Content area
Full text
ABSTRACT Complexes of proteins with small ligands are of utmost importance in biochemistry, and therefore equilibria, formation, and decay have been investigated extensively by means of biochemical and biophysical methods. Theoretical studies of the molecular dynamics of such systems in solution are restricted to 10 ns, i.e., to fast processes. Only recently new theoretical methods have been developed not to observe the process in real time, but to explore its pathway(s) through the energy landscape. From the profiles of free energy, equilibrium and kinetic quantities can be determined using transition-state theory. This study is dedicated to the pharmacologically relevant insulin-phenol complex. The distance of the center of mass chosen as a reaction coordinate allows a reasonable description over most of the pathway. The analysis is facilitated by analytical expressions we recently derived for distance-type reaction coordinates. Only the sudden onset of rotations at the very release of the ligand cannot be parameterized by a distance. They obviously require a particular treatment. Like a preliminary study on a peptide, the present case emphasizes the contribution of internal friction inside a protein, which can be computed from simulation data. The calculated equilibrium constant and the friction-corrected rates agree well with experimental data.
INTRODUCTION
In the present report, a novel approach is described to study protein-ligand binding and unbinding on the basis of molecular dynamics (MD) simulations with respect to the energy and geometry changes connected with the process. As a model system, the 2Zn insulin hexamer was chosen with phenol as a ligand. Phenol and other phenolic compounds were traditionally used as bacteriostatic preservatives in pharmaceutical insulin preparations long before it became known that they stabilize the structure of the insulin molecule (Wollmer et al., 1987) and reduce its chemical reactivity (Brange and Langkjaer, 1992). The protracted activity of phenolic complexes and its dependence on details of engineered insulin were the subject of a recent study (Berchtold and Hilgenfeld, 1999).
2Zn insulin hexamers exist in one of three structural states, all defined by x-ray analysis (Baker et al., 1988; Bentley et al., 1976; Derewenda et al., 1989), that in solution are related by dynamic equilibria: T^sub 6^ [Lef-right arrow] T^sub 3^R^sub 3^ [Lef-right arrow] R^sub 6^. In T-state subunits, the conformation of the N-terminal B-chain (residues...