Title: Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation.

Authors: Doulias, Paschalis-Thomas; Greene, Jennifer L; Greco, Todd M; Tenopoulou, Margarita; Seeholzer, Steve H; Dunbrack, Roland L; Ischiropoulos, Harry

Published In Proc Natl Acad Sci U S A, (2010 Sep 28)

Abstract: S-nitrosylation, the selective posttranslational modification of protein cysteine residues to form S-nitrosocysteine, is one of the molecular mechanisms by which nitric oxide influences diverse biological functions. In this study, unique MS-based proteomic approaches precisely pinpointed the site of S-nitrosylation in 328 peptides in 192 proteins endogenously modified in WT mouse liver. Structural analyses revealed that S-nitrosylated cysteine residues were equally distributed in hydrophobic and hydrophilic areas of proteins with an average predicted pK(a) of 10.01 ± 2.1. S-nitrosylation sites were over-represented in α-helices and under-represented in coils as compared with unmodified cysteine residues in the same proteins (χ(2) test, P < 0.02). A quantile-quantile probability plot indicated that the distribution of S-nitrosocysteine residues was skewed toward larger surface accessible areas compared with the unmodified cysteine residues in the same proteins. Seventy percent of the S-nitrosylated cysteine residues were surrounded by negatively or positively charged amino acids within a 6-Å distance. The location of cysteine residues in α-helices and coils in highly accessible surfaces bordered by charged amino acids implies site directed S-nitrosylation mediated by protein-protein or small molecule interactions. Moreover, 13 modified cysteine residues were coordinated with metals and 15 metalloproteins were endogenously modified supporting metal-catalyzed S-nitrosylation mechanisms. Collectively, the endogenous S-nitrosoproteome in the liver has structural features that accommodate multiple mechanisms for selective site-directed S-nitrosylation.

PubMed ID: 20837516

MeSH Terms: Amino Acid Motifs; Amino Acid Sequence; Animals; Cysteine/analogs & derivatives*; Cysteine/analysis; Cysteine/metabolism; Hydrophobic and Hydrophilic Interactions; Liver/metabolism*; Mice; Molecular Sequence Data; Protein Processing, Post-Translational*; Proteins/chemistry; Proteins/metabolism*; Proteome; Proteomics; S-Nitrosothiols/analysis; S-Nitrosothiols/metabolism*