Molecular Docking on Recomposed versus Crystallographic Structures of Zn-Dependent Enzymes and their Natural Inhibitors
Matrix metalloproteinases (MMP) are a class of
structural and functional related enzymes involved in altering the
natural elements of the extracellular matrix. Most of the MMP
structures are cristalographycally determined and published in
WorldWide ProteinDataBank, isolated, in full structure or bound to
natural or synthetic inhibitors. This study proposes an algorithm to
replace missing crystallographic structures in PDB database. We
have compared the results of a chosen docking algorithm with a
known crystallographic structure in order to validate enzyme sites
reconstruction there where crystallographic data are missing.
[1] S.D. Shapiro A concise yet informative stroll through matrix
metalloproteinases and TIMPs, J Cell Sci., 2000, 113:19,3355-3356.
[2] J.F. Woessner Jr., Matrix metalloproteinase inhibition. From the
Jurassic to the third millennium, 1999, Ann N Y Acad Sci., 30, 878,
pp.388-403, June 1999.
[3] K. Brew, D. Dinakarpandian, H. Nagase, Tissue inhibitors of
metalloproteinases: evolution, structure and function, Biochim Biophys
Acta, 2000, 1477, 1-2.
[4] L. Fang, F. Huber-Abel, M. Teuchert, C. Hendrich, J. Dorst, D.
Schattauer, H. Zettlmeissel, M. Wlaschek, K. Scharffetter-Kochanek, H.
Tumani, A.C. Ludolph, J. Brettschneider, Linking neuron and skin:
Matrix metalloproteinases in amyotrophic lateral sclerosis (ALS), J
Neurol Sci. 2009, e-pub.
[5] B.F. Ribeiro, D.P. Iglesias, G.J. Nascimento, H.C. Galvão, A.M.
Medeiros, R.A. Freitas, Immunoexpression of MMPs-1, -2, and -9 in
ameloblastoma and odontogenic adenomatoid tumor, Oral Dis., 2009, epub.
[6] E. Korpos, C. Wu, L. Sorokin, Multiple roles of the extracellular matrix
in inflammation, Curr Pharm Des., 2009, 15:12, 1349-57.
[7] A. Ando, Y. Hagiwara, M. Tsuchiya, Y. Onoda, H. Suda, E. Chimoto, E.
Itoi, Increased expression of metalloproteinase-8 and -13 on articular
cartilage in a rat immobilized knee model, Tohoku J Exp Med., 2009,
217:4, 27127-8.
[8] B. Gentner, A. Wein, R.S. Croner, I. Zeittraeger, R.M. Wirtz, F. Roedel,
A. Dimmler, L. Dorlaque, W. Hohenberger, E. G. Hahn, W.M. Brueckl,
Differences in the gene expression profile of matrix metalloproteinases
(MMPs) and their inhibitors (TIMPs) in primary colorectal tumors and
their synchronous liver metastases, Anticancer Res., 2009, 29:1, 67-74.
[9] V.P. Rajeshwar, H. Corwin, Matrix metalloproteinases (MMPs)
Chemical-biological functions and (Q)SARs, Bioorganic & Medicinal
Chemistry, 2007, 15:6, 2223-2268.
[10] B. Lovejoy, A. Cleasby, A.M. Hassell, K. Longley, M.A. Luther, D.
Weigl, G. McGeehan, A.B. McElroy, D. Drewry, M.H. Lambert, S.R.
Jorden, Structural Analysis of the Catalytic Domain of Human
Fibroblast Collagenase, Science, 1994, 263, 375.
[11] E. Morgunova, A. Tuuttila, U. Bergmann, K. Tryggvason, Structural
insight into the complex formation of latent matrix metalloproteinase 2
with tissue inhibitor of metalloproteinase 2. Proc Natl Acad Sci U S A.
2002, 28;99(11):7414-9.
[12] H.M. Berman, K. Henrick, H. Nakamura, Announcing the worldwide
Protein Data Bank Nature Structural Biology, 2003, 10 (12): 98
[13] W. Humphrey, A. Dalke, . K. Schulten, VMD - Visual Molecular
Dynamics, J. Molec. Graphics, 1996, 14: 33-38
[1] S.D. Shapiro A concise yet informative stroll through matrix
metalloproteinases and TIMPs, J Cell Sci., 2000, 113:19,3355-3356.
