Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational Plasticity within Organelles, Cells, and Tissues

Many proteins can exist in multiple conformational states in vivo to achieve distinct functional roles. These states
include alternative conformations, variable post-translational modifications
(PTMs), and associations with interacting
protein, nucleotide, and ligand partners. Quantitative chemical cross-linking
of live cells, organelles, or tissues together with mass spectrometry
provides the relative abundance of cross-link levels formed in two
or more compared samples, which depends both on the relative levels
of existent protein conformational states in the compared samples
and on the relative likelihood of the cross-link originating from
each. Because cross-link conformational state preferences can vary
widely, one expects intraprotein cross-link levels from proteins with
high conformational plasticity to display divergent quantitation among
samples with differing conformational ensembles. Here we use the large
volume of quantitative cross-linking data available on the public
XLinkDB database to cluster intraprotein cross-links according to
their quantitation in many diverse compared samples to provide the
first widescale glimpse of cross-links grouped according to the protein
conformational state(s) from which they predominantly originate. We
further demonstrate how cluster cross-links can be aligned with any
protein structure to assess the likelihood that they were derived
from it.