BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiP

Abstract

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.

Recent advances in the structural and mechanistic aspects of Hsp70 molecular chaperones

“…Application of these prediction algorithms reveals that there are potential DnaK-binding sites with high frequency (one every 40 residues) in the E. coli proteome. Analogous predictive algorithms have been developed for the eukaryotic Hsp70, BiP, using a combination of phage display and peptide array data (28,29). The results show that there may be some chaperone-to-chaperone variation in substrate preferences, but the ability to bind many sequences is a common Hsp70 property.…”

Members of the Hsp70 Family Recognize Distinct Types of Sequences to Execute ER Quality Control

“…BiP bound to multiple sequences above the Δins background signal in apyrase supplemented lysates, which was readily disrupted by ATP addition as expected for bona fide substrate binding to an Hsp70 chaperone. The frequent number of binding sites observed is consistant with in silico predictions (Knarr et al, 1995; Schneider et al, 2016) and in vivo experiments (Kaloff and Haas, 1995) revealing that BiP can bind multiple antibody domains. Unfortunately the apyrase treatment used to stabilize BiP binding resulted in partial cleavage of some of the peptides due to a contaminating protease activity.…”

Ca2+ binding induced sequential allosteric activation of sortase A: An example for ion-triggered conformational selection

“…The hydrogen and the heavy atoms were minimized consecutively using the SANDER module of Amber14. The systems were heated up to 300 K in the NVT ensemble, in a stepwise fashion as performed in our previous work applying a 3 kcal.mol -1 .A -2 force constant first on all heavy protein atoms (0-50K) and later on all backbone atoms (50-200K), respectively [ 44 , 45 ]. The SHAKE algorithm was used to constraint all bonds involving hydrogen atoms [ 46 ].…”