biophysical modeling

This study shows that bacterial flagellum assembly is optimized for energy efficiency and motility by balancing secretion rate and filament length.

This study investigates how psychostimulant derivatives modulate the prokaryotic pentameric ligand-gated ion channel sTeLIC through a vestibular pocket, revealing a structure-function mechanism for allosteric potentiation.

This paper constructs a biophysical model showing how loop extrusion by MukBEF and exclusion by MatP can establish left-ori-right chromosome order in E. coli without locus anchoring.

This study uses all-atom simulations to reveal that guanine in RNA has the strongest interaction with membranes, while base pairing reduces membrane binding.

This study identifies the caspase-11 CARD as a bipartite lipid-binding module that recognizes both self and nonself lipids, enabling the design of an LPS-binding domain.

This study uses atomic-level simulations to show how ligand binding modulates conformational dynamics of the M2 muscarinic receptor, revealing key aromatic residue interactions involved in activation.

The paper identifies MutT1 as a phosphatase that dephosphorylates sensor kinases in Mycobacterium tuberculosis, revealing a new regulatory mechanism in two-component signaling.

This study identifies MDC1 as a mediator of Pellino1 and Pellino2 recruitment to DNA double-strand breaks through phosphorylation-dependent interactions.

This study identifies how Bacillus velezensis 9912 promotes rice growth by modulating plant hormones and miRNA-mRNA regulatory networks.

This study identifies DGAT3 and FBN2 as key factors in powdery mildew exploitation of Arabidopsis plastoglobuli for pathogen proliferation.

This study investigates the function of FtsZ in a cell wall-less bacterium, showing that SeFtsZ forms ring-like structures in cell wall-less cells, suggesting a role in cell division independent of cell wall synthesis.

The paper identifies and validates an alternative to VSV-G for lentivector pseudotyping to improve in vivo T cell transgene delivery for tumor therapy.

This study identifies small molecule inhibitors of TOX protein that reverse T cell exhaustion and show cytotoxicity in T-ALL.

This study investigates how pH changes affect synaptogyrin-1 and -3 behavior, revealing their distinct responses and implications for synaptic function and neurodegenerative diseases.

This study shows that bird beak and body shapes are constrained by biophysical trade-offs, leading to specialized forms and faster evolutionary turnover at the extremes of morphospace.

The paper evaluates expression changes of PVT1, HULC, and HOTTIP in DLBCL patients before and after treatment, finding significant upregulation pre-treatment and normalization post-treatment.

This study characterizes prophages in Bacteroides and Phocaeicola using bioinformatic tools, revealing their diversity, broad host range, and temporal stability in the human gut.

The paper identifies leaky ribosomal scanning as the mechanism enabling tunable translation of bicistronic ORFs in green algae through bioinformatic and in vivo analyses.

This study identifies a distinct mechanism of RNA recognition by GATA1, showing competitive DNA/RNA binding through an overlapping surface involving the ARM-like domain.

This study identifies Txlnb as a centrosome-adapter protein that mediates proteostasis in cardiomyocytes, linking centrosomes to the ubiquitin-proteasome system and influencing cardiac stress responses.

This study investigates how AT8 phosphorylation affects Tau protein conformation and dynamics using biophysical experiments and simulations.

This study shows that intrinsically disordered proteins can exhibit different polymer-like behaviors in distinct regions of their conformational space.

This study shows mechanical strain in E. coli filaments affects Min system dynamics and division site positioning through mechanochemical feedback.

This study identifies the localization and functions of two pyrophosphatases in Plasmodium falciparum, showing their roles in pyrophosphate homeostasis across subcellular compartments.

This study shows that SPO11 dimerization is essential for meiotic DNA double-strand break formation, demonstrating that SPO11 can cleave DNA alone or with TOP6BL.

This paper develops a biophysical model of the glycocalyx's role in generating and sensing membrane curvature, showing how glycocalyx properties influence membrane shape and curvature sensing.

The paper identifies allosteric regulation of PSKH1 kinase activity by Ca2+ sensor proteins, showing both activation and suppression by different sensors.

The paper shows that non-stomatal regulation of transpiration occurs due to reduced plasma membrane conductance in the outside-xylem zone under moderate xylem water stress.

This study shows mechanical strain focuses at topological defects during Hydra regeneration, promoting head organizer formation through a feedback loop involving Wnt signaling and biophysical modeling.

The paper develops a biophysical model of the lung to quantify pulmonary surfactant's effect on lung compliance by simulating respiration and surfactant dysfunction.