Systematic Modeling, Prediction, and Comparison of Domain-Peptide Affinities: Does it Work Effectively With the Peptide QSAR Methodology?

Qian Liu,Shaozhou Wang,Li Mei,Li Wen,Jing Lin,Shuyong Shang,Peng Zhou

doi:10.3389/fgene.2021.800857

Abstract

The protein–protein association in cellular signaling networks (CSNs) often acts as weak, transient, and reversible domain–peptide interaction (DPI), in which a flexible peptide segment on the surface of one protein is recognized and bound by a rigid peptide-recognition domain from another. Reliable modeling and accurate prediction of DPI binding affinities would help to ascertain the diverse biological events involved in CSNs and benefit our understanding of various biological implications underlying DPIs. Traditionally, peptide quantitative structure-activity relationship (pQSAR) has been widely used to model and predict the biological activity of oligopeptides, which employs amino acid descriptors (AADs) to characterize peptide structures at sequence level and then statistically correlate the resulting descriptor vector with observed activity data via regression. However, the QSAR has not yet been widely applied to treat the direct binding behavior of large-scale peptide ligands to their protein receptors. In this work, we attempted to clarify whether the pQSAR methodology can work effectively for modeling and predicting DPI affinities in a high-throughput manner? Over twenty thousand short linear motif (SLiM)-containing peptide segments involved in SH3, PDZ and 14-3-3 domain-medicated CSNs were compiled to define a comprehensive sequence-based data set of DPI affinities, which were represented by the Boehringer light units (BLUs) derived from previous arbitrary light intensity assays following SPOT peptide synthesis. Four sophisticated MLMs (MLMs) were then utilized to perform pQSAR modeling on the set described with different AADs to systematically create a variety of linear and nonlinear predictors, and then verified by rigorous statistical test. It is revealed that the genome-wide DPI events can only be modeled qualitatively or semiquantitatively with traditional pQSAR strategy due to the intrinsic disorder of peptide conformation and the potential interplay between different peptide residues. In addition, the arbitrary BLUs used to characterize DPI affinity values were measured via an indirect approach, which may not very reliable and may involve strong noise, thus leading to a considerable bias in the modeling. The R prd 2 = 0.7 can be considered as the upper limit of external generalization ability of the pQSAR methodology working on large-scale DPI affinity data.

Highlights

Protein–protein interactions play a key role in cell life
There are several indicators that can be used to represent the binding affinity of domain–peptide interaction (DPI), such as the Kd that can be determined by fluorescence polarization (FP) and surface plasmon resonance (SPR) to indicate the apparent dissociation constant for domain–peptide complex formation, and the ΔG that can be measured using isothermal titration calorimetry (ITC) to denote free energy change upon the complex binding
The SPOT peptide synthesis in conjunction with light intensity assays has been used to rapidly screen effective domain binders against massive peptide candidates, where peptides matching the defined patterns were synthesized at high density on cellulose membranes by SPOT synthesis technology and the membranes were probed with GST-fused domain protein, which were revealed by an anti-GST antibody and by a secondary anti-IgG antibody coupled to horseradish peroxidase (POD) to derive the intensity of each SPOT quantitatively in Boehringer light unit (BLU) as an arbitrary light intensity unit (Landgraf et al, 2004)

Summary

Introduction

Protein–protein interactions play a key role in cell life. Through formation of the functionally complicated complexes between two or more interacting protein partners, they participate in a variety of signal cascades in cells, thereby regulating the life activities of cells and individuals (Slater et al, 2020). Intrinsically disordered proteins (IDP) often interacts with the peptide-recognition domain of target protein through a flexible peptide segment on its own surface (Dyson and Wright 2005). Different from the permanent and stable complexes that are commonly formed by binding with global rigid globulins, the domain–peptide complexes are generally transient and reversible due to the limited number of residues and small contact area involved in the complex interfaces. This feature makes domain–peptide interactions (DPIs) very suitable to serve as molecular switches in biological signaling pathways that require exquisitely dynamic regulation and are closely related to various cellular processes and major diseases

Methods

Results

Conclusion