ABSTRACT
BiP is the endoplasmic member of the Hsp70 family. BiP is regulated by several co-chaperones including the nucleotide-exchange factor (NEF) Bap (Sil1 in yeast). Bap is a two-domain protein. The interaction of the Bap C-terminal domain with the BiP ATPase domain is sufficient for its weak NEF activity. However, stimulation of the BiP ATPase activity requires full-length Bap, suggesting a complex interplay of these two factors. Here, single-molecule FRET experiments with mammalian proteins reveal that Bap affects the conformation of both BiP domains, including the lid subdomain, which is important for substrate binding. The largely unstructured Bap N-terminal domain promotes the substrate release from BiP. Thus, Bap is a conformational regulator affecting both nucleotide and substrate interactions. The preferential interaction with BiP in its ADP state places Bap at a late stage of the chaperone cycle, in which it coordinates release of substrate and ADP, thereby resetting BiP for ATP and substrate binding.
Subject(s)
Gene Expression Regulation , Guanine Nucleotide Exchange Factors/chemistry , Heat-Shock Proteins/chemistry , Molecular Chaperones/chemistry , Nucleotides/chemistry , Adenosine Diphosphate/chemistry , Adenosine Triphosphatases/chemistry , Adenosine Triphosphate/chemistry , Animals , Anisotropy , Area Under Curve , Endoplasmic Reticulum Chaperone BiP , Fluorescence Resonance Energy Transfer , HSP70 Heat-Shock Proteins/chemistry , Humans , Kinetics , Mice , Models, Molecular , Protein Binding , Protein Domains , Protein Structure, Secondary , Saccharomyces cerevisiae/metabolismABSTRACT
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.
Subject(s)
Carrier Proteins/chemistry , Heat-Shock Proteins/chemistry , Immunoglobulin Light Chains, Surrogate/chemistry , Peptides/chemistry , Vascular Endothelial Growth Factor A/chemistry , Amino Acid Sequence , Anisotropy , Binding Sites , Carrier Proteins/genetics , Carrier Proteins/metabolism , Endoplasmic Reticulum Chaperone BiP , Fluorescent Dyes/chemistry , Gene Expression , Heat-Shock Proteins/genetics , Heat-Shock Proteins/metabolism , Humans , Immunoglobulin Light Chains, Surrogate/genetics , Immunoglobulin Light Chains, Surrogate/metabolism , Isoquinolines/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Peptides/genetics , Peptides/metabolism , Protein Array Analysis , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , Spectrometry, Fluorescence , Structural Homology, Protein , Structure-Activity Relationship , Thermodynamics , Vascular Endothelial Growth Factor A/genetics , Vascular Endothelial Growth Factor A/metabolismABSTRACT
Hsp70s are molecular chaperones involved in the folding and assembly of proteins. They recognize hydrophobic amino acid stretches in their substrate binding groove. However, a detailed understanding of substrate specificity is still missing. Here, we use the endoplasmic reticulum-resident Hsp70 BiP to identify binding sites in a natural client protein. Two sites are mutually recognized and form stable Hsp70-substrate complexes. In silico and in vitro analyses revealed an extended substrate conformation as a crucial factor for interaction and show an unexpected plasticity of the substrate binding groove. The basic binding mechanism is conserved among different Hsp70s.
