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to be a trimer of the usual dimer of stalk proteins. This non-canonical
stalk structure seemed to be a peculiarity of the thermophilic ribosomes
studied (Fig. 6).
Protein-lipid interactions
An important aspect of structural mass spectrometry is in identifying
lipid ligands of proteins not readily discernible by other structural
methods. Lipids are structural components of biomembranes but they
also play significant roles in signal transduction and energy storage. As
regulatory molecules some have been found to be ligands of orphan
nuclear receptors (so called because their endogenous ligands were
unknown).
In the case of retinoid-X-receptor or RXR, which is a nuclear recep-
tor acting as a ligand activated transcription factor, the identification of
the ligand was done by MS (de Urquiza
et al
., 2000). Through a combi-
nation of biochemical work-up and bioassays of brain conditioned-
media, the isolation of an active component was achieved. Analysis of
an intense ion peak associated with active fractions as well as some
minor ones made it possible to deduce the molecular formula as C
22
H
32
O
2
.
This was later confirmed by identical fragmentation patterns from
MS/MS experiments of the intense ion peak (from active fractions) with
that of the standard cis-4,7,10,13,16,19-docosahexaenoic acid (DHA).
The true ligand binding activity of DHA was further confirmed by its
activation being very sensitive to mutations that alter the ligand-binding
specificity of RXR.
Another example is the case of horse myelin P2, which is an essen-
tial myelin (insulating membrane of neuronal axons) associated protein
belonging to the fatty acid binding protein family (FABP). It was possi-
ble not only to identify the ligands in the binding pocket but also preserve
the complex such that a higher than expected molecular weight was
accounted for by the presence of lauryl dimethylamine-N-oxide and
HEPES, both components of the crystallization buffer for this membrane
associated protein (Hunter
et al
., 2005). FABPs have been shown to have
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