On the evolution of protein-adenine binding

Aya Narunsky, Amit Kessel, Ron Solan, Vikram Alva, Rachel Kolodny, Nir Ben-Tal

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)4701-4709
Number of pages9
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number9
DOIs
StatePublished - 3 Mar 2020

Keywords

  • Computational biology
  • Ligand binding
  • Molecular evolution
  • Molecular recognition
  • Structural biology

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