Modeling alcohol metabolism with the DARC/CALPHI system.

We present our general system for QSAR search, CALPHI (Computer-Aided Law by Hyperstructure Investigation) set up in the context of the DARC structural language. We use it to construct global, fragmentary, and topological models of the capacity of alcohols to undergo glucuronidation. The DARC/PELCO model, more precisely and more significantly, explains 98% of the total variance with only three parameters, while treating the whole set of primary, secondary, and tertiary alcohols, whereas the best previously reported treatment restricted to primary alcohols, explains only 90% of the variance with two parameters. It provides an explicit and more precise interpretation of alcohol metabolism. The PELCO methodology is extended to evaluate the prediction reliability of both global and fragmentary models. PELCO leads to more predictions when comparison is made at the same level of reliability.

The different influences of ether and ester phospholipids on the conformation of gramicidin A. A molecular modelling study.

With AMBER (assisted model building with energy refinement) molecular modelling techniques, the interactions between lipids which differ in the type of chain linkage (e.g., ether or ester) and gramicidin were approximated. It was found, theoretically, that replacement of the ester function in dipalmitoylphosphatidylcholine (DPPC) by an ether moiety induces a shift in the rotameric distribution of the Trp-15 side-chain in gramicidin A. Concomitantly, the channel entrance is contracted by approx. 0.4 A. The perturbation can be related to the strong hydrogen-bond formed between the lipid carbonyl group and the indole proton of the Trp-15 residue of gramicidin. In the ether lipid-gramicidin assembly a weaker H-bond is formed between Trp-15 and the phosphate moiety. To obtain a first indication of the influence of the strength of this H-bond on gramicidin A, a preliminary experimental study was set up. The transport properties of gramicidin A were studied using efflux measurements through vesicle walls containing ether and ester lipids, respectively. A change in the permeability of gramicidin A was found when ether lipids were added to a bilayer composed of the ester lipid dioleoylphosphatidylcholine (DOPC).

Role of magnesium cations in the yeast orotate phosphoribosyltransferase catalyzed reaction. Mechanism of the inhibition by Cu++ and Ni++ ions.

The magnesium chelate of the N(3)H tautomer of orotate, L3Mg, is the true substrate in the biosynthesis of orotidine 5'-monophosphate (OMP) catalyzed by yeast orotate phosphoribosyltransferase (OPRTase, E.C. 2.4.210) with a Michaelis constant KmL3Mg equal to 12(2) muM. It is postulated that Mg++ cations activate the transport of orotate to the active site by neutralizing the orotate charges; the ligand N(3)H is then exchanged between the incoming cation and the cation bound to the enzyme, thus ensuring the stabilization of the appropriate isomeric structure of orotate. This scheme, together with kinetic and thermodynamic data on orotate complexation by Mg++ and Ca++, accounts for the role of Ca++ cations that neither activate nor inhibit OMP synthesis. Cu++ and Ni++ inhibiting properties arise from the formation of inert complexes of orotate. Ni++ complexes have a poor affinity for the protein, whereas Cu++ complexes have a Michaelis constant similar to that of the L3Mg active species. The inertness of these complexes is tentatively understood in terms of low phosphoribosyl transfer rates as postulated from the kinetic study of the protonation of the complexes in water.

Highly sensitive microwave temperature-jump apparatus.

A temperature-jump apparatus with repetitive microwave heating and spectrophotometric detection is described. Temperature jumps of 1.5 degrees C are achieved in a flow microcell within 1.5 mus (two shorter heating times of 0.5 and 0.25 mus are also available) at a repetition rate up to 50 Hz. On-line accumulation of the relaxation signals is performed with a PDP 11 processor, leading to very short recording times (more than 1000 signals accumulated in less than 50 s) and to a sensitivity better than 10(-4) optical density (OD) units. Nonlinear identification treatment permits processing the summed signal even when it is strongly blurred by noise. To demonstrate the capabilities of our apparatus, highly shifted fast prototropic equilibria in aqueous solutions of pyrimidine base have been studied.