Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 32, 2009, Pages 13248-13253

  Reymer, Anna ^a   Frykholm, Karolin ^a   Morimatsu, Katsumi ^a,b   Takahashi, Masayuki ^c   Nordén, Bengt ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITÉ DE NANTES   (France)

Author keywords

Homologous recombination; HsRad51

Indexed keywords

DOUBLE STRANDED DNA; MONOMER; NUCLEOPROTEIN; RAD51 PROTEIN; TYROSINE;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; DNA BINDING; DNA CONFORMATION; DNA RECOMBINATION; DNA STRAND; GENE MUTATION; HOMOLOGOUS RECOMBINATION; INTERCALATION COMPLEX; LINEAR DICHROISM; MOLECULAR DOCKING; MOLECULAR MODEL; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SPECTROSCOPY; VALIDATION PROCESS;

DNA; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; RAD51 RECOMBINASE; SPECTRUM ANALYSIS; TYROSINE;

EID: 69449083857     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0902723106     Document Type: Article

References (41)

1. Baumann P, West S (1998) Role of the human Rad51 protein in homologous recombination and double-stranded-break repair. Trends Biochem Sci 23:247-251. (Pubitemid 28343368)
2. Shinohara A, Ogawa H, Ogawa T (1992) Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell 69:457-470.
3. Bianco P, Tracy R, Kowalczykowski S (1998) DNA strand exchange proteins: A biochemical and physical comparison. Front Biosci 3:570-603.
4. Cox MM (1999) Recombinational DNA repair in bacteria and the RecA protein. Prog Nucleic Acid Res Mol Biol 63:311-366.
5. Prévost C, Takahashi M (2003) Geometry of the DNA strands within the RecA nucleo-filament: Role in homologous recombination. Q Rev Biophys 36:429-453. (Pubitemid 38902195)
6. Radding CM (1991) Helical interactions in homologous pairing and strand exchange driven by RecA protein. J Biol Chem 266:5355-5358.
7. Roca AI, CoxMM(1997) RecA protein: Structure, function, and role in recombinational DNA repair. Prog Nucleic Acid Res Mol Biol 56:129-223.
8. Takahashi M, Nordén B (1994) Structure of RecA-DNA complex and mechanism of DNA strand exchange reaction in homologous recombination. Adv Biophys 30:1-35.
9. Ogawa T, Yu X, Shinohara A, Egelman EH (1993) Similarity of the yeast Rad51 filament to the bacterial RecA filament. Science 259:1896-1899. (Pubitemid 23124460)
10. Yu X, Jacobs S, West S, Ogawa T, Egelman EH (2001) Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA. Proc Natl Acad Sci USA 98:8419-8424. (Pubitemid 32678044)
11. Story RM,Weber IT, Steitz TA (1992) The structure of the E. coli RecA protein monomer and polymer. Nature 355:318-325.
12. Aihara H, Ito Y, Kurumizaka H, Yokoyama S, Shibata T (1999) The N-terminal domain of the human Rad51 protein binds DNA: Structure and a DNA binding surface as revealed by NMR. J Mol Biol 290:495-504. (Pubitemid 29324833)
13. Conway AB, et al. (2004) Crystal structure of a Rad51 filament. Nat Struct Mol Biol 11:791-796.
14. Pellegrini L, et al. (2002) Insights into DNA recombination from the structure of a Rad51-BRCA2 complex. Nature 420:287-293. (Pubitemid 35398178)
15. Chen Z, Yang H, Pavletich NP (2008) Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature 453:489-494. (Pubitemid 351733325)
16. Morimatsu K, Takahashi M, Nordén B (2002) Arrangement of RecA protein in its active filament determined by polarized-light spectroscopy. Proc Natl Acad Sci USA 99:11688-11693. (Pubitemid 34994460)
17. VanLoock MS, et al. (2003) ATP-mediated conformational changes in the RecA filament. Structure 11:187-196.
