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Mass spectrometry (MS) was used to characterise the binding of the 58 kDa protein OppA to 11 peptides with diverse properties. Peptides with two, three and five amino acid residues were added to OppA, and the mass spectra showed that the highest-affinity complexes are formed between OppA and tripeptide ligands. Lower-affinity complexes were observed for OppA and dipeptide ligands, and no complex formation was detected with pentapeptides or a tripeptide in which the N-terminal amino group was acetylated. Tripeptides containing a single d amino acid residue were found not to bind to native OppA. Evidence from the peak width and the, charge in the spectra of the complexes suggests that the bound peptides are encapsulated by the protein in a solvent-filled cavity in the gas phase of the mass spectrometer. Analysis of the proportions of peptide-bound and free proteins under low-energy MS conditions shows a good correlation with solution-phase K(d) measurements where available. Increasing the internal energy of the gas-phase complex led to dissociation of the complex. The ease of dissociation is interpreted in terms of the intrinsic stability of the complex in the absence of the stabilising effects of bulk solvent. The results from this study demonstrate insensitivity to the hydrophobic and ionic properties, of the side-chains of the peptides, in contrast to the investigation of other protein ligand systems by MS. Moreover, these findings are in accord with the physiological role of this protein in allowing into the cell di- and tripeptides containing naturally occurring amino acids, regardless of their sequence, while barring access to potentially harmful peptide mimics.

Original publication




Journal article


J Mol Biol

Publication Date





269 - 279


Acetylation, Bacterial Proteins, Binding Sites, Carrier Proteins, Ligands, Lipoproteins, Mass Spectrometry, Models, Molecular, Molecular Weight, Oligopeptides, Protein Binding, Solvents, Static Electricity, Substrate Specificity, Thermodynamics, Water