Disordered Motifs and Domains in Cell Control - October 11-15, 2014

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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