Interplay between Conformational Entropy and Solvation Entropy in Protein–Ligand Binding

Abstract

Understanding the driving forces underlying molecular recognition is of fundamental importance in chemistry and biology. The challenge is to unravel the binding thermodynamics into separate contributions and to interpret these in molecular terms. Entropic contributions to the free energy of binding are particularly difficult to assess in this regard. Here we pinpoint the molecular determinants underlying differences in ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and molecular dynamics simulations followed by conformational entropy and grid inhomogeneous solvation theory (GIST) analyses. Using a pair of diastereomeric ligands that have essentially identical chemical potential in the unbound state, we reduced the problem of dissecting the thermodynamics to a comparison of the two protein–ligand complexes. While the free energies of binding are nearly equal for the R and S diastereomers, greater differences are observed for the enthalpy and entropy, which consequently exhibit compensatory behavior, ΔΔ H°(R – S) = −5 ± 1 kJ/mol and −TΔΔ S°(R – S) = 3 ± 1 kJ/mol. NMR relaxation experiments and molecular dynamics simulations indicate that the protein in complex with the S-stereoisomer has greater conformational entropy than in the R-complex. GIST calculations reveal additional, but smaller, contributions from solvation entropy, again in favor of the S-complex. Thus, conformational entropy apparently dominates over solvation entropy in dictating the difference in the overall entropy of binding. This case highlights an interplay between conformational entropy and solvation entropy, pointing to both opportunities and challenges in drug design.

Minimizing the Entropy Penalty for Ligand Binding: Lessons from the Molecular Recognition of the Histo Blood‐Group Antigens by Human Galectin‐3

“…Thebinding event usually takes place with aloss of conformational entropy,e specially for the ligand, [4] and as ac onsequence,l arge entropic penalties are generally observed. [5,6] Attempts to manipulate this thermodynamic balance have focused on the design of pre-organized ligands.H owever, chemically induced modifications have rather unpredictable thermodynamic consequences and in fact, most of these efforts have failed [7] by following the paradigm of the enthalpy/entropy compensation mechanism.…”

Minimizing the Entropy Penalty for Ligand Binding: Lessons from the Molecular Recognition of the Histo Blood‐Group Antigens by Human Galectin‐3

“…[1] From the chemical perspective,t hese interactions are generally weak, and except for isolated cases, [2] they are characterized by at hermodynamic profile in which the favorable binding enthalpy compensates for an unfavorable entropic contribution. Thebinding event usually takes place with aloss of conformational entropy,e specially for the ligand, [4] and as ac onsequence,l arge entropic penalties are generally observed. Thebinding event usually takes place with aloss of conformational entropy,e specially for the ligand, [4] and as ac onsequence,l arge entropic penalties are generally observed.…”

Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures

“…Coordinates, B-factors, occupancies and reection data of the complexes collected at 100 K and 298 K, were obtained from the protein data bank (PDB entries 6QGF and 6QGE for the cryo-structures and entries 6RHL and 6RHM for the roomtemperature structures of R and S, respectively). 25,26 The resolutions of these structures were 1.34Å and 1.16Å for the cryostructures and 1.30Å and 1.60Å for the room-temperature structures.…”

“…21,22 The C-terminal domain is easily crystallisable with various ligands. [23][24][25] We studied the binding of two diastereomeric ligands, (2R)-and (2S)…”

“…The simulations were set up in the same way as in our previous studies of galectin-3C. 24,25,29,30 In agreement with neutron structures, 31 all Glu and Asp residues were negatively charged and all Lys and Arg residues positively charged, whereas the other residues were assumed to be neutral. The His158 residue was protonated on the ND1 atom, whereas the other three His residues were protonated on the NE2 atom, in accordance with neutron crystal structures, NMR measurements and previous extensive test calculations with MD.…”