biophysical modeling

Small RNA ASpks2 Promote Mycobacterium tuberculosis Survival in Macrophages via Targeting Polyketide Synthase 2

The paper identifies a novel small RNA, ASpks2, in Mycobacterium tuberculosis that promotes bacterial survival in macrophages by targeting polyketide synthase 2.

Competing forms of protein-protein association and DNA binding exhibited by BrxC from the BREX phage restriction system

This study investigates the structural and functional properties of BrxC, a conserved AAA+ ATPase in the BREX phage restriction system, revealing its role in mediating competing protein associations and DNA binding that regulate host methylation and phage restriction.

Structural basis of substrate recognition for proteasome degradation by prokaryotic ubiquitin-like protein ligase PafA

The paper determines the structural basis of substrate recognition by PafA, showing that broad specificity arises from dynamic, geometrically compatible interactions rather than sequence-specific binding.

A Nonlinear Biomechanical Model for Prognostic Analysis of Clavicle Fractures

This paper develops a nonlinear biomechanical model to explain varying outcomes in clavicle fractures by analyzing stability and bifurcation mechanisms.

Hierarchical decoding of targeting tripeptide motif by the cytosolic iron-sulfur cluster assembly targeting complex

This paper defines the molecular basis for TCR peptide recognition by the CIA targeting complex using binding measurements, bioinformatics, and structural modeling, revealing a hierarchy of physicochemical determinants.

Structural and biochemical characterization of a novel inhibitor of NMNAT1, the gatekeeper of nuclear NAD+ biosynthesis

The paper identifies AMI-1 as an inhibitor of NMNAT1, shows its effect on NAD+ levels and cancer cell viability, and determines its binding mechanism via cryo-EM.

A Biophysical Model of Phagocytic Cup Dynamics: The Effect of Membrane Tension

The paper develops a biophysical model of phagocytic cup dynamics that incorporates membrane tension, showing it leads to slower engulfment and stalled engulfment, with implications for immune function and drug delivery.

Ancestral protein reconstruction reveals the mechanism of substrate specificity in FN3K-mediated deglycation.

This study uses ancestral protein reconstruction to uncover the molecular mechanism of substrate specificity in FN3K and KT3K enzymes, revealing an allosteric network that modulates substrate recognition.

Unconventional Interplay Between GPCRs and RTKs Signaling Pathways Through SH2 Domain-Containing Proteins

This study identifies a novel mechanism where Gq/11 and G12/13 activation causes SH2 domain-containing proteins to translocate from the plasma membrane to the nucleus, reducing RTK signaling activity.

Pearling Drives Mitochondrial DNA Nucleoid Distribution

The paper shows that mitochondrial DNA nucleoid distribution is controlled by pearling and cristae structure, revealing a mechanism for nucleoid spacing and segregation.

The small GTPase Rab5 inhibits actin polymerization mediated by the Legionella pneumophila effector VipA

This study identifies Rab5 as an interacting partner of the L. pneumophila effector VipA, showing that Rab5 binding inhibits VipA's ability to promote actin polymerization.

Th17 cells require the DNA repair sensor XPC to control oxidative DNA damage

This study identifies XPC as essential for protecting Th17 cells from oxidative DNA damage, showing its role in DNA repair, differentiation, and function.

Supercoiling twists Cas9 off-target discrimination when nicking and cleaving

This study investigates how DNA supercoiling affects Cas9 off-target cleavage by mapping cleavage rates and sites across different topologies using NucleaSeq and a biophysical model.

Domain-Specific Agonist Binding Affinities Explain Structural and Functional Regulation of TRPM2

This study quantifies the binding affinities of TRPM2 domains for ADPR analogs and shows that MHR1/2 drives activation while NUDT9H maintains structural integrity.

Decoding Mutually Induced Conformational Changes in Non-Canonical Recognition of U1 SL4 snRNA by ULD of SF3A1 during Early Spliceosome Assembly

This study investigates the structural and dynamic basis of non-canonical recognition between SF3A1 ULD and U1 snRNA SL4 during spliceosome assembly, revealing dual recognition mechanisms and the impact of mutations on protein-RNA interactions.

