The substitutions G245C and G245D in the Zn2+-binding pocket of the p53 protein result in differences of conformational flexibility of the DNA-binding domain

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 1, 2013, Pages 78-86

  Pintus, S S ^a   Ivanisenko, N V ^a   Demenkov, P S ^a   Ivanisenko, T V ^a   Ramachandran, S ^b   Kolchanov, N A ^a   Ivanisenko, V A ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

Binding site; Conformational flexibility; DNA binding domain (DBD); Molecular dynamics; P53 protein

Indexed keywords

MUTANT PROTEIN; PROTEIN P53; ZINC ION;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BETA SHEET; BINDING SITE; COMPLEX FORMATION; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA BINDING MOTIF; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN TERTIARY STRUCTURE; QUANTUM MECHANICS; STATISTICAL ANALYSIS; WILD TYPE;

AMINO ACID SUBSTITUTION; BINDING SITES; CARRIER PROTEINS; DNA; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN CONFORMATION; TUMOR SUPPRESSOR PROTEIN P53; ZINC;

EID: 84871254738     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.691364     Document Type: Conference Paper

References (33)

1. Alsner, J., Jensen, V., Kyndi, M., Offersen, B.V., Vu, P., Børresen-Dale, A.L., & Overgaard, J. (2008). A comparison between p53 accumulation determined by immunohistochemistry and TP53 mutations as prognostic variables in tumours from breast cancer patients. Acta Oncologica, 47, 600-607.
2. Amariglio, F., Tchang, F., Prioleau, M.N., Soussi, T., Cibert, C., & Méchali, M. (1997). A functional analysis of p53 during early development of Xenopus laevis. Oncogene, 18, 2191-2199.
3. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., & Haak, J.R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684-3690.
4. Butler, J.S., & Loh, S.N. (2003). Structure, function, and aggregation of the zinc-free form of the p53 DNA binding domain. Biochemistry, 42, 2396-2403.
5. Coi, A., Tonelli, M., Ganadu, M.L., & Bianucci, A.M. (2006). Binding free energy calculations of adenosine deaminase inhibitors. Bioorganic & Medicinal Chemistry, 14, 2636-2641.
6. Donehower, L.A. (1997). Genetic instability in animal tumorigenesis models. Cancer surveys, 29, 329-352.
7. Duan, J., & Nilsson, L. (2006). Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain. Biochemistry, 45, 7483-7492.
8. Esmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., & Pedersen, L.G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103, 8577-8592.
9. Ewald, P.P. (1921). The calculation of optical and electrostatic lattice potentials. Annalen der Physik, 64, 253-287.
10. Hainaut, P., & Mann, K. (2001). Zinc binding and redox control of p53 structure and function. Antioxidants & Redox Signaling, 3, 611-623.
11. Hess, B., Bekker, H., Berendsen, H.J.C., & Fraaije, J.G.E.M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463-1472.
12. Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, loadbalanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435-447.
13. Ivanisenko, V.A., Pintus, S.S., Grigorovich, D.A., & Kolchanov, N.A. (2004). PDBSiteScan: A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Research, 32, W549-W554.
14. Ivanisenko, V.A., Pintus, S.S., Grigorovich, D.A., & Kolchanov, N.A. (2005). PDBSite: A database of the 3D structure of protein functional sites. Nucleic Acids Research, 33, D183-D187.
15. Jorgensen, W., Chandrasekhar, J., Madura, J., Impey, R., & Klein, M. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926-935.
16. Jorgensen, W., Maxwell, D., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-Atom force field on conformational energetics and properties of organic liquids. Journal of American Chemical Society, 118, 11225-11236.
17. Jorgensen, W., & Tirado-Rives, J. (1988). The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of American Chemical Society, 110, 1657-1666.
18. Khazanov, N., & Levy, Y. (2011). Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-Talks between its constituent domains. Journal of molecular biology, 408, 335-355.
19. Levine, A.J. (1997). P53, the cellular gatekeeper for growth and division. Cell, 88, 323-331.
20. Lu, Q., Tan, Y.H., & Luo, R. (2007). Molecular dynamics simulations of p53 DNA-binding domain. The Journal of Physical Chemistry B, 111, 11538-11545.
21. Malkin, D., Li, F.P., Strong, L.C., Fraumeni, J.F. Jr, Nelson, C. E., Kim, D.H. Tainsky, M.A. (1990). Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science, 250, 1233-1238.
22. Méplan, C., Richard, M.J., & Hainaut, P. (2000a). Metalloregulation of the tumor suppressor protein p53: Zinc mediates the renaturation of p53 after exposure to metal chelators in vitro and in intact cells. Oncogene, 19, 5227-5236.
23. Méplan, C., Richard, M.J., & Hainaut, P. (2000b). Redox signalling and transition metals in the control of the p53 pathway. Biochemical Pharmacology, 59, 25-33.
24. Merabet, A., Houlleberghs, H., Maclagan, K., Akanho, E., Bui, T.T., Pagano, B.,Nikolova, P.V. (2010). Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: Structural and biochemical insights. Biochemical Journal, 427, 225-236.
25. Olivier, M., Langerød, A., Carrieri, P., Bergh, J., Klaar, S., Eyfjord, J.,Børresen-Dale, A.L. (2006). The clinical value of somatic TP53 gene mutations in 1,794 patients with breast cancer. Clinical Cancer Research, 12, 1157-1167.
26. Pavletich, N.P., Chambers, K.A., & Pabo, C.O. (1993). The DNA-binding domain of p53 contains the four conserved regions and the major mutation hot spots. Genes & Development, 7, 2556-2564.
27. Pintus, S.S., Fomin, E.S., Ivanisenko, V.A., & Kolchanov, N.A. (2006). Phylogenetic analysis of the family of p53. Biofizika, 51, 640-649.
28. Pintus, S.S., Fomin, E.S., Oshurkov, I.S., & Ivanisenko, V.A. (2007). Phylogenetic analysis of the p53 and p63/p73 gene families. In Silico Biology, 7, 319-332.
29. Prochazkova, J., Lichnovsky, V., Kylarova, D., Erdosova, B., & Vranka, P. (2004). Involvement of p53 and Bcl-2 family proteins in regulating programmed cell death and proliferation in human embryogenesis. General Physiology and Biophysics, 23, 209-229.
30. Rainwater, R., Parks, D., Anderson, M.E., Tegtmeyer, P., & Mann, K. (1995). Role of cysteine residues in regulation of p53 function. Molecular and Cellular Biology, 15, 3892-3903.
31. Schwede, T., Kopp, J., Guex, N., & Peitsch, M.C. (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research, 31, 3381-3385.
32. van Slooten, H.J., van De Vijver, M.J., Borresen, A.L., Eyfjörd, J.E., Valgardsdóttir, R., Scherneck, S.,Van Dierendonck, J.H. (1999). Mutations in exons 5-8 of the p53 gene, independent of their type and location, are associated with increased apoptosis and mitosis in invasive breast carcinoma. The Journal of Pathology, 189, 504-513.
33. Verhaegh, G.W., Parat, M.O., Richard, M.J., & Hainaut, P. (1998). Modulation of p53 protein conformation and DNA-binding activity by intracellular chelation of zinc. Molecular Carcinogenesis, 21, 205-214.