biophysical modeling

Interplay Between Protein-RNA Binding and Phase Separation Drives Emergent Behavior in RNP Condensates

The paper develops a model showing how protein-RNA binding and phase separation interact to influence RNP condensate behavior, revealing RNA's role as a scaffold and explaining condensation dynamics.

Small-molecule modulation of Beta-arrestins

This study identifies small-molecule inhibitors of beta-arrestins and elucidates their mechanism, offering a framework for modulating GPCR signaling.

Local sequence context determines the effect of glycine substitutions in collagen triple helices

The paper shows that glycine substitutions in collagen triple helices have varying effects based on local sequence context, with GP sites being especially restrictive.

Biophysical modeling for accurate T cell specificity prediction of viral and tumor antigens

The paper develops a biophysical model to predict T cell receptor specificity for viral and tumor antigens using structural data and sequence-based clustering.

A Type VII-secreted toxin enables inter-mycobacterial competition

The paper identifies a type VII-secreted toxin in mycobacteria that enables inter-bacterial competition by targeting arabinogalactan.

Modelling Plant Cortical Microtubules: Curvature Sensing from Bending Energy

This paper models plant cortical microtubules to show how curvature sensing from bending energy influences their organization on complex surfaces, revealing new roles for proteins in navigating high-curvature edges.

Non-Canonical Cytochrome P450 Enzymes in Nature

The paper identifies and characterizes non-canonical CYPs lacking the conserved cysteine ligand, revealing new ligands like serine and selenocysteine in microbial genomes.

Collagen Shapes Fingertip Surface Strains during Normal Loading

This study uses a biomechanical model to show that collagen anisotropy is essential for accurately simulating fingertip strain patterns during normal loading.

CD8-mediated organization of the TCR-pMHC interface shapes its force response and dissociation pathways

This study uses molecular dynamics simulations to show how CD8 modulates the mechanical stability and dissociation pathways of the TCR-pMHC complex.

Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments

The paper uses molecular dynamics simulations to show that phosphate release from actin filaments is limited by dissociation from Mg2+ and varies with subunit position and water molecule count.

Design and discovery of "tug-of-war" riboswitches

The paper designs and discovers a new modular transcriptional riboswitch architecture called 'tug-of-war' that suppresses intrinsic termination by ligand-stabilized RNA structures upstream of terminators.

High side chain promiscuity of the terminal enzyme in the homologation pathway for L-phenylalanine and L-tyrosine

This study investigates the substrate promiscuity of the enzyme HphB in the homologation pathway, showing it can accept diverse side chains while maintaining backbone specificity.

Highly diverged non-vertebrate Ki-67 proteins with conserved biophysical and functional properties

The paper identifies Ki-67-like proteins in non-vertebrate eukaryotes, showing conserved biophysical and functional properties despite low sequence homology.

Mapping binding landscape of allosteric inhibitor G6PDi-1 on human G6PD

This study investigates how the allosteric inhibitor G6PDi-1 affects G6PD activity by combining biochemical assays and computational methods, revealing binding sites and allosteric effects that disrupt oligomerization.

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation

The paper identifies sequence-encoded autoinhibition in fission yeast Dcp2 that regulates mRNA decapping activity and shows how conformational relief is propagated within phase-separated condensates.

IsdH binding to hemoglobin:haptoglobin is decoupled from iron acquisition in Staphylococcus aureus

This study shows IsdH binds HbHp but does not support S. aureus growth under iron restriction when HbHp is the sole iron source, suggesting HbHp recognition has roles beyond iron acquisition.

Intersegmental transfers drive target search in an RNA-targeting CRISPR system

This study shows that Cas13 uses intersegmental transfers to efficiently search for RNA targets, differing from DNA-binding proteins.

Multiaxial Biophysical Control of Oncogenic Phase Separation by Indoleamines: A Proof-of-Concept Synthesis of Landscape-Level Regulation

The paper identifies a network of 26 genes at the intersection of melatonin signaling and phase separation, showing melatonin suppresses oncogenic drivers and correlates with poorer survival in breast and gastric cancers.

Basement membrane turnover drives filopodial protease-independent invasion

This study shows that basement membrane turnover and filopodia can drive protease-independent invasion through mechanical deformation and pore enlargement.

The Warburg effect as a metabolic niche construction strategy in the tumor microenvironment

This paper models the Warburg effect's role in the tumor microenvironment, showing lactate secretion creates a growth-exclusion tradeoff resolved by pro-tumor stromal cross-feeding.

A framework for the organization of microtubules in developing neurons

This paper proposes a conceptual framework and biophysical model to explain how microtubule orientation emerges in developing neurons, showing how geometrical effects, parallel amplification, and polarization contribute to axon-dendrite differentiation.

Lipid Droplets Direct Amyloid Assembly and β-Cell Stress through Interfacial Control of Amylin Aggregation

This study shows lipid droplets modulate amylin aggregation and β-cell stress by controlling its conformational changes and interaction pathways.

Glutamine Tautomerization Drives RhoGAP-Aided GTP Hydrolysis in Small Rho GTPases

The paper resolves the mechanism of GTP hydrolysis in the RhoGAP-RhoA complex, revealing a tautomerization-driven process involving Gln63.

Tightly Knotted Enzymes Inhibit Protein-Protein Aggregation

This study shows that knotted protein structures inhibit aggregation by limiting expanded states and suppressing liquid-liquid phase separation.

A metabolic checkpoint coordinates bacterial cell envelope biosynthesis and c-di-GMP signaling

This study shows that acetyl-CoA inhibits PDEs in Pseudomonas aeruginosa, linking cell envelope biosynthesis to c-di-GMP signaling and biofilm formation.

Unlocking viral evasion: Luminal charge interactions in BoHV-1 UL49.5 allosterically control TAP degradation

This study identifies N-terminal electrostatic interactions in BoHV-1 UL49.5 as allosteric determinants of TAP degradation, showing that TAP degradation can be uncoupled from MHC class I downregulation.

Sequence-encoded H2A.Z nucleosome dynamics control DNA unwrapping and SUV420H1 recognition

This study shows that H2A.Z's sequence-encoded flexibility in specific regions enhances DNA unwrapping and enables SUV420H1 recognition, revealing a mechanism linking nucleosome dynamics to epigenetic enzyme specificity.

Human ASPDH is a 2-aminomuconate reductase that produces L-2-aminohex-3-enedioic acid in tryptophan catabolism

The paper identifies human ASPDH as a 2-aminomuconate reductase in tryptophan catabolism, revealing a new branch of the kynurenine pathway and an unknown amino acid.

Redox-regulated cysteine acylation governs β-lactam sensing by the Vibrio histidine kinase VbrK

This study reveals how β-lactam antibiotics interact with the histidine kinase VbrK through redox-dependent cysteine acylation, enabling bacterial resistance.

D-Retro-Inverso Peptide Candidates for Inhibiting SAA Cardiac Amyloidosis

The paper designs and evaluates D-amino acid-based peptides to inhibit SAA3 fibril formation in a mouse model of cardiac amyloidosis.