biophysical modeling

Towards understanding nitrate-reducing Fe(II) oxidation in Ferrigenium straubiae: spotlight on old and new key protein candidates

The paper identifies key proteins and metabolic pathways in Ferrigenium straubiae involved in nitrate-reducing Fe(II) oxidation using transcriptomic and genomic analyses.

Dimeric Alix nucleates ESCRT-III CHMP4 polymerization

This study shows dimeric Alix nucleates CHMP4 polymerization, essential for ESCRT-III membrane remodeling, and demonstrates that dimerization is required for plasma membrane repair.

Structural basis of substrate recognition and transport in bacterial ACS transporters

This study identifies substrate specificity of bacterial ACS transporters using genetics, biochemistry, and structural biology, revealing structural determinants of stereoselectivity in LgoT.

Physiological trade-offs drive the archaeal dominance and carbon turnover in deep subsurface

The paper shows archaea, specifically Bathyarchaeia, dominate deep sediments by prioritizing maintenance over growth, leading to long-term organic carbon preservation.

β-Ketoacyl Synthase II Homologs from a Ladderane-Producing Organism Form a Ketosynthase/Chain Length Factor-like functional heterodimer

This paper characterizes two FabF homologs from anammox bacteria that form a functional heterodimer involved in ladderane biosynthesis, revealing their unique mechanism and substrate specificity.

Durotactic Migration Driven by Anisotropic Matrix Stiffening and Mechanical Feedback

The paper develops a biomechanical model to study how cells remodel fibrous matrices to drive durotactic migration, showing collective behavior similar to cancer metastasis.

Advancing Liver Cancer Precision Medicine with TARGET-SL

This paper validates the TARGET-SL framework for predicting genetic events and drug sensitivities in liver cancer using cell lines and patient-derived organoids, showing potential to improve personalized drug screening.

A conserved structural logic underlies sensor-helper NLR communication in the NRC immune receptor network

The paper identifies conserved sensor-helper NLR interfaces in the NRC immune receptor network and validates their role in immune activation through structural and functional studies.

Molecular mechanism of a single stranded DNA-stimulated bacterial immune peptidase

The paper defines how the CapP peptidase is activated by single-stranded DNA, leading to transcriptional activation of immune operons in response to DNA damage.

Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system

The paper identifies a phage-encoded factor that activates the Hna anti-phage defense system by overcoming its auto-inhibition.

Mycobacteriophage TM4 requires XylR for successful infection in Mycobacterium smegmatis mc2155

This study identifies a phage resistance mechanism in Mycobacterium smegmatis involving XylR-mediated cell-envelope remodeling that impedes phage DNA injection.

Evolution of allostery without shape shifting: Internal dynamics drives functional diversification of a transcriptional repressor superfamily

The paper investigates how allostery evolves in the ArsR superfamily by showing that functional diversification arises from internal dynamics rather than large conformational changes.

Dimerization of MilM is essential for catalyzing the pyridoxal-5'-phosphate (PLP)-dependent Cγ-hydroxylation of L-arginine during mildiomycin biosynthesis

This paper investigates the dimerization and catalytic mechanism of MilM, a PLP-dependent enzyme involved in mildiomycin biosynthesis, revealing its role in substrate binding, catalysis, and product formation.

Structural basis for the intestinal protocadherin-based intermicrovillar adhesion complex

The paper determines the Cryo-EM structure of the intestinal IMAC complex, revealing its heterotetrameric composition and structural features that enable microvilli adhesion and resilience to shear stress.

Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation

This study identifies intramolecular loops that regulate SARS-CoV-2 N-protein self-association and nucleic acid binding through phosphorylation-dependent conformational changes.

Conformational dynamics of plasmepsin X during inhibitor binding

This paper investigates the conformational dynamics of plasmepsin X during inhibitor binding and unbinding using molecular dynamics simulations, revealing a dominant unbinding pathway involving flap conformational changes.

Processing of forked DNA activates a helicase-nuclease immune system

The paper shows that forked DNA activates a helicase-nuclease immune complex in type III Druantia through enzymatic processing, enabling phage defense without host toxicity.

TBK1 restricts IRGQ-mediated autophagy

This study identifies TBK1 as a regulator of IRGQ-mediated autophagy by disrupting the IRGQ-GABARAPL2 complex through phosphorylation of GABARAPL2.

Widespread genomic heterogeneity at the type II NAD(P)H dehydrogenase locus predisposes Cryptosporidium to clofazimine resistance

The paper identifies genomic heterogeneity at the NDH2 locus in Cryptosporidium species that contributes to clofazimine resistance through adaptive recombination.

Targeting an RNA Editor to Impede H3K27M+ Pediatric Gliomas

This study identifies ADAR as a key mediator of immune evasion in H3K27M+ pediatric gliomas and shows that ATRA can induce ADAR degradation, enhancing antiviral responses and tumor immunogenicity.

Diversity and evolution of a phase-variable multi-locus antigen in Neisseria gonorrhoeae

The paper uses long-read sequencing to analyze opa gene diversity in Neisseria gonorrhoeae genomes, revealing high variability and rapid evolution of these genes.

Neuronal calcium sensors emerge as novel adenylyl cyclase 8 regulators

This study identifies HPCAL1 as a Ca2+-dependent regulator of AC8, revealing a new mechanism for cAMP signaling regulation.

Hero11 Unlocks TDP-43 Condensate Fluidity via Targeting Inter-Helical Interactions

This study shows Hero11 disrupts TDP-43 condensate structure by targeting helix-helix interactions, altering condensate fluidity and dynamics.

Molecular anatomy of PLK1 master docking motifs

The paper identifies a high-affinity master docking motif on CENP-U that interacts extensively with PLK1's Polo-box domain, suggesting common features among master PLK1 docking motifs.

Structural basis of the two-photon photoactivation mechanism of orange carotenoid protein

The paper elucidates the structural basis of the two-photon photoactivation mechanism of orange carotenoid protein using a combination of structural and biochemical methods.

ILK binding to β1 Integrin is indirectly mediated by Kindlin-2

This study resolves the debate on how ILK binds to β1 integrin by showing ILK is recruited via K2, not directly, using interdisciplinary methods.

Schizokinen siderophores in the methylotrophy model organism Methylorubrum extorquens AM1

This study investigates Methylorubrum extorquens AM1's ability to produce siderophore-like molecules for lanthanide acquisition, finding that it produces schizokinen siderophores that do not chelate lanthanides.

Structural modelling and biophysical analyses reveal a dimeric coiled-coil architecture in the FAZ10 central region of Trypanosoma brucei

This study determines the dimeric coiled-coil structure of the FAZ10 central region in Trypanosoma brucei using structural modeling and biophysical analysis.

A phage-derived reconfigurable effector associated with an actinobacterial contractile nanomachine tailors bacterial responses to competition

The paper identifies a novel class of contractile injection system effectors in actinobacteria that enhance bacterial adaptation to competition by modulating proteomes and phenotypes.

ARHGEF7 S-glutathionylation promotes cancer cell migration through Rac1 activation

This study identifies ARHGEF7 S-glutathionylation at C312 as a redox-regulated mechanism that enhances cancer cell migration through Rac1 activation.