structural biology

LinearKnot: linear-time ensemble analysis of RNA density-2 pseudoknots under hierarchical folding

LinearKnot approximates CParty's hierarchical pseudoknot analysis with linear time complexity, achieving comparable accuracy for RNA structure prediction and ensemble calculations.

Endothelial protein C receptor is an entry receptor for Langya virus

This study identifies the endothelial protein C receptor (EPCR) as the entry receptor for Langya virus and reveals the molecular basis of its interaction with the viral attachment glycoprotein.

Contributions of Site Heterogeneity in Multi-site Brain-Phenotype Predictions

This paper evaluates how site heterogeneity affects brain-phenotype predictions in multi-site data, finding that larger sample sizes improve accuracy more than multi-site composition.

Connectome structure constrains neural activity across scales

The paper shows that coarse-grained connectome partitions can preserve functional predictions about neural activity even when path structure is lost.

FoXSight: Facilitating Computational Hit Identification in Crystallographic Fragment Screening Experiments

FoXSight identifies weak binding events in crystallographic fragment screening by detecting target-specific density features in noisy electron density maps.

Long-range allosteric restraint by the Spiral-Pincer scaffold gates oxidative activation of the ATM kinase

The paper investigates how the Spiral-Pincer scaffold regulates ATM kinase activation by oxidative stress, showing it restricts access to an oxidation-competent conformation.

Lesion-Derived Estimated Functional and Structural Connectomes Predict Post-Stroke Recovery Outcomes

The paper develops a pipeline to estimate structural and functional connectomes from lesion masks to predict post-stroke recovery outcomes, showing better performance than traditional methods.

BundleMorphometry: Spatially Resolved White Matter Bundle Shape Analysis Using Nonlinear Streamline-based Registration

BundleMorphometry quantifies local white matter bundle shape using nonlinear registration, revealing deformation patterns in glioma and Parkinson's disease datasets.

EigenBrain maps cortical molecular architecture from functional, geometric, and structural eigenmodes

The paper shows functional MRI eigenmodes can approximate specific receptor and transporter distributions in the cortex, while structural and geometric eigenmodes cannot, and applies this to detect molecular differences in autism and schizophrenia.

Antigenic landscape of a highly mutated SARS-CoV-2 Spike in ongoing viral evolution

This study examines how mutations in the N-terminal domain of SARS-CoV-2 Spike affect antigenic properties and immune escape, finding that structural flexibility and loss of heme-metabolite interaction reduce antibody neutralization.

Structural mechanism of metal-induced DNA release by an ArsR/SmtB transcriptional regulator

This study defines the structural mechanism of metal-induced DNA release by the ArsR/SmtB repressor CadC using crystal structures and biochemical analyses.

A directed TM->JM coupling in receptor tyrosine kinase dimers, set by activating mutations and the membrane environment

The paper uses MD simulations and computational methods to determine the direction of conformational coupling in RTK dimers, showing it correlates with receptor activity states.

A widespread bacterial toxin reveals a deeply divergent DNase family neutralized by diverse immunity proteins.

This study identifies Rehh as a widespread bacterial toxin with DNase activity, revealing its evolutionary divergence and mechanism of neutralization by immunity proteins.

Mechanism of GPR84 allosteric modulation at a helix 8-proximate site

This paper identifies a helix 8-proximate allosteric site in GPR84 and shows how it enables Gi-biased signalling through structural and dynamic mechanisms.

Temporal Hydrogen-Bond Network Analysis Reveals Substrate-Directed Connectivity in Dihydrofolate Reductase

The paper introduces a temporal hydrogen-bond network analysis framework to study ligand-directed connectivity in DHFR, revealing mutation-sensitive pathways and evolutionarily supported communication regions.

Conformational Ensembles of the Disordered 4E-BP2:eIF4E Complex Restrained by smFRET Experiments

The paper generates conformational ensembles of the 4E-BP2:eIF4E complex using smFRET and NMR data, revealing dynamic structural changes and new contact regions.

Substrate binding reorganizes the energetic landscape of Plasmodium falciparum hexose transporter PfHT1

This study shows how glucose binding reorganizes the conformational and energetic landscape of PfHT1, a malaria parasite transporter, using computational methods and experimental validation.

Structural basis of lipid-mediated self-regulation of Tissue Factor.

This paper identifies two lipid-mediated mechanisms of Tissue Factor self-regulation through structural analysis, revealing conformational changes and their impact on FVII binding.

Phosphoinositides protonation states dictate AKT1 binding with membrane

This study shows that phosphoinositide protonation microstates determine AKT1 membrane binding specificity and how mutations alter this interaction.

Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation

This paper investigates how the L405D mutation in SARS-CoV-2 nsp13 decouples ATP hydrolysis from RNA translocation by altering conformational dynamics.

Synergistic Effects of pH and Temperature on Dengue VirusEnvelope Dimers: Insights from Microsecond MolecularDynamics Simulations

This study uses molecular dynamics simulations to show how pH and temperature together destabilize dengue virus envelope dimers, revealing a 'compensatory embrace' mechanism and potential targets for antiviral drugs.

Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10

This study determines the structural basis of Trm10's specific tRNA methylation by capturing its post-catalytic states using cryo-EM and MD simulations.

Conformational dynamics of an intrinsically disordered receptor enable signal transduction

This study uses HS-AFM to directly observe conformational changes in FGFR1 during signal transduction, showing that autophosphorylation enables dynamic interactions with FRS2.

A Generic Numbering Scheme for TMEM16 Scramblases

This paper introduces a generic numbering scheme for TMEM16 scramblases to enable comparative analysis across paralogs with different sequence numbering systems.

Structural characterization the LlaI anti-phage defense system reveals insights into the evolution of nucleotide specificity and the organization of DNA binding in McrBC restriction complexes

The paper reports crystal structures of LlaI components, revealing nucleotide specificity evolution and DNA binding mechanisms in McrBC restriction complexes.

Molecular Interactions of Viral Insulin/IGF-like Peptides with Zebrafish Receptors

This study uses molecular dynamics simulations to analyze how viral insulin/IGF-like peptides bind to zebrafish receptors, identifying conserved and unique interactions.

A novel lipid-triggered allosteric site modulates LC3-LIR receptor binding activity

This study identifies a lipid-triggered allosteric site in LC3 that modulates receptor binding activity through conformational changes upon membrane engagement.

Development of force-field corrections for the RNA A-bulge motif

The paper develops a hydrogen-bond correction to improve RNA force fields' accuracy in modeling noncanonical motifs like the MAPT A-bulge.

Computational Structural Analysis of POLG Variants R627Q and W748S with Model-Variability Controls

This paper evaluates structural changes in POLG variants R627Q and W748S using AlphaFold2 models and experimental structures, finding no clear mutation-specific deformation but suggesting physicochemical hypotheses.

Ligand Binding Kinetics, Thermodynamics, and Gating of Insect Odorant Receptor

This study investigates the ligand binding kinetics, thermodynamics, and gating of the insect odorant receptor MhOR5 using molecular dynamics simulations, revealing key structural determinants and differences in ligand behavior.