Theoretical Evaluation of Sulfur-Based Reactions as a Model for Biological Antioxidant Defense

Abstract

Sulfur-containing amino acids, Methionine (Met) and Cysteine (Cys), are very susceptible to Reactive Oxygen Species (ROS). Therefore, sulfur-based reactions regulate many biological processes, playing a key role in maintaining cellular redox homeostasis and modulating intracellular signaling cascades. In oxidative conditions, Met acts as a ROS scavenger, through Met sulfoxide formation, while thiol/disulfide interchange reactions take place between Cys residues as a response to many environmental stimuli. In this work, we apply a QM/MM theoretical–computational approach, which combines quantum–mechanical calculations with classical molecular dynamics simulations to estimate the free energy profile for the above-mentioned reactions in solution. The results obtained, in good agreement with experimental data, show the validity of our approach in modeling sulfur-based reactions, enabling us to study these mechanisms in more complex biological systems.

Molecular Modeling of the Deamidation Reaction in Solution: A Theoretical–Computational Study

“…When the calculation is performed along the reaction coordinate (ξ), as in the present work, the Helmholtz free energy of the reaction can be calculated as a function of such a coordinate, as previously reported. 25 , 30 − 32 Thus, the perturbed free energy change (Δ A ), due to the movement from an initial position (i) to a subsequent point ( i + 1), along the reaction coordinate is where Δ U is the perturbed energy change, k B is the Boltzmann’s constant, and β = 1/ k B T . The sum of each free energy variation leads to the Δ A tot .…”

Modeling the Temperature Dependence of the Fluorescence Properties of Indole in Aqueous Solution

“…The theory behind the Perturbed Matrix Method (PMM) and Molecular Dynamics-Perturbed Matrix Method (MD-PMM, a QM/MM method [37,38] combining PMM and Molecular Dynamics) can be found in previous works [29][30][31]. A summary of these approaches, which provided accurate results in the past [14,[39][40][41], as well as the method used to obtain the vibronic absorption and emission spectra [39,42], is presented in Section S1 of the Supplementary Material.…”

Structural Design of π–d Conjugated TMxB3N3S6 (x=2, 3) Monolayer Toward Electrocatalytic Ammonia Synthesis

“…[12][13][14] These newly emerged catalysts can maximize the utilization of TM atoms with highly exposed active sites, results in superior high selectivity for NRR. [15][16][17] For examples, TM@MoS 2 , [18] TMs-g-C 9 N 4 , [19] TiN 4 -graphene, [20] Mo@g-GaN [21] and V-BN [22] have high catalytic activity for NRR.…”