Disordered Motifs and Domains in Cell Control
Tuesday Speaker Abstracts
Regulation by In-Complex Molecular Switching
Toby Gibson
.
EMBL, Heidelberg, Germany.
Proteomics has shown us that regulatory proteins spend most, often all, of their time in large
macromolecular complexes. This suggests that to understand cell regulation, we need to
understand the processes that occur within these complexes. The knowledge now being won
about the role of natively disordered polypeptide and short linear motifs, suggests that these
protein modules are assembled into molecular switch devices within these complexes. We have
reviewed and classified these switches by mechanism. We collate motif switches in the
switches.ELM database. In the talk, I will discuss the nature of cell regulation by molecular
switching and how we might move forward the computational representation of regulatory
pathways and complexes. In particular, it needs to be understood that protein complexes are units
of biochemical function as, at a different scale, are individual peptide modules (domains, motifs):
Regulatory proteins themselves are not, however, meaningful units of biochemical function but
are vehicles for bringing concatenated assemblies of functional peptide modules into the
regulatory complexes.
Entropic Exclusion Determines Allostery in a Major Family of Intrinsically Disordered
Bacterial Transcription Factors
Abel Garcia-Pino
.
Vrije Universiteit Brussel, Brussels, Belgium.
Phd is the paradigm of a recently discovered transcription regulation mechanism known as
conditional cooperativity. Under normal conditions transcription of classic type II toxin-antitoxin
operons occurs through a complex mechanism that allows for the toxin to act as a co-repressor at
low toxin:antitoxin ratios and become an activator at high toxin:antitoxin ratios. To address how
Phd recognizes its binding sites, we determined the crystal structures of phage P1 Phd in
complex with its operator box. The DNA-binding domain of the Phd dimer interacts with DNA
in a novel fashion where α-helix α1 “reads” the target sequence and the backbone of α-helices α1
and α2 interact with the phosphate backbone. Moreover the wing regions defined by loop b2b3
of each monomer bind to the minor groove of the DNA tethering the DNA to the protein. These
wing contacts communicate the N-terminal region of the protein to the intrinsically disordered C-
terminus and may explain the allosteric cross-talk between toxin binding and DNA regulation.
Our data reveal the intrinsically disordered domain of Phd acts as a master regulator by
subjecting the system to either negative or positive cooperativity, depending on the occurring
interaction. In absence of Doc, the intrinsically disordered part of the repressor bound to the
DNA acts as a "veil" covering the second site and precluding the binding of a second Phd
molecule, resulting in strong negative cooperativity and weak repression. When Doc is present it
acts as an anchor point for the second Phd that folds upon binding leading to positive
cooperativity and strong repression. Such cooperativity switch enables the condition-specific
tuning of transcription that regulates the operon.
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