BiPPred: Combined sequence- and structure-based prediction of peptide binding to the Hsp70 chaperone BiP.
Substrate binding to Hsp70 chaperones is involved in many biological processes, and the identification of potential substrates is important for a comprehensive understanding of these events. We present a multi-scale pipeline for an accurate, yet efficient prediction of peptides binding to the Hsp70 chaperone BiP by combining sequence-based prediction with molecular docking and MMPBSA calculations. First, we measured the binding of 15mer peptides from known substrate proteins of BiP by peptide array (PA) experiments and performed an accuracy assessment of the PA data by fluorescence anisotropy studies. Several sequence-based prediction models were fitted using this and other peptide binding data. A structure-based position-specific scoring matrix (SB-PSSM) derived solely from structural modeling data forms the core of all models. The matrix elements are based on a combination of binding energy estimations, molecular dynamics simulations, and analysis of the BiP binding site, which led to new insights into the peptide binding specificities of the chaperone. Using this SB-PSSM, peptide binders could be predicted with high selectivity even without training of the model on experimental data. Additional training further increased the prediction accuracies. Subsequent molecular docking (DynaDock) and MMGBSA/MMPBSA-based binding affinity estimations for predicted binders allowed the identification of the correct binding mode of the peptides as well as the calculation of nearly quantitative binding affinities. The general concept behind the developed multi-scale pipeline can readily be applied to other protein-peptide complexes with linearly bound peptides, for which sufficient experimental binding data for the training of classical sequence-based prediction models is not available. Proteins 2016; 84:1390-1407. © 2016 Wiley Periodicals, Inc.
Department Biowissenschaftliche Grundlagen, Technische Universität München, Freising, Germany.
Markus
M
Schneider
Department Chemie, Technische Universität München, Garching, Germany.
Mathias
M
Rosam
Department Biowissenschaftliche Grundlagen, Technische Universität München, Freising, Germany.
Manuel
M
Glaser
Department Biowissenschaftliche Grundlagen, Technische Universität München, Freising, Germany.|Center for Integrated Protein Science, Departments of Bioscience, Technische Universität München, Munich, Germany.
Atanas
A
Patronov
Department Biowissenschaftliche Grundlagen, Technische Universität München, Freising, Germany.
Harpreet
H
Shah
Department Chemie, Technische Universität München, Garching, Germany.
Katrin Christiane
KC
Back
Department Chemie, Technische Universität München, Garching, Germany.
Marina Angelika
MA
Daake
Department Chemie, Technische Universität München, Garching, Germany.|Center for Integrated Protein Science, Department of Chemistry, Technische Universität München, Munich, Germany.
Johannes
J
Buchner
Department Biowissenschaftliche Grundlagen, Technische Universität München, Freising, Germany. antes@tum.de.|Center for Integrated Protein Science, Departments of Bioscience, Technische Universität München, Munich, Germany. antes@tum.de.
Iris
I
Antes
D000595:Amino Acid Sequence; D016880:Anisotropy; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000091342:Endoplasmic Reticulum Chaperone BiP; D005456:Fluorescent Dyes / Q000737:chemistry; D015870:Gene Expression; D006360:Heat-Shock Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D054444:Immunoglobulin Light Chains, Surrogate / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D007546:Isoquinolines / Q000737:chemistry; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D040081:Protein Array Analysis; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D013050:Spectrometry, Fluorescence; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D042461:Vascular Endothelial Growth Factor A / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
D002352:Carrier Proteins; D000091342:Endoplasmic Reticulum Chaperone BiP; D005456:Fluorescent Dyes; D006360:Heat-Shock Proteins; D054444:Immunoglobulin Light Chains, Surrogate; D007546:Isoquinolines; D010455:Peptides; C467484:VEGFA protein, human; C515639:VPREB1 protein, human; D042461:Vascular Endothelial Growth Factor A; C029702:prolactin-binding protein; C017475:lucifer yellow
Hsp70-substrate specificity; MMGBSA calculations; MMPBSA calculations; peptide binding prediction; protein-peptide docking