Selective Stabilization of Aspartic Acid Protonation State within a Given Protein Conformation Occurs via Specific “Molecular Association”
journal contributionposted on 19.06.2020, 14:10 by Debashree Bandyopadhyay, Akshay Bhatnagar, Shobhit Jain, Prabhav Pratyaksh
Proteins involved in proton-/electron-transfer processes often possess “functional” aspartates/aspartic acids (Asp) with variable protonation states. The mechanism of Asp protonation–deprotonation within proteins is unclear. Two questions were askedthe possible types of determinants responsible for Asp protonation–deprotonation and the spatial arrangements of the determinants leading to selective stabilization. The questions were analyzed using nine different solvent models, which scanned the complete protein dielectric range, and four protein models, which illustrated the spatial arrangements around Asp, termed as “molecular association”. The methods employed were quantum chemical calculations and constant pH simulations. The types of the determinants identified were charge–charge interaction, H bonding, dipole−π interaction, extended electronic conjugation, dielectric effect, and solvent accessibility. All solvent-exposed Asp [buried fraction (BF) less than 0.5] were aspartates, and buried Asp were either aspartic acids or aspartates, each having a different “molecular association”. The exposed aspartates were stabilized via a H-bonding network with bulk water, buried aspartates via salt bridge or, minimum, two intramolecular H bonds, and buried aspartic acids via, minimum, one intramolecular H bond. An “acid–alcohol pair” (involving Ser/Thr/Tyr) was a common determinant to any “functional” buried aspartate/aspartic acid. Higher energy “molecular associations” observed within proteins compared to those within water, presumably, indicated easy molecular restructuring and alteration of the Asp protonation states during a protein-mediated proton/electron transfer.