ct6b00101_si_001.pdf (2.46 MB)
Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets
journal contribution
posted on 2016-07-11, 00:00 authored by Daria B. Kokh, Paul Czodrowski, Friedrich Rippmann, Rebecca C. WadeSimulations of the long-time scale motions of a ligand binding
pocket in a protein may open up new perspectives for the design of
compounds with steric or chemical properties differing from those
of known binders. However, slow motions of proteins are difficult
to access using standard molecular dynamics (MD) simulations and are
thus usually neglected in computational drug design. Here, we introduce
two nonequilibrium MD approaches to identify conformational changes
of a binding site and detect transient pockets associated with these
motions. The methods proposed are based on the rotamerically induced
perturbation (RIP) MD approach, which employs perturbation of side-chain
torsional motion for initiating large-scale protein movement. The
first approach, Langevin-RIP (L-RIP), entails a series of short Langevin
MD simulations, each starting with perturbation of one of the side-chains
lining the binding site of interest. L-RIP provides extensive sampling
of conformational changes of the binding site. In less than 1 ns of
MD simulation with L-RIP, we observed distortions of the α-helix
in the ATP binding site of HSP90 and flipping of the DFG loop in Src
kinase. In the second approach, RIPlig, a perturbation is applied
to a pseudoligand placed in different parts of a binding pocket, which
enables flexible regions of the binding site to be identified in a
small number of 10 ps MD simulations. The methods were evaluated for
four test proteins displaying different types and degrees of binding
site flexibility. Both methods reveal all transient pocket regions
in less than a total of 10 ns of simulations, even though many of
these regions remained closed in 100 ns conventional MD. The proposed
methods provide computationally efficient tools to explore binding
site flexibility and can aid in the functional characterization of
protein pockets, and the identification of transient pockets for ligand
design.