Intrinsically disordered protein domains do not
fold on their own into α-helices or β-sheets/turns. Structural genomics
studies and prediction algorithms together indicate that thousands of
eukaryotic proteins contain one or more intrinsically disordered regions,
including a large fraction involved in genome regulation. Not surprisingly,
the determinants of function of intrinsically disordered regions appear to
be different than for typical globular proteins. In particular,
intrinsically disordered regions have a distinctive amino acid composition
that includes being enriched in like charged residues and deficient in nonpolar residues. For example, the unusual amino acid composition of the
linker histone CTDs is shown in the table below
Our laboratory has been studying intrinsically
disordered proteins for over a decade, through our investigations of the
core histone N-terminal tail domains, linker histone CTD, ySir3p and MeCP2.
The core and linker histones have unstructured terminal regions that serve
as combinatorial interaction domains. In contrast, yeast SIR3p and MeCP2
have long internal intrinsically disordered regions.
A major challenge that we have undertaken is determining how intrinsic
disorder is linked to protein function at the biochemical level. While
interaction-induced disorder to order transitions and specific amino acid
composition are thought to be involved, the structure/function relationships
that pertain to intrinsically disordered proteins remain poorly understood.
The tertiary structure of intrinsically disordered proteins cannot be
determined by x-ray crystallography or NMR. Consequently, solution
physicochemical approaches, e.g., circular dichroism, analytical
ultracentrifugation, hydrogen exchange, small angle x-ray scattering have
proven to be most useful in our studies. The approach we take is to mutate
key properties of intrinsically disordered regions and ask how the mutations
affect protein structure and function. For example, in the case of the core
histone NTDs we have altered the chare density and length, while for the CTD
we have scrambled the amino acid composition and moved the location of key
functional elements relative to the winged helix. The combination of
targeted mutagenesis followed by solution physicochemical analyses holds
major promise for deciphering how intrinsically disordered proteins work.
Our work in this area is funded by both NIH grants R01 GM45916 and GM66834.