Reactivity-based analysis of domain structures in native replication protein A

Biochemistry

Volumn 45, Issue 32, 2006, Pages 9804-9818

  Nuss, Jonathan E ^a,b   Sweeney, Deacon J ^a   Alter, Gerald M ^a  

^a WRIGHT STATE UNIVERSITY   (United States)

^b University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CONFORMATIONS; DNA; NUCLEAR MAGNETIC RESONANCE;

DNA BINDING PROTEIN; NATIVE PROTEIN STRUCTURE; SOLUTION-STATE PROTEIN;

PROTEINS;

AMINO ACID; DNA BINDING PROTEIN; REPLICATION PROTEIN A; SINGLE STRANDED DNA;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL MODIFICATION; CONFORMATIONAL TRANSITION; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; HUMAN; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN MODIFICATION; PROTEIN STRUCTURE; STRUCTURAL PROTEOMICS; THREE DIMENSIONAL IMAGING; X RAY ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; DNA; FREE RADICALS; HUMANS; HYDROXYLATION; KINETICS; MASS SPECTROMETRY; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; REPLICATION PROTEIN A; TIME FACTORS;

EID: 33747455702     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi052397v     Document Type: Article

References (60)

1. Iftode, C., Daniely, Y., and Borowiec, J. A. (1999) Replication protein A (RPA): the eukaryotic SSB, Crit. Rev. Biochem. Mol. Biol. 34, 141-180.
2. Wold, M. S. (1997) Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism, Annu. Rev. Biochem. 66, 61-92.
3. Kim, C., Paulus, B. F., and Wold, M. S. (1994) Interactions of human replication protein A with oligonucleotides, Biochemistry 33, 14197-14206.
4. Kim, C., and Wold, M. S. (1995) Recombinant human replication protein A binds to polynucleotides with low cooperativity, Biochemistry 34, 2058-2064.
5. Gomes, X. V., Henricksen, L. A., and Wold, M. S. (1996) Proteolytic mapping of human replication protein A: evidence for multiple structural domains and a conformational change upon interaction with single-stranded DNA, Biochemistry 35, 5586-5595.
6. Treuner, K., Ramsperger, U., and Knippers, R. (1996) Replication protein A induces the unwinding of long double-stranded DNA regions, J. Mol. Biol. 259, 104-112.
7. Thoma, B. S., and Vasquez, K. M. (2003) Critical DNA damage recognition functions of XPC-hHR23B and XPA-RPA in nucleotide excision repair, Mol. Carcinog. 38, 1-13.
8. Robison, J. G., Elliott, J., Dixon, K., and Oakley, G. G. (2004) Replication protein A and the Mre11.Rad50.Nbs1 complex colocalize and interact at sites of stalled replication forks, J. Biol. Chem. 279, 34802-34810.
9. 2+-dependent activation of gelsolin by using synchrotron footprinting, Proc. Natl. Acad. Scie. U.S.A. 100, 3942-3947.
10. Murzin, A. G. (1993) OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for nonhomologous sequences, EMBO J. 12, 861-867.
11. Bochkareva, E., Korolev, S., Lees-Miller, S. P., and Bochkarev, A. (2002) Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA, EMBO J. 21, 1855-1863.
12. Bochkarev, A., Bochkareva, E., Frappier, L., and Edwards, A. M. (1999) The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding, EMBO J. 18, 4498-4504.
13. Bochkarev, A., Pfuetzner, R. A., Edwards, A. M., and Frappier, L. (1997). Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA, Nature 385, 176-181.
14. Jacobs, D. M., Lipton, A. S., Isern, N. G., Daughdrill, G. W., Lowry, D. F., Gomes, X., and Wold, M. S. (1999) Human replication protein A: global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker, J. Biomol. NMR 14, 321-331.
15. Mer, G., Bochkarev, A., Gupta, R., Bochkareva, E., Frappier, L., Ingles, C. J., Edwards, A. M., and Chazin, W. J. (2000) Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA, Cell 103, 449-456.
16. Bochkareva, E., Belegu, V., Korolev, S., and Bochkarev, A. (2001) Structure of the major single-stranded DNA-binding domain of replication protein A susgests a dynamic mechanism for DNA binding, EMBO J. 20, 612-618.
17. Peterson, J. J., Young, M. M., and Takemoto, L. J. (2004) Probing alpha-crystallin structure using chemical cross-linkers and mass spectrometry, Mol. Vision 10, 857-866.
