StACKER, A TOOL FOR SYSTEMS LEVEL ANALYSIS OF BASE STACKING IN NUCLEOTIDE-RICH STRUCTURES

Abstract

Nucleic acid macromolecules can undergo significant structural changes--often mediated by nucleotide modification or molecular interactions. These alterations can be critical to their function. An ongoing challenge is to develop useful tools to quantify system-wide changes in nucleic acid-rich structures. We introduce StACKER, a robust Python package for observing conformational changes in a nucleic acid structure through its pi-stacking of base rings. StACKER creates System Stacking Fingerprints (SSFs) which highlight the landscape of pi-stacking throughout a molecule and can be used to show widespread conformational adjustments. Additionally, StACKERs Pairwise Stacking Fingerprint (PSF) can further characterize pi-stacking in a select residue pair, showing how the effects of localized residue changes spread through a nucleic acid system. We apply StACKER to molecular dynamics (MD) simulations of a subsystem of the ribosome to reveal that alternative codons at the ribosome A-site and 3 adjacent +1 codon position induce allosteric structure changes in the decoding center neighborhood, leading to a toggle between two conformational states. Through previous analysis of ribosome profiling data, we link these states to an observed fast/slow translation phenotype (Sun et al. 2024). We benchmark StACKER alongside other lenses for observing allostery to demonstrate its use in assessing allosteric shifts and its relevance to future structure-to-function studies.