Comparative analysis of binding sites of human meprins with hydroxamic acid derivative by molecular dynamics simulation study

Acknowledgments

References

• Abramowitz, N., Schechter, I., & Berger, A. (1967). On the size of the active site in proteases. II. Carboxypeptidase-A. Biochemical and Biophysical Research Communications, 29, 862–867.
   PubMed Web of Science ®Google Scholar
• Accelrys Discovery Studio Visualiser v 3.5.0.12158, San Diego: Accelrys Software Inc.
   Google Scholar
• Bella, J., & Humphries, M. J. (2005). Calpha-H...O=C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions. BMC Structural Biology, 5: 4.
   PubMed Web of Science ®Google Scholar
• Bode, W., Gomis-Rüth, F. X., Huber, R., Zwilling, R.,& Stöcker, W. (1992). Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases. Nature, 358, 164–167.
   PubMed Web of Science ®Google Scholar
• Bode, W., Reinemer, P., Huber, R., Kleine, T., Schnierer, S., & Tschesche, H. (1994). The X-ray crystal structure of the catalytic domain of human neutrophil collagenase inhibited by a substrate analogue reveals the essentials for catalysis and specificity. EMBO Journal, 13, 1263–1269.
   PubMed Web of Science ®Google Scholar
• Bond, J. S., & Beynon, R. B. (1995). The astacin family of metalloendopeptidases. Protein Science, 4, 1247–1261.
   PubMed Web of Science ®Google Scholar
• Broder, C., & Becker-Pauly, C. (2013). The metalloproteases meprin α and meprin β: unique enzymes in inflammation, neurodegeneration, cancer and fibrosis. Biochemistry Journal, 450, 253–264.
   PubMed Web of Science ®Google Scholar
• Brunger, A., Brooks III, C. L., & Karplus, M. (1984). Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chemical Physics Letters, 105, 495–500.
   Web of Science ®Google Scholar
• Dumermuth, E., Sterchi, E. E., Jiang, W. P, Wolz, R. L., Bond, J. S., Flannery, A. V., & Beynon, R. J. (1991). The astacin family of metalloendopeptidases. Journal of Biological Chemistry, 266, 21381–21385.
   PubMed Web of Science ®Google Scholar
• Durham, E., Dorr, B., Woetzel, N., Staritzbichler, R., & Meiler, J. (2009). Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Journal of Molecular Modeling, 15, 1093–1108.
   PubMed Web of Science ®Google Scholar
• Eman, M. D., Amr, H. M., Mohamed, S. A. E., Ahmed, H. El-K., Michael, W. L., & Khaled, A. A. (2012). Applying ligands profiling using multiple extended electron distribution based field templates and feature trees similarity searching in the discovery of new generation of urea-based antineoplastic kinase inhibitors. PLoS ONE, 7, e49284.
   PubMed Web of Science ®Google Scholar
• Feller, S. E., & Mackerell, A. D. (2000). An improved empirical potential energy function for molecular simulations of phospholipids. Journal of Physical Chemistry B, 104, 7510–7515.
   Web of Science ®Google Scholar
• Grams, F., Dive, V., Yiotakis, A., Yiallouros, I., Vassiliou, S., Zwilling, R., …, Stocker, W. (1996). Structure of astacin with a transition-state analogue inhibitor. Naturel Structural Biology, 3, 671–675.
   PubMedGoogle Scholar
• Hopkins, D. R., Keles, S., & Greenspan, D. S. (2007). The bone morphogenetic protein 1/Tolloid-like metalloproteinases. Matrix Biology, 26, 508–523.
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926–935.
   Web of Science ®Google Scholar
• Kessler, E., Takahara, K., Biniamov, L., Brusel, M., & Greenspan, D. S. (1996). Bone morphogenetic protein-1: the type I procollagen C-proteinase Science, 271, 360–362.
   PubMed Web of Science ®Google Scholar
• Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., … Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948.
   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, 283–291.
   Web of Science ®Google Scholar
• Mackerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D. … Karplu, M. (1998). All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. Journal of Physical Chemistry B, 102, 3586–3616.
   PubMed Web of Science ®Google Scholar
• Marti-Renom, M. A., Stuart, A., Fiser, A., Sanchez, R., Melo, F., & A., Sali (2000). Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29, 291–325.
   PubMedGoogle Scholar
• Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins: Structure, Function and Genetics, 12, 345–364.
   PubMed Web of Science ®Google Scholar
• Quesada, V., Sanchez, L. M., Alvarez, J., & Lopez-Otin, C. (2004). Identification and characterization of human and mouse ovastacin: A novel metalloproteinase similar to hatching enzymes from arthropods, birds, amphibians, and fish. Journal of Biological Chemistry, 279, 26627–26634.
   PubMed Web of Science ®Google Scholar
• Rawling, N. D., & Barrett, A. J. (1995). Evolutionary families of metallopeptidases. Methods in Enzymology, 248, 183–228.
   PubMedGoogle Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian Equations of Motion of a System with Constraints. Journal of Computational Physics, 23, 327–341.
   Web of Science ®Google Scholar
• Sali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234, 779–815.
   PubMed Web of Science ®Google Scholar
• Schechter, I., & Berger, A. (1967). On the size of the active site in proteases. I. Papain. Biochemical and Biophysical Research Communications, 27, 157–162.
   PubMed Web of Science ®Google Scholar
• Stocker, W., Gomis-Ruth, F. X., Bode, W., & Zwilling, R. (1993). Implications of the three-dimensional structure of astacin for the structure and function of the astacin family of zinc-endopeptidases. European Journal of Biochemistry, 214, 215–231.
   PubMedGoogle Scholar
• Stocker, W., Wolz, R. L., Zwilling, R., Strydom, D. J., & Auld, D. S. (1988). Astacus protease - a zinc metalloenzyme. Biochemistry, 27, 5026–5032.
   Google Scholar
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673–4680.
   PubMed Web of Science ®Google Scholar
• Titani, K., Torff, H. J, Hormel, S., Kumar, S., Walsh, K. A., Rödl, J., … Zwilling, R. (1987). Amino acid sequence of a unique protease from the crayfish Astacus fluviatilis. Biochemistry, 26, 222–226.
   PubMed Web of Science ®Google Scholar
• Xu, D., Tsai, C. J., & Nussinov, R. (1997). Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engineering, 10, 999–1012.
   PubMedGoogle Scholar