Binding of buried structural water increases the flexibility of proteins

Abstract

Water deeply buried in proteins is considered to be an integral part of the folded structure. Such structural water molecules make strong H bonds with polar groups of the surrounding protein and therefore are believed to tighten the protein matrix. Surprisingly, our computational analysis of the binding of a buried water molecule to bovine pancreatic trypsin inhibitor shows that the protein actually becomes more flexible, as revealed by an increase in the vibrational entropy. We find that this effect must be common in proteins, because the large entropic cost of immobilizing a single water molecule [-TDeltaS = 20.6 kcal/mol (1 kcal = 4.18 kJ) for the lost translational and rotational degrees of freedom] can only be partly compensated by water-protein interactions, even when they are nearly perfect, as in the case of bovine pancreatic trypsin inhibitor (DeltaE = -19.8 kcal/mol), leaving no room for a further decrease in entropy from protein tightening. This study illustrates the importance of considering changes in protein flexibility (which in this case favor binding by 3.5 kcal/mol) for the prediction of ligand binding affinities.

Figure 1

(a) Vibrational spectra of unbound (P) and complexed (PW) bovine pancreatic trypsin inhibitor (cannot be distinguished on this scale). The vibrational frequencies ν_i correspond to the normal modes of the energy-minimized structure (20) obtained by diagonalizing the mass-weighted matrix of the second derivatives of the energy (21). (b) Cumulative change of the vibrational entropy ΔS(n) = ∑_i=1ⁿ ΔS_i on water binding, where ΔS_i = (S_i^PW − S_i^P) is the contribution of the ith vibration mode. The Inset shows ΔS_i for the first 100 modes. S_i = [hν_i/T/(e^hν_i/kT − 1) − kln(1 − e^−hνi/kT)] is the entropic content of one vibration mode i (12).