Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues

Abstract

The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a given protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the Escherichia coli proteome using several proteomic methodologies and globally measured oxidation rates of methionine residues in the presence and absence of tertiary structure, as well as the folding stabilities of methionine-containing domains. These data indicated that buried methionines have a wide range of protection factors against oxidation that correlate strongly with folding stabilities. Consistent with this, we show that in comparison to E. coli, the proteome of the thermophile Thermus thermophilus is significantly more stable and thus more resistant to methionine oxidation. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and propose a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Overall, these results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability. The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a given protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the Escherichia coli proteome using several proteomic methodologies and globally measured oxidation rates of methionine residues in the presence and absence of tertiary structure, as well as the folding stabilities of methionine-containing domains. These data indicated that buried methionines have a wide range of protection factors against oxidation that correlate strongly with folding stabilities. Consistent with this, we show that in comparison to E. coli, the proteome of the thermophile Thermus thermophilus is significantly more stable and thus more resistant to methionine oxidation. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and propose a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Overall, these results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability. Sidechains of methionine and cysteine residues contain sulfur atoms that are readily oxidizable by reactive oxygen species (ROS). While not as well-studied as cysteine oxidation, methionine oxidation is an important enzymatically reversible posttranslational modification that has been shown to play a role in a number of physiological processes and cellular pathways (1Levine R.L. Moskovitz J. Stadtman E.R. Oxidation of methionine in proteins: Roles in antioxidant defense and cellular regulation.IUBMB Life. 2000; 50: 301-307Crossref PubMed Scopus (325) Google Scholar, 2Levine R.L. Mosoni L. Berlett B.S. Stadtman E.R. Methionine residues as endogenous antioxidants in proteins.Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 15036-15040Crossref PubMed Scopus (865) Google Scholar, 3Stadtman E.R. Van Remmen H. Richardson A. Wehr N.B. Levine R.L. Methionine oxidation and aging.Biochim. Biophys. Acta. 2005; 1703: 135-140Crossref PubMed Scopus (317) Google Scholar, 4Moskovitz J. Roles of methionine suldfoxide reductases in antioxidant defense, protein regulation and survival.Curr. Pharm. 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Oxidation of methionine in proteins: Roles in antioxidant defense and cellular regulation.IUBMB Life. 2000; 50: 301-307Crossref PubMed Scopus (325) Google Scholar, 2Levine R.L. Mosoni L. Berlett B.S. Stadtman E.R. Methionine residues as endogenous antioxidants in proteins.Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 15036-15040Crossref PubMed Scopus (865) Google Scholar, 4Moskovitz J. Roles of methionine suldfoxide reductases in antioxidant defense, protein regulation and survival.Curr. Pharm. Des. 2005; 11: 1451-1457Crossref PubMed Scopus (71) Google Scholar). This that surface methionines can oxidized by to more oxidation in the protein other other oxidized methionines can be enzymatically by methionine sulfoxide reductases a for the of J. Methionine sulfoxide enzymes in antioxidant defense, protein and of Biophys. 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The to the and folding stabilities within the proteomes of the Escherichia coli and the thermophile Thermus The globally the influence of folding stabilities on methionine oxidation rates and the proteome stabilities and optimal growth temperatures of these two Oxidation of protein-bound methionines that are can from the state of the protein of the native these and neighboring residue effects strongly influence the of oxidation. we that for buried methionine of the native is to the sulfur to oxidation In this protein be the in the oxidation where the folding is in a to the oxidation the folding be to the of oxidation and This is to the model used to where the of of are to correlate with folding stabilities the stability of a protein by Biol. Google Scholar). and folding stability can influence the of methionine oxidation, and the of on the properties of the methionine To the of of these to oxidation of protein-bound we proteomic to globally the rates of methionine oxidation within rates of methionine oxidation within native and folding stabilities of methionine-containing protein domains. To for methionine oxidation in E. coli protein with to with with of at for and by the of levels of oxidation levels with by of and using a this for of methionine oxidation the effects of oxidation that during and S. of in methionine oxidation of the human Res. PubMed Scopus Google Scholar). measured by the oxidation and of using a We to methionines and cysteine residues in to the effects of methionine oxidation and cysteine oxidation. In we to for methionine-containing of with a of is in with measured oxidation rates for methionine at this temperature J. Brems D.N. of antioxidants on the oxidation of methionine residues in and human Res. 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