Discovery of the Xenon–Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability

The
intermolecular interactions of noble gases in biological systems
are associated with numerous biochemical responses, including apoptosis,
inflammation, anesthesia, analgesia, and neuroprotection. The molecular
modes of action underlying these responses are largely unknown. This
is in large part due to the limited experimental techniques to study
protein–gas interactions. The few techniques that are amenable
to such studies are relatively low-throughput and require large amounts
of purified proteins. Thus, they do not enable the large-scale analyses
that are useful for protein target discovery. Here, we report the
application of stability of proteins from rates of oxidation (SPROX)
and limited proteolysis (LiP) methodologies to detect protein–xenon
interactions on the proteomic scale using protein folding stability
measurements. Over 5000 methionine-containing peptides and over 5000
semi-tryptic peptides, mapping to ∼1500 and ∼950 proteins,
respectively, in the yeast proteome, were assayed for Xe-interacting
activity using the SPROX and LiP techniques. The SPROX and LiP analyses
identified 31 and 60 Xe-interacting proteins, respectively, none of
which were previously known to bind Xe. A bioinformatics analysis
of the proteomic results revealed that these Xe-interacting proteins
were enriched in those involved in ATP-driven processes. A fraction
of the protein targets that were identified are tied to previously
established modes of action related to xenon’s anesthetic and
organoprotective properties. These results enrich our knowledge and
understanding of biologically relevant xenon interactions. The sample
preparation protocols and analytical methodologies developed here
for xenon are also generally applicable to the discovery of a wide
range of other protein–gas interactions in complex biological
mixtures, such as cell lysates.