18. Renodon-Corniere A, et al. (2008) Structural analysis of the human Rad51 protein-DNA complex filament by tryptophan fluorescence scanning analysis: Transmission of allosteric effects between ATP binding and DNA binding. J Mol Biol 383:575-587.
19. Yu X, VanLoock MS, Yang S, Reese JT, Egelman EH (2004) What is the structure of the RecA-DNA filament? Curr Protein Pept Sci 5:73-79. (Pubitemid 38380054)
20. Nordén B, et al. (1992) Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples. J Mol Biol 226:1175-1191.
21. Frykholm K, Morimatsu K, Nordén B (2006) Conserved conformation of RecA protein after executing the DNA strand-exchange reaction. a site-specific linear dichroism structure study. Biochemistry 45:11172-11178. (Pubitemid 44413664)
22. Larkin MA, et al. (2007) ClustalW and ClustalX version 2.0. Bioinformatics 23:2947-2948.
23. Shinohara A, et al. (1993) Cloning of human, mouse and fission yeast recombination genes homologous to Rad51 and RecA. Nat Genet 4:239-243. (Pubitemid 23205171)
24. Matsuo Y, Sakane I, TakizawaY, Takahashi M, KurumizakaH(2006) Roles of the human Rad51 L1 and L2 loops in DNA binding. FEBS J 273:3148-3159.
25. Prasad T, Yeykal C, Greene E (2006) Visualizing the assembly of human Rad51 filaments on double-stranded DNA. J Mol Biol 363:713-728. (Pubitemid 44488687)
26. Selmane T, et al. (2004) Identification of the subunit-subunit interface of Xenopus Rad51.1 protein: Similarity to RecA. J Mol Biol 335:895-904. (Pubitemid 38091599)
27. Galkin V, et al. (2005) BRCA2 BRC motifs bind Rad51-DNA filaments. Proc Natl Acad Sci USA 102:8537-8542. (Pubitemid 40862771)
28. Kinebuchi T, et al. (2004) Structural basis for octameric ring formation and DNAinteraction of the human homologous-pairing protein DMC1. Mol Cell 14:363-374. (Pubitemid 38591407)
29. Shin DS, et al. (2003) Full-length archaeal Rad51 structure and mutants: Mechanisms for Rad51 assembly and control by BRCA2. EMBO J 22:4566-4576.
30. Simmerling C, Strockbine B, Roitberg AE (2002) All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 124:11258-11259.
31. Fiser A, Do R, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773.
32. Benson F, Stasiak A, West S (1994) Purification and characterization of the human Rad51 protein, an analog of E. coli RecA. EMBO J 13:5764-5771. (Pubitemid 24363044)
33. Kurumizaka H, Aihara H, Kagawa W, Shibata T, Yokoyama S (1999) Human Rad51 amino acid residues required for Rad52 binding. J Mol Biol 291:537-548. (Pubitemid 29392632)
34. Berman H, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242.
35. Kaplan W, Littlejohn TG (2001) Swiss-PDB Viewer (Deep View). Brief Bioinform 2:195-197.
36. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 31:3381-3385. (Pubitemid 37442164)
37. Case D, et al. (2008) AMBER 10 (University of California, San Francisco).
38. Pettersen E, et al. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612.
39. Kim HK, Morimatsu K, Nordén B, ArdhammarM, TakahashiM(2002) ADP stabilizes the human Rad51-single stranded DNA complex and promotes its DNA annealing activity. Genes Cells 7:1125-1134. (Pubitemid 35256334)
40. Bullock WO, Fernandez JM, Short JM (1987) XL1-Blue-a high-efficiency plasmid transforming RecA Escherichia-coli strain with beta-galactosidase selection. BioTechniques 5:376-379.
41. Nordén B, Kubista M, Kurucsev T (1992) Linear dichroism spectroscopy of nucleic acids. Q Rev Biophys 25:51-170.