Start2Fold: A database of protein folding and stability data

Hydrogen/deuterium exchange (HDX) experiments are used to probe the tertiary structures and folding pathways of proteins. The rate of proton exchange between a given residue’s backbone amide proton and the surrounding solvent depends on the solvent exposure of the residue. By refolding a protein under exchange conditions, these experiments can identify which regions quickly become solvent-inaccessible, and which regions undergo exchange for longer, providing information about the refolding pathway.

Although there are many examples of individual HDX experiments in the literature, the heterogeneous nature of the data has deterred comprehensive analyses. Start2Fold (Start2Fold.eu) [1] is a curated database that aims to present protein folding and stability data derived from solvent-exchange experiments in a comparable and accessible form. For each protein entry, residues are classified as early/intermediate/late based on folding data, or strong/medium/weak based on stability data. Each entry includes the PDB code, length, and sequence of the protein, as well as details of the experimental method. The database currently includes 57 entries, most of which have both folding and stability data. Hopefully, this database will grow as scientists add their own experimental data, and reveal useful information about how proteins refold.

The folding data available in Start2Fold is visualised in the figure below, with early, intermediate and late folding residues coloured light, medium and dark blue, respectively.

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[1] Pancsa, R., Varadi, M., Tompa, P., Vranken, W.F., 2016. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. Nucleic Acids Res. 44, D429-34.