Impact of the Cellular Environment on Adenosine Triphosphate Conformations

Meredith M. Rickard, Haolin Luo, Ashley De Lio, Martin Gruebele, Taras V. Pogorelov

Research output: Contribution to journalArticlepeer-review


The cytoplasm is an environment crowded by macromolecules and filled with metabolites and ions. Recent experimental and computational studies have addressed how this environment affects protein stability, folding kinetics, and protein-protein and protein-nucleic acid interactions, though its impact on metabolites remains largely unknown. Here we show how a simulated cytoplasm affects the conformation of adenosine triphosphate (ATP), a key energy source and regulatory metabolite present at high concentrations in cells. Analysis of our all-atom model of a small volume of the Escherichia coli cytoplasm when contrasted with ATP modeled in vitro or resolved with protein structures deposited in the Protein Data Bank reveals that ATP molecules bound to proteins in cell form specific pitched conformations that are not observed at significant concentrations in the other environments. We hypothesize that these interactions evolved to fulfill functional roles when ATP interacts with protein surfaces.

Original languageEnglish (US)
Pages (from-to)9809-9814
Number of pages6
JournalJournal of Physical Chemistry Letters
Issue number42
StatePublished - Oct 27 2022

ASJC Scopus subject areas

  • General Materials Science
  • Physical and Theoretical Chemistry


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