMed Web of Science ®Google Scholar
• Carugo, O., & Djinovic-Carugo, K. (2013). Half a century of Ramachandran plots. Acta Crystallographica Section D Biological Crystallography, 69(8), 1333–1341. doi: 10.1107/S090744491301158X
   PubMedGoogle Scholar
• Cheng, F., Shen, J., Xu, X., Luo, X., Chen, K., Shen, X., & Jiang, H. (2009). Interaction models of a series of oxadiazole-substituted alpha-isopropoxy phenylpropanoic acids against PPARalpha and PPARgamma: Molecular modeling and comparative molecular similarity indices analysis studies. Protein & Peptide Letters, 16(2), 150–162. doi: 10.2174/092986609787316207
   PubMed Web of Science ®Google Scholar
• Chou, K. C., Wei, D. Q., & Zhong, W. Z. (2003). Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochemical and Biophysical Research Communications, 308(1), 148–151.
   PubMed Web of Science ®Google Scholar
• Das, A., & Mukhopadhyay, C. (2007). Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study. Journal of Chemical Physics, 127(16), 165103. doi: 10.1063/1.2796165
   PubMed Web of Science ®Google Scholar
• de Groot, B. L., Daura, X., Mark, A. E., & Grubmuller, H. (2001). Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. Journal of Molecular Biology, 309(1), 299–313. doi: 10.1006/jmbi.2001.4655
   PubMed Web of Science ®Google Scholar
• Diamond, R. H., Cressman, D. E., Laz, T. M., Abrams, C. S., & Taub, R. (1994). PRL-1, a unique nuclear protein tyrosine phosphatase, affects cell growth. Molecular and Cellular Biology, 14(6), 3752–3762. doi: 10.1128/MCB.14.6.3752
   PubMed Web of Science ®Google Scholar
• Dror, R. O., Dirks, R. M., Grossman, J. P., Xu, H., & Shaw, D. E. (2012). Biomolecular simulation: A computational microscope for molecular biology. Annual Review of Biophysics, 41(1), 429–452. doi: 10.1146/annurev-biophys-042910-155245
   PubMed Web of Science ®Google Scholar
• Fiordalisi, J. J., Keller, P. J., & Cox, A. D. (2006). PRL tyrosine phosphatases regulate rho family GTPases to promote invasion and motility. Cancer Research, 66(6), 3153–3161. doi: 10.1158/0008-5472.CAN-05-3116
   PubMed Web of Science ®Google Scholar
• Forner, A., Llovet, J. M., & Bruix, J. (2012). Hepatocellular carcinoma. Lancet, 379(9822), 1245–1255. doi: 10.1016/S0140-6736(11)61347-0
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. doi: 10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Grant, B. J., Rodrigues, A. P., ElSawy, K. M., McCammon, J. A., & Caves, L. S. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22(21), 2695–2696. doi: 10.1093/bioinformatics/btl461
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Jiao, Y., Ye, D. Z., Li, Z., Teta-Bissett, M., Peng, Y., Taub, R., … Kaestner, K. H. (2015). Protein tyrosine phosphatase of liver regeneration-1 is required for normal timing of cell cycle progression during liver regeneration. American Journal of Physiology-Gastrointestinal and Liver Physiology, 308(2), G85–G91. doi: 10.1152/ajpgi.00084.2014
   PubMed Web of Science ®Google Scholar
• Jin, S., Wang, K., Xu, K., Xu, J., Sun, J., Chu, Z., … Yin, D. (2014). Oncogenic function and prognostic significance of protein tyrosine phosphatase PRL-1 in hepatocellular carcinoma. Oncotarget, 5(11), 3685–3696. doi: 10.18632/oncotarget.1986
   PubMedGoogle Scholar
• Jin, W. Y., Ma, Y., Li, W. Y., Li, H. L., & Wang, R. L. (2018). Scaffold-based novel SHP2 allosteric inhibitors design using receptor–ligand pharmacophore model, virtual screening and molecular dynamics. Computational Biology and Chemistry, 73, 179–188. doi: 10.1016/j.compbiolchem.2018.02.004
   PubMed Web of Science ®Google Scholar
• Kadam, P. D., & Chuan, H. H. (2016). Erratum to: Rectocutaneous fistula with transmigration of the suture: A rare delayed complication of vault fixation with the sacrospinous ligament. International Urogynecology Journal, 27(3), 505. doi: 10.1007/s00192-016-2952-5
