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Predicting the redox state and secondary structure of cysteine residues in proteins using NMR chemical shifts
Author(s) -
Wang ChingCheng,
Chen JuiHung,
Yin ShihHis,
Chuang WoeiJer
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20875
Subject(s) - cysteine , redox , chemistry , protein secondary structure , chemical shift , crystallography , stereochemistry , biochemistry , organic chemistry , enzyme
We report 2D cluster analyses of 1 H α , 1 H N , 13 C α , and 13 C′ versus 13 C β NMR chemical shifts (CSs) that can be used to predict the redox state and secondary structure of cysteine residues in proteins. A database of cysteine 1 H α , 1 H β2 , 1 H β3 , 1 H N , 13 C α , 13 C β , 13 C′, and 15 N H CSs as a function of secondary structure and redox state was constructed from BioMagResBank entries. One‐dimensional statistical analysis showed that cysteine 1 H α , 1 H N , 13 C α , 13 C′, and 15 N H CSs reflected the secondary structure, and that cysteine C β CS is extremely sensitive to the redox state. In contrast, cysteine 1 H β CS was not correlated with its redox state or secondary structure. Two‐dimensional cluster analysis revealed that 2D C α /C β , C′/C β , H N /C β , and H α /C β clusters were helpful in distinguishing both the redox state and secondary structure of cysteine residues. Based on these results, we derived rules using a score matrix to predict the redox state and secondary structure of cysteines using their CSs. The score matrix predicts the redox state and secondary structure of cysteine residues in proteins with ∼90% accuracy. This suggests that the redox state and secondary structure of cysteine residues in peptides and proteins can be obtained from their CSs without recourse to nuclear Overhauser effect measurements. Proteins 2006. © 2006 Wiley‐Liss, Inc.