Bacillus toyonensis biovar Thuringiensis: an overlooked entomopathogen?

The paper identifies Bacillus toyonensis biovar Thuringiensis as a potential entomopathogen capable of producing insecticidal crystals, challenging previous classifications of related strains.

A NOD2-Encoded Toggle Switch Resolves the Host-Microbe Battle Over Cyclic AMP Control

This paper identifies a host-encoded toggle switch involving NOD2 and GIV that controls cAMP levels in macrophages, converting tolerant cells into microbicidal machines to restore microbial clearance and gut barrier integrity.

TRiC folds the giant ciliary protein IFT172 via a non-canonical open-state mechanism

This study reveals how TRiC folds the large ciliary protein IFT172 using a non-canonical open-state mechanism involving Z-shaped bending and fold-and-eject dynamics.

Staying in the loop to make ends meet: roles and regulation of GlmR in Bacillus subtilis

This study investigates GlmR's role in carbon regulation, cell morphology, and stress response in Bacillus subtilis, revealing its post-translational regulation and enzymatic function.

The CRISPR ring nuclease Csx15 oligomerises on cyclic nucleotide binding to regulate antiviral defence

This study investigates the structural and biochemical properties of Csx15, a ring nuclease that binds cyclic nucleotides and regulates antiviral defense by modulating cOA levels.

Localization-dependent activation of the DEAD-box ATPase Vasa by eLOTUS domains

This study identifies how eLOTUS domains activate Vasa by promoting its RNA and ATP binding through a charged disordered sequence, revealing a localization-dependent regulatory mechanism.

Kinetic logic of uridylation-mediated RNA decay

This study investigates how uridylation mediates RNA decay in Drosophila by showing how Tailor generates oligo(U) intermediates and how Dis3l2 decodes these to initiate decay.

A molecular switch in NAC prevents mitochondrial protein mistargeting by SRP

This study identifies a molecular switch in NAC that prevents mitochondrial protein mistargeting by SRP, showing that mutations disrupt this mechanism and cause ER stress.

Dissecting the interactions of the ISG15-USP18-STAT2 inhibitory complex

This study investigates the ISG15-USP18-STAT2 inhibitory complex's structure and function using AlphaFold and biochemical methods, revealing critical residues and patient mutations affecting its interaction.

A codon-sensitive conformational switch gates commitment to translation start sites

The paper identifies a conformational switch in eIF5 that regulates translation initiation at AUG and non-AUG codons by stabilizing or destabilizing the initiation complex.

Hydration-Controlled Proton Transport in Respiratory Complex I

This study uses simulations to show that hydration dynamics enable proton transport in Complex I by aligning with excess protons, revealing a coupling between water and proton movement.

Ghostbusting the national bird checklist: integrative evidence shows that Pionus fuscus does not occur in Colombia

The paper reassesses the historical record of Pionus fuscus in Colombia using multiple lines of evidence, concluding it does not occur there.

Characterisation of novel Campylobacter jejuni Type VI secretion system (T6SS) effectors and exploration of the roles of the C. jejuni T6SS in bacterial antagonism and human host cell interaction

This study identifies two novel T6SS effectors in C. jejuni and shows their role in bacterial antagonism and host cell interaction.

Structural, biophysical, and virological mechanistic characterization of HIV-1 capsid-targeting antivirals

The paper characterizes structural, biophysical, and virological properties of HIV-1 capsid-targeting antivirals, showing improved potency and stability through chemical modifications of PF74.

Unraveling Viral peptide-G4 Interactions: the NS3 Protease Domain of Yellow Fever Virus Binds G-Quadruplexes with High Specificity and Affinity

This study identifies the NS3 protease domain of Yellow Fever Virus as a high-affinity G4 binder, revealing its interaction mechanism and potential as an antiviral target.