Molecular dynamics simulations for "Evolutionary Dynamics of RuBisCO: Emergence of the Small Subunit and its Impact Through Time"

This repository contains the molecular dynamics simulation files for the extant and ancestral RuBisCOs, presented in Amritkar2024 et. al.

There are two separate folders, one for the regular MD simulations and the other for MD simulations with gas trajectories.

Both folders have the simulation trajectory `.dcd` files and the `.pdb` for their corresponding protein structures.

The trajectory files are dried, i.e. water molecules have been removed from them.

The data encompasses over 7 extant (pdb ids: 1BWV, 3ZXW, 6FTL, 6URA, 7SNV, 8RUC, 9RUB) and 8 ancestral (Anc-I/I', Anc-I', Anc-I, Anc-IAB, Anc-ICD, Anc-IA, Anc-IB, Anc-I-without-RbcS) RuBisCO complexes.

This study performed three types of simulations: with water molecules (labeled as exp01), with water + CO2 molecules (labeled as exp02), and with water + O2 molecules (labeled as exp04).

There are two replicates for the exp01 simulations and the simulation length for each is 250 ns.

The exp02 and exp04 files are not present for the RbcS-less (Anc-I/I', Anc-I', Anc-I-without_RbcS, 6URA, and 9RUB) RuBisCOs. The simulation length for the gas simulations is 75 ns and one replicate.

Each file is named "RuBisCO-system"."simulation-type".md"replicate-number".dry."pdb or dcd".

The files are named with respect to each RuBisCO-id in small (No caps). Anc-I/I' is represented as "anciip" and Anc-I' is represented as "ancip".