Gábor Náray-Szabó

Application of neural networks in structure–activity relationships

Methodology and application of artificial neural networks in structure–activity relationships are reviewed focusing on the most frequently used three‐layer feedforward back‐propagation procedure. Two applications of neural networks are presented and a comparison of the performance with those of CoMFA and a classical QSAR analysis is also discussed.

Mechanism of Action of D-Xylose Isomerase

The present knowledge on the stereochemical mechanism of action of glucose (or xylose) isomerase, one of the highest tonnage industrial enzymes, is summarized. First we deal shortly with experimental methods applied to study the structure and function of this enzyme: enzyme kinetics, protein engineering, X-ray crystallography, nuclear magnetic and electron paramagnetic resonance spectroscopy. Computational methods like homology modeling, molecular orbital, molecular dynamics and continuum electrostatic methods are also shortly treated. We discuss mostly those results and their contribution to the elucidation of the mechanism of action that have been published in the last decade. Structural characteristics of free xylose isomerase as well as its complexes with various ligands are depicted. This information provides a tool for the study of structural details of the enzyme mechanism. We present a general mechanism where the first step is ring opening, which is followed by the extension of the substrate to an open-chain conformation, a proton shuttle with the participation of a structural water molecule and the rate-determining hydride shift. The role of metal ions in the catalytic process is discussed in detail. Finally we present main trends in efforts of engineering the enzyme and delineate the prospective future lines. The review is completed by an extended bibliography with over 100 citations.

Computational approaches to biochemical reactivity

Preface A. Warshel, G. Naray-Szabo. 1. Quantum Mechanical Models for Reactions in Solution J. Tomasi, et al. 2. Free Energy Perturbation Calculations within Quantum Mechanical Methodologies R.S. Standon, et al. 3. Hybrid Potentials for Molecular Systems in the Condensed Phase M.J. Field. 4. Molecular Mechanics and Dynamics Simulations of Enzymes R.H. Stote, et al. 5. Electrostatic Interactions in Proteins K.A. Sharp. 6. Electrostatic Basis of Enzyme Catalysis G. Naray-Szabo, et al. 7. On the Mechanisms of Proteinases A. Goldblum. 8. Modelling of Proton Transfer Reactions in Enzymes J. Aqvist. 9. Protein-Ligand Interactions T.P. Lybrand. Subject Index.

Bond orbital framework for rapid calculation of environmental effects on molecular potential surfaces

Abstract A procedure is outlined to calculate rapidly potential surfaces of very large (bio) molecules. Using strictly localized orbitals as a basis set, the molecule is divided into a central part, treated at the SCF level, and the environment where the strictly localized character of the orbitals is maintained. Conformation of the active serine sidechain in α-chymotrypsin is discussed.

Electrostatic complementarity in molecular associations.

In this paper, I attempt to summarize the main qualitative features of electrostatic complementarity and similarity, important determinants of molecular recognition. The two aspects, Coulombic and hydrophobic matching, can be formulated in terms of molecular electrostatic potentials and fields. The Coulombic aspect is equivalent to the requirement to produce a potential pattern in the host cavity that is opposite in sign to that emerging from a guest. Hydrophobic complementarity is best described by the similis simili gaudet principle. This means that field patterns near the interacting molecular surfaces must be of similar magnitude. The above rules, which may find useful application in molecular graphics, were studied for different cases of enzyme-ligand interactions in trypsin. A further example, a noncovalent structural model of the catalytic diad in Streptomyces Griseus protease A, supports the observation that the same molecular entities form similar associations even in different environments, as is the case in the complex of small species in a crystal and amino acid residues with structural water molecules in a protein.

Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods

Abstract A comparative study of the pH-dependent redox mechanisms of several members of the cytochrome c3 family has been carried out. In a previous work, the molecular determinants of this dependency (the so-called redox-Bohr effect) were investigated for one species using continuum electrostatic methods to find groups with a titrating range and strength of interaction compatible with a mediating role in the redox-Bohr effect. Here we clarify these aspects in the light of new and improved pKa calculations, our findings supporting the hypothesis of propionate D from heme I being the main effector in the pH-dependent modulation of the cytochrome c3 redox potentials in all the c3 molecules studied here. However, the weaker (but significant) role of other titrating groups cannot be excluded, their importance and identity changing with the particular molecule under study. We also calculate the relative redox potentials of the four heme centers among the selected members of the c3 family, using a continuum electrostatic method that takes into account both solvation and interaction effects. Comparison of the calculated values with available data for the microscopic redox potentials was undertaken, the quality of the agreement being dependent upon the choice of the dielectric constant for the protein interior. We find that high dielectric constants give best correlations, while low values result in better magnitudes for the calculated potentials. The possibility that the crystallographic calcium ion in c3 from Desulfovibrio gigas may be present in the solution structure was tested, and found to be likely.

