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Oxidation increases the strength of the methionine-aromatic interaction

Nature Chemical Biology volume 12, pages 860–866 (2016)Cite this article

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Abstract

Oxidation of methionine disrupts the structure and function of a range of proteins, but little is understood about the chemistry that underlies these perturbations. Using quantum mechanical calculations, we found that oxidation increased the strength of the methionine-aromatic interaction motif, a driving force for protein folding and protein-protein interaction, by 0.5–1.4 kcal/mol. We found that non-hydrogen-bonded interactions between dimethyl sulfoxide (a methionine analog) and aromatic groups were enriched in both the Protein Data Bank and Cambridge Structural Database. Thermal denaturation and NMR spectroscopy experiments on model peptides demonstrated that oxidation of methionine stabilized the interaction by 0.5–0.6 kcal/mol. We confirmed the biological relevance of these findings through a combination of cell biology, electron paramagnetic resonance spectroscopy and molecular dynamics simulations on (i) calmodulin structure and dynamics, and (ii) lymphotoxin-α binding toTNFR1. Thus, the methionine-aromatic motif was a determinant of protein structural and functional sensitivity to oxidative stress.

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Figure 1: Structural informatics search of the CSD and PDB and interaction energy.
Figure 2: 1H-1H rotating frame Overhauser effect NMR spectroscopy (ROESY) and chemical shift analysis of α-helical peptide mixtures of two diasteriomers containing the R and S sulfoxide of methionine.
Figure 3: REMD simulations and EPR spectroscopy measurements of CaM.
Figure 4: Oxidation of LTα, but not TNF ablated its interaction with TNFR1.
Figure 5: Molecular dynamics simulations of LTα with Met120 oxidized showed that competitive interaction of Met120 with Tyr96 prevented its interaction with Trp107.

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Acknowledgements

This work was supported by grants to J.N.S. (US National Institutes of Health (NIH) R01 GM107175), D.D.T. (NIH R37 AG26160), W.C.K.P. (US National Science Foundation (NSF)-CAREER CHE-1352091) and A.H. (NSF-CAREER MCB-0845676). This work was carried out in part using computing resources at the University of Minnesota Supercomputing Institute. EPR spectroscopy and CD experiments were performed at the Biophysical Spectroscopy Center, University of Minnesota. We thank J.F. Evans for discussion and guidance regarding the principal component analysis of our CD data.

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Authors and Affiliations

  1. Department of Biomedical Engineering, University of Minnesota–Twin Cities, Minneapolis, Minnesota, USA

    Andrew K Lewis, Tiffany L Senkow, Christopher C Valley & Jonathan N Sachs

  2. Department of Chemistry and Biochemistry, University of Minnesota-Duluth, Duluth, Minnesota, USA

    Katie M Dunleavy, Benjamin T Horn, Mark A Jersett, Ryan Mahling, Alessandro Cembran & Anne Hinderliter

  3. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota–Twin Cities, Minneapolis, Minnesota, USA

    Cheng Her, Megan R McCarthy, Christine B Karim & David D Thomas

  4. Department of Chemistry, University of Minnesota–Twin Cities, Minneapolis, Minnesota, USA

    Gabriella T Perell, Jiali Gao & William C K Pomerantz

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Contributions

Project conception and production was directed by J.N.S. PDB search, molecular dynamics simulations, experimental and computational LTα work, and computational CaM work were performed by A.K.L., T.L.S., C.C.V. and J.N.S. CSD search and NMR spectroscopy were performed by G.T.P. and W.C.K.P. Quantum calculations were performed by M.A.J., A.C. and J.G. CD was performed by R.M., B.T.H., K.M.D. and A.H. Peptides were synthesized by C.B.K. CaM work was carried out by M.R.M, C.H. and D.D.T.

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Correspondence to Alessandro Cembran, Anne Hinderliter or Jonathan N Sachs.

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Lewis, A., Dunleavy, K., Senkow, T. et al. Oxidation increases the strength of the methionine-aromatic interaction. Nat Chem Biol 12, 860–866 (2016). https://doi.org/10.1038/nchembio.2159

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