A multifaceted computational investigation of a prospective universal chemical role of water in enzyme catalysis

Abstract

The functionality of enzymes is intricately linked to their solvation environment, yet the role of water within enzyme active sites remains insufficiently understood, particularly regarding its direct chemical involvement in catalysis. This dissertation investigates the presence and significance of water molecules within enzyme active sites, combining structural and quantum mechanical analyses to elucidate their potential catalytic roles. First, an extensive survey of 1013 enzyme crystals, resolved to high resolution (< 1.5 angstrom) using X-ray crystallography, revealed that 98% of these structures possess water-filled tunnels connecting the active sites to bulk water. This structural insight suggests a ubiquitous presence of water molecules intricately positioned within the catalytic cores of enzymes. Building upon these structural findings, analysis of 1179 enzyme crystal structures demonstrated that the average electric field experienced by water molecules in enzyme active sites is greater in magnitude than that of water molecules elsewhere in or near enzymes, and substantially larger than those in bulk solvent. Moreover, a classical molecular dynamics simulation of triose phosphate isomerase and its substrate in bulk water showed that the electric fields incurred by water hydrogen near the enzyme-bound substrate are significantly greater than those near the unbound substrate. Lastly, measuring these fields in eight enzyme active sites during quantum molecular dynamics calculations showed greater variance in the magnitude of the electric field incurred along water hydroxyl bonds relative to those in bulk solvent, implicating heterogeneity of the electrostatic profiles of enzyme active sites. During these 100 fs atom centered density matric propagation simulations, water ionizing events were observed in two of the eight enzyme active sites, which is remarkable considering the slow ionization rate of pure liquid water. The combined structural and electrostatic evidence presented in this study supports the hypothesis that water molecules within enzyme active sites contribute critically to the catalytic efficiency and specificity of enzymatic reactions. By highlighting the chemically active nature of these water molecules, this research advances our understanding of enzymatic catalysis and opens new avenues for exploring enzyme function and design.