Halogenated Benzenes Bound within a Non-polar Cavity in T4 Lysozyme Provide Examples of I•••S and I•••Se Halogen-bonding

We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume similar to 150 angstrom(3) that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystallography and related techniques to analyze the binding of halogen-incorporated benzenes typified by C6F5X, where X=H, F, Cl, Br or I, and C6H5X, where X=H or I was also studied. Because of the increased electron density of fluorine relative to hydrogen, the geometry of binding of the fluoro, compounds can often be determined more precisely than their hydrogen-containing analogs. All of the ligands bind in essentially the same plane but the center of the phenyl ring can translate by up to 1.2 angstrom. In no case does the ligand rotate freely within the cavity. The walls of the cavity consist predominantly of hydrocarbon atoms, and in several cases it appears that van der Waals interactions define the geometry of binding. In comparing the smallest 3 with the largest ligand, the cavity volume increases from 181 angstrom(3) to 245 angstrom(3). This shows that the protein is flexible and adapts to the size and shape of the ligand. There is a remarkably close contact of 3.0 angstrom between the iodine atom on C6F5I and the sulfur or selenium atom of Met or SeMet102. This interaction is 1.0 angstrom less than the sum of the van der Waals radii and is a clear example of a so-called halogen bond. Notwithstanding this close approach, the increase in binding energy for the halogen bond relative to a van der Waals contact is estimated to be only about 0.5-0.7 kcal/mol. (C) 2008 Elsevier Ltd. All rights reserved.