Modulation of allostery by protein intrinsic disorder

Abstract

Allostery is an intrinsic property of many globular proteins and enzymes that is indispensable for cellular regulatory and feedback mechanisms. Recent theoretical1 and empirical2 observations indicate that allostery is also manifest in intrinsically disordered proteins (IDPs), which account for a significant proportion of the proteome3,4. Many IDPs are promiscuous binders that interact with multiple partners and frequently function as molecular hubs in protein interaction networks. The adenovirus early region 1A (E1A) oncoprotein is a prime example of a molecular hub IDP5. E1A can induce drastic epigenetic reprogramming of the cell within hours after infection, through interactions with a diverse set of partners that include key host regulators like the general transcriptional coactivator CREB binding protein (CBP), its paralog p300, and the retinoblastoma protein (pRb)6,7. Little is known about the allosteric effects at play in E1A-CBP-pRb interactions, or more generally in hub IDP interaction networks. Here, we utilized single-molecule Förster/fluorescence resonance energy transfer (smFRET) to study coupled binding and folding processes in the ternary E1A system. The low concentrations used in these high-sensitivity experiments proved essential for these studies, which are challenging due to a combination of E1A aggregation propensity and high-affinity binding interactions. Our data revealed that E1A-CBP-pRb interactions display either positive or negative cooperativity, depending on the available E1A interaction sites. This striking cooperativity switch enables fine-tuning of the thermodynamic accessibility of the ternary vs. binary E1A complexes, and may permit a context-specific tuning of associated downstream signaling outputs. Such a modulation of allosteric interactions is likely a common mechanism in molecular hub IDP function.

Protein conformational dynamics dictate the binding affinity for a ligand

“…There has recently been growing interest in the regulation of protein functions in an allosteric manner 19,25,[28][29][30][31][32] . However, the operational mechanism of the allosteric regulation remains poorly understood.…”

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

“…IDRs such as the SF3b155 ULM-containing region often coordinate the synergistic action of multiple weak binding sites to modulate positive or negative allostery, as recently exemplified for coordination of host CBP or pRB proteins by the adenoviral protein E1A (Ferreon et al 2013). The ULM-containing region of SF3b155 adjoins its binding site for p14, an RRM-like U2 snRNP subunit that ultimately contacts the branch point sequence of the pre-mRNA Cass and Berglund 2006;Schellenberg et al 2006;Spadaccini et al 2006).…”

Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors

“…This improves the affinity of the second binding event (because binding need no longer pay the unfavorable cost associated with folding), leading to positive allosteric behavior. Ferreon et al (24), for example, have shown that the intrinsically disordered oncoprotein adenovirus early region 1A (E1A) folds upon binding either of its two (different) target ligands (CREB binding protein or retinoblastoma protein), thus increasing the affinity with which the second ligand binds and rendering the system heterotropically allosteric. In addition, Furukawa et al (25) have shown that the partially intrinsically disordered protein STIM 1 exhibits strongly homotropic allosteric binding to calcium.…”

“…Specifically, both theoretical (23) and experimental (24,25) studies have demonstrated that the global conformation change these proteins undergo upon an initial ligand binding event provides a convenient means of preorganizing a second, distal ligand binding site. This improves the affinity of the second binding event (because binding need no longer pay the unfavorable cost associated with folding), leading to positive allosteric behavior.…”