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The methionine-aromatic motif plays a unique role in stabilizing protein structure.

ABSTRACT: Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1-1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins.

SUBMITTER: Valley CC

PROVIDER: S-EPMC3471747 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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The methionine-aromatic motif plays a unique role in stabilizing protein structure.

Valley Christopher C CC Cembran Alessandro A Perlmutter Jason D JD Lewis Andrew K AK Labello Nicholas P NP Gao Jiali J Sachs Jonathan N JN

The Journal of biological chemistry 20120801 42

Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif ...[more]

PMID: 22859300

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Project description:Campylobacter concisus, an emerging pathogen found throughout the human oral-gastrointestinal tract, is able to grow under microaerobic or anaerobic conditions; in the latter case, N- or S-oxides could be used as terminal electron acceptors (TEAs). Analysis of 23 genome sequences revealed the presence of multiple (at least two and up to five) genes encoding for putative periplasmic N- or S-oxide reductases (N/SORs), all of which are predicted to harbor a molybdopterin (or tungstopterin)-bis guanine dinucleotide (Mo/W-bisPGD) cofactor. Various N- or S-oxides, including nicotinamide N-oxide, trimethylamine N-oxide , biotin sulfoxide, dimethyl sulfoxide, and methionine sulfoxide (MetO), significantly increased anaerobic growth in two C. concisus intestinal strains (13826 and 51562) but not in the C. concisus oral (type) strain 33237. A collection of mutants was generated to determine each N/SOR substrate specificity. Surprisingly, we found that disruption of a single gene, annotated as "bisA" (present in strains Cc13826 and Cc51562 but not in Cc33237), abolished all N-/S-oxide-supported respiration. Furthermore, ΔbisA mutants showed increased sensitivity to oxidative stress and displayed cell envelope abnormalities, suggesting BisA plays a role in protein MetO repair. Indeed, purified recombinant CcBisA was able to successfully repair MetO residues on a commercial protein (β-casein), as shown by mass spectrometry. Our results suggest that BisA plays a dual role in C. concisus, by allowing the pathogen to use N-/S-oxides as TEAs and by repairing periplasmic protein-bound MetO residues, therefore essentially being a periplasmic methionine sulfoxide reductase (Msr). This is the first report of a Mo/W-bisPGD-containing Msr enzyme in a pathogen. IMPORTANCE Campylobacter concisus is an excellent model organism to study respiration diversity, including anaerobic respiration of physiologically relevant N-/S-oxides compounds, such as biotin sulfoxide, dimethyl sulfoxide, methionine sulfoxide (MetO), nicotinamide N-oxide, and trimethylamine N-oxide. All C. concisus strains harbor at least two, often three, and up to five genes encoding for putative periplasmic Mo/W-bisPGD-containing N-/S-oxide reductases. The respective role (substrate specificity) of each enzyme was studied using a mutagenesis approach. One of the N/SOR enzymes, annotated as "BisA", was found to be essential for anaerobic respiration of both N- and S-oxides. Additional phenotypes associated with disruption of the bisA gene included increased sensitivity toward oxidative stress and elongated cell morphology. Furthermore, a biochemical approach confirmed that BisA can repair protein-bound MetO residues. Hence, we propose that BisA plays a role as a periplasmic methionine sulfoxide reductase. This is the first report of a Mo/W-bisPGD-enzyme supporting both N- or S-oxide respiration and protein-bound MetO repair in a pathogen.

Dataset Information

The methionine-aromatic motif plays a unique role in stabilizing protein structure.

Publications

The methionine-aromatic motif plays a unique role in stabilizing protein structure.

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