R. V. Pappu

This paper introduces a dominance analysis framework to determine the molecular mechanism of condensate modulation, demonstrating its application to G3BP1/RNA condensates disrupted by suramin.

This study uses multiple techniques to characterize the structural properties of biomolecular condensates, revealing network fluid behavior with spatial inhomogeneities.

The paper shows that glutamate reveals distinct energy and length scales for phase separation and clustering of FET family proteins in sub-saturated solutions.

This paper demonstrates how crowder titrations can quantify intrinsic driving forces for macromolecular phase separation by measuring saturation concentrations and second virial coefficients.

This paper introduces a formalism to identify dominant energetic contributions to biomolecular condensate formation in multicomponent systems by analyzing phase separation data.

This study quantifies collective interactions in biomolecular phase separation by analyzing dilute phase concentrations and free energy, revealing how salts and small molecules modulate condensate formation.

This study investigates how sequence-specific interactions influence the viscoelastic properties and aging dynamics of protein condensates formed by prion-like low-complexity domains.

FIREBALL fits protein phase diagrams using mean-field theories to analyze phase separation parameters from experimental or computed data.

This paper investigates phase separation of mixtures of prion-like low complexity domains using simulations and experiments, finding that homotypic and heterotypic interactions drive condensate formation.

SOURSOP is a Python package for analyzing simulated conformational ensembles of intrinsically disordered proteins, offering tools to quantify sequence-specific properties.

This study uses single-fluorogen imaging to reveal that biomolecular condensates have hydrophobic internal environments and spatially inhomogeneous molecular organization.

This study shows that pyrimidine-rich RNAs act as adsorbents enabling wetting transitions in condensates formed by purine-rich RNAs, revealing orientation differences between scaffolds and adsorbents.

The paper investigates how charge regulation affects the stability of single alpha helices, finding that uncharged glutamate residues and conformational buffering contribute to pH insensitivity.

This study identifies dynamical control as a mechanism enabling the formation of demixed biomolecular condensates by showing that asynchronous molecular production is required for their coexistence.

The paper identifies molecular grammars in intrinsically disordered regions of nucleolar proteins that drive phase separation to form nucleolar substructures.

The paper shows RNAs undergo phase transitions with lower critical solution temperatures, driven by Mg2+ and phosphate backbone interactions, and can suppress RNase P activity.

This paper develops an analytical HPLC method to quantify coexisting phase concentrations in multi-component phase-separating systems, enabling reconstruction of coexistence curves.

This paper investigates how sequence patterns in the disordered C-terminal linker (CTL) of Bacillus subtilis FtsZ influence autoregulatory interactions and bacterial cell division.

This study shows that disordered protein condensates form small-world networks with interface-specific conformational expansions and orientations.

This study investigates cluster formation in subsaturated solutions of RNA binding proteins with prion-like domains and finds that cluster formation and phase separation are coupled through sequence-specific interactions.

This paper uses atomistic simulations to show polyampholytic IDPs exhibit two-state behavior between globules and self-avoiding walks, with sequence-specific temperature-dependent preferences.

This study reconstitutes mitochondrial transcriptional condensates in vitro and shows that RNA production alters their phase behavior and leads to non-equilibrium structures.

This paper introduces a q-canonical ensemble framework to analyze potentiometric titration data and determine mesostate pKa values and populations for proteins with multiple ionizable residues.

The paper investigates how sequence grammars of unfolded globular proteins drive phase separation and formation of UPODs, highlighting the role of hydrophobic residues and their impact on disease-related interactions.

This paper introduces NARDINI, a computational method to identify non-random binary patterns in intrinsically disordered proteins by comparing sequence patterns to null models.

The paper identifies conformational buffering as a mechanism that conserves spatial dimensions in disordered protein regions despite sequence variation, enabling functional selection.

This study shows that a specific sequence motif in the Whi3 protein promotes dilute phase oligomerization, which opposes phase separation and alters the composition and material properties of ribonucleoprotein condensates.

The paper shows that prion-like domain-containing endocytic coat proteins form viscoelastic condensates that enable actin-independent membrane remodeling and endocytosis in yeast.

The paper estimates hydration free energies of model compounds mimicking charged amino acid sidechains using TCPD and AMOEBA simulations, revealing structural and thermodynamic differences between acidic and basic residues.

The paper identifies how specific amino acid compositions influence phase separation in prion-like domains and develops a model to simulate these behaviors.