Numerical computation of the electrostatic interaction energy between methanol and the dyad water-imidazole

peer reviewedThe electrostatic interaction energy between methanol and the dyad water-imidazole has been computed numerically at three levels of approximation from 3D grids of the charge density of one partner and the electrostatic potential of the other. The minimum positions and energy values thus obtained compare well with those calculated analytically. The numerical procedure is especially interesting for the prediction of the stable conformers

Mechanism of acyl transfer by the class A serine β-lactamase of Streptomyces albus G

Optimization by energy minimization of stable complexes occurring along the pathway of hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase has highlighted a proton shuttle that may explain the catalytic mechanism of the beta-lactamases of class A. Five residues, S70, S130, N132, T235 and A237, are involved in ligand binding. The gamma-OH group of T235 and, in the case of benzylpenicillin, the gamma-OH group of S130 interact with the carboxylate group, on one side of the ligand molecule. The side-chain NH2 group of N132 and the carbonyl backbone of A237 interact with the exocyclic CONH amide bond, on the other side of the ligand. The backbone NH groups of S70 and A237 polarize the carbonyl group of the scissile beta-lactam amide bond. Four residues, S70, K73, S130 and E166, and two water molecules, W1 and W2, perform hydrolysis of the bound beta-lactam compound. E166, via W1, abstracts the proton from the gamma-OH group of S70. While losing its proton, the O-gamma atom of S70 attacks the carbonyl carbon atom of the beta-lactam ring and, concomitantly, the proton is delivered back to the adjacent nitrogen atom via W2, K73 and S130, thus achieving formation of the acyl-enzyme. Subsequently, E166 abstracts a proton from W1. While losing its proton, W1 attacks the carbonyl carbon atom of the S70 ester-linked acyl-enzyme and, concomitantly, re-entry of a water molecule W'1 replacing W1 allows E166 to deliver the proton back to the same carbonyl carbon atom, thus achieving hydrolysis of the beta-lactam compound and enzyme recovery. The model well explains the differences found in the kcat. values for hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase. It also explains the effects caused by site-directed mutagenesis of the Bacillus cereus beta-lactamase I [Gibson, ChristensenPeer reviewe

Site-Directed Mutagenesis of the Streptomyces R61 Dd-Peptidase. Catalytic Function of the Conserved Residues around the Active Site and a Comparison with Class-a and Class-C Beta-Lactamases

The importance of various residues in the Streptomyces R61 penicillin-sensitive DD-peptidase has been assessed by site-directed mutagenesis. The replacement of the active Ser62 by a Cys residue yielded an inactive protein which was also unable to recognize penicillin. The activity of the Lys65 → Arg mutant with the peptide and thiol ester substrates was decreased 100-200-fold and the rate of penicillin inactivation was decreased 20 000-fold or more. The mutant thus behaved as a poor, but penicillin-resistant, DD-peptidase. The other studied mutations, the mutations Phe358 → Leu, Tyr90 → Asn, Thr101 → Asn, Phe164 → Ala, Asp225 → Glu and Asp225 → Asn had little influence on the catalytic and penicillin-binding properties. The Asp225 mutants did not exhibit an increased sensitivity to cefotaxime. The Phe164 → Ala mutant was significantly more unstable than the wild-type enzyme

Catalytic Properties of Class a Beta-Lactamases: Efficiency and Diversity

beta-Lactamases are the main cause of bacterial resistance to penicillins, cephalosporins and related beta-lactam compounds. These enzymes inactivate the antibiotics by hydrolysing the amide bond of the beta-lactam ring. Class A beta-lactamases are the most widespread enzymes and are responsible for numerous failures in the treatment of infectious diseases. The introduction of new beta-lactam compounds, which are meant to be 'beta-lactamase-stable' or beta-lactamase inhibitors, is thus continuously challenged either by point mutations in the ubiquitous TEM and SHV plasmid-borne beta-lactamase genes or by the acquisition of new genes coding for beta-lactamases with different catalytic properties. On the basis of the X-ray crystallography structures of several class A beta-lactamases, including that of the clinically relevant TEM-1 enzyme, it has become possible to analyse how particular structural changes in the enzyme structures might modify their catalytic properties. However, despite the many available kinetic, structural and mutagenesis data, the factors explaining the diversity of the specificity profiles of class A beta-lactamases and their amazing catalytic efficiency have not been thoroughly elucidated. The detailed understanding of these phenomena constitutes the cornerstone for the design of future generations of antibiotics

