Poster Presentation 2014 International Biophysics Congress

Exploring the free-energy profile for MDM2 in complex with a peptide using Brownian dynamics fluctuation dissipation theorem (#678)

Guodong Hu 1 , Tao Liang 1 , Jihua Wang 1
  1. Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, Dezhou, China

A problem of central importance in computational biology is predicting the free-energy profile of binding with sufficient accuracy for reliable estimates of both thermodynamics and kinetics. The hybrid steer molecular dynamics simulation (hSMD) combined with Brownian-dynamics fluctuation-dissipation theorem (BD-FDT) was used to calculate the free-energy profile for MDM2 in complex with a peptide (PDB ID: 1YCR). The hSMD simulations include steering more than one centers of the peptide and equilibrating the system with and without biasing it. In this work, the path from bound state to the dissociated state was divided into 16 sections. Within a given section, four forward and four reverse pulling paths were sampled along which the work done to the system was recorded. Three centers of peptide were steered for the complex peptide with 13 residues. The pulling speed was 0.005Å/ps. The MD runs were implemented using NAMD. All the atomistic interactions are represented by the CHARMM36 force field. The potential of mean force shows that there is no the energy barrier along the pulling path from the bound state to the dissociated state. The computed absolutely binding free energies are slightly higher than the experimental data. However, our results obtained with BD-FDT are closer to the experimental data than those obtained with the JE method.