biophysical modeling

This study investigates the Zdhhc5-GOLGA7 protein complex involved in non-apoptotic cancer cell death induced by CIL56, revealing key residues critical for complex formation and cell death.

The paper investigates how extracellular K+ and Na+ ions differentially regulate TCR signaling by modulating ZAP-70 recruitment, affecting T cell function and development.

The paper constructs a synthetic signalosome using Death Domains and shows that its function depends on polymer stability and avidity, demonstrating these properties are tunable and not restricted to specific motifs.

The paper identifies teichuronic acid oligosaccharides as the receptor for umbrella toxins and shows targeting specificity arises from lectin domain recognition of variable TUA-WTA structures.

This study elucidates the mechanism of MBOAT-SGNH acyltransferases in Gram-negative bacteria, showing that a tyrosine-containing peptide shuttles acyl groups from MBOAT to SGNH active sites for peptidoglycan O-acetylation.

This study identifies a trade-off between PAM recognition breadth and CRISPR-Cas9 editing efficiency, proposing a two-step target capture mechanism to improve genome editing.

The paper determines cryo-EM structures of CpaF in different conformations and proposes a rotary mechanism of catalysis for Tad pilus assembly and disassembly.

The paper identifies proteins and amino acid patterns associated with iodine binding in human tissues to improve μCT imaging contrast.

This study maps the free energy landscape of K-Ras4B dimerization using simulations, revealing multiple interfaces and showing the G12D mutant forms more diverse dimers than wild-type.

This study characterizes the RNA virome of Tuta absoluta, identifying ten novel insect-specific viruses and highlighting greater viral diversity in field populations compared to lab samples.

This paper determines the structure of the palladin-actin complex using crosslinking, docking, NMR, and SAXS, revealing how palladin stabilizes F-actin at the interface between two actin monomers.

This study identifies that floral handedness in Cyanella alba is determined by phyllotactic spiral direction and auxin-induced differential cell elongation, not genetics.

This paper shows that MA-5 improves hearing loss and extends lifespan in mice by increasing NAD+ and SIRT1 through DNA-PK activation and mitochondrial function.

The paper investigates whether reported miRNAs in cancer are functionally active, finding many are not incorporated into RISC and lack endogenous silencing capability.

This study investigates how environmental factors like pH and ionic strength affect the conformational and amyloidogenic properties of DPF3a using biophysical and molecular dynamics methods.

This study shows IP6 binding influences the kinetic switch of the HIV-1 capsid's TVGG motif between coil and helix conformations, essential for pentamer formation.

This study identifies biomechanical compartmentalization in the regenerating intestine and shows vascular Piezo1 influences angiogenesis and stem cell proliferation across species.

This study investigates the structural dynamics of DENV2 NS5 interacting with SLA using SPR, HDX-MS, computational modeling, and cryoEM, revealing conformational changes and a conserved binding mode.

The paper develops nanobodies that bind Cavin1's HR1 domain, revealing structural flexibility and regulated interactions important for caveolae assembly.

This study reveals the activation mechanism of human mitochondrial ClpP protease through structures showing how inhibitors induce an allosteric transition to the active state, with implications for cancer therapy.

This study identifies how AGR2 chaperone forms a dimer to repress IRE1β dimerization and suppress the UPR by blocking its activating conformation.

This study shows that the picornavirus 3C protease binds RNA and induces liquid-liquid phase separation, which may have implications for viral replication and stress granule dynamics.

This paper shows P-Rex1 limits agonist-induced GPCR internalisation through its PDZ, DEP, and IP4P domains, independent of its Rac-GEF activity, by inhibiting phosphorylation and interacting with Grk2.

This paper develops a biophysical model to show glycocalyx can induce membrane tube formation through critical grafting density and polymer length, facilitated by actin forces and line tension.

This study identifies YebC2 as a translation factor that resolves ribosome stalling at polyprolines independently of EF-P and YfmR in B. subtilis.

In DT40 cells, condensins displace extrusive cohesin, bypass cohesive cohesin and stall against each other while extruding ~1-3 kb/sec, yielding irregular helical chromatids of consecutive loops.

This study shows that cargo-sensitive TPR switch in kinesin-1 controls its conformational dynamics by dislocating the TPR shoulder, promoting motor domain activation and microtubule binding.

The paper reveals a beta-relay signaling mechanism in prokaryotic Argonautes that activates the SPARDA defense system to degrade invading DNA and host DNA, preventing plasmid spread.

This study investigates how BSEP mutations cause PFIC2 by analyzing protein stability and structure, identifying a key interface affected by disease-causing variants.

The paper compares the mechanical behavior of two TCRs recognizing the same pMHC using MD simulations, showing differences in load response due to dynamic allostery.