Michael E. Colvin

Immunoreactivity of organic mimeotopes of the E2 component of pyruvate dehydrogenase: connecting xenobiotics with primary biliary cirrhosis.

In primary biliary cirrhosis (PBC), the major autoepitope recognized by both T and B cells is the inner lipoyl domain of the E2 component of pyruvate dehydrogenase. To address the hypothesis that PBC is induced by xenobiotic exposure, we took advantage of ab initio quantum chemistry and synthesized the inner lipoyl domain of E2 component of pyruvate dehydrogenase, replacing the lipoic acid moiety with synthetic structures designed to mimic a xenobiotically modified lipoyl hapten, and we quantitated the reactivity of these structures with sera from PBC patients. Interestingly, antimitochondrial Abs from all seropositive patients with PBC, but no controls, reacted against 3 of the 18 organic modified autoepitopes significantly better than to the native domain. By structural analysis, the features that correlated with autoantibody binding included synthetic domain peptides with a halide or methyl halide in the meta or para position containing no strong hydrogen bond accepting groups on the phenyl ring of the lysine substituents, and synthetic domain peptides with a relatively low rotation barrier about the linkage bond. Many chemicals including pharmaceuticals and household detergents have the potential to form such halogenated derivatives as metabolites. These data reflect the first time that an organic compound has been shown to serve as a mimeotope for an autoantigen and further provide evidence for a potential mechanism by which environmental organic compounds may cause PBC.

X̃ 1A1, ã 3B1, and à 1B1 electronic state of silylenes. Structures and vibrational frequencies of SiH2, and SiHF, and SiF2

Abstract The spectroscopic characteristics of the three lowest-lying electronic states of SiH 2 , SiHF, and SiF 2 have been predicted via a priori quantum-mechanical methods. Where experimental results are available, the theoretical predictions usually agree well. Specifically Raos identification of the 3 B 1 state of SiF 2 is confirmed here. Also Milligan and Jacoxs very tentative assignment of an absorption at 2032 cm −1 to ν 1 (SiH 2 ) is shown to be reasonable. Many spectroscopic features have been predicted for which there are no experimental observations at present.

Infrared intensities of H3O+, H2DO+, HD2O+, and D3O+

Infrared intensities of isotopic molecular ions H3O+, H2DO+, and D3O+ are reported.(AIP)Infrared intensities of isotopic molecular ions H3O+, H2DO+, and D3O+ are reported.(AIP)

Quantitative structure-activity relationship of flavonoids for inhibition of heterocyclic amine mutagenicity.

The mutagenic/carcinogenic heterocyclic amines formed during the cooking of protein foods have been determined to be a potential risk to human health. Therefore, mitigation measures are beginning to be studied. A recent finding is that the induction of mutation in Salmonella by these amines can be inhibited by the addition of flavonoids to the assay. This study combines data on the inhibitory process with structural, ab initio quantum chemical, hydropathic, and antioxidant factors to develop a quantitative structure‐activity relationship (QSAR) database and statistical analysis. For 39 diverse flavonoids the inhibitory potency varied approximately 100‐fold. Three predictive variables, in order of decreasing contribution to variance, are: (1) a large dipole moment; (2) after geometric minimization of energy, a small departure from planarity (i.e., small dihedral angle between the benzopyran nucleus and the attached phenyl ring), and a low rotational energy barrier to achieving planarity; and (3) fewer hydroxyl groups on the phenyl ring. However, these variables account for less than half of the variance in inhibitory potency of the flavonoids. Frontier orbital energies and antioxidant or radical scavenging properties showed little or no relationship to potency. We conclude that interference by the flavonoids with cytochrome P450 activation of the promutagens is the probable mechanism for inhibition of mutagenesis, and suggest avenues for further research. Environ. Mol. Mutagen. 35:279–299, 2000 Published 2000 Wiley‐Liss, Inc.

Chemical and biological factors affecting mutagen potency

This review surveys the chemical and biological factors that are correlated with the mutagenic activity of the aromatic and heterocyclic amines. Particular attention is given to the predicted quantum chemical properties of the parent amines and their metabolites. A number of chemical properties have been found to correlate well with measured mutagenic potency, including log P, the energies of the frontier orbitals of the parent amines, and the thermodynamic stability of the nitrenium ion, possibly the ultimate DNA-binding species. These correlations are intriguing clues to the mutagenic activity of the aromatic amines; however, many factors still await final explanation, including the exact mechanisms of the metabolic enzymes, the identity(s) of the ultimate DNA-binding species, the reaction mechanism in the DNA-adduction, the role of sequence context in the covalent and non-covalent binding of the adducts, and the role of DNA repair.

