Start2Fold

The database of hydrogen/deuterium exchange data on protein folding and stability

Welcome to Start2Fold!

There are 57 entries in Start2Fold as of July 28, 2016. We welcome additional data submissions! Please fill in and send the template below to mvaradi at ebi.ac.uk: XML template 

What is here?

Start2Fold is a comprehensive collection of carefully curated and classified residue- or segment-level data on the folding and/or stability proteins that have been previously investigated by solvent exchange-based measurements. Besides the classification of residues based on their exchange protection levels, all entries contain the detailed descriptions of the underlying experimental procedures, sample components, measurement conditions, cross references to other databases, references to the original publications and instant visualisation of the relevant residue groups on the 3D structures of the corresponding proteins.

Why is it relevant?

Proteins are dynamic molecules that display a wide range of behaviours and fulfil many functions in the cell; understanding how they fold into complex three-dimensional structures and how these structures remain stable is essential for the interpretation of their overall behaviour. This database reports on the folding and stability of proteins based on hydrogen deuterium exchange (HDX) and oxidative labelling experimental data extracted from literature.

Folding

The protons of the backbone amide of amino acid residues exchange with protons of the solvent (water) at neutral or acidic pH. If these amide protons are in residues that are part of the folding nuclei of proteins, they become protected from solvent at a very early stage during the folding process and stop exchanging. These 'protection rates' of amide protons can be detected by a range of methods that follow their solvent exchange from the completely unfolded state throughout the entire folding course: for example pulsed labelling, quenched flow and competition-based HDX measurements (coupled with either NMR or MS) as well as oxidative labelling experiments provide invaluable information on the folding mechanisms of proteins.

Stability

On the other hand, the native exchange experiments investigate proteins in their folded or partially folded states and report on the stability of existing hydrogen bonds to the amide protons based on their resistance to solvent exchange. By varying the environmental conditions, like pH or denaturant concentrations, such measurements can also provide quantitative information on the protection levels of the individual amide protons in function of changes in the conformation of the protein. Comparing these values can distinguish more stable from less stable regions of the protein fold.

Please cite the database by referring to R. Pancsa and M. Varadi, P. Tompa, W. Vranken: Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability Nucleic Acids Research, November 2015, Database issue