Feb 12 – 16, 2024
EPN Campus
Europe/Paris timezone

High-throughput prediction of ATP synthase rotor ring stoichiometries

Feb 16, 2024, 9:30 AM
30m
IBS seminar room (EPN Campus)

IBS seminar room

EPN Campus

71 avenue des Martyrs 38000 Grenoble
Talk CAPRI

Speaker

Ivan Gushchin (Moscow Institute of Physics and Technology)

Description

Rotary ATP synthases are large enzyme complexes present in every living cell. They consist of a transmembrane and a soluble domain, each comprising multiple subunits. The transmembrane part contains an oligomeric rotor ring (c-ring), whose stoichiometry defines the ratio between the number of synthesized ATP molecules and the number of ions transported through the membrane. Here, we present an easy-to-use high-throughput computational approach based on AlphaFold that allows us to estimate the stoichiometry of all homooligomeric c-rings, whose sequences are present in genomic databases. We validate the approach on the available experimental data, obtaining the correlation of 0.96 for the reference set of c-rings with stoichiometry from 8 to 15, and use it to predict the existence of c-rings with stoichiometry varying from 8 to 27. We then conduct molecular dynamics simulations of selected c-rings to corroborate the machine learning-based predictions. Our work highlights the usability of AlphaFold-based approaches for modeling homooligomeric proteins.

Submitting to: 8th CAPRI assessment meeting

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