Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations

The biological functions of protein S-sulfhydration in eukaryotes and the ever-increasing understanding of its effects on bacteria

As a critical endogenous signaling molecule, hydrogen sulfide may induce reversible post-translational modifications on cysteine residues of proteins, generating a persulfide bond known as S-sulfhydration. A systemic overview of the biofunctions of S-sulfhydration will equip us better to characterize its regulatory roles in antioxidant defense, inflammatory response, and cell fate, as well as its pathological mechanisms related to cardiovascular, neurological, and multiple organ diseases, etc. Nevertheless, the understanding of S-sulfhydration is mostly built on mammalian cells and animal models. We subsequently summarized the mediation effects of this specific post-transcriptional modification on physiological processes and virulence in bacteria. The high-sensitivity and high-throughput detection technologies are required for studying the signal transduction mechanism of H₂S and protein S-sulfhydration modification. Herein, we reviewed the establishment and development of different approaches to assess S-sulfhydration, including the biotin-switch method, modified biotin-switch method, alkylation-based cysteine-labelled assay, and Tag-switch method. Finally, we discussed the limitations of the impacts of S-sulfhydration in pathogens-host interactions and envisaged the challenges to design drugs and antibiotics targeting the S-sulfhydrated proteins in the host or pathogens.

The curious case of DMSO: A CCSD(T)/CBS(aQ56+d) benchmark and DFT study

This work addresses the pathological behavior of the energetics of dimethyl sulfoxide and related sulfur-containing compounds by providing the computational benchmark energetics of R₂E₂ species, where R = H/CH₃ and E = O/S, with bent and pyramidal geometries using state-of-the-art methodologies. These 22 geometries were fully characterized with coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)], second-order Møller-Plesset perturbation theory (MP2), and 22 density functional theory (DFT) methods with 8, 12, and 12, respectively, correlation consistent basis sets of double-, triple-, or quadruple-ζ quality. The relative energetics were determined at the MP2 and CCSD(T) complete basis set (CBS) limits using 17 basis sets up to sextuple-ζ and include augmented, tight-d, and core-valence correlation consistent basis sets. The relative energies of oxygen-/sulfur-containing compounds exhibit exceptionally slow convergence to the CBS limit with canonical methods as well as significant basis set dependence. CCSD(T) with quadruple-ζ basis sets can give qualitatively incorrect relative energies. Explicitly correlated MP2-F12 and CCSD(T)-F12 methods dramatically accelerate the convergence of the relative energies to the CBS limit for these problematic compounds. The F12 methods with a triple-ζ quality basis set give relative energies that deviate no more than 0.41 kcal mol^-1 from the benchmark CBS limit. The correlation consistent Composite Approach (ccCA), ccCA-TM (TM for transition metals), and G3B3 deviated by no more than 2 kcal mol^-1 from the benchmark CBS limits. Relative energies for oxygen-/sulfur-containing systems fully characterized with DFT are quite unreliable even with triple-ζ quality basis sets, and 13 out of 45 combinations fortuitously give a relative energy that is within 1 kcal mol^-1 on average from the benchmark CCSD(T) CBS limit for these systems.

Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H2O2 and H2O

Long associated with cell death, hydrogen peroxide (H₂O₂) is now known to perform many physiological roles. Unraveling its biological mechanisms of action requires atomic-level knowledge of its association with proteins and lipids, which we address here. High-level [MP2(full)/6-311++G(3df,3pd)] ab initio calculations reveal skew rotamers as the lowest-energy states of isolated H₂O₂ (ϕ_HOOH ∼ 112°) with minimum and maximum electrostatic potentials (kcal/mol) of -24.8 (V_s,min) and 36.5 (V_s,max), respectively. Transition-state, nonpolar trans rotamers (ϕ_HOOH ∼ 180°) at 1.2 kcal/mol higher in energy are poorer H-bond acceptors (V_s,min = -16.6) than the skew rotamers, while highly polar cis rotamers (ϕ_HOOH ∼ 0°) at 7.8 kcal/mol are much better H-bond donors (V_s,max = 52.7). Modeling H₂O₂ association with neutral and charged analogs of protein residues and lipid groups (e.g., ester, phosphate, choline) reveals that skew rotamers (ϕ_HOOH = 84-122°) are favored in the neutral and cationic complexes, which display gas-phase interaction energies (E^CP, kcal/mol) of -1.5 to -18. The neutral and cationic complexes of H₂O exhibit a similar range of stabilities (E^CP ∼ -1 to -18). However, considerably higher energies (E^CP ∼ -14 to -36) are found for the H₂O₂ complexes of the anionic ligands, which are stabilized by charge-assisted H-bond donation from cis and distorted cis rotamers (ϕ_HOOH = 0-60°). H₂O is a much poorer H-bond donor (V_s,max = 33.4) than cis-H₂O₂, so its anionic complexes are significantly weaker (E^CP ∼ -11 to -20). Thus, by dictating the rotamer preference of H₂O₂, functional groups in biomolecules can discriminate between H₂O₂ and H₂O. Finally, exploiting the present ab initio data, we calibrated and validated our published molecular mechanics model for H₂O₂ (Orabi, E. A.; English, A. M. J. Chem. Theory Comput. 2018, 14, 2808-2821) to provide an important tool for simulating H₂O₂ in biology.

New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology

Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)_n clusters, for n = 3-7; various clusters of HF and H₂O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H₂O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.