Parallel algorithms for quantum chemistry. I. Integral transformations on a hypercube multiprocessor

For many years it has been recognized that fundamental physical constraints such as the speed of light will limit the ultimate speed of single processor computers to less than about three billion floating point operations per second (3 GFLOPS). This limitation is becoming increasingly restrictive as commercially available machines are now within an order of magnitude of this asymptotic limit. A natural way to avoid this limit is to harness together many processors to work on a single computational problem. In principle, these parallel processing computers have speeds limited only by the number of processors one chooses to acquire. The usefulness of potentially unlimited processing speed to a computationally intensive field such as quantum chemistry is obvious. If these methods are to be applied to significantly larger chemical systems, parallel schemes will have to be employed. For this reason we have developed distributed‐memory algorithms for a number of standard quantum chemical methods. We are current...

Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process

Replication and related processes in eukaryotic cells require replication factor C (RFC) to load a molecular clamp for DNA polymerase in an ATP‐driven process, involving multiple molecular interactions. The detailed understanding of this mechanism is hindered by the lack of data regarding structure, mutual arrangement, and dynamics of the players involved. In this study, we analyzed interactions that take place during loading onto DNA of either the PCNA clamp or the Rad9‐Rad1‐Hus1 checkpoint complex, using computationally derived molecular models. Combining the modeled structures for each RFC subunit with known structural, biochemical, and genetic data, we propose detailed models of how two of the RFC subunits, RFC1 and RFC3, interact with the C‐terminal regions of PCNA. RFC1 is predicted to bind PCNA similarly to the p21‐PCNA interaction, while the RFC3‐PCNA binding is proposed to be similar to the E. coli δ‐β interaction. Additional sequence and structure analysis, supported by experimental data, suggests that RFC5 might be the third clamp loader subunit to bind the equivalent PCNA region. We discuss functional implications stemming from the proposed model of the RFC1‐PCNA interaction and compare putative clamp‐interacting regions in RFC1 and its paralogs, Rad17 and Ctf18. Based on the individual intermolecular interactions, we propose RFC and PCNA arrangement that places three RFC subunits in association with each of the three C‐terminal regions in PCNA. The two other RFC subunits are positioned at the two PCNA interfaces, with the third PCNA interface left unobstructed. In addition, we map interactions at the level of individual subunits between the alternative clamp loader/clamp system, Rad17‐RFC2–5/Rad9‐Rad1‐Hus1. The proposed models of interaction between two clamp/clamp loader pairs provide both structural framework for interpretation of existing experimental data and a number of specific findings that can be subjected to direct experimental testing.

Heterocyclic amine formation and the impact of structure on their mutagenicity

The occurrence and formation of heterocyclic amines in foods is discussed in light of the consistent finding of a new class of imidazopyridines. In addition, a quantitative structure-activity relationship will be presented correlating the potency of these imidazopyridines to predicted chemical properties. Although no strong linear correlation is found between the potency and the chemical properties, a low dipole moment is found to be a qualitative predictor of high mutagenic potency.

Experimental and simulation studies of heat flow and heterocyclic amine mutagen/carcinogen formation in pan-fried meat patties.

Heterocylic amine (HA) compounds formed in the cooking of certain foods have been shown to be bacterial mutagens and animal carcinogens, and may be a risk factor for human cancer. To help explain the variation observed in HA formation under different cooking conditions, we have performed heat-flow simulations and experiments on the pan-frying of beef patties. The simulations involve modeling the heat flow within a meat patty using empirically derived thermal transport coefficients for the meat. The predicted temperature profiles are used to integrate the Arrhenius rate equation to estimate the concentration of HAs formed in the meat. We find that our simulations accurately model experimentally determined temperature profiles, cooking times, HA spatial distributions and total HA formation in patties that are flipped once during the pan-frying process. For patties flipped every 60 s, the simulations qualitatively agree with experiment in predicting reduced cooking times and HA formation relative to the singly-flipped patties. However, the simulations overestimate the effect of rapid flipping on cooking times and underestimate the effect of flipping on total HAs formed. These results suggest that the dramatic reductions in HA formation due to rapid flipping may be due to factors other than the heating process or that there is a critical feature of the flipping process that is not captured in our model.

The Dynamics, Structure, and Conformational Free Energy of Proline-Containing Antifreeze Glycoprotein

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.