Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling.

CONTEXT: In cellular environments, the reduction of disulfide bonds is pivotal for protein folding and synthesis. However, the intricate enzymatic mechanisms governing this process remain poorly understood. This study addresses this gap by investigating a disulfide bridge reduction reaction, serving as a model for comprehending electron and proton transfer in biological systems. Six potential mechanisms for reducing the dimethyl disulfide (DMDS) bridge through electron and proton capture were explored. Thermodynamic and kinetic analyses elucidated the sequence of proton and electron addition. MD-PMM, a method that combines molecular dynamics simulations and quantum-chemical calculations, was employed to compute the redox potential of the mechanism. This research provides valuable insights into the mechanisms and redox potentials involved in disulfide bridge reduction within proteins, offering an understanding of phenomena that are challenging to explore experimentally. METHODS: All calculations used the Gaussian 09 software package at the MP2/6-311 + g(d,p) theory level. Visualization of the molecular orbitals and electron densities was conducted using Gaussview6. Molecular dynamics simulations were performed using GROMACS with the CHARMM36 force field. The PyMM program (Python Program for QM/MM Simulations Based on the Perturbed Matrix Method) is used to apply the Perturbed Matrix Method to MD simulations.

Theoretical study of methyl group transfer assisted by proton transfer reaction in the N-acylated imidates.

The single methyl group transfer (MGT), double MGT and single MGT assisted by proton transfer (PT) that occurs in small biological systems N-methoxy methylene formamide and N-hydroxy methylen formamide (NMMF-NHMF) have been investigated completely in the present study using density functional theory (DFT) and Möller-Plesset perturbation (MP2) methods with a 6-31G(d) basis set. The barrier height for MGT assisted by PT is significantly lower than those of the single and double MGT. Polar solvents decrease the energy barriers.

Insight on the interaction of polychlorobiphenyl with nucleic acid-base.

The interaction between one polychlorobiphenyl (3,3',4,4',-tetrachlorobiphenyl, coded PCB77) and the four DNA nucleic acid-base is studied by means of quantum mechanics calculations in stacked conformations. It is shown that even if the intermolecular dispersion energy is the largest component of the total interaction energy, some other contributions play a non negligible role. In particular the electrostatic dipole-dipole interaction and the charge transfer from the nucleobase to the PCB are responsible for the relative orientation of the monomers in the complexes. In addition, the charge transfer tends to flatten the PCB, which could therefore intercalate more easily between DNA base pairs. From these seminal results, we predict that PCB could intercalate completely between two base pairs, preferably between Guanine:Cytosine pairs.