Complete Extraction of Protein Dynamics Information in Hydrogen/Deuterium Exchange Mass Spectrometry Data

Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) has been used to study protein conformation and conformational dynamics. A continuous labeling experiment, followed by proteolytic digestion and MS analysis, generates a large amount of data, containing information on protein conformation and conformational dynamics. Lacking appropriate computational methods, information hidden inside the isotope distribution is often omitted and not extracted. In this work, a computational model is described to simulate the determined isotope pattern for each proteolytic peptide at each labeling time. Optimizing the model with experimental data yields conformational protection as well as protein unfolding/folding kinetics. With this method, complete extraction of protein dynamics information in the HDX–MS data is achieved. Information derived from the method is reliable as the model is mostly based on first-principles with very few assumptions. It is demonstrated that the protein dynamics information extracted from one or two labeling time points approaches or exceeds the information derived from an entire deuterium uptake time course by the traditional method. Application of the computational method to an IgG1 antibody under mild denaturing conditions indicates that the unfolding of each immunoglobulin domain can be explained by a simple two-state unfolding process, with different unfolding rate for each domain.