structural biology

Conformational Dynamics in Insulin Receptor Kinase Reveals a Type III Allosteric Pocket

This study identifies a type III allosteric pocket in the insulin receptor kinase through molecular dynamics simulations and shows its structural features and inhibitor binding dynamics.

Small molecule activator of phosphatase PP2A remodels scaffold PR65 structural dynamics to promote holoenzyme assembly

The paper investigates how SMAPs bind to PR65, showing that S2 is a stable binding site while S1 is not, and that binding promotes an extended PR65 conformation favorable for PP2A holoenzyme assembly.

Catalytic and Structural Insights into Neil3-Dependent Unhooking of Endogenous Abasic DNA Crosslink

This study clarifies the mechanism of NEIL3 in unhooking Ap-ICLs by showing that a processed form of NEIL3 efficiently removes crosslinks without generating strand breaks.

SF3B1 Phosphorylation Prompts U2AF2 Dissociation for Widespread Control of pre-mRNA Splicing

This study shows SF3B1 phosphorylation reduces its binding to U2AF2, enabling widespread control of pre-mRNA splicing by promoting U2AF2 dissociation.

Structural analysis of OCT4 Binding to Human LIN28B Nucleosomes

The paper shows OCT4 binds to LIN28B nucleosomes assembled with human histones similarly to those assembled with Xenopus histones, using cryogenic electron microscopy.

Structure and signaling mechanism of Helicobacter pylori transducer-like protein D

The paper presents high-resolution structures of Helicobacter pylori TlpD, revealing how ligand-binding perturbations propagate through coiled-coils to regulate kinase interfaces.

Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies

The paper shows that 2'-O-methylation alters ribozyme active site geometries and reaction mechanisms, challenging assumptions about its role in stabilizing pre-catalytic conformations.

Cooperativity and Communication between the Active Sites of the Dimeric SARS-CoV-2 Main Protease

This study investigates how the two active sites of SARS-CoV-2 Mpro communicate and cooperate in catalysis using enzymatic assays, crystal structures, and engineered mutations.

A single methylation site regulates HRSV nucleocapsid architecture and replication

This study identifies R27 methylation as a regulator of HRSV nucleocapsid structure and replication through molecular dynamics and cryo-EM analyses.

Structural Basis of Glycolytic Control in Trypanosoma cruzi: Insights from Enolase and PGI

The paper reports high-resolution structures of T. cruzi glycolytic enzymes and identifies potential inhibitors through structural analysis and virtual screening.

Sequence constraints predispose Class D GPCRs to follow an atypical activation mechanism

This study identifies sequence constraints that predispose Class D GPCRs to an atypical activation mechanism involving TM7 displacement and TM6 inward movement.

Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling

This study investigates how pathogenic mutations in SHP2's SH2 domains alter conformational dynamics, leading to hyperactivation by stabilizing a zipped β-sheet state.

Visualization of the complete primosome reveals the structural mechanisms governing DNA replication restart

The paper presents two primosome structures in Escherichia coli, revealing mechanisms of DNA replication restart and a similarity between DnaT and DnaA.

Improved protein binder design using -pairing targeted RFdiffusion

Conditioning RFdiffusion on edge beta-strand pairing yields specific binders to polar targets, with in silico success above 9.2% versus 0.98% for hotspot-only conditioning.

A fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase

This study identifies a fold switch in ONNV nsP4 that regulates its conformation, RNA binding, and polymerase activity through proteolytic cleavage and fold switching.

Molecular mechanism of exchange coupling in CLC chloride/proton antiporters

The paper provides a mechanistic model for the 2:1 Cl-/H+ exchange in CLC transporters using structural and computational methods.

Molecular insights into bulk lipid transport from structural studies of the bridge-like protein VPS13A complexed with the scramblase XKR1

The paper uses cryo-EM to study the VPS13A-XKR1 complex, revealing how it facilitates lipid transfer between membranes and how this process is enhanced by membrane properties.

Structural investigation of an engineered feruloyl esterase with improved MHET degrading properties

The paper investigates the structural changes in an engineered feruloyl esterase that enhances its ability to degrade MHET, revealing hydrogen bonding and peptide bond isomerization.

Structural transitions in kinesin minus-end directed microtubule motility

This paper reports high-resolution structures of kinesin-14 motor proteins during different mechanochemical states, revealing structural transitions that drive force generation and the power stroke.

The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation

This paper identifies how a human AGO-miRNA-trigger complex binds ZSWIM8 for CUL3-mediated polyubiquitylation, leading to target-directed miRNA degradation.

P-Rex2 exhibits unique structural features and regulatory mechanisms distinct from the closely related RhoGEF P-Rex1

This study determines the structure of P-Rex2 and identifies unique regulatory features compared to P-Rex1, revealing differences in autoinhibition and dynamics.

From fibril to framework: P. abyssi AbpX illuminates a calcium-responsive family of microbial biomatrix proteins that form thermostable hydrogels

This paper investigates AbpX, a microbial biomatrix protein that forms thermostable hydrogels through calcium ion-dependent self-assembly and provides an atomic model of its fibril lattice.

'Zipper' Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II

The paper defines the minimal sequence requirements of RNA polymerase II CTD across transcriptional stages using structural analysis and synthetic constructs, revealing a 'zipper' model for PIC assembly and transcription progression.

Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways

PRISM clusters molecular pathways using structural medoids and geometric dissimilarities, showing robust clustering across complex biomolecular transitions.

Inhibition mechanism of pancreatic KATP channels by centipede toxins

This paper identifies centipede toxins SpTx1 and Sm3a as inhibitors of human pancreatic KATP channels, revealing their binding mechanism and therapeutic potential for neonatal diabetes.

Structural dynamics in the CENP-A nucleosome impacted by protein-protein interactions with centromere protein N

This study uses molecular dynamics simulations to analyze how CENP-N interacts with CENP-A nucleosomes, revealing structural changes and their impact on conformational states and protein interactions.

Accurate interdomain contacts in mixed folded proteins from NMR-guided coarse-grained simulations

The paper improves the accuracy of interdomain contacts in mixed folded-disordered proteins using NMR-guided coarse-grained simulations.

Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins

This study maps allosteric communication networks in SARS-CoV-2 Delta and Omicron spike proteins, revealing variant-specific changes in conformational dynamics and signaling pathways.

Structural insights into the specific recognition of H2A.Z-H2B dimer by the catalytic subunit of SRCAP chromatin remodeling complex

The paper determines the crystal structure of SRCAP-Z domain bound to H2A.Z-H2B dimer, revealing hydrophobic interactions and a conserved structural basis for recognition.

Structural basis of quinone-sensing by the MarR-type repressor MhqR in Staphylococcus aureus

This paper identifies the quinone-binding pocket of SaMhqR and elucidates its mechanism of inactivation through structural and mutational analyses.