[2] J.F. Woessner Jr., Matrix metalloproteinase inhibition. From the
Jurassic to the third millennium, 1999, Ann N Y Acad Sci., 30, 878,
pp.388-403, June 1999.
[3] K. Brew, D. Dinakarpandian, H. Nagase, Tissue inhibitors of
metalloproteinases: evolution, structure and function, Biochim Biophys
Acta, 2000, 1477, 1-2.
[4] L. Fang, F. Huber-Abel, M. Teuchert, C. Hendrich, J. Dorst, D.
Schattauer, H. Zettlmeissel, M. Wlaschek, K. Scharffetter-Kochanek, H.
Tumani, A.C. Ludolph, J. Brettschneider, Linking neuron and skin:
Matrix metalloproteinases in amyotrophic lateral sclerosis (ALS), J
Neurol Sci. 2009, e-pub.
[5] B.F. Ribeiro, D.P. Iglesias, G.J. Nascimento, H.C. Galvão, A.M.
Medeiros, R.A. Freitas, Immunoexpression of MMPs-1, -2, and -9 in
ameloblastoma and odontogenic adenomatoid tumor, Oral Dis., 2009, epub.
[6] E. Korpos, C. Wu, L. Sorokin, Multiple roles of the extracellular matrix
in inflammation, Curr Pharm Des., 2009, 15:12, 1349-57.
[7] A. Ando, Y. Hagiwara, M. Tsuchiya, Y. Onoda, H. Suda, E. Chimoto, E.
Itoi, Increased expression of metalloproteinase-8 and -13 on articular
cartilage in a rat immobilized knee model, Tohoku J Exp Med., 2009,
217:4, 27127-8.
[8] B. Gentner, A. Wein, R.S. Croner, I. Zeittraeger, R.M. Wirtz, F. Roedel,
A. Dimmler, L. Dorlaque, W. Hohenberger, E. G. Hahn, W.M. Brueckl,
Differences in the gene expression profile of matrix metalloproteinases
(MMPs) and their inhibitors (TIMPs) in primary colorectal tumors and
their synchronous liver metastases, Anticancer Res., 2009, 29:1, 67-74.
[9] V.P. Rajeshwar, H. Corwin, Matrix metalloproteinases (MMPs)
Chemical-biological functions and (Q)SARs, Bioorganic & Medicinal
Chemistry, 2007, 15:6, 2223-2268.
[10] B. Lovejoy, A. Cleasby, A.M. Hassell, K. Longley, M.A. Luther, D.
Weigl, G. McGeehan, A.B. McElroy, D. Drewry, M.H. Lambert, S.R.
Jorden, Structural Analysis of the Catalytic Domain of Human
Fibroblast Collagenase, Science, 1994, 263, 375.
[11] E. Morgunova, A. Tuuttila, U. Bergmann, K. Tryggvason, Structural
insight into the complex formation of latent matrix metalloproteinase 2
with tissue inhibitor of metalloproteinase 2. Proc Natl Acad Sci U S A.
2002, 28;99(11):7414-9.
[12] H.M. Berman, K. Henrick, H. Nakamura, Announcing the worldwide
Protein Data Bank Nature Structural Biology, 2003, 10 (12): 98
[13] W. Humphrey, A. Dalke, . K. Schulten, VMD - Visual Molecular
Dynamics, J. Molec. Graphics, 1996, 14: 33-38
@article{"International Journal of Biological, Life and Agricultural Sciences:60046", author = "Tudor Petreuş and Andrei Neamţu and Cristina Dascălu and Paul Dan Sîrbu and Carmen E. Cotrutz", title = "Molecular Docking on Recomposed versus Crystallographic Structures of Zn-Dependent Enzymes and their Natural Inhibitors", abstract = "Matrix metalloproteinases (MMP) are a class of
structural and functional related enzymes involved in altering the
natural elements of the extracellular matrix. Most of the MMP
structures are cristalographycally determined and published in
WorldWide ProteinDataBank, isolated, in full structure or bound to
natural or synthetic inhibitors. This study proposes an algorithm to
replace missing crystallographic structures in PDB database. We
have compared the results of a chosen docking algorithm with a
known crystallographic structure in order to validate enzyme sites
reconstruction there where crystallographic data are missing.", keywords = "matrix metalloproteinases, molecular docking, structure superposition, surface complementarity.", volume = "4", number = "8", pages = "617-4", }
