Biomedical subjects
Publications and source records attributed to Ruth Pachter.
A quinoidal porphyrin has been synthesised with such a curved pi-system that pi-pi stacking leads to the formation of cyclic trimer aggregates in the crystal, which pack to generate cylindrical channels with an internal diameter of 1.0 nm.
Molecular dynamics (MD) simulations were carried out to study the conformational rearrangement induced by deprotonation of the fluorescent chromophore in GFP, as well as the associated changes in the hydrogen-bonding network. For both the structures with either a neutral or an anionic chromophore, it was found that the beta-barrel was stable and rigid, and the conformation of the chromophore was consistent with the available x-ray structure. The conformational change in Thr203 due to deprotonation was also found to be consistent with the three-state isomerization model. Although GFP is highly fluorescent, denatured-GFP is nonfluorescent, indicating that the environment of the protein plays an important role in its fluorescence behavior. Our MD simulations, which explore the effect of the protein shell on the conformation of the chromophore, find the flexibility of the central chromophore to be significantly restricted due to the rigid nature of the protein shell. The hydrogen-bonding between the chromophore and neighboring residues was also shown to contribute to the chromophore rigidity. In addition to the MD studies, quantum mechanics/molecular mechanics (QM/MM) ONIOM calculations were carried out to investigate the effect of the beta-barrel on the internal rotation in the chromophore. Along with providing quantitative values for torsional rotation barriers about the bridging bond in the chromophore, the ONIOM calculations also validate our MD force field parameters.
We present the performance of the fast classical molecular dynamics (MD) code, fast molecular dynamics (FMD), designed for efficient, object-oriented, and scalable large scale simulations, and summarize its application to a liquid crystalline cluster. FMD uses an implementation of the three-dimensional fast multipole method, developed in our group. The fast multipole method offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus, enabling more realistic simulations of large molecular systems. Performance testing was carried out on IBM SP2, SGI Origin 2000, and CRAY T3E massively parallel systems using the MPI massage passing library. The electrostatic forces were tested on models of up to 100,000 randomly placed charges, and on protein and liquid crystalline molecular systems of over 99,000 atoms. Tests on the stability of the method are presented, along with comparisons with direct calculations, the NAMD2 code, and the physical multipole-based cell-multipole method.
Hydrazine propellants pose a substantial operational concern to the U.S. Air Force and to the aerospace industry because of their toxicity. In our continuing efforts to develop methods for the prediction of the toxicological response to such materials, we have measured in vitro toxicity endpoints for a series of high-energy chemicals (HECs) that were recently proposed as propellants. The HECs considered are structurally diverse and can be classified into four chemical types (hydrazine-based, amino-based, triazoles, and a quaternary ammonium salt), although most are hydrazine derivatives. We measured the following endpoints in primary cultures of isolated rat hepatocytes: mitochondrial function (MTT), lactate dehydrogenase leakage (LDH), generation of reactive oxygen species (ROS), and total glutathione content (GSH). In several instances, effective concentrations (EC) were indeterminate, and only lower limits to the measured endpoints could be ascertained. Using molecular descriptors calculated with a semiempirical molecular orbital method, quantitative structure-activity relationships (QSARs) were derived for MTT (EC25) and for GSH (EC50). Correlation coefficients for 2- and 3-parameter QSARs of about 0.9 enable us to predict the toxicity for similar compounds. Furthermore, except in one case, predicted EC values for the uncertain endpoints were consistent with experiment. Descriptors comprising the QSARs for MTT were consistent with the biophysical mechanism of toxic response found experimentally for hydrazine derivatives. Application of our derived QSARs will assist in predicting toxicity for newly proposed propellants.
The toxic effects from exposure to halogenated hydrocarbons (HAs), which are produced in large amounts and used in a variety of applications, are well-known. Previously, QSARs for the toxicity of a series of HAs in vitro have been studied extensively. In this work, using a composite toxicity metric calculated from a set of five in vitro hepatotoxicity endpoints determined for 20 HAs, we find that QSARs derived using quantum descriptors calculated from the neutral HA species are statistically similar to QSARs calculated from HA metabolites. In most cases, QSARs derived using descriptors calculated from both neutral HAs and metabolites are statistically superior to those derived using either neutral-HA descriptors or metabolite descriptors. However, to properly utilize metabolite descriptors, multiple QSARs, each of which utilizes a set of HAs that form unique metabolites, must be derived and toxicity values calculated therefrom must be averaged. These average toxicity values agree better with experiment than those calculated from the neutral-HA QSARs.