Osmolyte structural and thermodynamic effects across the protein folding landscape

Supplementary data files for the article "Osmolyte structural and thermodynamic effects across the protein folding landscape" Ander Francisco Pereira and Leandro Martínez Institute of Chemistry and Center for Computing in Engineering & Sciences - Universidade Estadual de Campinas (UNICAMP) https://doi.org/10.1021/jacsau.5c00813 Contains: 1. PULCHRA generated structures, equilibrated structures, and resulting solvation analyses performed with ComplexMixtures.jl for all 5000 models of each protein/cosolvent system. These files contain, for each protein (`SH3` or `BdpA`), and for each cosolvent `Urea` or `TMAO`: a) the reconstruction of the SBM model by Pulchra. b) The equilibrated structure model, used to initiate production runs for the simulations of solvation. c) The final solvation analyzes of solvation, performed with ComplexMixtures.jl, including two files: `results_water.json` and `results_urea.json` or `results_tmao.json`, which contain the analyzes of distributions of each solvent component, performed over the trajectories. Files: SH3_TMAO.zip SH3_Urea.zip BdpA_TMAO.zip BdpA_Urea.zip 2. Resulting solvation analsyses with ComplexMixtures.jl for all simulations performed for the determination of the transfer free energies: The files contain, for each concentration, the output of the ComplexMixtures.jl calculation that appends the distribution functions and results of all simulation replicas for that concentration. The files are in the ".json" format, and must be read with `ComplexMixtures.load("file.json")`. Files with `Water` identifiers correspond to the calculations for the water as the solvent. The files without `Water` correspond to computing the distributions considering the cosolute (`Urea` or `TMAO`) as the solvents. `SH3` and `BdpA` indicate which protein is analyzed. Files: SH3_ComplexMixtures-Transfer-WaterUrea.zip SH3_ComplexMixtures-Transfer-WaterTMAO.zipSH3_ComplexMixtures-Transfer-Urea.zipSH3_ComplexMixtures-Transfer-TMAO.zip BdpA_ComplexMixtures-Transfer-WaterUrea.zip BdpA_ComplexMixtures-Transfer-WaterTMAO.zipBdpA_ComplexMixtures-Transfer-Urea.zipBdpA_ComplexMixtures-Transfer-TMAO.zip 3. CSV data tables with the m-values and zeta-angle analyses for all 5000 models of each protein/cosolvent system, with: 3.1. mvalue-estimates and contributions of the side-chains and backbones for the estimates. 3.2. Exposed surface area for every type of residue, in each of the models. 3.4. fraction of zeta angles within 2 standard deviations of expected values, computed for the PULCHRA and equlibrated models. Files: SH3_mvalues_zeta.zip BdpA_mvalues_zeta.zip Additional files, simulation trajectories, and analysis scripts may be obtained upon request to authors.