   PubMed Web of Science ®Google Scholar
• Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652. doi: 10.1038/nsb0902-646
   PubMedGoogle Scholar
• Khoddami, M., Nadri, H., Moradi, A., & Sakhteman, A. (2015). Homology modeling, molecular dynamic simulation, and docking based binding site analysis of human dopamine (D4) receptor. Journal of Molecular Modeling, 21(2), 36. doi: 10.1007/s00894-015-2579-3
   PubMed Web of Science ®Google Scholar
• Koska, J., Spassov, V. Z., Maynard, A. J., Yan, L., Austin, N., Flook, P. K., & Venkatachalam, C. M. (2008). Fully automated molecular mechanics based induced fit protein–ligand docking method. Journal of Chemical Information and Modeling, 48(10), 1965–1973. doi: 10.1021/ci800081s
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Open Source Drug Discovery, Consortium, & Lynn, A. (2014). g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. doi: 10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Larue, L., & Bellacosa, A. (2005). Epithelial–mesenchymal transition in development and cancer: Role of phosphatidylinositol 3' kinase/AKT pathways. Oncogene, 24(50), 7443–7454. doi: 10.1038/sj.onc.1209091
   PubMed Web of Science ®Google Scholar
• Lazo, J. S., McQueeney, K. E., Burnett, J. C., Wipf, P., & Sharlow, E. R. (2018). Small molecule targeting of PTPs in cancer. International Journal of Biochemistry & Cell Biology, 96, 171–181. doi: 10.1016/j.biocel.2017.09.011
   PubMed Web of Science ®Google Scholar
• Lewis, J. A., Mongan, J., McCammon, J. A., & Cohen, S. M. (2006). Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor. ChemMedChem, 1(7), 694–697. doi: 10.1002/cmdc.200600102
   PubMed Web of Science ®Google Scholar
• Li, C., Jiang, Y., Miao, R., Qu, K., Zhang, J., & Liu, C. (2018). MicroRNA-1271 functions as a metastasis and epithelial–mesenchymal transition inhibitor in human HCC by targeting the PTP4A1/c-Src axis. International Journal of Oncology, 52(2), 536–546. doi: 10.3892/ijo.2017.4224
   PubMed Web of Science ®Google Scholar
• Li, W. Y., Wei, H. Y., Sun, Y. Z., Zhou, H., Ma, Y., & Wang, R. L. (2018). Exploring the effect of E76K mutation on SHP2 cause gain-of-function activity by a molecular dynamics study. Journal of Cellular Biochemistry, 119(12), 9941–9956. doi: 10.1002/jcb.27316
   PubMed Web of Science ®Google Scholar
• Linse, B., & Linse, P. (2014). Tuning the smooth particle mesh Ewald sum: Application on ionic solutions and dipolar fluids. Journal of Chemical Physics, 141(18), 184114. doi: 10.1063/1.4901119
   PubMed Web of Science ®Google Scholar
• Ma, Y., Wang, S. Q., Xu, W. R., Wang, R. L., & Chou, K. C. (2012). Design novel dual agonists for treating type-2 diabetes by targeting peroxisome proliferator-activated receptors with core hopping approach. PLoS One, 7(6), e38546. doi: 10.1371/journal.pone.0038546
   PubMed Web of Science ®Google Scholar
• Martin, A. J., Vidotto, M., Boscariol, F., Di Domenico, T., Walsh, I., & Tosatto, S. C. (2011). RING: Networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics, 27(14), 2003–2005. doi: 10.1093/bioinformatics/btr191
   PubMed Web of Science ®Google Scholar
• Mehla, K., & Ramana, J. (2016). Travelers' diarrhea-associated enterotoxigenic Escherichia coli gyrA mutants and quinolone antibiotic affinity: A molecular dynamics simulation and residue interaction network analysis. OMICS, 20(11), 635–644. doi: 10.1089/omi.2016.0104
   PubMed Web of Science ®Google Scholar
• Miller, A., Carchman, R., Long, R., & Denslow, S. A. (2012). La Crosse viral infection in hospitalized pediatric patients in Western North Carolina. Hospital Pediatrics, 2(4), 235–242. doi: 10.1542/hpeds.2012-0022
   PubMedGoogle 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
• Ramachandran, G. N., & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Advances in Protein Chemistry, 23, 283–438.
