Protein oxidation in crowded environments

Proteins are the most abundant macromolecules in biological systems. This high abundance and the presence of electron-rich side-chains make proteins a major target for biological oxidants. Protein oxidation encompasses a complex set of reactions that, depending on protein structure and the chemical properties of the oxidant, can trigger specific and reversible modifications, or can irreversibly damage multiple side-chains. Therefore, understanding protein oxidation from a mechanistic and kinetic perspective is important to illuminate the molecular basis of physiological (e.g. redox signaling) and pathological processes (e.g. cardiovascular disease and neurodegenerative diseases). However, an existing conundrum in the redox biochemistry field is whether (and how) intrinsic properties of biological environments, such as the crowded intracellular conditions resulting from the high abundance of macromolecules and protein confinement, modulate oxidation rates and pathways. These obvious, but often neglected, aspects of biological environments have begun to be systematically addressed, suggesting that the crowded intracellular conditions would be an important player in the oxidative biology of proteins. This review outlines the importance of protein oxidation in physiology and pathology. Then, thoroughly discusses the modulatory effect that crowding exerts on biochemical processes that involve proteins, particularly on the oxidative modification of proteins. Finally, evidence that illustrates the interplay that would exist between crowding, protein oxidation, and protein confinement by phase separation is discussed. The author proposes that the transition from using dilute in vitro studies to an experimental workflow that takes into account the crowded and heterogeneous conditions encountered is the cell is mandatory to rigorously investigate protein oxidation.