Comparison of protein electrostatic potential along the catalytic triad of serine proteinases

Intraproteic electrostatic potentials along the catalytic triad in serine proteinases are compared for eight enzymes for which three-dimensional co-ordinates are available. We used our bond-increment method to calculate the potential and we considered all protein atoms, including hydrogens. It was found that counter ions which may be located in the vicinity of charged surface side chains play a decisive role in determining enzymatic action. If ionizable side chains are neutralized the electrostatic potential curve across the catalytic triad is of minimum character in all investigated enzymes. It stabilizes the (-+-) charge distribution which models the Ser- -His+ -Asp- transition state structure which is formed during the catalytic process. Based on the close similarity of the electrostatic pattern in various enzymes we call attention to the possibility that convergent evolution produced not only the effective catalytic triad but also a minimum-type potential which accelerates the enzymatic reaction.

Construction of a 3D model of oligopeptidase B, a potential processing enzyme in prokaryotes.

A three dimensional structural model of oligopeptidase B (OpB) was constructed by homology modeling. High resolution X-ray structure of prolyl oligopeptidase (PEP), the only protein with sequential and functional homology was used as a template. Initial models of OpB were built by the MODELLER and were analysed by the PROCHECK programs. The best quality model was chosen for further refinement by two different techniques--either constrained molecular dynamics simulations or simulated annealing calculations starting from 500 K. The overall quality of each of the refined models was evaluated and the simulated annealing procedure found to be more effective. The refined model was analysed by different protein analysis programs including PROCHECK for the evaluation of the Ramachandran plot quality, PROSA for testing interaction energies and WHATIF for the calculation of packing quality. This structure was found to be satisfactory and also stable at room temperature as demonstrated by a 300 ps long unconstrained molecular dynamics simulation. Calculation of molecular electrostatic potentials revealed that the binding site of OpB is more negative than that of PEP, in accordance with the experimentally observed selectivity of OpB towards proteolysis at dibasic sites. A recently developed Monte Carlo docking method was used provide a structural rationale for the affinity differences measured between Z-Arg and Z-Arg-Arg substrates.

Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase

Acylaminoacyl peptidase from Aeropyrum pernix is a homodimer that belongs to the prolyl oligopeptidase family. The monomer subunit is composed of one hydrolase and one propeller domain. Previous crystal structure determinations revealed that the propeller domain obstructed the access of substrate to the active site of both subunits. Here we investigated the structure and the kinetics of two mutant enzymes in which the aspartic acid of the catalytic triad was changed to alanine or asparagine. Using different substrates, we have determined the pH dependence of specificity rate constants, the rate-limiting step of catalysis, and the binding of substrates and inhibitors. The catalysis considerably depended both on the kind of mutation and on the nature of the substrate. The results were interpreted in terms of alterations in the position of the catalytic histidine side chain as demonstrated with crystal structure determination of the native and two mutant structures (D524N and D524A). Unexpectedly, in the homodimeric structures, only one subunit displayed the closed form of the enzyme. The other subunit exhibited an open gate to the catalytic site, thus revealing the structural basis that controls the oligopeptidase activity. The open form of the native enzyme displayed the catalytic triad in a distorted, inactive state. The mutations affected the closed, active form of the enzyme, disrupting its catalytic triad. We concluded that the two forms are at equilibrium and the substrates bind by the conformational selection mechanism.

Ultraviolet photoelectron spectra of group IV hexamethyl derivatives containing a metal-metal bond

Abstract The He(I) photoelectron spectra of some organometallic compounds of general formula (CH 3 ) 3 M—M′(CH 3 ) 3 (M  M′ C, Si, Ge, and Sn) are presented and assigned by comparison with those of simple related molecules and with the aid of CNDO/2 calculations. The HOMO is highly localized at the central metal—metal bond, and its energy is linearly related to the M′—M+ ionic bond dissociation energy.