18. Novak, P., Krappa, G. H., Young, M. M., and Schoeniger, J. (2004) A top-down method for the determination of residue-specific solvent accessibility in proteins, J. Mass Spectrom. 39, 322-328.
19. Kruppa, G. H., Schoeniger, J., and Young, M. M. (2003) A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry, Rapid Commun. Mass Spectrom. 17, 155-162.
20. Guan, J. Q., Vorobiev, S., Almo, S. C., and Chance, M. R. (2002) Mapping the G-actin binding surface of cofilin using synchrotron protein footprinting. Biochemistty 41, 5765-5775.
21. Guan, J. Q., Almo, S. C., Reisler, E., and Chance, M. R. (2003) Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent, Biochemistry 42, 11992-12000.
22. D'Ambrosio, C., Talamo, F., Vitale, R. M., Amodeo, P., Tell, G., Ferrara, L., and Scaloni, A. (2003) Probing the dimeric structure of porcine aminoacylase 1 by mass spectrometric and modeling procedures, Biochemistry 42, 4430-4443.
23. Goldsmith, S. C., Guan, J. Q., Almo, S., and Chance, M. (2001) Synchrotron protein foolprinting: a technique to investigate protein-protein interactions, J. Biomol. Struct. Dyn. 19, 405-418.
24. Liu, R., Guan, J. Q., Zak, O., Aisen, P., and Chance, M. R. (2003) Structural reorganization of the transferrin C-lobe and transferrin receptor upon complex formation: the C-lobe binds to the receptor helical domain, Biochemistry 42, 12447-12454.
25. Maleknia, S. D., Ralston, C. Y., Brenowitz, M. D., Downard, K. M., and Chance, M. R. (2001) Determination of macromolecular folding and structure by synchrotron X-ray radiolysis techniques, Anal. Biochem. 289, 103-115.
26. Nukuna, B. N., Sun, G., and Anderson, V. E. (2004) Hydroxyl radical oxidation of cytochrome c by aerobic radiolysis, Free Radical Biol. Med. 37, 1203-1213.
27. Henricksen, L. A., Umbricht, C. B., and Wold, M. S. (1994) Recombinant replication protein A: expression, complex formation, and functional characterization, J. Biol. Chem. 269, 11121-11132
28. [erratum: (1994) J. Biol. Chem. 269, 16519].
29. Bochkareva, E., Korolev, S., and Bochkarev, A. (2000) The role for zinc in replication protein A, J. Biol. Chem. 275, 27332-27338.
30. Salvucci, M. E. (1993) Covalent modification of a highly reactive and essential lysine residue of ribulose-1,5-bisphosphate carboxylase/oxygenase activase, Plant Physiol. 103, 501-508.
31. Nuss, J. E., Patrick, S. M., Oakley, G. G., Alter, G. M., Robison, J. G., Dixon, K., and Turchi, J. J. (2005) DNA damage induced hyperphosphorylation of replication protein A. I. Identification of novel sites of phosphorylation in response to DNA damage, Biochemistiy 44, 8428-8437.
32. Nuss, J. E., and Alter, G. M. (2004) Denaturation of replication protein A reveals an alternative conformation with intact domain structure and oligonucleotide binding activity, Protein Sci. 13, 1365-1378.
33. Tsunematsu, H., Imamura, T., and Makisumi, S. (1983) Kinetics of hydrolysis of Nα-benzoyl-p-guanidino-L-phenylalanine p-nitroanilide by trypsin, J. Biochem. 94, 123-128.
34. Pozsgay, M., Szabo, G., Bajusz, S., Simonsson, R., Gaspar, R., and Elodi, P. (1981) Investigation of the substrate-binding site of trypsin by the aid of tripeptidyl-p-nitroanilide substrates, Eur. J. Biochem. 115, 497-502.
35. Nagata, K., Yoshida, N., Ogata, F., Araki, M., and Noda, K. (1991) Subsite mapping of an acidic amino acid-specific endopeptidase from Streptomyces griseus, GluSGP, and protease V8, J. Biochem. 110, 859-862.
36. Houmard, J. (1976) Kinetic investigation of the staphylococcal protease-catalyzed hydrolysis of synthetic substrates. Eur. J. Biochem. 68, 621-627.
37. Tang, C. L., Xie, L., Koh, I. Y., Posy, S., Alexov, E., and Honig, B. (2003) On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles, J. Mol. Biol. 334, 1043-1062.
38. Zhao, L., Cox, A. G., Ruzicka, J. A., Bhat, A. A., Zhang, W., and Taylor, E. W. (2000) Molecular modeling and in vitro activity of an HIV-1-encoded glutathione peroxidase, Proc. Natl. Acad. Sci. U.S.A. 97, 6356-6361.
