Data from: Molecular exaptation by the integrin αI domain

Integrins bind ligands between their alpha (α) and beta (β) subunits and
transmit signals through conformational changes. Early in chordate
evolution, some α subunits acquired an "inserted" (I) domain
that expanded integrin’s ligand-binding repertoire but obstructed the
ancestral ligand pocket, seemingly blocking conventional integrin
activation. To understand the ancestral conformational dynamics of the
integrin I domain, we performed all-atom molecular dynamics simulations on
a representative sample of integrin I domains, sister clade
collagen-derived vWFA domains, and the ancestral reconstruction AncI. We
further investigated the effect of amino acid substitution on the internal
ligand of αLβ2 bound with ICAM-1 and αEβ7 bound to E-cadherin. All
simulations were performed using OpenMM 7.7.0 (I-domain systems) or OpenMM
8.2.0 (integrin headpiece systems) employing AMBER19ffSB force field, OPC
water model, and 12-6-4 Li Merz ion parameters. Simulations were performed
on either the Fred Hutch Cancer Center clusters on Nvidia GTX 2080 or
in-house workstations on Nvidia GTX 3090. Trajectory snapshots were saved
every 100 ps during production simulations.