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Research Article

Computational insights into the interaction mechanism of transcription cofactor vestigial-like protein 4 binding to TEA domain transcription factor 4 by molecular dynamics simulation and molecular mechanics generalized Born/surface area) calculation

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Pages 2538-2545 | Received 11 Nov 2017, Accepted 06 Jun 2018, Published online: 09 Nov 2018

References

  • Avruch, J., Zhou, D., & Bardeesy, N. (2012). YAP oncogene overexpression supercharges colon cancer proliferation. Cell Cycle, 11, 1090–1096.
  • Bae, J. S., Kim, S. M., & Lee, H. (2017). The Hippo signaling pathway provides novel anti-cancer drug targets. Oncotarget, 8, 16084–16098.
  • 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, 235–242.
  • Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668–1688.
  • Chen, F., Liu, H., Sun, H., Pan, P., Li, Y., Li, D., & Hou, T. (2016). Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking. Physical Chemistry Chemical Physics, 18, 22129–22139.
  • 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.
  • Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., … Kollman, 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.
  • Ehmer, U., & Sage, J. (2016). Control of proliferation and cancer growth by the Hippo signaling pathway. Molecular Cancer Research, 14, 127.
  • Felley-Bosco, E., & Stahel, R. (2014). Hippo/YAP pathway for targeted therapy. Translational Lung Cancer Research, 3, 75–83.
  • Halder, G., & Johnson, R. L. (2011). Hippo signaling: Growth control and beyond. Development, 138, 9–22.
  • Harvey, K., & Tapon, N. (2007). The Salvador-Warts-Hippo pathway – An emerging tumour-suppressor network. Nature Reviews Cancer, 7, 182–191.
  • Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry, 32, 866–877.
  • Jiao, S., Wang, H., Shi, Z., Dong, A., Zhang, W., Song, X., … Zhou, Z. (2014). A peptide mimicking VGLL4 function acts as a YAP antagonist therapy against gastric cancer. Cancer Cell, 25, 166–180.
  • 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.
  • Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., … Cheatham, T. E., 3rd (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33, 889–897.
  • Li, C., Yang, D., Cao, X., Wang, F., Jiang, H., Guo, H., … Yin, X. (2016). LFG-500, a newly synthesized flavonoid, attenuates lipopolysaccharide-induced acute lung injury and inflammation in mice. Biochemical Pharmacology, 113, 57–69.
  • Li, N., Yu, N., Wang, J., Xi, H., Lu, W., Xu, H., … Liu, H. (2015). miR-222/VGLL4/YAP-TEAD1 regulatory loop promotes proliferation and invasion of gastric cancer cells. American Journal of Cancer Research, 5, 1158–1168.
  • Nagashima, S., Bao, Y. & Hata, Y. (2017). The Hippo pathway as drug targets in cancer therapy and regenerative medicine. Current Drug Targets, 18, 447–454.
  • Onufriev, A., Bashford, D. & Case, D. A. (2004). Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins, 55, 383–394.
  • Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.
  • 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, 22035–22045.
  • 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, 16719–16729.
  • SYBYL_X2.1 is available from Tripos Associates Inc., S. H. R., St. Louis, MO 631444, USA.
  • 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.
  • Xu, L., Sun, H., Li, Y., Wang, J. & Hou, T. (2013). Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models. The Journal of Physical Chemistry B, 117, 8408–8421.
  • Yang, J., Li, C., Ding, L., Guo, Q., You, Q. & Jin, S. (2012). Gambogic acid deactivates cytosolic and mitochondrial thioredoxins by covalent binding to the functional domain. Journal of Natural Products, 75, 1108–1116.
  • Ye, S., & Eisinger-Mathason, T. S. (2016). Targeting the Hippo pathway: Clinical implications and therapeutics. Pharmacological Research, 103, 270–278.
  • Zeng, Q., & Hong, W. (2008). The emerging role of the hippo pathway in cell contact inhibition, organ size control, and cancer development in mammals. Cancer Cell, 13, 188–192.
  • Zhang, W., Gao, Y., Li, P., Shi, Z., Guo, T., Li, F., … Ji, H. (2014). VGLL4 functions as a new tumor suppressor in lung cancer by negatively regulating the YAP-TEAD transcriptional complex. Cell Research 24, 331–343.
  • Zhang, Y., Shen, H., Withers, H. G., Yang, N., Denson, K. E., Mussell, A. L., … Zhang, J. (2017). VGLL4 selectively represses YAP-dependent gene induction and tumorigenic phenotypes in breast cancer. Scientific Reports 7, 6190.

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