Assessing the functional impact of protein binding site definition

Abstract

Many biomedical applications, such as classification of binding specificities or bioengineering, depend on the accurate definition of protein binding interfaces. Depending on the choice of method used, substantially different sets of residues can be classified as belonging to the interface of a protein. A typical approach used to verify these definitions is to mutate residues and measure the impact of these changes on binding. Besides the lack of exhaustive data this approach generates, it also suffers from the fundamental problem that a mutation introduces an unknown amount of alteration into an interface, which potentially alters the binding characteristics of the interface. In this study we explore the impact of alternative binding site definitions on the ability of a protein to recognize its cognate ligand using a pharmacophore approach, which does not affect the interface. The study also provides guidance on the minimum expected accuracy of interface definition that is required to capture the biological function of a protein.

Optimal selection of suitable templates in protein interface prediction

“…In this article, we explored how much one can improve template-based interface prediction for proteins whose homologs share low sequence identity. The method developed in this article was motivated by the recent observation that the minimum interface prediction accuracy needs to be at least 70% correct to capture the biological function of a protein, as assessed by its ability to reliably recognize its cognate binding partner(s) ( Nandigrami and Fiser 2023 ). This goal is a trivial task for proteins that share more than 35% sequence identity with a functionally characterized known template ( Fig.…”

“…In interface prediction, one would need to consider how incorrectly an interface can be defined while still capturing its biological function. A recent study addressing this issue reported that for an interface prediction method to be useful, it must capture at least 70% of the true biological interface of the protein ( Nandigrami and Fiser 2023 ). This suggests that the currently available best approaches still do not reach the desired level of accuracy for practical applications.…”