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.