title: A physical model for PDZ-domain/peptide interactions.
abstract: The PDZ domain is an interaction motif that recognizes and binds the C-terminal peptides of target proteins. PDZ domains are ubiquitous in nature and help assemble multiprotein complexes that control cellular organization and signaling cascades. We present an optimized energy function to predict the binding free energy (ΔΔG) of PDZ domain/peptide interactions computationally. Geometry-optimized models of PDZ domain/peptide interfaces were built using ROSETTA: , and protein and peptide side chain and backbone degrees of freedom are minimized simultaneously. Using leave-one-out cross-validation, ROSETTA: 's energy function is adjusted to reproduce experimentally determined ΔΔG values with a correlation coefficient of 0.66 and a standard deviation of 0.79 kcal mol(-1). The energy function places an increased weight on hydrogen bonding interactions when compared to a previously developed method to analyze protein/protein interactions. Binding free enthalpies (ΔΔH) and entropies (ΔS) are predicted with reduced accuracies of R = 0.60 and R = 0.17, respectively. The computational method improves prediction of PDZ domain specificity from sequence and allows design of novel PDZ domain/peptide interactions.
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
authors.forename: Kristian
authors.initials: K
authors.lastname: Kaufmann
authors.forename: Nicole
authors.initials: N
authors.lastname: Shen
authors.forename: Laura
authors.initials: L
authors.lastname: Mizoue
authors.forename: Jens
authors.initials: J
authors.lastname: Meiler
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D019277:Entropy; D006860:Hydrogen Bonding; D008958:Models, Molecular; D054731:PDZ Domains; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D010455:Peptides
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