Biology subjects

Ahn, S. Y.

Publications and source records attributed to Ahn, S. Y..

3 recordsLinked to original sources

bioRxiv2026

Dynamics of synthetic transcriptional condensates emerge from RNA synthesis and degradation

At sites of active gene expression, dynamic compartments known as transcriptional condensates assemble and dissolve on timescales relevant to RNA synthesis and degradation. Yet how the non-equilibrium dynamics of these condensates emerge from the coupling of RNA concentration and phase separation remains poorly understood. Here we engineer synthetic active condensates in which T7 RNA polymerase transcribes RNA in situ, triggering phase separation with a cationic scaffold protein. By using RNA concentration as a tunable parameter, we drive condensates along defined paths through a characterized phase diagram. This reaction-phase separation coupling gives rise to three emergent dynamic phenomena not accessible in passive systems: a rapid switch-like nucleation burst, RNA-mediated positive and negative feedback regulation of transcription, and oscillatory condensate formation in which RNA degradation spontaneously renucleates condensates. Together, these results show that the dynamic functions of transcriptional condensates emerge from their reaction-driven paths through phase space, providing a quantitative framework for understanding how RNA flux governs condensate dynamics in living cells.

biophysics↗

bioRxiv2026

Electrostatic Self-Assembly of Protein Nanoparticles from Intrinsically Disordered Polypeptide and Globular Protein Pairs

Intracellular delivery of folded, functional proteins remains a critical barrier to realizing the full potential of protein therapeutics. We present a fully aqueous, genetically encoded platform for assembling micellar protein nanoparticles via electrostatic coacervation between anionic globular proteins and multi-domain intrinsically disordered proteins (IDPs) composed of a neutral elastin-like polypeptide (ELP) domain and a cationic disordered histone-derived domain (H5). This biosynthetic system allows modular control over charge density, neutral domain length, and stoichiometry, enabling the formation of homogeneous micellar nanoparticles with high protein payload retention under mild, biologically relevant conditions without organic solvents or covalent modification. Unlike amphiphilic micelle systems, globular proteins in this approach act as both cargo and assembly drivers, providing a direct handle to tune encapsulation. Nanoparticle assembly was characterized with a suite of complementary techniques including DLS, FCS, TEM, and SAXS, enabling detailed analysis of nanoparticle structure, size, and composition. The system exhibits remarkable tolerance to different formulations, consistently producing well-defined particles with low dispersity. This expanded design space arises from the use of structured, charge-regulating proteins and confers exceptional versatility in formulation. Different charge fractions modulate not only nanoparticle size but also physicochemical properties such as core density and cargo loading, which may be critical for tuning nanoparticle stability and performance. Together, these features establish a robust and programmable platform for protein-based nanoparticle engineering with potential application in intracellular protein delivery.

bioengineering↗

bioRxiv2024

Selectivity of Complex Coacervation in Multi-Protein Mixtures

Liquid-liquid phase separation of biomolecules is increasingly recognized as relevant to various cellular functions, and complex coacervation of biomacromolecules, particularly proteins, is emerging as a key mechanism for this phenomenon. Complex coacervation is also being explored as a potential protein purification method due to its potential scalability, aqueous operation, and ability to produce a highly concentrated product. However, to date most studies of complex coacervation have evaluated the phase behavior of a binary mixture of two oppositely charged macromolecules. Therefore, a comprehensive understanding of the phase behavior of complex biological mixtures has yet to be established. To address this, a panel of engineered proteins was designed to allow for quantitative analysis of the complex coacervation of individual proteins within a multi-component mixture. The behavior of individual proteins was evaluated using a defined mixture of proteins that mimics the charge profile of the E. coli proteome. To allow for direct quantification of proteins in each phase, spectrally separated fluorescent proteins were used to construct the protein mixture. From this quantitative analysis, we observed that the coacervation behavior of individual proteins in the mixture was consistent with each other, which was distinctive from the behavior when each protein was evaluated in a single-protein system. Subtle differences in biophysical properties between the proteins became noticeable in the mixture, which allowed us to elucidate parameters for protein complex coacervation. With this understanding, we successfully designed methods to enrich a range of proteins of interest from a mixture of proteins.

biophysics↗