39. Bates, P. A., Kelley, L. A., MacCallum, R. M., Sternberg, M. J. (2001) Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM, Proteins, Suppl. 5, 39-46.
40. Means, G., and Feenery, R. (1971) Chemical Modification of Proteins, Holden-Day, San Francisco, CA.
41. Gomes, X., Henricksen, L., and Wold, M. (1996) Proteolytic mapping of human replication protein A: evidence fro multiple structureal domains and a contormational change upon interaction with single-stranded DNA, Biochemistry 35, 5586-5595.
42. Fraczkiewicz, R., and Braun, W. (1998) Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules, J. Comput. Chem. 19, 319-333.
43. Pearlman, D. A. C., Caldwell, J. W., Ross, W. R., Cheatham, T. E., III. DeBolt, S., Ferguson, D., Seibel, G., and Kollman, P. (1995) AMBER, a computer program for applying molecular mechanics, normal-mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules, Comput. Phys. Commun. 91, 1-41.
44. Letner, C., and Alter, G. (1994) The evolution of lactate dehydrogenase conformation during molecular dynamics simulation, in Proceedings of the First Electronic Computational Chemistry Conference, ARInternet.
45. Zhang, K., Tang, H., Huang, L., Blankenship, J. W., Jones, P. R., Xiang, F., Yau, P. M., and Burlingame, A. L. (2002) Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry, Anal. Biochem. 306, 259-269.
46. Deleted in proof.
47. Ellison, D., Hinton, J., Hubbard, S. J., and Beynon, R. J. (1995) Limited proteolysis of native proteins: the interaction between avidin and proteinase K, Protein Sci. 4, 1337-1345.
48. Hubbard, S. J., Campbell, S. F., and Thornton, J. M. (1991) Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors, J. Mol. Biol. 220, 507-530.
49. Hubbard, S. J., Beynon, R. J., and Thornton, J. M. (1998) Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures, Protein Eng. 11, 349-359.
50. Mustard, D., and Ritchie, D. W. (2005) Docking essential dynamics eigenstructures, Proteins: Struct., Funct., Bioinf. 60, 269-274.
51. Ritchie, D. W. (2003) Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2, Proteins 52, 98-106.
52. Ritchie, D. W., and Kemp, G. J. (2000) Protein docking using spherical polar Fourier correlations, Proteins 39, 178-194.
53. Creighton, T. (1993) Proteins: Structure and Molecular Properties, W. H. Freeman, New York.
54. Doneanu, C. E., et al. (2004) Mass spectrometry of UV-cross-linked protein-nucleic acid complexes: Identification of amino acid residues in the single-stranded DNA-binding domain of human replication protein A, Anal. Chem. 76, 5667-5676.
55. Park, J. S., Wang, M., Park, S. J., and Lee, S. H. (1999) Zinc finger of replication protein A, a non-DNA binding element, regulates its DNA binding activity through redox, J. Biol. Chem. 274, 29075-29080.
56. Walther, A. P., Gomes, X. V., Lao, Y., Lee, C. G., and Wold, M. S. (1999) Replication protein A interactions with DNA. I. Functions of the DNA-binding and zinc-finger domains of the 70-kDa subunit, Biochemistry 38, 3963-3973.
57. Lao, Y., Lee, C. G., and Wold, M. S. (1999) Replication protein A interactions with DNA. 2. Characterization of double-stranded DNA-binding/helix-destabilization activities and the role of the zinc-finger domain in DNA interactions, Biochemistry 38, 3974-3984.
58. Eckerieh, C., Fackelmayer, F. O., and Knippers, R. (2001) Zinc affects the conformation of nucleoprotein filaments formed by replication protein A (RPA) and long natural DNA molecules, Biochim. Biophys. Acta 1538, 67-75.
59. Pestryakov, R., Weisshart, K., Schlott, B., Khodyreva, S., Kremmer, E., Grossie, F., Larvrik, O., and Nasheuer, H. (2003) The C-terminal RPA70 and the central RPA32 domains are involved in the interactions with the 3′-end of a primer-template DNA, J. Biol. Chem. 278, 17515-17524.
60. Blackwell, L. J., Borowiec, J. A., and Masrangelo, I. A. (1996) Single-stranded-DNA binding alters human replication protein A structure and facilitates interaction with DNA-dependent protein kinase, Mol. Cell. Biol. 16, 4798-4807.