Roger J. Pachter

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We have determined the solution structures and examined the dynamics of the Escherichia coli trp repressor (a 25-kDa dimer), with and without the co-repressor L-tryptophan, from NMR data. This is the largest protein structure thus far determined by NMR. To obtain a set of data sufficient for a structure determination it was essential to resort to isotopic(More)
The INDO atomic charges q and Wiberg bond indices p (in electrons) were calculated for aflatoxin B1, sterigmatocystin and versicolorin A. The C-2-C-3 bond in these compounds has the same bond order and is predicted to be the most reactive towards epoxidation. The electronic effects do not explain the observed differences in mutagenicity and toxicity.
The structure of the Hydra head activator (HHA) neuropeptide has been previously studied using NMR, CD, and Raman spectroscopy and determined to contain 62-67% anti-parallel beta-pleated sheet, and predicted to assume a beta-turn near the amino terminus. We have utilized spectroscopic data with the Double-Iterated Kalman Filter (DIFK) technique and CHARMm(More)
The effects of selective deuteration on calculated NOESY intensities have been analyzed for the structure of the E. coli trp aporepressor, a 25 kDa protein. It is shown that selectively deuterated trp aporepressor proteins display larger calculated NOESY intensities than those for the same interproton distances in the natural abundance protein. The(More)
Proton transfer to the [Fe-Fe](H) sub-cluster in the Desulfovibrio desulfuricans (DdH) and Clostridium pasteurianum (CpI) [Fe-Fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. Pathways that can be inferred from the X-ray crystal structures of DdH and CpI, i.e.,(More)
Today's CA tools are not self-contained. The development of a concept from engineering to final product requires a variety of specialized tools. In order to connect these different vendor tools (large and small) at the applications level, integration capability is necessary. True integration can only be accomplished with the development of standards in the(More)
Sequence-specific 1H NMR assignments are reported for the active L-tryptophan-bound form of Escherichia coli trp repressor. The repressor is a symmetric dimer of 107 residues per monomer; thus at 25 kDa, this is the largest protein for which such detailed sequence-specific assignments have been made. At this molecular mass the broad line widths of the NMR(More)
In order to improve Quantitative Structure-Activity Relationships (QSARs) for halogenated aliphatics (HA) and to better understand the biophysical mechanism of toxic response to these ubiquitous chemicals, we employ improved quantum-mechanical descriptors to account for HA electrophilicity. We demonstrate that, unlike the lowest unoccupied molecular orbital(More)
The design processes are basically the same at all levels of applications - chip, board and system. Many businesses involved with design find themselves with a combination of manual methods and a variety of CA tools to accomplish different portions of this process. This implies that the information, or database, is found in a variety of media forms: on(More)
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