QM/MM methods were used to study the isomerization step from (2R)-methylmalonyl-CoA to succinyl-CoA. A pathway via a "fragmentation-recombination" mechanism is ruled out on energetic grounds. For the other radicalic pathway, involving an addition recombination step, geometries and vibrational contributions have been determined, and a barrier height of 11.
View Article and Find Full Text PDFA nonoriented hydrated film of poly(dG-dC) with ?20 water molecules per nucleotide (called B* by Loprete and Hartman (Biochem. 32, 4077-4082 (1993)) was studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated sample between 290 and 270 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200 and 220 K. IR spectral changes on isothermal relaxation at 200 and 220 K, caused by interconversion of two conformer substates, are revealed by difference spectra.
View Article and Find Full Text PDFHuman plasma afamin, the fourth member of the albumin gene family, is shown to be a specific binding protein for vitamin E. A radio ligand-binding assay followed by Scatchard and Hill analysis are used to show that afamin has a binding affinity for both alpha-tocopherol and gamma-tocopherol, two of the most important forms of vitamin E, in vitro. The binding-dissociation constant was determined to be 18 microM, indicating that afamin plays a role as vitamin E carrier in body fluids such as human plasma and follicular fluid under physiological conditions.
View Article and Find Full Text PDFWe investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened.
View Article and Find Full Text PDFAlthough the trp-repressor-operator complex is one of the best studied transcriptional controlling systems, some questions regarding the specific recognition of the operator by the repressor remain. We performed a 2.35 ns long molecular dynamics simulation to clarify the influence of the two B-DNA backbone conformational substates B(I) and B(II) on complexation.
View Article and Find Full Text PDFDry carbonic acid has recently been shown to be kinetically stable even at room temperature. Addition of water molecules reduces this stability significantly, and the decomposition (H2CO3 + nH2O --> (n+1)H2O + CO2) is extremely accelerated for n = 1, 2, 3. By including two water molecules, a reaction rate that is a factor of 3000 below the experimental one (10 s(-1)) at room temperature was found.
View Article and Find Full Text PDFThis paper presents geometries of copper(II) chelates with L-alanine, L-leucine, and L-N,N-dimethylvaline optimized by the hybrid density functional method B3LYP. According to the molecular quantum mechanics results, a square-planar copper(II) coordination geometry is electronically favored in vacuo. Deviations from the planar configuration observed in the crystal state should be attributed to sterical intramolecular and/or intermolecular effects.
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