biophysical modeling

Competitive resource allocation drives asynchronous and rapid nuclear multiplication in the malaria parasite

This study identifies a mechanism of asynchronous nuclear division in Plasmodium falciparum that enhances proliferation by minimizing resource idling through sequential allocation of a limiting replication resource.

Rational Redesign of an Fc-Binding Peptide for Multivalent Antibody Assembly

This paper redesigns an Fc-binding peptide to enable multivalent antibody assembly without altering the IgG scaffold, showing enhanced stability and functional utility.

Simulations of an extended Tau/tubulins interface reveal a complex disorder-disorder interplay mediated by the C-terminal tails

The paper uses molecular dynamics simulations to study the dynamic interactions between Tau protein and tubulin C-terminal tails, revealing sequence-dependent effects and disorder-disorder interplay.

Structural and mechanistic basis for membrane recognition and activation of the vacuolar lipase Atg15

This study identifies structural and mechanistic principles of Atg15 activation and membrane recognition using MD simulations and experimental validation.

Cholesteryl Esters Modulate Lipid Droplet Rigidity and Monolayer Organization during Liver Cancer Progression

This study uses molecular dynamics simulations to show that cholesteryl esters increase lipid droplet rigidity and monolayer organization in liver cancer.

Multiscale Biomechanical and Electrophysiological Modeling of Nociceptive Activation in Musculoskeletal Joint Disorders: Insights from the Temporomandibular Joint

This study develops a multiscale computational model linking TMJ structural changes to nociceptive activation by integrating biomechanics, neural morphology, and electrophysiology.

Membrane Remodeling by the Collective Action of Caveolin-1

This study develops a coarse-grained model to investigate how caveolin-1 proteins drive membrane curvature through collective interactions.

Structural and Biochemical Analysis of the CABIT1 Domain of THEMIS

This study reports the crystal structure of the THEMIS CABIT1 domain and shows that LCK phosphorylation enables its interaction with SHP1 and protects SHP1 from ROS inhibition.

A molecular description of plant cellulose biosynthesis inhibition

This study identifies thaxtomin A as a potent cellulose biosynthesis inhibitor with broad-spectrum activity and elucidates its mechanism of action through structural and functional analyses.

Structural and evolutionary insights into DAF-12 interactions with transcriptional coactivators in parasitic nematodes

This study investigates DAF-12 interactions with transcriptional coactivators in parasitic nematodes using structural and bioinformatic approaches, revealing conserved and nematode-specific mechanisms of coactivator recruitment.

Molecular and biophysical requirements for B cell receptor dependent enhancement of dengue virus infection

This study identifies BCR-dependent enhancement (BDE) as a mechanism by which DENV infects B cells, showing that BCR-E protein interactions and dynamin-mediated entry are critical for viral replication in these cells.

The mechanism of biofilm degradation by a detachable tailspike of gene transfer agents

This study identifies TspA, a biofilm-degrading enzyme from Rhodobacter capsulatus GTA, which enhances gene transfer by clearing biofilms and navigating the extracellular matrix.

Cysteine Redox State Governs the Condensation Pathway of Hendra Virus W Protein and Differentially Impacts Type I IFN and NF-κB signaling

Structural elements required for the efficient loading and activation of HELB on RPA-coated single-stranded DNA

This paper identifies two structural elements in HELB essential for its interaction with RPA-coated ssDNA, showing how they facilitate RPA displacement and DNA loop formation.

Total Biosynthesis of Pseudomonas aeruginosa-Derived Azabicyclocarbamates Identifies Distinct Dehydrating Condensation Family Proteins

The paper identifies a new family of dehydrating condensation domain proteins involved in the biosynthesis of azabicyclocarbamates in Pseudomonas aeruginosa.

ZnF-UBP domains regulate deubiquitinase activity by relieving ubiquitin product inhibition

The paper investigates ZnF-UBP domains in USP DUBs, showing they relieve product inhibition by facilitating Ub release, thereby regulating enzyme activity.

VDAC2 stabilizes a membrane-inserted, primed intermediate of BAX activation

This study identifies VDAC2 as a regulator of BAX activation by stabilizing a primed, membrane-inserted intermediate in the BAX activation pathway.

How the terminal glucoside of the N-glycan donor affects the catalytic efficiency of the eukaryotic oligosaccharyltransferase

This study investigates how the terminal Glc-(1-2)- in the LLO donor affects OST catalytic efficiency through molecular dynamics simulations of yeast OST with and without this motif.

A multiscale cytoskeletal network model for shear rheological property and its evolutionary mechanism

This study develops a multiscale cytoskeletal network model to simulate shear rheological properties and their evolutionary mechanisms, revealing how chemo-mechanical coupling and actin filament dynamics influence cellular mechanical responses.

Substrate biasing in UCHL5 proteoforms

This study identifies substrate biasing in UCHL5 proteoforms, showing N-terminal ubiquitination activates the enzyme toward monoubiquitin substrates and regulates debranching activity.

Feedback between filament spacing, crosslinker binding, and self-organization in cytoskeletal bundles

The paper develops a biophysical model showing how crosslinker binding and filament spacing feedback to self-organize cytoskeletal bundles into specific geometries.

Hidden Structural Bias in Proteomics: Sonication-induced Selective Fragmentation of Intrinsically Disordered Regions

This study shows sonication causes selective fragmentation of intrinsically disordered proteins in proteomics, leading to structural bias and potential misinterpretation of protein size and stability.

Structural basis for the unexpected activity of rifamycin B against rifampicin-resistant RNA polymerase

This study reveals the structural basis for Rifamycin B's activity against rifampicin-resistant RNA polymerase, showing its unique binding mechanism and potential for drug development.

Conserved core RNAi machinery in trematode-vectoring snails indicates gene silencing potential in the absence of classical systemic and amplification effectors

The paper identifies conserved RNAi effector genes in trematode-vectoring snails, suggesting potential for RNAi-based disease control despite lacking classical systemic and amplification components.

Tn3-derived inverted-repeat miniature elements (TIMEs) that mobilize antibiotic resistance genes

This study identifies new TIME-COMP-like structures containing antibiotic resistance genes in Enterobacteriaceae genomes, highlighting the role of TIMEs in ARG mobilization.

A DNA-scaffolded Retron Ring Mediates Antiphage Immunity

This study defines the structure and mechanism of retron type IX, revealing how its DNA-scaffolded ring assembly mediates antiphage immunity through phage-encoded nuclease-triggered activation.

Antagonistic activity of AEA on TAT treated Human Astrocytes identify Inflammaging pathways

This study investigates how Anandamide affects microRNA expression in HIV1 TAT-stimulated human astrocytes, identifying miRNAs involved in anti-inflammatory pathways.

CenIR, an essential BlaIR-family regulatory system in C. difficile

This paper identifies CenIR as an essential BlaIR-family regulatory system in C. difficile that lacks a β-lactam-binding domain and is required for viability, with its regulon containing genes involved in peptidoglycan hydrolase and cell envelope maintenance.

Electrostatics and Local Aromatic Residues Govern Lipid Binding and Membrane Penetration of Synaptotagmin C2 Domains

This study identifies electrostatic and aromatic residues as key determinants of lipid binding and membrane penetration in synaptotagmin C2 domains through molecular dynamics simulations.

From biofilms to birth: Quantitative murburn rationale for hydrated polymer-centred biological transduction, coherence, and evolution of complex life

The paper uses quantitative modeling to show how hydrated polymer systems regulate oxygen delivery and reactive species buffering across biological processes, from amphibian development to human reproduction and disease.