Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

Highly charged intrinsically disordered proteins can form complexes with very high affinity in which both binding partners fully retain their disorder and dynamics, exemplified by the positively charged linker histone H1.0 and its chaperone, the negatively charged prothymosin α. Their interaction exhibits another surprising feature: The association/dissociation kinetics switch from slow two-state-like exchange at low protein concentrations to fast exchange at higher, physiologically relevant concentrations. Here we show that this change in mechanism can be explained by the formation of transient ternary complexes favored at high protein concentrations that accelerate the exchange between bound and unbound populations by orders of magnitude. Molecular simulations show how the extreme disorder in such polyelectrolyte complexes facilitates (i) diffusion-limited binding, (ii) transient ternary complex formation, and (iii) fast exchange of monomers by competitive substitution, which together enable rapid kinetics. Biological polyelectrolytes thus have the potential to keep regulatory networks highly responsive even for interactions with extremely high affinities.

No abstract

Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin α. Consequently, prothymosin α can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation.

Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin α. Consequently, prothymosin α can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation. 3 A large fraction of the human genome codes for proteins that contain substantial disordered regions or even lack any well-defined three-dimensional structure 1 . These intrinsically disordered proteins are involved in many cellular processes and mediate key interactions with other proteins or nucleic acids 2 . DNA-and RNA-binding proteins often contain disordered regions highly enriched in positively charged residues 3,4 , which are expected to facilitate electrostatic interactions with their cellular targets, the highly negatively charged nucleic acids 3 . The affinities can be remarkably high, even if no structure is formed upon binding 5,6 . Such polyelectrolyte interactions have long been known in the field of soft matter physics 7 , but their importance in biology has only recently started to be recognized 5,6,[8][9][10][11] and is thus largely unexplored.A ubiquitous group of proteins with long disordered positively charged regions are the histones, which are responsible for packaging DNA into chromatin. Among these, the linker histones are particularly remarkable 12 : They are largely disordered and highly positively charged, with two disordered regions flanking a small folded globular domain. By binding to the linker DNA on the nucleosome (Fig. 1a), linker histones contribute to chromatin condensation and transcriptional regulation 12,13 . However, the role of protein disorder in the complex between nucleosome and linker histone and the functional consequences have remained unclear. Here, by integrating single-molecule experiments and simulations, we establish a molecular model of the linker histone-nucleosome complex and show that disorder enables an unexpected mechanism that regulates linker histone binding: The highly negatively charged and disordered human protein prothymosin α (ProTα), a histone chaperone 14-17 that forms a high-affinity disordered complex with linker histone H1 5 , can efficiently...