Photochemical surface mapping of C14S-Sml1p for constrained computational modeling of protein structure

Analytical Biochemistry

Volumn 340, Issue 2, 2005, Pages 201-212

  Sharp, Joshua S ^a,d   Guo, Jun Tao ^b   Uchiki, Tomoaki ^a   Xu, Ying ^b   Dealwis, Chris ^c   Hettich, Robert L ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b University of Georgia ^*  (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

^d NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

de novo computational modeling; Mass spectrometry; Photochemical surface mapping; Protein structure; Sml1p protein; Solvent accessibility

Indexed keywords

AMINO ACIDS; COMPUTATION THEORY; MAPPING; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; PROTEINS; REACTION KINETICS; YEAST;

COMPUTATIONAL MODEL; HYDROXYL RADICAL REACTIONS; NUCLEAR MAGNETIC RESONANCE(NMR); PROTEIN STRUCTURES; SOLVENT ACCESSIBILITY; SOLVENT-EXPOSED REGIONS; SURFACE MAPPING; TRYPTOPHAN FLUORESCENCE;

SOLVENTS;

AMINO ACID; PROTEIN SML1P; PROTEIN SUBUNIT; UNCLASSIFIED DRUG;

ARTICLE; MASS SPECTROMETRY; MATHEMATICAL MODEL; NUCLEAR MAGNETIC RESONANCE; PHOTOCHEMICAL EFFICIENCY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 17444402478     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ab.2005.02.005     Document Type: Article

References (46)

