Intrinsically disordered proteins and their dynamic multivalent interactions 

Dr. Sean Devenish

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June 20, 2024

The fuzziness of intrinsically disordered proteins

Protein–protein interactions (PPIs) are fundamental to all cellular functions. The mechanism by which we understand these interactions has evolved from the early “lock and key” model [1] to the “induced fit” [2] and “conformational selection [3] which now considers protein dynamics. In the past approximately thirty years, however, a new type of protein has become recognized which does not adhere to these established models. The emergence of intrinsically disordered proteins/regions (IDPs/IDRs) have emerged as a new protein class that takes part in many PPIs.

Unlike ordered globular proteins, IDPs have no fixed structure and can interact with binding partners in a multitude of ways. IDPs bind to their partners through so-called “fuzzy” interactions, and in doing so still retain various degrees of disorder [4]. The concept of “fuzziness” initially referred to differing levels of structural heterogeneity and flexibility in the complexes formed by intrinsically disordered proteins and regions.

The concept of “fuzziness” has evolved over time. In 2017 the importance of multiple interaction sites in facilitating the function of IDPs was highlighted [5], and subsequently this concept developed into a new term: dynamic multivalent interaction (DMI), which aimed to include the importance of dynamism in the interactions of IDPs [6]. DMIs of IDPs result in a dynamic ensemble of protein complexes with heterogeneous conformation, promiscuous binding, stoichiometry and kinetics. In short, DMIs allow for a plethora of subtly variable interactions that serve in promiscuous functional roles.

Figure 1: . A) DMI with specific site pairing. B) DMIs facilitating the transport of a protein. C) DMI with binding promiscuity. D) DMI exhibiting heterogeneous stoichiometry. E) Highly fuzzy interactions between a pair of IDPs. Adapted from Weng & Wang, 2020 [6].

DMI with a specific binding site pairing

As shown in Fig 1A there is one type of DMI where the binding sites on the IDP and its partner are one-to-one. The binding site pairs may have different affinities and the bound IDP exhibits residual dynamics from binding/rebinding at weak binding sites to local conformational fluctuation. An example consistent with this binding model is the TAZ1/TAD-STAT2 complex. Briefly, the weakly binding part of TAD-STAT2 was found to undergo fast binding/rebinding, which is a property that could be important for binding to multiple partners [7].

DMI and heterogeneous stoichiometry

In instances where IDPs and/or their binding partners have multiple binding motifs which can bind to the same or similar target sites/motifs, the interaction could lead to heterogenous stoichiometry of the complex [6]. The formation of a dynamic complex which possesses heterogenous stoichiometry has now been proven to be a mechanism for tuning transcriptional regulation [8]. Another example showing heterogeneous stoichiometry is the DMI between the intrinsically disordered protein tau and tubulin [9].

Characterizing intrinsically disordered protein DMIs

The protein-protein interactions of classical ordered, regular proteins form an extensive interaction network. Significant complexity is being added to this interaction landscape due to DMIs between IDPs. Current technologies that measure binding affinities between proteins are best suited to those ordered and globular in shape. These technologies are, to a variable extent, ill-equipped to characterize the binding between IDPs and regular ordered proteins. This is further compounded by the emerging importance of DMIs with their variable stoichiometry and dynamic nature adding to the difficulty of experimental characterization.

However, the solution to such characterization could be found in microfluidic technology. Falke et al. used microfluidic diffusional sizing (MDS) to characterize the interaction of an IDP involved in Parkinson’s disease, α-synuclein, with lipid particles [10]. By using MDS, they were able to develop a detailed molecular picture of the protein-lipid interaction in native and solution-phase conditions.

Watch the video below to learn more about MDS or contact us to discuss how MDS can help characterize IDP DMIs. 

References 

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    7. Lindström, I.; Dogan, J. Dynamics, Conformational Entropy, and Frustration in Protein–Protein Interactions Involving an Intrinsically Disordered Protein Domain. ACS Chem. Biol. 2018, 13, 1218–1227. https://doi.org/10.1021/acschembio.7b01105
    8. Clark, S.; Myers, J.B.; King, A.; Fiala, R.; Novacek, J.; Pearce, G.; Heierhorst, J.; Reichow, S.L.; Barbar, E.J. Multivalency Regulates Activity in an Intrinsically Disordered Transcription Factor. eLife 2018, 7, e36258. https://doi.org/10.7554/eLife.36258
    9. Li, X.-H.; Rhoades, E. Heterogeneous Tau-Tubulin Complexes Accelerate Microtubule Polymerization. Biophys. J. 2017, 112, 2567–2574. https://doi.org/10.1016/j.bpj.2017.05.006
    10. Falke, M.; Victor, J.; Wördehoff, M.M.; Peduzzo, A.; Zhang, T.; Schröder, G.F.; Buell, A.K.; Hoyer, W.; Etzkorn, M. α-Synuclein-Derived Lipoparticles in the Study of α-Synuclein Amyloid Fibril Formation. Chem. Phys. Lipids 2019, 220, 57–65. https://doi.org/10.1016/j.chemphyslip.2019.02.009
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