Proton and tritium NMR relaxation studies of peptide inhibitor binding to bacterial collagenase: conformation and dynamics

Tritium NMR: A compilation of data and a practical guide

The present review is focused on experimental methods and structural applications of tritium NMR. It consists of five parts covering accordingly, introduction, brief overview, early (based on the papers appearing before 2000), more recent (based on the papers appeared in the interim of 2000 to 2015), and recent (based on the papers that appeared after 2015) reports. A special interest in this review is focused on practical aspects of tritium NMR spectroscopy, which is thoroughly illustrated by its numerous applications in chemistry and biochemistry.

Use of nuclear magnetic resonance in probing ligand-macromolecule interactions

Nuclear magnetic resonance techniques can be used to study ligand-macromolecule interactions under a wide variety of conditions. There are a number of different approaches, which are generally applicable under different conditions of exchange rate and binding constant. In the tight binding limit direct structural studies using NOE are possible using labeled ligand (13C, 15N) and/or labeled macromolecule. In the intermediate exchange regime, line broadening complicates the analysis of bound conformations of ligands. However, a good deal of information can be obtained about the binding kinetics and about the number and nature of binding modes when several are present. In such cases it is often best to use an NMR active nucleus which can be directly detected, with high sensitivity. Tritium has good characteristics in this respect, and has been effective in a number of cases. In the fast exchange limit it is often best to use the rapid dissociation of the ligand to transfer structural information from the bound form to the free, where it can be sensitively and selectively detected, often by direct observation of 1H values. There are a number of conditions on the binding kinetics which must be met, and systems with multiple binding sites generally cannot be analyzed. The large number of different NMR approaches which can be used, often only under special conditions of exchange, complicates planning of NMR studies of ligand-macromolecule interactions. However, once the characteristics of binding affinity and exchange rate have been determined, it is usually possible to apply NMR spectroscopy to obtain information about the binding. The instrumental demands for carrying out ligand-macromolecule interactions are generally not more than those required for studies of the macromolecules alone.

Human thimet oligopeptidase

We have purified human thimet oligopeptidase to homogeneity from erythrocytes, and compared it with the enzyme from rat testis and chicken liver. An antiserum raised against rat thimet oligopeptidase also recognized the human and chicken enzymes, suggesting that the structure of the enzyme has been strongly conserved in evolution. Consistent with this, the properties of the human enzyme were very similar to those for the other species. Thus human thimet oligopeptidase also is a thiol-dependent metallo-oligopeptidase with M(r) about 75,000. Specificity for cleavage of a number of peptides was indistinguishable from that of the rat enzyme, but Ki values for the four potent reversible inhibitors tested were lower. In discussing the results, we consider the determinants of the complex substrate specificity of thimet oligopeptidase. We question whether substrates containing more than 17 amino acid residues are cleaved, as has been suggested. We also point out that the favourable location of a proline residue and a free C-terminus in the substrate may be as important as the hydrophobic residues in the P2, P1 and P3' positions that have been emphasized in the past.

Peptide inhibitors of E. collagenolyticum bacterial collagenase--effect of N-methylation. Consequences on biological activity and conformational properties

Peptide inhibitors of E. collagenolyticum bacterial collagenase, HS-CH2-CH2-CO-Pro-Yaa (Yaa = Ala, Leu, Nle), have been N-methylated at the Yaa position. The N-methylation slightly increases the inhibitory potency of the modified peptides as compared to the parent compounds. The conformational effects of the N-methylation have been investigated by both 1H 2D-NMR and molecular mechanics energy minimization. Three low-energy conformers have been predicted for the unmethylated parent compounds (Yaa = Ala, Leu, Nle). They are characterized by the psi value of the central proline residue: psi Pro = 150 degrees (trans' conformation), psi Pro = 70 degrees (C7 conformation) and psi Pro = -50 degrees (cis' conformation). The N-methylation has been found to strongly increase the energy of the C7 conformer and to a less extent the energy of the cis' conformer. This leaves the trans' conformation as the only low-energy conformer. The ROESY experiments have established that both the N-methyl peptides and the parent compounds adopt the same preferred backbone conformation in water solution, i.e. the trans' conformation. Based on these results, the activities of the N-methyl peptides are discussed and a possible conformation of the inhibitor in the bound state is proposed.