Distonic radical anion species in cysteine oxidation processes

Abstract

<p>Oxidation of cysteine residues constitutes an important regulatory mechanism in the function of biological systems. Much of this behavior is controlled by the specific chemical properties of the thiol side-chain...</p>

PTM‐Psi: A python package to facilitate the computational investigation of post‐translational modification on protein structures and their impacts on dynamics and functions

“…Post‐translational modification (PTM) is a critical mechanism for regulating protein functions by chemically modifying the side chains of amino acids (Paulsen & Carroll, 2013 ). These site‐specific PTMs on the protein structures perturb or even modify the activity state (Zhang et al, 2021 ), the Energy Landscape (Garrido Ruiz et al, 2022 ), and the dynamics that affect functions by regulating the signaling processes in profound ways (Harris et al, 2020 ; Liu et al, 2022 ; Qin et al, 2020 ). While some PTMs, such as phosphorylation, require specific enzymes to characterize cellular behaviors, oxidation–reduction (redox)‐based PTMs (i.e., redox PTMs) (Kitatani et al, 2006 ) of thiol‐containing cysteines (Jumper et al, 2021 ) are the most common in microbes for regulating metabolic pathways for their rapid responses to shifting redox conditions.…”

“…Mass spectrometry (MS)‐based redox proteomics has enabled quantitative profiling of redox proteomics for the measurement of cysteine thiol PTMs stoichiometrically (Ahdritz et al, 2022 ). However, because multiple PTM forms, potentially transient or labile (Qin et al, 2020 ), can be present at a single cysteine site, the coverage of cysteine oxidation in protein structures, biophysics, and simulations is still an underdeveloped area (Garrido Ruiz et al, 2022 ). One of the major hurdles in computer simulations is the highly electronegative cysteine thiols that react swiftly with the reactive oxygen species in the local environment.…”

“…Such an effect can potentially alter the molecular interactions between proteins and promote or impede the formation of quaternary complexes. Other quantum mechanical (QM) approaches were also used for modeling PTMs on enzymatic reactions (Qin et al, 2020 ). However, the scope of these computer simulations is often limited to the structural arrangement of the surrounding atoms at the reaction site.…”

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

“…A recent tandem mass spectrometry and dynamics simulations indicated that gaseous deprotonated L-cysteine S-sulfate anion [cysS-SO 3 ] − is a precursor for the generation of the cysteine sulfenic intermediate [cysSO] − via low-energy collision-induced dissociation [ 3 ]. This pioneering, mass spectrometry-based observation has stimulated spectroscopic characterization of the electronic structure of [cysSO] − , proven to be a distonic radical anion [ 4 ]. Despite the importance of [cysS-SO 3 ] − in numerous biological processes, its intrinsic molecular properties have not yet been characterized.…”

Structural Elucidation of C6H4+. Using Chemical Reaction Monitoring: Charge Transfer Versus Bond Forming Reactions

“…However, these thermodynamic quantities were most precisely obtained from benzyne anions using negative ion photoelectron spectroscopy [27] . Indeed, negative ion photoelectron spectroscopy has proven to be a powerful tool to retrieve the structures of (di)radicals including distonic species from their corresponding anionic counterparts [28–30] . Finally, computational and laser spectroscopic explorations of the C 6 H 4 +.…”