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 ..., , # Data from: Molecular exaptation by the integrin αI domain

## Provided Files

The dataset contains molecular dynamics trajectories analyzed for the manuscript titled \"Molecular exaptation by the integrin αI domain\", Science Advances, 2015. Two sets of simulations were performed: 1) simulations of various integrin I-domains initially bound to different divalent cations (`i-domains/`), and 2) simulations of the αEβ7 and LFA1 headpiece simulations (`aEb7-LFA1/`).

* `i-domains.zip/` files for I-domain simulations. Includes:
* `strip-traj/` - trajectories in `.xtc` file format
* `ref/` - reference trajectories for RMS analysis
* `prmtop/` - topology file in `.prmtop` file format
* `aEb7_LFA1.zip/` files for αEβ7 and LFA1 simulations. Includes:
* `wrap-traj/` - trajectories in `.xtc` file format
* `ref/` - reference trajectories for RMS analysis
* `prmtop/` - topology file in `.prmtop` file format

### Simulation details

All simulations were performed using OpenMM 7.7.0 (I-dom...,