Protonation and pK changes in protein–ligand binding

Abstract

Formation of protein-ligand complexes causes various changes in both the receptor and the ligand. This review focuses on changes in pK and protonation states of ionizable groups that accompany protein-ligand binding. Physical origins of these effects are outlined, followed by a brief overview of the computational methods to predict them and the associated corrections to receptor-ligand binding affinities. Statistical prevalence, magnitude, and spatial distribution of the pK and protonation state changes in protein-ligand binding are discussed in detail, based on both experimental and theoretical studies. While there is no doubt that these changes occur, they do not occur all the time; the estimated prevalence varies, both between individual complexes and by method. The changes occur not only in the immediate vicinity of the interface, but sometimes far away. When receptor-ligand binding is associated with protonation state change at particular pH, the binding becomes pH dependent: we review the interplay between sub-cellular characteristic pH and optimum pH of receptor-ligand binding. It is pointed out that there is a tendency for protonation state changes upon binding to be minimal at physiologically relevant pH for each complex (no net proton uptake/release), suggesting that native receptor-ligand interactions evolved to reduce the energy cost associated with ionization changes. As a result, previously reported statistical prevalence of these changes – typically computed at the same pH for all complexes – may be higher than what may be expected at optimum pH specific to each complex. We also discuss whether proper account of protonation state changes appears to improve practical docking and scoring outcomes relevant to structure-based drug design. An overview of some of the existing challenges in the field is provided in conclusion.

Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase

“…Conversely, inhibitor binding perturbs the 113S loop, which is propagated to affect the sidechain rotation of His45, resulting in a shift in the protonation equilibrium. Thus, our finding adds a new dimension to the allosteric regulation framework 34 and confirms a long-standing hypothesis based on the pioneering work of Alexov 31,32 and later Onufriev and coworkers 25,30 using Poisson-Boltzmann calculations. The proposed mechanism can be experimentally verified by testing whether mutating His45 to a charged amino acid such as Lys would increase the binding affinity of BACE1.…”

“…The existence of long-range coupling between protein/ligand binding and receptor protonation through a conformational mechanism has been previously hypothesized by Alexov and later Onufriev based on the Poisson-Boltzmann calculations. 25,30–32 The p K a shift of His45 in BACE1 binding is reminiscent of an experimentally known case: a distal residue His164 in plasmepsin II (another aspartyl protease) shifts its p K a from 6 to 7.5 upon pepstatin binding. 31,33 …”

Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations

“…Proton transfer is among the most common mechanisms in biomolecules (Ben-Shimon et al, 2013 andAlexov, 2013). It is a step that proves very important in several organisms (Ben-Shimon et al, 2013 andAlexov, 2013).…”

“…It is a step that proves very important in several organisms (Ben-Shimon et al, 2013 andAlexov, 2013). However, modeling and simulating this phenomenon 'in silico' is extremely complex.…”

Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions

“…103 Likewise, accuracy of individual charge-charge interactions is key for successful continuum electrostatic estimates of biomolecular p K values. 13,104–106 …”