On the evolution of protein–adenine binding

Abstract

Proteins’ interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein–adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein–adenine interactions in the Watson–Crick edge of adenine and shows that all of adenine’s edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments (“themes”) that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

“…The alternative binding mode can be explained by the N3 substitution of adenine on this fragment, which prevents formation of the canonical N1-Ile23 H-bond. This pattern of hydrogen bonds to the protein has not been previously observed in adenines linked through N9 ( 58 ).…”

“…The alternative binding mode can be explained by the N3 substitution of adenine on this fragment, which prevents formation of the canonical N1-Ile23 H-bond. This pattern of hydrogen bonds to the protein has not been previously observed in adenines linked through N9 (58). We also observed diverse fragments without adenine-like motifs binding at this site, including succinimides, amides, thiazoles, diamino-pyridines, pyrazoles, pyrroles, and ureas ( Fig.…”

Bridging themes: short protein segments found in different architectures

“…For cases of shared ancestry, we now speculate about the turn of events that could have led to such current-day patterns. One possibility is that in the ancient past, a short ancestral theme existed on its own, i.e., without the segments that flank it in the intact, contemporary domain, perhaps bound to an ion or mineral (e.g., Figures , 6, 7, 2S, and [1]), a nucleotide [77], or RNA [5,16]. Over time, it may have duplicated, the two copies diverged (albeit not beyond the level of detection), and protein segments accumulated before and/or after both variations.…”

“…In other words, the themes, and specifically, their reconstructed ancestral sequences, may be good candidates for protein engineering (in contrast with the contemporary variations, that may have lost the contextual agility [45,83]). Themes with ligand binding function are particularly attractive candidates [77,84].…”

Defining a Global Map of Functional Group Based 3D Ligand-binding Motifs

“…For example, the phosphate-binding loop (P-loop) motif (Saraste et al, 1990;Via et al, 2000), in which the residues are highly conserved in terms of amino acid types as well as spatial positions among diverse phosphate-binding proteins. Conserved 3D motifs were also reported for other FGs such as adenine ring (Denessiouk et al, 2001;Narunsky et al, 2020;Nebel et al, 2007), heme group (Ferousi et al, 2019;Zubieta et al, 2007) and prosthetic groups (Nebel, 2006). However, these motifs were either uncovered through manual analysis of a small set of protein structures by an expert (e.g.…”