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Matteo Dal Peraro

Publications and source records attributed to Matteo Dal Peraro.

7 recordsLinked to original sources
PubMed2007

Proton shuttles and phosphatase activity in soluble epoxide hydrolase.

Recently, a novel metal Mg2+-dependent phosphatase activity has been discovered in the N-terminal domain of the soluble epoxide hydrolase (sEH), opening a new branch of fatty acid metabolism and providing an additional site for drug targeting. Importantly, the sEH N-terminal fold belongs to the haloacid dehalogenase (HAD) superfamily, which comprises a vast majority of phosphotransferases. Herein, we present the results of a computational study of the sEH phosphatase activity, which includes classical molecular dynamics (MD) simulations and mixed quantum mechanical/molecular mechanics (QM/MM) calculations. On the basis of experimental results, a two-step mechanism has been proposed and herein investigated: (1) phosphoenzyme intermediate formation and (2) phosphoenzyme intermediate hydrolysis. Building on our earlier work, we now provide a detailed description of the reaction mechanism for the whole catalytic cycle along with its free energy profile. The present computations suggest metaphosphate-like transition states for these phosphoryl transfers. They also reveal that the enzyme promotes water deprotonation and facilitates shuttling of protons via a metal-ligand connecting water bridge (WB). These WB-mediated proton shuttles are crucial for the activation of the solvent nucleophile and for the stabilization of the leaving group. Moreover, due to the conservation of structural features in the N-terminal catalytic site of sEH and other members of the HAD superfamily, we suggest a generalization of our findings to these other metal-dependent phosphatases.

Catalysis↗
PubMed2006

Polarization effects and charge transfer in the KcsA potassium channel.

The electronic structure of the selectivity filter of KcsA K(+) channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].

Bacterial Proteins↗
PubMed2004

Water-assisted reaction mechanism of monozinc beta-lactamases.

Hybrid Car-Parrinello QM/MM calculations are used to investigate the reaction mechanism of hydrolysis of a common beta-lactam substrate (cefotaxime) by the monozinc beta-lactamase from Bacillus cereus (BcII). The calculations suggest a fundamental role for an active site water in the catalytic mechanism. This water molecule binds the zinc ion in the first step of the reaction, expanding the zinc coordination number and providing a proton donor adequately oriented for the second step. The free energy barriers of the two reaction steps are similar and consistent with the available experimental data. The conserved hydrogen bond network in the active site, defined by Asp120, Cys221, and His263, not only contributes to orient the nucleophile (as already proposed), but it also guides the second catalytic water molecule to the zinc ion after the substrate is bound. The hydrolysis reaction in water has a relatively high free energy barrier, which is consistent with the stability of cefotaxime in water solution. The modeled Michaelis complexes for other substrates are also characterized by the presence of an ordered water molecule in the same position, suggesting that this mechanism might be general for the hydrolysis of different beta-lactam substrates.

Bacillus cereus↗
PubMed2004

Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus.

Structure and dynamics of substrate binding (cefotaxime) to the catalytic pocket of the mononuclear zinc-beta-lactamase from Bacillus cereus are investigated by molecular dynamics simulations. The calculations, which are based on the hydrogen-bond pattern recently proposed by Dal Peraro et al. (J Biol Inorg Chem 2002; 7:704-712), are carried out for both the free and the complexed enzyme. In the resting state, active site pattern and temperature B-factors are in agreement with crystallographic data. In the complexed form, cefotaxime is accommodated into a stable orientation in the catalytic pocket within the nanosecond timescale, interacting with the enzyme zinc-bound hydroxide and the surrounding loops. The beta-lactam ring remains stable and very close to the hydroxide nucleophile agent, giving a stable representation of the productive enzyme-substrate complex.

Bacillus cereus↗
PubMed2003

Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis.

The determination of the protonation state of enzyme active sites may be crucial for the investigation of their mechanism of action. In the bizinc beta-lactamase family of enzymes, no consensus has been reached on the protonation state of a fully conserved amino acid present in the active site, Asp120. To address this issue, we carry out here density functional theory (DFT) calculations on large models (based on Bacteroides fragilis X-ray structure) which include the metal coordination polyhedron and groups interacting with it. Our calculations suggest that Asp120 is ionized. The relevance of this finding for site-directed mutagenesis experiments on the 120 position and on the mechanism of action is discussed.

Aspartic Acid↗
PubMed2002

Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site.

Zinc(II)-beta-lactamases are among the latest generation of antibiotic-resistant enzymes developed by bacteria against beta-lactams. Here we have used density functional theory to provide the full structure of the catalytic site from Bacillus cereus mononuclear beta-lactamase II. Calculations are carried out on relative large models built on the X-ray structure of the free enzyme at the highest available resolution (1.7 A, PDB entry 3BC2). The most stable conformation emerging from our calculations consists of a Zn(II)-bound hydroxide, which acts as nucleophilic agent in the enzymatic reaction, highly stabilized by a complex hydrogen-bond network, in which the protonation state of Asp90 plays a major role. The pattern differs from that previously proposed on the basis of smaller models. Furthermore, the calculations confirm that Arg91 contributes to determine the orientation and the protonation state of Asp90, as recently suggested by mutagenesis experiments.

Amino Acids↗