Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes

Abstract

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.

On the specificity of protein–protein interactions in the context of disorder

“…At low concentration, the complex forms a 1 : 1 complex of nM affinity. At higher concentration, the dynamics of the complex makes it possible for a second ligand (of either partner) to enter the complex, forming ternary (or higher order) complexes of lower affinity ( Figure 4 ) [ 125 ]. The trimers are only transient, and one of the ligands sharing the interaction will remain and reestablish a new nM affinity 1 : 1 complex.…”

“…This can happen much faster than one would expect from a ‘normal' nM affinity interaction with long-lived established contacts at the interface, and with a concentration dependent dissociation rate constant. As a result, the exchange rate in the complex changes more than 45-fold compared with a two-state reaction [ 125 ], which has implications for affinity measurement at higher protein concentrations [ 124 ]. This mechanism has been referred to as facilitated ligand exchange via competitive substitution [ 125 , 126 ].…”

Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins

“…This information is not unlike the spatial coordinates obtained from biomolecular simulations, which in some ways can simply be viewed as single-molecule distance measurements performed in silico . As such, several notable strategies have been developed during the last 10 years to combine the strengths of these two methods [ 24 , 69 – 85 ]. These strategies vary depending on the type of biochemical information desired.…”

“…The results of these dilute-solution studies were then used to both optimize and validate a coarse-grained model of the three interacting species for MD simulations. Here, structure-based models of the nucleosome and the globular domain of H1 were used in conjunction with polymer-like representations of H1 and ProTα [ 84 , 85 ], where each amino acid is represented by single bead of the appropriate charge and each nucleotide represented by three beads. Importantly, the interaction between H1, ProTα, and the nucleosome were governed by a potential energy function containing electrostatic and generic short-range attractive terms, the latter of which was adjusted via a single parameter to maximize agreement with the experimental FRET data.…”

Microbiome dysbiosis in lung cancer: from composition to therapy

“…Dysregulation of host metabolism by microbiome alterations have been intensively studied in the intestinal tract 52 – 54 . The carcinogen acetaldehyde and deoxycholic acid produced by microbiome were reported to be involved in esophagus and liver carcinogenesis 55 , 56 .…”