R. V. Pappu

Tunable metastability of condensates reconciles their dual roles in amyloid fibril formation

The paper shows that separable interactions in A1-LCD allow tunable metastability of condensates, which can suppress amyloid fibril formation even with ALS mutations.

Linking modulation of bio-molecular phase behaviour with collective interactions

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.

Biomolecular condensates form spatially inhomogeneous network fluids

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

Glutamate helps unmask the differences in driving forces for phase separation versus clustering of FET family proteins in sub-saturated solutions

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

Crowder titrations enable the quantification of driving forces for macromolecular phase separation

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

Dominance Analysis: A formalism to uncover dominant energetic contributions to biomolecular condensate formation in multicomponent systems

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

Quantifying collective interactions in biomolecular phase separation

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.

Sequence-specific interactions determine viscoelasticity and aging dynamics of protein condensates

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: A tool to fit protein phase diagrams based on mean-field theories for polymer solutions

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

Phase Separation in Mixtures of Prion-Like Low Complexity Domains is Driven by the Interplay of Homotypic and Heterotypic Interactions

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: A Python package for the analysis of simulations of intrinsically disordered proteins

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

Single fluorogen imaging reveals distinct environmental and structural features of biomolecular condensates

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

Adsorption of RNA to interfaces of biomolecular condensates enables wetting transitions

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.

Uncovering the contributions of charge regulation to the stability of single alpha helices

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.

Dynamical control enables the formation of demixed biomolecular condensates

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.

Uncovering molecular grammars of intrinsically disordered regions that organize nucleolar fibrillar centers

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

RNAs undergo phase transitions with lower critical solution temperatures

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.

Quantifying coexistence concentrations in multi-component phase-separating systems using analytical HPLC

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

Connecting sequence features within the disordered C-terminal linker of B. subtilis FtsZ to function and bacterial cell division

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

Condensates of disordered proteins have small-world network structures and interfaces defined by expanded conformations

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

Phase separating RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions

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.

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

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.

Structure-function relationships in mitochondrial transcriptional condensates

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

Quantifying charge state heterogeneity for proteins with multiple ionizable residues

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.

Sequence grammar underlying unfolding and phase separation of globular proteins

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.

Uncovering non-random binary patterns within sequences of intrinsically disordered proteins

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

Conformational buffering underlies functional selection in intrinsically disordered protein regions

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

Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate

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.

Proteins with prion-like domains can form viscoelastic condensates that enable membrane remodeling and endocytosis

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

Uncovering Differences in Hydration Free Energies and Structures for Model Compound Mimics of Charged Sidechains of Amino Acids

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.