Adenosine Triphosphate Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks

Abstract

Adenosine triphosphate (ATP) is an abundant molecule with crucial cellular roles as the energy currency and a building block of nucleic acids and for protein phosphorylation.Here we show that ATP mediates the phase separation of basic intrinsically disordered proteins (bIDPs). In the resulting condensates, ATP is highly concentrated (apparent partition coefficients up to 7700) and serves as bridges between bIDP chains. These liquid-like droplets have some of the lowest interfacial tension (∼25 pN/μm) but high zero-shear viscosities (1−15 Pa s) due to the bridged protein networks, and yet their fusion has some of the highest speeds (∼1 μm/ms). The rapid fusion manifests extreme shear thinning, where the apparent viscosity is lower than zero-shear viscosity by over 100-fold, made possible by fast reformation of the ATP bridges. At still higher concentrations, ATP does not dissolve bIDP droplets but results in aggregates and fibrils.

Fundamental Aspects of Phase-Separated Biomolecular Condensates

“…A similar situation was found in the all-atom simulations of a condensate formed by mixing ATP with protamine, a 33-residue IDP containing 21 Arg residues (Figure b) . ATP bridges protamine chains, forming contacts with 2.5 chains on average, via extensive interactions between Arg side chains and all parts of ATP molecules, including multilayered cation−π and π–π and stacks.…”

“…Yet their fusion is very fast, implicating extreme shear thinning. Kota et al proposed that the fast fusion is made possible by rapid reformation of ATP bridges between the protamine chains during the fusion process (Subsection ).…”

“…The green plane represents the viscocapillary model; blue circles display data points above the plane, implicating shear thinning; red triangles display data points below the plane, implicating shear thickening. Data from refs , , , , , , , and . Cyan squares display the data on the interfacial tension–viscosity plane; also included are points, shown as orange squares, where interfacial tension was deduced from viscosity and fusion speed by applying the viscocapillary model. , …”

“…In both the Jeffreys and Burgers models, the zero-shear viscosity is given by η = η 0 + η 1 . These models have been used to analyze viscoelasticity data for biomolecular condensates. ,,,,, …”

Adenosine Triphosphate: The Primordial Molecule That Controls Protein Homeostasis and Shapes the Genome–Proteome Interface

“…Briefly, ATP serves as a bridging agent, cross-linking bIDP chains to create mesh-like networks that manifest as liquid-like droplets. These droplets exhibit unusual physicochemical characteristics, such as very high ATP concentrations within the droplets, rapid fusion rates, low interfacial tension, and high viscosities, thus resulting in extreme shear-thinning behavior [105].…”