A. S. Holehouse

This paper introduces GOOSE, a computational framework for designing intrinsically disordered proteins, and demonstrates its ability to create IDRs with specific functional responses.

The paper investigates how sequence variation in intrinsically disordered regions (IDRs) can still encode functional specificity in RNA binding, using coronavirus nucleocapsid proteins as a model.

This study shows that helical structure in a tardigrade IDP is necessary for desiccation tolerance, but not sufficient on its own.

This study identifies a mechanism by which tardigrade CAHS D proteins form gels to protect cells during desiccation, showing that gelation reduces molecular motion and metabolic activity, with reversible effects.

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

This paper develops ALBATROSS, a deep learning model that predicts ensemble conformational properties of intrinsically disordered proteins from sequence, enabling proteome-wide analysis.

The paper introduces the analytical Flory Random Coil (AFRC) model as a reference for unfolded proteins, enabling comparison of experimental and simulation data.

The paper identifies a common toxic mechanism in positively charged peptides across species and develops a machine learning tool to detect it.

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

This study investigates how the disordered N-terminal tail of the SARS-CoV-2 Nucleocapsid protein enhances RNA binding affinity and modulates interactions with RNA.

This study identifies TTDN1's role in linking intron lariat processing to the spliceosome, showing its defect causes splicing and gene expression issues in NP-TTD.

This study develops CRISPRburst to measure how 92 human transcription factors affect transcriptional bursting kinetics and identifies kinetic signatures that classify TFs and predict their regulatory roles.

The paper shows that adding other components to liquid-like condensates can stabilize protein dynamics, mediated by weak interactions among multiple components.

The paper investigates how sequence- and chemical specificity enable functional IDR diversity despite poor sequence conservation.

The paper shows that structural biases in intrinsically disordered proteins persist in human cells and can respond to intracellular changes.

This study identifies CAHS D as a tardigrade protein that protects against desiccation through multiple mechanisms involving water coordination and slowed molecular motion.

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

The paper shows TRF2 drives single telomere condensation and multi-telomere phase separation, with hRap1 modulating these processes.

This study uses number and brightness analysis to examine how IDR amino acid composition affects ARF19 condensate morphology and material properties, but not oligomeric state.

This study shows that arrested P body condensates in Drosophila oocytes prevent premature mRNA release, supporting mRNA regulation during early development.

The paper identifies design principles for biomolecular condensates using PopZ and applies them to create synthetic condensates in human cells.

This study identifies cholesterol's essential role in SARS-CoV-2 membrane fusion and syncytia formation, suggesting statins may benefit COVID-19 patients.

This study develops a framework to characterize how intrinsically disordered proteins (IDRs) respond to their chemical environment, finding sequence-dependent sensitivity and potential regulatory roles.

This study identifies FLOE1, a prion-like protein in Arabidopsis thaliana, whose hydration-dependent phase separation regulates seed germination under water stress.

This study investigates the SARS-CoV-2 nucleocapsid protein's dynamics, disorder, and RNA phase separation using single-molecule spectroscopy and simulations, revealing its multivalent RNA binding properties and phase separation behavior.

This study analyzes survey data from faculty job applicants to assess how various metrics correlate with hiring outcomes and highlights issues with the academic job application process.

The paper introduces a computational approach to predict sequence-specific phase diagrams for intrinsically disordered proteins by combining simulations with Gaussian cluster theory.

This study shows that nonstop mRNA proteins accumulate in nucleoli, disrupting their structure and function, and links this to neurodegeneration mechanisms.

The paper identifies sequence features of mixed-charge domains that govern nuclear speckle condensation and function in mRNA processing.

This study introduces a computational method to alter solution conditions and control residual structure in intrinsically disordered proteins, offering an alternative to mutational studies.