RESUMEN
We have investigated the importance of polarization by the enzyme dihydrofolate reductase (DHFR) on its substrates, folate and dihydrofolate, using a series of quantum mechanical (QM) techniques (Hartree-Fock (HF), Møller-Plesset second-order perturbation theory (MP2), local density approximation (LDA) and generalized gradient approximation (GGA) density functional theory (DFT) calculations) in which the bulk enzyme is included in the calculations as point charges. Polarization, in terms of both charges on components (residues) of the folate and dihydrofolate molecules and changes in the electron density, particularly of the pterin ring of the substrates, and the implications for the catalytic reduction are discussed. Significant differences in polarization behavior are observed for the different theoretical methods employed. The consequences of this, particularly for choosing an appropriate model for quantum mechanical/molecular mechanical (QM/MM) calculations, are pointed out. The HF and MP2 QM methods show small polarizations (approximately 0.04 electrons) of the pterin ring but quite large polarizations with both LDA and GGA DFT methods (0.3-0.5 electrons). This large difference in polarization for both folate and dihydrofolate arises as a result of substantial differences between the charge distributions for the gasphase DFT and HF calculations, specifically the charges on the dianionic glutamate side chain. Some recent literature reports of incorrect representation of anionic systems by DFT methods are noted. The DFT results are similar to the previously reported LDA DFT results of Bajorath et al. predicting a large polarization of the pterin ring of folate (Proteins 9:217-224, 1991) and dihydrofolate (PNAS 88:6423-6426, 1991) of approximately 0.5-0.6 electrons.
Asunto(s)
Escherichia coli/química , Ácido Fólico/análogos & derivados , Tetrahidrofolato Deshidrogenasa/química , Ácido Fólico/química , Mecánica , Modelos Moleculares , Conformación Proteica , Electricidad Estática , Especificidad por SustratoRESUMEN
A desktop PC-based graphics package, UNIVIS, for visualization of three-dimensional numerical data is described. Apart from routine molecular model visualization, the package provides for a host of other features such as extraction of various surfaces, planar cross-sections of the three-dimensional data, and property texturing. Fast rendering and transparency are the strengths of the present package. These features are comprehensively discussed. The salient features of UNIVIS are presented in the form of visualization of a variety of molecular properties, which are of immense importance in understanding molecular structure and reactivity patterns.