Active-site mutants of class B beta-lactamases: substrate binding and mechanistic study

Increased resistance to beta-lactam antibiotics is mainly due to beta-lactamases. X-ray structures of zinc beta-lactamases unraveled the coordination of the metal ions, but their mode of action remains unclear. Recently, enzymes in which one of the zinc ligands was mutated have been characterized and their catalytic activity against several beta-lactam antibiotics measured. A molecular modeling study of these enzymes was performed here to explain the catalytic activity of the mutants. Coordination around the zinc ions influences the way the tetrahedral intermediate is bound; any modification influences the first recognition of the substrate by the enzyme. For all the studied mutants, at least one of the interactions fails, inducing a loss of catalytic efficiency compared to the wild type. The present studies show that the enzyme cavity is a structure of high plasticity both structurally and mechanistically and that local modifications may propagate its effects far from the mutated amino acid

On the structural analogy between D-alanyl-D-alanine terminated peptides and β-lactam antibiotics

Structural analogy between D-alanyl-D-alanine terminated peptides (and analogues) of varying substrate activity toward D-alanyl-D-alanine-cleaving peptidases, and bicyclic fused ring azetidinone structures of varying inactivating potency toward the same enzymes has been exa-mihed by comparing the relative spatial disposition of the carboxylate function at the C-terminal position and the amide function at the N-terminal position with respect to the scissile amide bond at the central position. The observed variations in the geometric parameters and the molecular electrostatic potential maps generated by these functional groups suggest multiple modes of binding. In the monobactam sulfazecin, the relative disposition of at least the scissile amide bond and the terminal sulphamate group is comparable to that of the corresponding functions in the bicyclic β-lactams.Le degré d'analogie structurale entre, d'une part, peptides se terminant par la séquence D-alanyl-D-alanine (et analogues) et doués d'activité de substrat variable vis-à-vis des DD-peptidases et, d'autre part, β-lactamines bicycliques douées de pouvoir inactivateur variable vis-à-vis de ces mêmes enzymes a été examiné en comparant la disposition spatiale relative des fonctions carboxylate et amide qui se situent, respectivement, en position C-terminale et en position N-terminale par rapport à la liaison peptidique (amidique) sensible. Les paramètres géométriques et les cartes de potentiel électrostatique générées par ces trois fonctions suggèrent des modes multiples de fixation aux centres actifs de ces enzymes. La disposition relative du groupement sulfamate terminal et de la liaison amidique sensible dans la β-lactamine monocyclique, sulfazecine, est comparable à celle des fonctions correspondantes dans les β-lactamines bicycliques

Streptomyces albus G serine β-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes

In previous studies, several amino acids of the active site of class A , β-lactamases have been modified by site-directed mutagenesis. On the basis of the catalytic mechanism proposed for the Streptomyces albus G , β-lactamase [Lamotte- Brasseur, Dive, Dideberg, Charlier, Frere & Ghuysen (1991) Biochem. J. 279, 213-221], the influence that these mutations exert on the hydrogen-bonding network of the active site has been analysed by molecular mechanics. The results satisfactorily explain the effects of the mutations on the kinetic parameters of the enzyme's activity towards a set of substrates. The present study also shows that, upon binding a properly structured ,β-lactam compound, the impaired cavity of a mutant enzyme can readopt a functional hydrogen-bonding-network configuration