Dynamic Flexibility of Protein−Inhibitor Complexes: A Study of the HIV-1 Protease/KNI-272 Complex

Abstract

The dynamics and flexibility of protein−ligand complexes is central to understanding and predicting binding geometries and energetics. We have calculated various measures of the dynamic flexibility of a pseudo-C2-symmetric protein, HIV-1 protease, complexed with the asymmetric inhibitor KNI-272 based on molecular dynamics simulations. This system is expected to be an excellent candidate for observing asymmetric dynamics between the two monomers due to the differences in the interactions between the two monomers of the protease and the inhibitor. Experimental methods have thus far been unable to observe the expected asymmetry in this system. Our calculated results are in excellent agreement with the available experimental data for the main-chain order parameters from a parallel 15N NMR study of the same inhibitor−protein complex, as well as the Debye−Waller temperature factors from X-ray crystallography. In our simulations, asymmetry between the monomers is found almost exclusively in the side-chain order parameters of the inhibitor and protease (especially residues 84A and 84B), for which experimental data are not yet available. We analyze the dynamic information obtained from the different methods and discuss protein−ligand interactions responsible for the dynamical behavior of the complex.