Nitric oxide synthase (NOS) in mammals is a family of
multidomain
proteins in which interdomain electron transfer (IET) is controlled
by domain–domain interactions. Calmodulin (CaM) binds to the
canonical CaM-binding site in the linker region between the FMN and
heme domains of NOS and allows tethered FMN domain motions, enabling
an intersubunit FMN-heme IET in the output state for NO production.
Our previous cross-linking mass spectrometric (XL MS) results demonstrated
site-specific protein dynamics in the CaM-responsive regions of rat
neuronal NOS (nNOS) reductase construct, a monomeric protein [Jiang
et al., Biochemistry, 2023, 62, 2232–2237].
In this work, we have extended our combined approach of XL MS structural
mapping and AlphaFold structural prediction to examine the homodimeric
nNOS oxygenase/FMN (oxyFMN) construct, an established model of the
NOS output state. We employed parallel reaction monitoring (PRM) based
quantitative XL MS (qXL MS) to assess the CaM-induced changes in interdomain
dynamics and interactions. Intersubunit cross-links were identified
by mapping the cross-links onto top AlphaFold structural models, which
was complemented by comparing their relative abundances in the cross-linked
dimeric and monomeric bands. Furthermore, contrasting the CaM-free
and CaM-bound nNOS samples shows that CaM enables the formation of
the intersubunit FMN-heme docking complex and that CaM binding induces
extensive, allosteric conformational changes across the NOS regions.
Moreover, the observed cross-links sites specifically respond to changes
in ionic strength. This indicates that interdomain salt bridges are
responsible for stabilizing and orienting the output state for efficient
FMN-heme IET. Taken together, our targeted qXL MS results have revealed
that CaM and ionic strength modulate specific dynamic changes in the
CaM/FMN/heme complexes, particularly in the context of intersubunit
interdomain FMN-heme interactions.