Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: A molecular dynamics study

Proteins: Structure, Function and Genetics

Volumn 66, Issue 1, 2007, Pages 69-86

  Gough, Craig A ^a   Gojobori, Takashi ^a,b   Imanishi, Tadashi ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Binding entropy; Breast cancer; Disease mutations; Protein protein interactions; Quasiharmonic analysis

Indexed keywords

MUTANT PROTEIN;

ARTICLE; BINDING SITE; BREAST CANCER; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; ENTROPY; GENE MUTATION; LIGAND BINDING; MOLECULAR DYNAMICS; ONCOGENE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS; VIBRATION;

ALGORITHMS; BINDING SITES; BRCA1 PROTEIN; BREAST NEOPLASMS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; ENTROPY; FEMALE; HUMANS; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

EID: 33845602076     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21188     Document Type: Article

References (39)

1. Venkitaraman A. Cancer susceptibility and the functions of BRCA1 and BRCA2. Cell 2002;108:171-182.
2. Williams R, Chasman D, Hau D, Hui B, Lau A, Glover J. Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. J Biol Chem 2003;278:53007-53016.
3. Gayther SA, Warren W, Mazoyer S, Russell PA, Harrington PA, Chiano M, Seal S, Hamoudi R, van Rensburg EJ, Dunning AM, Love R, Evans G, Easton D, Clayton D, Stratton MR, Ponder BA. Germline mutations of the BRCA1 gene in breast and ovarian cancer families provide evidence for a genotype-phenotype correlation. Nat Genet 1995;11:428-433.
4. Bork P, Hofmann K, Bucher P, Neuwald A, Altschul S, Koonin EA. Superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J 1997;11:68-76.
5. Callebaut I, Mornon J. From BRCA1 to RAP1: a widespread BRCT module closely associated with DNA repair. FEBS Lett 1997;400: 25-30.
6. Caldecott K, McKeown C, Tucker J, Ljungquist S, Thompson L. An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III. Mol Cell Biol 1994;14:68-76.
7. Nash R, Caldecott K, Barnes D, Lindahl T. XRCC1 protein interacts with one of two distinct forms of DNA ligase III. Biochemistry 1997;36:5207-5211.
8. Taylor R, Wickstead B, Cronin S, Caldecott K. Role of a BRCT domain in the interaction of DNA ligase III-α with the DNA repair protein XRCC1. Curr Biol 1998;8:877-880.
9. Cantor S, Bell D, Ganesan S, Kass E, Drapkin R, Grossman S, Wahrer D, Sgroi D, Lane W, Haber D, Livingston D. BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell 2001;105:149-160.
10. Yu X, Chini C, He M, Mer G, Chen J. The BRCT domain is a phospho-protein binding domain. Science 2003;302:639-642.
11. Yu X, Wu L, Bowcock A, Aronheim A, Baer R. The C-terminal (BRCT) domains of BRCA1 interact in vivo with CtIP, a protein implicated in the CtBP pathway of transcriptional repression. J Biol Chem 1998;273:25388-25392.
12. Joo W, Jeffrey P, Cantor S, Finnin M, Livingston D, Pavletich N. Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure. Genes Dev 2002;16:583-593.
13. Derbyshire D, Basu B, Serpell L, Joo W, Date T, Iwabuchi K, Doherty A. Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor. EMBO J 2002;21:3863-3872.
14. Clapperton J, Manke I, Lowery D, Ho T, Haire L, Yaffe M, Smerdon S. Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Nat Struct Mol Biol 2004;11:512-518.
15. Williams R, Lee M, Hau D, Glover J. Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1. Nat Struct Mol Biol 2004;11:519-525.
16. Williams R, Green R, Glover J. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Nat Struct Biol 2001;8:838-842.
17. Monteiro AN, August A, Hanafusa H. Common BRCA1 variants and transcriptional activation. Am J Human Genet 1997;61:761, 762.
18. Scully R, Ganesan S, Vlasakova K, Chen J, Socolovsky M, Livingston D. Genetic analysis of BRCA1 function in a defined tumor cell line. Mol Cell 1999;4:1093-1099.
19. Case D, Pearlman D, Caldwell J, Cheatham TI, Wang J, Ross W, Simmerling C, Darden T, Merz K, Stanton R, Cheng A, Vincent J, Crowley M, Tsui V, Gohlke H, Radmer R, Duan Y, Pitera J, Massova I, Seibel G, Singh U, Weinger P, Kollman P. AMBER 7. San Francisco: University of California; 2002.
20. Pearlman D, Case D, Caldwell J, Ross W, Cheatham TI, DeBolt S, Ferguson S, Seibel G, Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
21. Allen M, Tildesley D. Computer simulation of liquids, Oxford: Clarendon; 1987. pp. 24-27.
22. Jorgensen W, Chandrasekar J, Madura J, Impey R, Klein M. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
23. Sagui C, Darden T. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu Rev Biophys Biomol Struct 1999;28:155-179.
24. Wang JPC, Kollman P. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000; 21:1049-1074.
25. Homeyer N, Horn A, Lanig H, Sticht H. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J Mol Model 2006;12:281-289.
26. Ryckaert J-P, Ciccotti G, Berendsen H. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
27. Berendsen H, Postmas J, van Gunsteren W, DiNola A, Haak J. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
28. Williams R, Glover J. Structural consequences of a cancer-causing BRCA1-BRCT missense mutation. J Biol Chem 2003;278:2630-2635.
29. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P. The protein data bank. Nucleic Acids Res 2000;28:235-242.
30. Sali A, Blundell T. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
31. Fiser A, Do R, Sali A. Modeling of loops in protein structures. Protein Sci 2000;9:1753-1773.
32. Marti-Renom M, Stuart A, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000;29:291-325.
33. Huang C, Couch G, Pettersen E, Ferrin T. Chimera: an extensible molecular modeling application constructed using standard components. Pac Symp Biocomput 1996;1:724.
34. 2+-induced transition: a study of the regulatory domain of skeletal troponin-C. Biophys J 2003;84:82-101.
35. Teeter M, Case D. Harmonic and quasiharmonic descriptions of crambin. J Phys Chem 1990;94:8091-8097.
36. Kitao A, Go N. Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 1999;9:164-169.
37. Gaiser O, Ball L, Schmieder P, Leitner D, Strauss H, Wahl M, Kuhne R, Oschkinaat H, Heinermann U. Solution structure, backbone dynamics, and association behavior of the C-terminal BRCT domain from the breast cancer-associated protein BRCA1. Biochemistry 2004;43:15983-15985.
38. Rapp C, Pollack R. Crystal packing effects on protein loops. Proteins: Struct Funct Bioinformatics 2005;60:103-109.
39. Gohlke H, Kiel C, Case DA. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 2003; 330:891-913.