Please use this identifier to cite or link to this item: http://hdl.handle.net/123456789/218
Title: Structure-Based Multiscale Approach for Identification of Interaction Partners of PDZ Domains
Authors: Mohanty, Debasisa
Tiwari, Garima
Keywords: Bioinformatics
Issue Date: Apr-2014
Publisher: American Chemical Society
Abstract: PDZ domains are peptide recognition modules which mediate specific protein−protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ−peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ−peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ−peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ−peptide binding data for training.
URI: http://hdl.handle.net/123456789/218
Appears in Collections:Bioinformatics Centre, Publications



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