Enthalpy of hydrogen bond formation in aprotein-ligand binding reaction.

Abstract

Parallel measurements of the thermodynamics (free-energy, enthalpy, entropy and heat-capac change) of ligand binding to FK506 binding protein First suggested >70 years ago (1, 2) and particularly emphasized by Pauling et al. (3,4), the hydrogen bond is now recognized as an interaction of fundamental importance in determining the structures of proteins and their complexes with ligands (5). Nevertheless, conflicting views are still held on the relative energetic contributions ofhydrogen bonds and interactions involving nonpolar groups to the thermodynamics of protein folding and ligand binding (6-8). Models have been presented arguing that the overall enthalpic contribution of interactions involving nonpolar moieties (at 250C) to the process of protein folding is highly unfavorable (7, 9), highly favorable (8), or essentially zero (10, 11). Arguments have also been advanced stating that the overall contribution of amide hydrogen-bond formation to the enthalpy of protein folding (or ligand-protein binding) at 250C is favorable (7), negligible (12) and possibly unfavorable (8,13). Clarification of the present controversy requires estimates of the enthalpies of formation of specific hydrogen bonds in particular regions of known protein structures. Such measurements are essential for understanding the energetic basis of protein folding and for obtaining structure-based predictions of the energies of ligand binding for the purpose of drug design.Part of the difficulty in dissecting the relative energetic contribution of hydrogen bonds to folding or binding reactions of proteins is that the formation of hydrogen bonds between atoms in reaction products is often accompanied by the release ofwater molecules that were hydrogen-bonded to these atoms prior to reaction. Tacrolimus (also known as FK506) and rapamycin are large macrocyclic compounds each of which binds with high affinity to a common cytosolic protein of 12 kDa known as FK506 binding protein . Recently, the structures of FKBP-12 in solution and in the crystalline state have been determined (14, 15), as have the crystal structures of the tacrolimus-FKBP-12 and rapamyci-FKBP-12 complexes (16-18). One of the structural features common to both protein-ligand complexes is a hydrogen bond between the Tyr-82 hydroxyl hydrogen (donor) and the amide carbonyl oxygen (acceptor) of either rapamycin or tacrolimus, buried in the hydrophobic interface (Fig. 1). As determined by x-ray crystallography, an important feature of the unliganded protein structure is the welldefined hydration of this tyrosine hydroxyl group. Furthermore, the NMR structure of tacrolimus in chloroform has been reported by Karuso et al. (19); the low solubility of tacrolimus prevents the determination of its structure in water. However, the interaction of unbound tacrolimus with water has been investigated through molecular dynamics simulation (20). The simulation reveals that the amide carbonyl oxygen of tacrolimus is exposed to solvent and makes an average of 1.6 hydrogen bonds with water mol...

Interactions Between a Helical Residue and Tertiary Structures: Helix Propensities in Small Peptides and in Native Proteins

“…In a recent experiment, Eberhardt & Raines (1994) determined the relative strengths of amide-amide and amide-water hydrogen bonds. In another study of protein-ligand interaction, Connelly et al (1994) suggested that forming an interior hydrogen bond involves dehydration, which is enthalpically unfavorable.…”

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

“…Yet, they can form hydrogen bonds and contribute significantly to the stability of a receptor-ligand complex. Cysteine residues d o not normally form covalent bonds between the binding species, and here they are only considered in the context of noncovalent intermolecular binding Connelly et al (1994) have noted that the mutation Y82F in the FK506 binding protein exhibits a slight destabilizing effect on the protein-ligand complex. The ligand binds through an interaction between a carbonyl group and the tyrosine hydroxyl group.…”

Thermodynamic consequences of disrupting a water‐mediated hydrogen bond network in a protein:pheromone complex

“…For example, in the binding of the protein FKBP-12 to its macrocyclic ligands (Connelly et al 1994), residue Tyr-82 forms three hydrogen bonds to ordered water molecules in the free form of the protein, but they are replaced by a hydrogen bond to a ligand carbonyl group in the complex. Thermodynamic binding data for wild-type and mutant (Y82F) FKBP-12 collected in H 2 O and D 2 O indicated that the three water-totyrosine hydrogen bonds are (in combination) enthalpically more favorable but entropically destabilizing relative to the tyrosine-to-ligand hydrogen bond that replaces them.…”