Biology subjects

Shum, H. C.

Publications and source records attributed to Shum, H. C..

8 recordsLinked to original sources

bioRxiv2026

Adenosine 5'-triphosphate (ATP) forms protein-free and responsive condensates in crowded environments

Adenosine 5-triphosphate (ATP) is found to form biomolecular condensates with proteins. However, without complementary proteins, the small size and high charge density of ATP molecules create substantial electrostatic and entropic barriers that prevent them from forming condensates. Here, we find that macromolecular crowding overcomes these energetic barriers, promoting ATP molecules to self-associate and form protein-free liquid-like condensates through screened electrostatic repulsion and enhanced hydrogen bonding. Importantly, ATP condensates are responsive to multiple stimuli and create distinct microenvironments that selectively enrich various guest molecules and protect ribonucleic acids from DNAzyme cleavage. These findings uncover important roles of ATP in forming dynamic, chemically distinct condensates via homotypic interactions, potentially expanding its classical view beyond a canonical energy carrier to a structural and regulatory architect in cellular physiology and prebiotic chemistry.

biophysics↗

bioRxiv2026

Coacervate Droplets as a Liquefier for the Solid-to-Liquid Transition of RNA Aggregates

Biomolecular condensates are functionally gated by their material properties. While RNA is a primary structural scaffold, its sequence-specific interactions can aberrantly drive condensates into dysfunctional solid aggregates. Yet, actively reversing this solidification to restore function remains a fundamental challenge, impeding progress in synthetic biology and therapeutics interventions. Here, we establish that complex coacervates can be engineered as liquefiers to actively remodel solid RNA-peptide aggregates into functional liquid droplets. Integrating systematic experiments with all-atom simulations, we decode a multiscale mechanism: coacervate infiltration at the micrometer scale mediates molecular buffering at the nanometer scale, which fluidizes the crosslinked network to drive macroscopic liquefaction. This capability is governed by a design rule, where coacervates formed by small-molecular anions exhibit optimal efficacy. We deploy this principle to functionally rescue silenced RNA within a model of pathologically solidified ribonucleoprotein assemblies. Our work provides a general framework for the active, compositional control of biomolecular phase behavior, with direct implications for managing pathological aggregation and engineering functional condensates in synthetic and living systems.

biophysics↗

bioRxiv2025

Endogenous flow and dialytaxis govern aging of Adenosine 5'-triphosphate (ATP) condensates

Biomolecular condensates are increasingly recognized as pivotal regulators of cellular physiology, yet their pathological aging underlies numerous diseases. However, the mechanisms governing this condensate aging remain largely elusive. Liquid-liquid phase separation of minimal biomolecular building blocks, such as small peptides or nucleotides, offers ideal model systems to dissect the mechanisms underlying condensate formation and aging. Here, we report that condensates formed by Adenosine 5-triphosphate (ATP) undergo liquid-to-solid phase transitions (LSPT) in macromolecularly crowded environments, evolving from dynamic liquid droplets into urchin-like fibrillar aggregates. In the initial stages of aging, small aggregates actively engulf surrounding droplets via direct contact and rapid wetting-driven merging. As aging progresses, internal flows emerge within condensates, with velocities oriented toward the nearest aggregate core. These flows arise endogenously from ATP fibrillization through the Marangoni effect and result in a long-range chemotaxis ripening process that facilitates transport of ATP molecules from peripheral droplets to a central aggregate. The Marangoni effect also drives the long-range motion of liquid droplets on hydrophobic surfaces towards the aggregates, representing a novel form of dialytaxis. These findings provide crucial and previously unrecognized dynamic behaviors and insights into the physical principles underlying condensate aging.

biophysics↗

bioRxiv2025

Pentose Sugars Encode Sequence-Dependent DNA-RNA Segregation for Biomimetic Multiphase Condensates

The nucleus segregates DNA and RNA with high precision to safeguard genome stability and gene regulation despite their homologous structures, yet the underlying molecular principles have long evaded both understanding and synthetic translation. Here we show that a single atomic difference between the pentose sugars, a 2-OH in RNA versus a 2-H in DNA, suffices to drive their phase segregation with cationic peptides. This subtle chemical distinction makes RNA bind peptides more strongly than sequence-identical DNA, generating an asymmetry that, when modulated by sequence-encoded homotypic interactions, drives the formation of core-shell multiphase condensates. Using a supervised machine-learning approach, we distill these molecular principles into a predictive design rule and harness it to program a library of oligonucleotide pairs, termed SEGREGamers, that self-assemble into droplets with coexisting DNA- and RNA-rich domains. These synthetic condensates recapitulate nuclear compartment functions, including selective molecular partitioning and enhanced RNA catalysis. Our results establish a chemically encoded platform for engineering synthetic nuclear mimics and programmable biomolecular condensates, and suggest that sugar identity may have served as an ancient physical mechanism for organizing nucleic acids.

