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PubMed2005

Two contact-point chiral distinction: model CHFClBr dimers.

Dimers of the simple chiral molecule CHFClBr have been studied using a variety of computational approaches, including HF, MP2, and DFT B3LYP and the 6-31G*, 6-31++G**, and 6-311++G** basis sets. Both heterochiral and homochiral dimers were studied to allow analysis of the chiral distinction in these systems. The dimers were arranged in edge-to-edge orientations with assorted combinations of two contact-points ("2:2e") between the dimers. The monomers were constrained to tetrahedral symmetry. We demonstrate that chiral distinction does indeed occur in these two contact-point models. While the stabilization energies are driven by the interactions of the nearest atoms (contacts) in the complexes, the degree of chiral distinction is driven by the profile of changing atoms, which, in the present systems, are often the distal atoms of the complexes. Moreover, the chiral distinction does not correlate with the stabilization energies. The terms contact-points and interactions are defined.

Journal Article↗

PubMed2002

Two-point contact chiral distinction--a theoretical appraisal.

Ab initio calculations reveal chiral distinction in two-point contact CHFCIBr dimers, with chiral distinction energy of 1.5 kJ mol-1 between the SR and SS dimers fully optimized at the MP2/6-311++G** level.

Journal Article↗

PubMed2002

Threading with chemostructural restrictions method for predicting fold and functionally significant residues: application to dipeptidylpeptidase IV (DPP-IV).

We present a new method for more accurate modeling of protein structure, called threading with chemostructural restrictions. This method addresses those cases in which a target sequence has only remote homologues of known structure for which sequence comparison methods cannot provide accurate alignments. Although remote homologues cannot provide an accurate model for the whole chain, they can be used in constructing practically useful models for the most conserved-and often the most interesting-part of the structure. For many proteins of interest, one can suggest certain chemostructural patterns for the native structure based on the available information on the structural superfamily of the protein, the type of activity, the sequence location of the functionally significant residues, and other factors. We use such patterns to restrict (1) a number of possible templates, and (2) a number of allowed chain conformations on a template. The latter restrictions are imposed in the form of additional template potentials (including terms acting as sequence anchors) that act on certain residues. This approach is tested on remote homologues of alpha/beta-hydrolases that have significant structural similarity in the positions of their catalytic triads. The study shows that, in spite of significant deviations between the model and the native structures, the surroundings of the catalytic triad (positions of C(alpha) atoms of 20-30 nearby residues) can be reproduced with accuracy of 2-3 A. We then apply the approach to predict the structure of dipeptidylpeptidase IV (DPP-IV). Using experimentally available data identifying the catalytic triad residues of DPP-IV (David et al., J Biol Chem 1993;268:17247-17252); we predict a model structure of the catalytic domain of DPP-IV based on the 3D fold of prolyl oligopeptidase (Fulop et al., Cell 1998;94:161-170) and use this structure for modeling the interaction of DPP-IV with inhibitor.

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