Side chain dynamics and alternative hydrogen bonding in the mechanism of protein thermostabilization.

To elucidate the mechanism of protein thermostabilization, the thermodynamic properties of small monomeric proteins from mesophilic and thermophilic organisms have been analyzed. Molecular dynamics simulations were employed in the study of dynamic features of charged and polar side chains of amino acid residues. The basic conclusion has been made: surface charged and polar side chains with high conformational mobility can form alternative hydrogen bonded (H-bonded) donor-acceptor pairs. The correlation between the quantitative content of alternative H-bonds per residue and the temperature of maximal thermostability of proteins has been found. The proposed mechanism of protein thermostabilization suggests continuous disruption of the primary H-bonds and formation of alternative ones, which maintain constant the enthalpy value in the native state and prevent a rapid increase of the conformational entropy with the rising temperature. The analysis of the results show that the more residues located in the N- and C-terminal regions and in the extended loops that are capable of forming alternative longer-range H-bonded pairs, the higher the protein thermostability.

Ab initio and density functional evaluations of the molecular conformations of beta-caryophyllene and 6-hydroxycaryophyllene.

The four conformations of beta-caryophyllene (alphaalpha, alphabeta, betaalpha, and betabeta) were investigated ab initio at the 6-31G/HF and MP2 levels and additionally with density functional methods (B3LYP/6-31G), as it concerns their relative thermodynamic stabilities. The alphaalpha is predicted to be the most stable geometry, in agreement with low-temperature NMR measurements. In the case of 6-hydroxycaryophyllene, the alphaalpha is still the most stable conformation when the configuration at C-6 is S, but when the configuration is reversed to R the betabeta geometry becomes the most stable one. This is again in agreement with NMR data. On the other hand, for both molecules the AM1 semiempirical model Hamiltonian fails to predict the alphaalpha as a low-energy geometry, mainly due to an incorrect description of the cyclobutane ring puckering. The interconversion paths among the different minima are also analyzed and discussed. The solvent effect (either chloroform or water) on the stability of the different conformers of beta-caryophyllene and 6-hydroxycaryophyllene was studied in the polarizable continuum model framework.

A theoretical study on reaction pathways to carbanions.

Different substituents (NO2, C6H5, NH2, NH-CH=CH-CHO) to a methylene group were taken into account to investigate under which conditions the mechanism of formation of carbanions by proton transfer to a base (methylamine) can be favorable, as a preliminary study of the reaction catalyzed by semicarbazide-sensitive amine oxidases. Three different approaching paths of methylamine to C(alpha) in NO2-C(alpha)H2-NO2, and the relevant potential energy surfaces, were examined at the SCF/3-21G and 6-31G* levels. The proton transfer along the first two paths occurred with a similar barrier, which became fairly consistent after including the MP2 correlation correction, with either basis set, while the last approaching path was abandoned. For the other model systems the minimum was searched only at the 3-21G level in the vicinity of the first reaction path. The substitution of a nitro group with a phenyl group sharply raised the barrier for the proton transfer to methylamine. Also by substituting the second nitro group with either -NH2 or -NH-CH=CH-CHO, a steep uphill pathway was found. A more realistic model of the substrate-cofactor complex, namely the Schiff base between benzylamine and pyridoxal, again produced a barrier, almost matching that obtained for C6H5-C(alpha)H2-NO2. In both cases, the energy profiles for the rotation about the CC(alpha)NC dihedral and the proton shift tautomers were also considered at the 3-21G and 6-31G* levels. A preliminary scan of the effect of methyl (or methylphosphate) substitutions to the pyridoxal ring was performed and the stability of the Schiff bases involving other cofactors was also considered.

4-Diazinyl- and 4-pyridinylimidazoles: potent angiotensin II antagonists. A study of their activity and computational characterization.

A series of N-[biphenylyl(tetrazolyl)methyl]-2-butylimidazoles containing variously substituted diazine or pyridine moieties either as their free bases or N-oxide derivatives attached to the 4-position of the imidazole ring was synthesized and tested for interaction with the AT1 receptors of rat adrenal cortex membranes (receptor binding assay). Some compounds were then chosen for further evaluation in vivo in the A II-induced pressor response in conscious normotensive rats. The most potent in the AT1 binding assay were found to be compounds in which the diazine or pyridine ring nitrogen is adjacent to the point of attachment between the two heteroaromatic rings such as 2-butyl-4-(3,6-dimethylpyrazin-2-yl)-1-[[2'-(1H-tetrazol-5-y l)-biphenyl-4- yl]methyl]-1H-imidazole (3b) or 2-butyl-4-[5-(methoxycarbonyl)pyrid-2-yl]-1-[[2'-(1H-tetrazol++ +-5- yl)biphenyl-4-yl]methyl]-1H-imidazole (6c). The binding affinities and oral activities of the pyridine N-oxide imidazoles in which a stabilizing group ortho to the pyridine ring nitrogen is present were markedly improved as in 2-butyl-4-[(3-methoxycarbonyl)-6-methyl-N-oxopyridin-2-yl]-1-[[2'- (1H- tetrazol-5-yl)biphenyl-4-yl]methyl]-1H-imidazole 31b. Molecular modeling studies were carried out to determine the molecular electrostatic potential values of related model systems and to correlate their receptor interaction energies with the observed activities of our compounds.

Simple model for the effect of Glu165----Asp165 mutation on the rate of catalysis in triose phosphate isomerase.

We present an ab-initio self-consistent field calculation with a 4-31G basis set on a simple model for proton abstraction from hydroxyacetone (a model for dihydroxyacetone phosphate; DHAP) by formate, which is a model for Glu165 in triose phosphate isomerase. Earlier, we showed that the electrophilic groups on the enzyme (the NH3+ of Lys13 and the NH of His95) were essential to efficient catalysis by triose phosphate isomerase. These groups stabilized the enediolate formed by proton abstraction from the DHAP model so that proton transfer from this molecule to Glu165 became likely. In this study, we carry this analysis one step further. First, we re-examine the energy profile for proton transfer, using the fact that our earlier calculations showed that the combined effect of His95 and Lys13 on the reactant DHAP and intermediate enediolate was to make them equal in energy. Then, we analyze the likely effect of changing Glu165 to Asp165 and relate this to experiments on the kinetics of enzyme catalysis by the Glu165----Asp165 mutant.