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

References

• Alsner , J. , Jensen , V. , Kyndi , M. , Offersen , B.V. , Vu , P. , Børresen-Dale , A.L. and 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 .
   PubMed Web of Science ®Google Scholar
• Amariglio , F. , Tchang , F. , Prioleau , M.N. , Soussi , T. , Cibert , C. and Méchali , M. 1997 . A functional analysis of p53 during early development of Xenopus laevis . Oncogene , 18 : 2191 – 2199 .
   Google Scholar
• Berendsen , H.J.C. , Postma , J.P.M. , van Gunsteren , W.F. and Haak , J.R. 1984 . Molecular dynamics with coupling to an external bath . Journal of Chemical Physics , 81 : 3684 – 3690 .
   Web of Science ®Google Scholar
• Butler , J.S. and Loh , S.N. 2003 . Structure, function, and aggregation of the zinc-free form of the p53 DNA binding domain . Biochemistry , 42 : 2396 – 2403 .
   PubMed Web of Science ®Google Scholar
• Coi , A. , Tonelli , M. , Ganadu , M.L. and Bianucci , A.M. 2006 . Binding free energy calculations of adenosine deaminase inhibitors . Bioorganic & Medicinal Chemistry , 14 : 2636 – 2641 .
   PubMedGoogle Scholar
• Donehower , L.A. 1997 . Genetic instability in animal tumorigenesis models . Cancer surveys , 29 : 329 – 352 .
   PubMedGoogle Scholar
• Duan , J. and Nilsson , L. 2006 . Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain . Biochemistry , 45 : 7483 – 7492 .
   PubMedGoogle Scholar
• Esmann , U. , Perera , L. , Berkowitz , M.L. , Darden , T. , Lee , H. and Pedersen , L.G. 1995 . A smooth particle mesh Ewald method . Journal of Chemical Physics , 103 : 8577 – 8592 .
   Web of Science ®Google Scholar
• Ewald , P.P. 1921 . The calculation of optical and electrostatic lattice potentials . Annalen der Physik , 64 : 253 – 287 .
   Web of Science ®Google Scholar
• Hainaut , P. and Mann , K. 2001 . Zinc binding and redox control of p53 structure and function . Antioxidants & Redox Signaling , 3 : 611 – 623 .
   PubMed Web of Science ®Google Scholar
• Hess , B. , Bekker , H. , Berendsen , H.J.C. and Fraaije , J.G.E.M. 1997 . LINCS: A linear constraint solver for molecular simulations . Journal of Computational Chemistry , 18 : 1463 – 1472 .
   Web of Science ®Google Scholar
• Hess , B. , Kutzner , C. , van der Spoel , D. and Lindahl , E. 2008 . GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation . Journal of Chemical Theory and Computation , 4 : 435 – 447 .
   PubMed Web of Science ®Google Scholar
• Ivanisenko , V.A. , Pintus , S.S. , Grigorovich , D.A. and 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 .
   PubMedGoogle Scholar
• Ivanisenko , V.A. , Pintus , S.S. , Grigorovich , D.A. and Kolchanov , N.A. 2005 . PDBSite: A database of the 3D structure of protein functional sites . Nucleic Acids Research , 33 : D183 – D187 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , W. , Chandrasekhar , J. , Madura , J. , Impey , R. and Klein , M. 1983 . Comparison of simple potential functions for simulating liquid water . Journal of Chemical Physics , 79 : 926 – 935 .
   Web of Science ®Google Scholar
• Jorgensen , W. , Maxwell , D. and 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 .
   Web of Science ®Google Scholar
• Jorgensen , W. and 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 .
   PubMed Web of Science ®Google Scholar
• Khazanov , N. and 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 .
   PubMedGoogle Scholar
• Levine , A.J. 1997 . P53, the cellular gatekeeper for growth and division . Cell , 88 : 323 – 331 .
   PubMed Web of Science ®Google Scholar
• Lu , Q. , Tan , Y.H. and Luo , R. 2007 . Molecular dynamics simulations of p53 DNA-binding domain . The Journal of Physical Chemistry B , 111 : 11538 – 11545 .
   PubMed Web of Science ®Google Scholar
• Malkin , D. , Li , F.P. , Strong , L.C. , Fraumeni , J.F. Jr , Nelson , C.E. , Kim , D.H. , … and Tainsky , M.A. 1990 . Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms . Science , 250 : 1233 – 1238 .
   PubMed Web of Science ®Google Scholar
• Méplan , C. , Richard , M.J. and 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 .
   PubMed Web of Science ®Google Scholar
• Méplan , C. , Richard , M.J. and Hainaut , P. 2000b . Redox signalling and transition metals in the control of the p53 pathway . Biochemical Pharmacology , 59 : 25 – 33 .
   PubMed Web of Science ®Google Scholar
• Merabet , A. , Houlleberghs , H. , Maclagan , K. , Akanho , E. , Bui , T.T. , Pagano , B. , … and 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 .
   PubMedGoogle Scholar
• Olivier , M. , Langerød , A. , Carrieri , P. , Bergh , J. , Klaar , S. , Eyfjord , J. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Pavletich , N.P. , Chambers , K.A. and 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 .
   PubMed Web of Science ®Google Scholar
• Pintus , S.S. , Fomin , E.S. , Ivanisenko , V.A. and Kolchanov , N.A. 2006 . Phylogenetic analysis of the family of p53 . Biofizika , 51 : 640 – 649 .
   PubMedGoogle Scholar
• Pintus , S.S. , Fomin , E.S. , Oshurkov , I.S. and Ivanisenko , V.A. 2007 . Phylogenetic analysis of the p53 and p63/p73 gene families . In Silico Biology , 7 : 319 – 332 .
   PubMedGoogle Scholar
• Prochazkova , J. , Lichnovsky , V. , Kylarova , D. , Erdosova , B. and 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 .
   PubMedGoogle Scholar
• Rainwater , R. , Parks , D. , Anderson , M.E. , Tegtmeyer , P. and Mann , K. 1995 . Role of cysteine residues in regulation of p53 function . Molecular and Cellular Biology , 15 : 3892 – 3903 .
   PubMed Web of Science ®Google Scholar
• Schwede , T. , Kopp , J. , Guex , N. and Peitsch , M.C. 2003 . SWISS-MODEL: An automated protein homology-modeling server . Nucleic Acids Research , 31 : 3381 – 3385 .
   PubMed Web of Science ®Google Scholar
• van Slooten , H.J. , van De Vijver , M.J. , Borresen , A.L. , Eyfjörd , J.E. , Valgardsdóttir , R. , Scherneck , S. , … and 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 .
   PubMed Web of Science ®Google Scholar
• Verhaegh , G.W. , Parat , M.O. , Richard , M.J. and Hainaut , P. 1998 . Modulation of p53 protein conformation and DNA-binding activity by intracellular chelation of zinc . Molecular Carcinogenesis , 21 : 205 – 214 .
   PubMed Web of Science ®Google Scholar