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Prediction of the Binding Affinities of PSD95 PDZ Domain in Complex with the CRIPT Peptide

Junmei Wang
Green Centers for System Biology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
Abstract—In this work, we have applied the state of artmolecular dynamics simulations in combination withsolvation free energy and conformational entropycalculations to predict the binding affinities of PSD95 PDZdomain in complex with the CRIPT peptide. Four diffidentcomputational protocols were evaluated on reproducing therelative binding free energies of the wild type PDZ and itsfive mutants. The protocol of MM-GB/SA in combinationwith normal mode analysis (NMA), which has a correlationcoefficient square of 0.84, apparently outperforms theothers especially for the two MM-PB/SA-based protocols.Free energy decomposition was also performed in order toidentify the hot spots that contribute significantly to thebinding.  

Index Terms—MD Simulations, MMPB/SA, MMGB/SA,NMA, WSAS, PDZ Domain

Cite: Junmei Wang, "Prediction of the Binding Affinities of PSD95 PDZ Domain in Complex with the CRIPT Peptide", Journal of Medical and Bioengineering, vol. 2, no. 2, pp.137-141, 2013. doi: 10.12720/jomb.2.2.137-141
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