Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein–Ligand Binding: Binding Site Variability

Abstract

The thermodynamic driving forces behind small molecule-protein binding are still not well understood, including the variability of those forces associated with different types of ligands in different binding pockets. To better understand these phenomena we calculate spatially resolved thermodynamic contributions of the different molecular degrees of freedom for the binding of propane and methanol to multiple pockets on the proteins Factor Xa and p38 MAP kinase. Binding thermodynamics are computed using a statistical thermodynamics based end-point method applied on a canonical ensemble comprising the protein-ligand complexes and the corresponding free states in an explicit solvent environment. Energetic and entropic contributions of water and ligand degrees of freedom computed from the configurational ensemble provides an unprecedented level of detail into the mechanisms of binding. Direct protein-ligand interaction energies play a significant role in both non-polar and polar binding, which is comparable to water reorganization energy. Loss of interactions with water upon binding strongly compensates these contributions leading to relatively small binding enthalpies. For both solutes, the entropy of water reorganization is found to favor binding in agreement with the classical view of the “hydrophobic effect”. Depending on the specifics of the binding pocket, both energy-entropy compensation and reinforcement mechanisms are observed. Notable is the ability to visualize the spatial distribution of the thermodynamic contributions to binding at atomic resolution showing significant differences in the thermodynamic contributions of water to the binding of propane versus methanol.

Water models for biomolecular simulations

“…Some of these options will be discussed here in detail. Atomistic simulations—which are the main focus here—are among the most widely used methods in biologically motivated theoretical/computational research . Structure‐based drug design and protein structure prediction and refinement are just two examples of biomedical applications of the methodology.…”

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking

“…Water is an indispensable participant in the binding process of a protein and a small molecule [1,2,3,4,5,6,7,8]. In an in vivo environment, the active sites of a proteins are filled with water molecules, and thermodynamics of these water molecules are diverse and quite different from those of bulk water [9,10,11]. When a small molecule binds to a protein, it causes the displacement of water molecules from the active site to the bulk region, and the thermodynamics of this displacement process is a principal source of binding free energy of ligands [12,13,14].…”

Solvent effects on ligand binding to a serine protease

“…114,115 We attempted both these approaches for our system, but did not succeed in obtaining statistically precise results due to the large fluctuations and slow decorrelation times. Methods that directly estimate enthalpies and entropies for large protein systems have been reported, 34,39 but to facilitate convergence they require (i) strong restraints to suppress conformational flexibility of the protein, and (ii) the use of unrealistic ionization states of solvent-exposed amino acids to maintain an overall neutral charge of the system without counterions. Especially the first approximation is rather drastic.…”

“…Detailed interpretations of the underlying driving forces are thus highly non-trivial, underlining the importance of developing theoretical methods to describe solvation effects. [25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] In many experiments, some form of enthalpy-entropy (H/S) compensation has been reported and used to explain the observed partitioning of the free energy into enthalpic and entropic components. 16,[41][42][43][44][45][46][47][48][49][50][51][52][53] H/S compensation has even been invoked as a general principle, 41 as it seems to play a role for many different processes, ranging from partitioning of small molecules between polar and apolar phases to protein folding/unfolding and protein-protein as well as protein-ligand binding.…”