Extreme Fuzziness: Direct Interactions between Two IDPs

Abstract

Protein interactions involving intrinsically disordered proteins (IDPs) greatly extend the range of binding mechanisms available to proteins. In interactions employing coupled folding and binding, IDPs undergo disorder-to-order transitions to form a complex with a well-defined structure. In many other cases, IDPs retain structural plasticity in the final complexes, which have been defined as the fuzzy complexes. While a large number of fuzzy complexes have been characterized with variety of fuzzy patterns, many of the interactions are between an IDP and a structured protein. Thus, whether two IDPs can interact directly to form a fuzzy complex without disorder-to-order transition remains an open question. Recently, two studies of interactions between IDPs (4.1G-CTD/NuMA and H1/ProTα) have found a definite answer to this question. Detailed characterizations combined with nuclear magnetic resonance (NMR), single-molecule Förster resonance energy transfer (smFRET) and molecular dynamics (MD) simulation demonstrate that direct interactions between these two pairs of IDPs do form fuzzy complexes while retaining the conformational dynamics of the isolated proteins, which we name as the extremely fuzzy complexes. Extreme fuzziness completes the full spectrum of protein-protein interaction modes, suggesting that a more generalized model beyond existing binding mechanisms is required. Previous models of protein interaction could be applicable to some aspects of the extremely fuzzy interactions, but in more general sense, the distinction between native and nonnative contacts, which was used to understand protein folding and binding, becomes obscure. Exploring the phenomenon of extreme fuzziness may shed new light on molecular recognition and drug design.

Keywords: binding mechanism; extremely fuzzy complex; intrinsic disordered protein; protein interaction.

Figure 1

(a) The domain organization of 4.1G and nuclear mitotic apparatus (NuMA). (b) The contact maps between 4.1G-C-terminal domain (CTD) and NuMA in the top five clusters of 4.1G-CTD/NuMA structure ensemble based on replica exchange molecular dynamics (REMD) simulations in [38]. FERM: four.one–ezrin–radixin–moesin domain; FA: FERM adjacent domain; SAB: spectrin–actin binding domain.

Figure 2

Charge hydropathy ratio for proteins. The dotted line represents an empirically determined charge/hydropathy relationship that distinguishes most ordered globular and intrinsically disordered proteins. The ratio was calculated using the Predictor of Natural Disordered Regions (PONDR) and the data of ordered proteins and disordered proteins were taken from PONDR website [48].

Figure 3

NuMA binding does not reduce the local frustrated interactions in 4.1G-CTD. Frustrations of pair interactions in the top three clusters of 4.1G/NuMA complex are evaluated. The green lines indicate minimally frustrated interactions, while the red lines indicate highly frustrated interactions. Representations in the left column are free form 4.1G-CTD and the ones in the right column are 4.1G/NuMA complex. NuMA peptide is colored orange and 4.1G is colored according to its secondary structure.