   PubMedGoogle Scholar
• Saiz-Urra, L., Cabrera, M. A., & Froeyen, M. (2011). Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: Protein–ligand interactions in the light of the alanine scanning and free energy decomposition methods. Journal of Molecular Graphics and Modelling, 29(5), 726–739. doi: 10.1016/j.jmgm.2010.12.005
   PubMed Web of Science ®Google Scholar
• Schuttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(Pt 8), 1355–1363. doi: 10.1107/S0907444904011679
   PubMedGoogle Scholar
• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., … Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504. doi: 10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Sun, J. P., Luo, Y., Yu, X., Wang, W. Q., Zhou, B., Liang, F., & Zhang, Z. Y. (2007). Phosphatase activity, trimerization, and the C-terminal polybasic region are all required for PRL1-mediated cell growth and migration. Journal of Biological Chemistry, 282(39), 29043–29051. doi: 10.1074/jbc.M703537200
   PubMed Web of Science ®Google Scholar
• Sun, J.-P., Wang, W.-Q., Yang, H., Liu, S., Liang, F., Fedorov, A. A., … Zhang, Z.-Y. (2005). Structure and biochemical properties of PRL-1, a phosphatase implicated in cell growth, differentiation, and tumor invasion. Biochemistry, 44(36), 12009–12021. doi: 10.1021/bi0509191
   PubMed Web of Science ®Google Scholar
• Swaminathan, S., Harte, W. E., & Beveridge, D. L. (1991). Investigation of domain structure in proteins via molecular dynamics simulation: Application to HIV-1 protease dimer. Journal of the American Chemical Society, 113(7), 2717–2721. doi: 10.1021/ja00007a054
   Web of Science ®Google Scholar
• Tung-Ping Poon, R., Fan, S. T., & Wong, J. (2000). Risk factors, prevention, and management of postoperative recurrence after resection of hepatocellular carcinoma. Annals of Surgery, 232(1), 10–24. doi: 10.1097/00000658-200007000-00003
   PubMed Web of Science ®Google Scholar
• Upadhyay, S. K. (2014). Dynamics of Gal80p in the Gal80p–Gal3p complex differ significantly from the dynamics in the Gal80p–Gal1p complex: Implications for the higher specificity of Gal3p. Molecular BioSystems, 10(12), 3120–3129. doi: 10.1039/C4MB00371C
   PubMedGoogle Scholar
• Wang, N., Jiang, J., Li, X., Tan, H., Zheng, J., Chen, G., & Jia, Z. (2015). Molecular dynamics simulation studies of dTTP binding and catalysis mediated by YhdE dimerization. PLoS One, 10(8), e0134879. doi: 10.1371/journal.pone.0134879
   PubMed Web of Science ®Google Scholar
• Werner, S. R., Lee, P. A., DeCamp, M. W., Crowell, D. N., Randall, S. K., & Crowell, P. L. (2003). Enhanced cell cycle progression and down regulation of p21(Cip1/Waf1) by PRL tyrosine phosphatases. Cancer Letters, 202(2), 201–211. doi: 10.1016/S0304-3835(03)00517-2
   PubMed Web of Science ®Google Scholar
• Yoon, J., Blumer, A., & Lee, K. (2006). An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality. Bioinformatics, 22(24), 3106–3108. doi: 10.1093/bioinformatics/btl533
   PubMed Web of Science ®Google Scholar
• Zeng, Q., Dong, J.-M., Guo, K., Li, J., Tan, H.-X., Koh, V., … Hong, W. (2003). PRL-3 and PRL-1 promote cell migration, invasion, and metastasis. Cancer Research, 63(11), 2716–2722.
   PubMed Web of Science ®Google Scholar
• Zhou, Y., Zhang, N., Chen, W., Zhao, L., & Zhong, R. (2016). Underlying mechanisms of cyclic peptide inhibitors interrupting the interaction of CK2alpha/CK2beta: Comparative molecular dynamics simulation studies. Physical Chemistry Chemical Physics, 18(13), 9202–9210. doi: 10.1039/C5CP06276D
   PubMed Web of Science ®Google Scholar