Brian L. Baker

The molecular conformation of methyl methacrylate — an infrared and ab initio study

Abstract An infrared study of methyl methacrylate trapped in low temperature matrixes has been carried out. Ab initio SCF calculations of harmonic frequencies at the fully optimized geometries of the planar cis and trans rotamers have been performed at the Hartree-Fock 4-31G∗∗ and 6-31G∗∗ basis set levels, with inclusion of electron correlation by second order perturbation theory (MP2). Scaled 4-31G∗∗ anharmonic frequencies have been used as an aid to the assignment of the experimental spectrum over the spectral region 400–4000 cm −1 . The computed spectrum is in excellent agreement with experiment, and confirms the co-existence of two planar rotamers (cis and trans) of nearly equal energy.

Quantification of the interaction of lysolecithin with phosphatidylcholine vesicles using bovine serum albumin: Relevance to the activation of phospholipase A2

The activity of soluble phospholipase A2 to hydrolyze phosphatidylcholine vesicles increases abruptly after a lag time of several minutes. The onset of this apparent activation event probably results from the accumulation of a threshold mole fraction of the hydrolysis products (lysolecithin and fatty acid) in the bilayer. One important observation relevant to the mechanism of this activation process is the biphasic dependence of the lag time on vesicle concentration. To test whether this dependence can be attributed entirely to the strength of partitioning of the lysolecithin into the phosphatidylcholine bilayer, we estimated the apparent partition coefficient of lysophospholipid in the membrane of phosphatidylcholine vesicles. Based on competition between bovine serum albumin and the vesicles for the lysophospholipid, we estimated the partition coefficient to be about 5.10(-7) for palmitoyl lipids at 39 degrees C and about 9.10(-7) for myristoyl lipids at 22 degrees C. These values were able to rationalize the behavior of the lag time with dipalmitoylphosphatidylcholine vesicles, but they were unable to predict the behavior with dimyristoylphosphatidylcholine. Therefore, it appears that the complete dependence of the lag phase on vesicle concentration must be explained by additional means such as the possible contribution of nascent fatty acid or previously proposed kinetic activation mechanisms.

FTIR studies of conformational isomerism in acrylates and acrylic acids

Abstract Acrylates have the possibility of existing in two heavy-atom planar structures (s-cis and s-trans), and research has shown that in many instances these conformations have somewhat similar energies. In the case of monomeric acrylic acid trapped in an inert matrix at low temperatures, two independent studies have shown that irradiation by UV light results in interconversion of the two rotamers. An interpretation of this phenomenon has been proposed in terms of hindered internal rotation about the central C–O bond. Our experimental observations on methacrylic acid (as reported in this paper), and methyl methacrylate demonstrate that the former compound shows a behavior similar to that of acrylic acid, but that UV irradiation has no effect on the interconversion of conformers in methyl methacrylate. An alternative mechanism for the interconversion of the isomers in the acrylic acids involving proton transfer is proposed.

Infrared spectrum of divinyl telluride and theoretical analysis of divinyl group VI compounds

Abstract The infrared spectrum of divinyl telluride (DVT) has been studied for the gaseous, liquid and solid phases as well as in inert matrices at low temperatures. HF-SCF calculations (using triple-zeta quality basis sets) have been carried out on DVT and on the oxygen, sulfur and selenium analogs. In each instance the calculations predict two relatively stable conformations, with the cis/trans form being the more stable for divinyl ether and a near-planar trans/trans form being the more stable for the other three compounds. The infrared spectrum of DVT is consistent with the presence of two rotameric forms of the molecule, and assignments of many of the absorptions are made to normal modes.

Quantification of the interaction between lysolecithin and phospholipase A2

The rate of hydrolysis of phosphatidylcholine bilayers by phospholipase A2 may be either enhanced or inhibited by the presence of lysolecithin depending on the experimental conditions examined. To further understand the relationship of lysolecithin to phospholipase A2 activity, the binding of lysolecithin to phospholipase A2 from the venom of Agkistrodon piscivorus piscivorus was examined by fluorescence spectroscopy. The tryptophan emission intensity of the enzyme was enhanced by 70% upon addition of lysolecithin. The binding isotherm for lysolecithin to the phospholipase A2 estimated from the fluorescence change was biphasic, with a clear break in the curve occurring at the critical micelle concentration of the lysolecithin. Several observations suggested that the phospholipase A2 was capable of hydrolyzing the lysolecithin although at a rate far below that of phospholipid hydrolysis. These experiments were repeated using several other species of phospholipase A2, and the results were found to be general among the enzymes except the lys-49 isozyme from A. p. piscivorus which displayed neither the dependence on the critical micelle concentration for binding nor the ability to hydrolyze lysolecithin. These results were used as the basis for a quantitative analysis of enzyme fluorescence changes that occur during the time course of phospholipid hydrolysis and of the mechanism whereby lysolecithin inhibits the hydrolysis of phosphatidylcholine bilayers by phospholipase A2.

Reversibility of the activation of soluble phospholipase A2 on lipid bilayers: Implications for the activation mechanism

The time-courses of hydrolysis of large vesicles of dipalmitoylphosphatidylcholine were compared using four species of phospholipase A2 (Agkistrodon piscivorus piscivorus, Crotalus adamanteus and Naja naja venoms and porcine pancreatic). In all four cases, the hydrolysis rate suddenly increases 10 to 100-fold at the time (tau) when a specific mole fraction of reaction products has accumulated. The intrinsic fluorescence emission of the three venom enzymes also increases suddenly at time tau. Both the activation and the fluorescence change are reversible with a half-time of about 50 s for the activity and 2 to 6 s for the fluorescence. These reversal rates and the vesicle concentration dependence of tau are considered for monomer and dimer enzyme activation models. Apparently, at least three states of the enzyme exist beyond the initial unbound state: (1) inactive and bound, (2) inactive with high fluorescence and (3) active. The dimer model already contains the necessary number of states but requires that the activation rate be much lower than the reversal rate to account for the vesicle concentration dependence of tau. Success of the monomer model requires an enzyme state additional to those proposed previously. Although these results do not exclude either the monomer or dimer models conclusively, they do impose important constraints on each model.

Elucidation of Protein Structural and Pharmacophore Features Based on Sequence Clustering by Common Neighbor Comparisons

INTRODUCTION. Genome sequencing projects have dramatically increased our understanding of the pathways and proteins involved in biological systems. The NAD(P)-utilizing family of enzymes is one of the most important gene families representing 15% of all known enzyme functions. We have performed a complete characterization of this gene family on a sequence, structural, and NAD(P)-pharmacophore level. Genome-wide analysis was performed to gain a complete understanding of the structures and functional importance of NAD(P)-utilizing enzymes in 17 different genomes.