biophysics↗

bioRxiv2024

Sidechain chemistry-encoded solid/liquid phase transitions of condensates

Nature effectively leverages multivalent interactions among fundamental building blocks in solvents to create remarkable materials for various purposes. One prominent example is the formation of biomolecular condensates through the phase separation of proteins and nucleic acids. In particular, these condensates play crucial roles in regulating cellular functions and constructing natural materials. During the phase separation, solvents not only provide liquid environments for solvating molecules but play crucial roles in affecting the material properties of condensates. However, it remains controversial in the literature that alcohol molecules, as one type of solvents, can solidify some condensates while also melting others, leading to liquid-to-solid phase transition (LSPT) or solid-to-liquid phase transitions (SLPT), respectively. The mechanism underlying the alcohol-induced solid/liquid phase transitions of condensates remains poorly understood. Here, we combine systematic experimental characterizations with molecular dynamics simulations to demonstrate that the phase transitions of condensates depend on their sidechain chemistry and dominant molecular interactions. Specifically, "hydrophilic" condensates, which consist of many charged sidechains, undergo LSPT by adding alcohols due to strengthened electrostatic interactions. In contrast, "hydrophobic" condensates comprised of abundant aromatic sidechains undergo SLPT with the addition of alcohols because of weakened cation-{pi} and {pi}-{pi} interactions. Importantly, these findings are generally applicable for predicting phase transitions of a wide range of condensates formed by synthetic polyelectrolytes and intrinsically disordered proteins based on their sidechain hydrophobicity or amino acid compositions. Our work not only reconciles a conundrum in the literature but provides a fundamental framework for understanding the responsiveness of condensates to environmental stimuli. These insights are instrumental for developing therapeutic drugs to treat pathological aggregates and engineering stimuli-responsive biomaterials from the perspective of sidechain chemistry and molecular interactions.

biophysics↗

bioRxiv2023

Merging-limited coarsening governs long-term stability of nanoscale condensates

Droplet coarsening is a long-standing phenomenon widely observed in our daily life and industrial processes. This process is typically governed by classic theories, such as Brownian motion-induced coalescence and Ostwald ripening, predicting continuous and rapid droplet growth. However, recent studies revealed that nanoscale biomolecular condensates, formed by liquid-liquid phase separation (LLPS), often defy this expectation, exhibiting remarkable long-term stability in cells and in vitro systems. Here, we reveal a merging-limited coarsening mechanism that underpins this anomalously slow growth. Using experiments, theory, and simulations, we demonstrate that nanoscale coacervates formed at neutral stoichiometry remain stable over extended periods due to size-dependent merging inefficiency. This inefficiency stems from entropic charge separation caused by asymmetric chain lengths of oppositely charged polymers, which induces interfacial charge accumulation and inter-coacervate electrostatic repulsion. Our findings reframe LLPS as a kinetically constrained process evolving over a rugged energy landscape, in which merging barriers trap condensates in metastable, long-lived states. This framework offers a physical basis for condensate size control in cells and a design principle for stable synthetic biomolecular assemblies.

biophysics↗

bioRxiv2021

Combinatorial engineering of bulk-assembled monodisperse coacervate droplets towards logically integrated protocells

Bottom-up synthetic biology seeks to construct artificial cells from simple building blocks for exploring origin and principles of cellular life and material design. Although cellular life may have emerged spontaneously, programmable integration of building blocks into size, membrane property-controlled compartments (liposome or coacervate) towards cellular organization, without using specialized devices, has proven difficult. Here, we report a self-templated route to monodisperse complex droplets in bulk solution from coacervate-liposome synergy, with nanoliposome controlling coacervate size and coacervate templating on-surface nanoliposome fusion. Nanoliposome-coated monodisperse coacervates are self-assembled within 30 seconds, which are sealed by fusing nanoliposomes into size-controlled giant unilamellar vesicles (GUVs), with model building blocks combinatorially integrated into droplets. Defect-free membrane is established on coacervate, which render these complex GUVs surviving at extreme osmotic, salty and pH conditions (4 M NaCl, 100 mM HCl, 1 M NaOH), while providing homeostasis for enzymatic reactions, reminiscent of extremophiles.

synthetic biology↗

bioRxiv2019

Multi-ATOM: Ultrahigh-throughput single-cell quantitative phase imaging with subcellular resolution

A growing body of evidence has substantiated the significance of quantitative phase imaging (QPI) in enabling cost-effective and label-free cellular assay, which provides useful insights into understanding biophysical properties of cells and their roles in cellular functions. However, available QPI modalities are limited by the loss of imaging resolution at high throughput and thus run short of sufficient statistical power at the single cell precision to define cell identities in a large and heterogeneous population of cells - hindering their utility in mainstream biomedicine and biology. Here we present a new QPI modality, coined multi-ATOM that captures and processes quantitative label-free single-cell images at ultra-high throughput without compromising sub-cellular resolution. We show that multi-ATOM, based upon ultrafast phase-gradient encoding, outperforms state-of-the-art QPI in permitting robust phase retrieval at a QPI throughput of >10,000 cell/sec, bypassing the need for interferometry which inevitably compromises QPI quality under ultrafast operation. We employ multi-ATOM for large-scale, label-free, multi-variate, cell-type classification (e.g. breast cancer sub-types, and leukemic cells versus peripheral blood mononuclear cells) at high accuracy (>94%). Our results suggest that multi-ATOM could empower new strategies in large-scale biophysical single-cell analysis with applications in biology and enriching disease diagnostics.

bioengineering↗