Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences ...
Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.
Related Citations:
The Role of Water in Sequence-Independent Ligand Binding by an Oligopeptide Transporter Protein Tame, J.R.H., Sleigh, S.H., Wilkinson, A.J., Ladbury, J.E. (1996) Nat Struct Biol 3: 998
The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands Tame, J.R.H., Dodson, E.J., Murshudov, G., Higgins, C.F., Wilkinson, A.J. (1995) Structure 3: 1395
Structure Determination of Oppa at 2.3 Angstroms Resolution Using Multiple Wavelength Anomalous Methods Glover, I.D., Denny, R., Nguti, N.D., McSweeney, S., Thompson, A., Dodson, E., Wilkinson, A.J., Tame, J.R.H. (1995) Acta Crystallogr D Biol Crystallogr 51: 39
The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein Tame, J.R.H., Murshudov, G.N., Dodson, E.J., Neil, T.K., Dodson, G.G., Higgins, C.F., Wilkinson, A.J. (1994) Science 264: 1578
Organizational Affiliation:
Structural Biology Centre Department of Chemistry, University of York, York, YO10 5DD, UK.
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