Photochemical surface mapping of C14S-Sml1p for constrained computational modeling of protein structure.
Photochemically generated hydroxyl radicals were used to map solvent-exposed regions in the C14S mutant of the protein Sml1p, a regulator of the ribonuclease reductase enzyme Rnr1p in Saccharomyces cerevisiae. By using high-performance mass spectrometry to characterize the oxidized peptides created by the hydroxyl radical reactions, amino acid solvent-accessibility data for native and denatured C14S Sml1p that revealed a solvent-excluding tertiary structure in the native state were obtained. The data on solvent accessibilities of various amino acids within the protein were then utilized to evaluate the de novo computational models generated by the HMMSTR/Rosetta server. The top five models initially generated by the server all disagreed with both published nuclear magnetic resonance (NMR) data and the solvent-accessibility data obtained in this study. A structural model adjusted to fit the previously reported NMR data satisfied most of the solvent-accessibility constraints. Through minor adjustment of the rotamers of two amino acid side chains for this latter structure, a model that not only provided a lower energy conformation but also completely satisfied previously reported data from NMR and tryptophan fluorescence measurements, in addition to the solvent-accessibility data presented here, was generated.
Sharp
Joshua S
JS
Graduate School of Genome Science and Technology, The University of Tennessee and Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830-8026, USA.
Guo
Jun-tao
JT
Uchiki
Tomoaki
T
Xu
Ying
Y
Dealwis
Chris
C
Hettich
Robert L
RL
D000595:Amino Acid Sequence; D019295:Computational Biology; D017665:Hydroxyl Radical / Q000737:chemistry; D013058:Mass Spectrometry; D008958:Models, Molecular; D010084:Oxidation-Reduction; D010777:Photochemistry / Q000379:methods*; D011489:Protein Denaturation; D017434:Protein Structure, Tertiary; D012264:Ribonucleotide Reductases / Q000037:antagonists & inhibitors; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*
C115052:SML1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D017665:Hydroxyl Radical; D012264:Ribonucleotide Reductases