posted on 2019-01-08, 00:00authored byMaria Luisa Verteramo, Olof Stenström, Majda Misini Ignjatović, Octav Caldararu, Martin A. Olsson, Francesco Manzoni, Hakon Leffler, Esko Oksanen, Derek T. Logan, Ulf J. Nilsson, Ulf Ryde, Mikael Akke
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,
ΔΔH°(R –
S) = −5 ± 1 kJ/mol and −TΔΔS°(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.