1. X. Zhao, E.G. Muller, and R. Rothstein A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools Mol. Cell 2 1998 329 340
2. A. Chabes, V. Domkin, and L. Thelander Yeast Sml1, a protein inhibitor of ribonucleotide reductase J. Biol. Chem. 274 1999 36679 36683
3. X. Zhao, A. Chabes, V. Domkin, L. Thelander, and R. Rothstein The ribonucleotide reductase inhibitor Sml1 is a new target of the Mec1/Rad53 kinase cascade during growth and in response to DNA damage EMBO J. 20 2001 3544 3553
4. Ouspenski, II, S.J. Elledge, B.R. Brinkley, New yeast genes important for chromosome integrity and segregation identified by dosage effects on genome stability, Nucleic Acids Res. 27 (1999) 3001-3008
5. T.A. Weinert, G.L. Kiser, and L.H. Hartwell Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair Genes Dev. 8 1994 652 665
6. T.A. Weinert, and L.H. Hartwell Cell cycle arrest of cdc mutants and specificity of the RAD9 checkpoint Genetics 134 1993 63 80
7. X. Zhao, B. Georgieva, A. Chabes, V. Domkin, J.H. Ippel, J. Schleucher, S. Wijmenga, L. Thelander, and R. Rothstein Mutational and structural analyses of the ribonucleotide reductase inhibitor Sml1 define its Rnr1 interaction domain whose inactivation allows suppression of mec1 and rad53 lethality Mol. Cell. Biol. 20 2000 9076 9083
8. J. Moult, T. Hubbard, S.H. Bryant, K. Fidelis, and J.T. Pedersen Critical assessment of methods of protein structure prediction (CASP): round II Proteins Suppl. 1 1997 2 6
9. J. Moult, T. Hubbard, K. Fidelis, and J.T. Pedersen Critical assessment of methods of protein structure prediction (CASP): round III Proteins Suppl. 3 1999 2 6
10. J. Moult, K. Fidelis, A. Zemla, and T. Hubbard Critical assessment of methods of protein structure prediction (CASP): round IV Proteins Suppl. 5 2001 2 7
11. P.E. Bourne CASP and CAFASP experiments and their findings Methods Biochem. Anal. 44 2003 501 507
12. C. Venclovas, A. Zemla, K. Fidelis, and J. Moult Assessment of progress over the CASP experiments Proteins 53 Suppl. 6 2003 585 595
13. L.N. Kinch, J.O. Wrabl, S.S. Krishna, I. Majumdar, R.I. Sadreyev, Y. Qi, J. Pei, H. Cheng, and N.V. Grishin CASP5 assessment of fold recognition target predictions Proteins 53 Suppl. 6 2003 395 409
14. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242
15. V. Gupta, C.B. Peterson, L. Dice, T. Uchiki, J. Guo, Y. Xu, R. Hettich, X. Zhao, R. Rothstein, and C. Dealwis Sml1p is a dimer in solution: characterization of denaturation and renaturation of recombinant Sml1p Biochemistry 43 2004 8568 8578
16. A.M. Lesk, L. Lo Conte, and T.J. Hubbard Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts Proteins Suppl. 5 2001 98 118
17. K.T. Simons, R. Bonneau, I. Ruczinski, and D. Baker Ab initio protein structure prediction of CASP III targets using ROSETTA Proteins Suppl. 3 1999 171 176
18. K.T. Simons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J. Mol. Biol. 268 1997 209 225
19. D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96
20. P.M. Bowers, C.E. Strauss, and D. Baker De novo protein structure determination using sparse NMR data J. Biomol. NMR 18 2000 311 318
21. Y. Xu, D. Xu, O.H. Crawford, and J.R. Einstein A computational method for NMR-constrained protein threading J. Comput. Biol. 7 2000 449 467
22. S.D. Maleknia, C.Y. Ralston, M.D. Brenowitz, K.M. Downard, and M.R. Chance Determination of macromolecular folding and structure by synchrotron x-ray radiolysis techniques Anal. Biochem. 289 2001 103 115
23. S.D. Maleknia, J.G. Kiselar, and K.M. Downard Hydroxyl radical probe of the surface of lysozyme by synchrotron radiolysis and mass spectrometry Rapid Commun. Mass Spectrom. 16 2002 53 61
24. J.G. Kiselar, S.D. Maleknia, M. Sullivan, K.M. Downard, and M.R. Chance Hydroxyl radical probe of protein surfaces using synchrotron X-ray radiolysis and mass spectrometry Int. J. Radiat. Biol. 78 2002 101 114
25. J.S. Sharp, J.M. Becker, and R.L. Hettich Protein surface mapping by chemical oxidation: Structural analysis by mass spectrometry Anal. Biochem. 313 2003 216 225
26. J.S. Sharp, J.M. Becker, and R.L. Hettich Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry Anal. Chem. 76 2004 672 683
27. S.D. Maleknia, M. Brenowitz, and M.R. Chance Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry Anal. Chem. 71 1999 3965 3973
28. W.M. Garrison Reaction-Mechanisms in the Radiolysis of Peptides, Polypeptides, and Proteins Chem. Rev. 87 1987 381 398
29. G.V. Buxton, C.L. Greenstock, W.P. Helman, and A.B. Ross Critical-Review of Rate Constants for Reactions of Hydrated Electrons, Hydrogen-Atoms and Hydroxyl Radicals (.Oh/.O-) in Aqueous-Solution J. Phys. Chem. Reference Data 17 1988 513 886
30. J.G. Kiselar, P.A. Janmey, S.C. Almo, and M.R. Chance Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprinting Proc. Natl. Acad. Sci. USA 100 2003 3942 3947
31. S.C. Goldsmith, J.Q. Guan, S. Almo, and M. Chance Synchrotron protein footprinting: a technique to investigate protein-protein interactions J. Biomol. Struct. Dyn. 19 2001 405 418
32. H. Rashidzadeh, S. Khrapunov, M.R. Chance, and M. Brenowitz Solution structure and interdomain interactions of the Saccharomyces cerevisiae TATA binding protein (TBP) probed by radiolytic protein footprinting Biochemistry 42 2003 3655 3665
33. J.Q. Guan, S. Vorobiev, S.C. Almo, and M.R. Chance Mapping the G-actin binding surface of cofilin using synchrotron protein footprinting Biochemistry 41 2002 5765 5775
34. J.Q. Guan, S.C. Almo, E. Reisler, and M.R. Chance Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent Biochemistry 42 2003 11992 12000
35. R. Liu, J.Q. Guan, O. Zak, P. Aisen, and M.R. Chance Structural reorganization of the transferrin C-lobe and transferrin receptor upon complex formation: the C-lobe binds to the receptor helical domain Biochemistry 42 2003 12447 12454
36. M.R. Chance Unfolding of apomyoglobin examined by synchrotron footprinting Biochem. Biophys. Res. Commun. 287 2001 614 621
37. T. Uchiki, R. Hettich, V. Gupta, and C. Dealwis Characterization of monomeric and dimeric forms of recombinant Sml1p-histag protein by electrospray mass spectrometry Anal. Biochem. 301 2002 35 48
38. C. Bystroff, V. Thorsson, and D. Baker HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins J. Mol. Biol. 301 2000 173 190
39. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
40. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723
41. R. Fraczkiewicz, and W. Braun Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules J. Computat. Chem. 19 1998 319 333
42. S.D. Maleknia, M.R. Chance, and K.M. Downard Electrospray-assisted modification of proteins: a radical probe of protein structure Rapid Commun. Mass Spectrom. 13 1999 2352 2358
43. P. Reichard Interactions between deoxyribonucleotide and DNA synthesis Annu. Rev. Biochem. 57 1988 349 374
44. D. Chivian, D.E. Kim, L. Malmstrom, P. Bradley, T. Robertson, P. Murphy, C.E. Strauss, R. Bonneau, C.A. Rohl, and D. Baker Automated prediction of CASP-5 structures using the Robetta server Proteins 53 Suppl. 6 2003 524 533
45. R. Bonneau, J. Tsai, I. Ruczinski, D. Chivian, C. Rohl, C.E. Strauss, and D. Baker Rosetta in CASP4: progress in ab initio protein structure prediction Proteins Suppl. 5 2001 119 126
46. Y. Xu, and D. Xu Protein threading using PROSPECT: design and evaluation Proteins 40 2000 343 354