Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain

Journal of Molecular Biology
Tingjun HouWei Wang

Abstract

Many important protein-protein interactions are mediated by peptide recognition modular domains, such as the Src homology 3 (SH3), SH2, PDZ, and WW domains. Characterizing the interaction interface of domain-peptide complexes and predicting binding specificity for modular domains are critical for deciphering protein-protein interaction networks. Here, we propose the use of an energetic decomposition analysis to characterize domain-peptide interactions and the molecular interaction energy components (MIECs), including van der Waals, electrostatic, and desolvation energy between residue pairs on the binding interface. We show a proof-of-concept study on the amphiphysin-1 SH3 domain interacting with its peptide ligands. The structures of the human amphiphysin-1 SH3 domain complexed with 884 peptides were first modeled using virtual mutagenesis and optimized by molecular mechanics (MM) minimization. Next, the MIECs between domain and peptide residues were computed using the MM/generalized Born decomposition analysis. We conducted two types of statistical analyses on the MIECs to demonstrate their usefulness for predicting binding affinities of peptides and for classifying peptides into binder and non-binder categories. First, combi...Continue Reading

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Citations

Dec 12, 2012·Journal of Computer-aided Molecular Design·Lingling GengBozhen Chen
Sep 17, 2011·Journal of Chemical Information and Modeling·Yuanhua ChengChen-Ho Tung
Sep 25, 2012·Journal of Chemical Information and Modeling·Lin LiTingjun Hou
Dec 25, 2012·Journal of Chemical Information and Modeling·Bo DingWei Wang
Apr 30, 2013·Journal of Chemical Information and Modeling·Wei CuiMing-Juan Ji
Mar 26, 2013·Journal of Chemical Information and Modeling·Peichen PanTingjun Hou
Aug 21, 2012·PloS One·T Andrew BinkowskiAndrzej Joachimiak
Feb 3, 2016·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Huiqun WangMingjuan Ji
Oct 22, 2009·Chemical Biology & Drug Design·Yuanchao LiQingwu Yang

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