structural biology

Predicting Capsid Protein Binding Sites in Single-Stranded RNA Viruses Using Machine Learning from Local Geometric Features

This paper develops a machine learning framework to predict capsid protein binding sites in ssRNA viruses using local geometric features from RNA structures, achieving high accuracy with and without experimental data.

Distinct atypical chemokine receptor 1 determinants underlie bacterial toxins recognition and pore formation

This study identifies distinct determinants of ACKR1 recognition by bacterial toxins, revealing a two-step mechanism involving sulfotyrosine binding and extracellular vestibule interaction.

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.

Structure of the human mitochondrial RNA degradosomereveals a distinct mode of helicase-nuclease coupling

The paper determines the cryo-EM structure of the human mitochondrial RNA degradosome, revealing a unique helicase-nuclease coupling mechanism.

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.

Discovery and structural analysis of glycoside hydrolase family 176 α-1,2 glucosidase from Arthrobacter humicola A8F5

This paper discovers and structurally analyzes a novel -1,2-glucosidase from Arthrobacter humicola A8F5, revealing its unique mechanism and structural features for cleaving rare -1,2-glucosidic bonds.

Architecture of a DNA-guided Cas12a

The paper presents the cryo-EM structure of AsCas12a bound to a pseudo-DNA guide and RNA target, revealing its mechanism of DNA-guided RNA recognition.

The MscS channel from Corynebacterium glutamicum uses a non-canonical gating mechanism

This study shows that CgMscS from Corynebacterium glutamicum opens at higher membrane tension than EcMscS and uses a distinct gating mechanism not based on the 'lipids-move-first' model.

Molecular basis of N2 fixation in a hyperthermophilic archaeon

This study investigates the N2-fixing system of Methanocaldococcus infernus, revealing structural insights into its thermostable nitrogenase and unifying mechanistic principles across nitrogenase types.

Structure of NO16, a marine non-tailed vibriophage with a global distribution

This study characterizes the structure of the non-tailed vibriophage NO16, revealing its capsid organization and potential host interaction mechanisms.

A widespread NADase domain links bacterial immunity with human TEP1

The paper identifies a conserved NADase domain, NIR, in bacterial immunity and eukaryotic proteins like human TEP1, linking bacterial defense mechanisms to eukaryotic functions.

Clathrin differentially adapts its trimerisation domain during mammalian evolution to traffic the insulin-responsive GLUT4 glucose transporter

The paper identifies an alternatively-spliced form of CHC17 (CHC17-SAS) that compensates for the absence of CHC22 in some vertebrates, enabling GLUT4 trafficking.

Structural basis for P-TEFb association with BRD4

This study identifies the structural basis of BRD4 interaction with P-TEFb and shows how BRD4 and AFF4 regulate P-TEFb activity through distinct mechanisms.

A 13-subunit c-ring in the Chlamydomonas chloroplast ATP synthase lowers the H⁺/ATP cost of carbon fixation

This paper reports a 13-subunit c-ring in the Chlamydomonas chloroplast ATP synthase, which lowers the H+/ATP cost of carbon fixation compared to the 14-subunit structure in spinach.

Steric control of signaling bias in the immunometabolic receptor GPR84

The paper identifies ligands with varying steric profiles that exhibit different β-arrestin recruitment capacities at GPR84, revealing a mechanism for controlling signaling bias.

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.

Structural and functional insights into QueC-family protein in QatABCD anti-phage system

The paper investigates the structural and functional role of QueC-family protein QatC in the QatABCD anti-phage system, showing its role in protein modification similar to type IV CBASS.

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.

Structural mechanism governing radiationless energy transfer in Renilla bioluminescence

This study reports co-crystal structures of a bioluminescent energy-transfer complex in Renilla reniformis, revealing the spatial arrangement of donor-acceptor chromophores and their role in efficient radiationless energy transfer.

Metabolic regulation and structural mechanism of glutamine synthetase AMPylation

This study investigates how metabolic signals regulate glutamine synthetase AMPylation in Herbaspirillum seropedicae and reveals the structural mechanism of enzyme inhibition by AMPylation.

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.

Structures of pUG-fold RNA bound to DNMT1 reveal a mechanism for RNA-mediated epigenetic regulation

This study determines the cryo-EM structures of DNMT1 bound to pUG-fold RNA, revealing two RNA-binding modes and their role in inhibiting DNMT1 activity.

Snapshots from the Catalytic Landscape of Chalcone Isomerase

This study investigates the dynamic conformational changes of chalcone isomerase using structural and biochemical methods, revealing how flexibility in the active site facilitates substrate rearrangements during catalysis.

Structural insights into how metallochaperones UreE and UreG interact to deliver a toxic metal to urease

This study determines the crystal structure of the UreE2G2 complex bound with nickel ions and GMPPNP, revealing how GTP and nickel binding regulate nickel transfer between metallochaperones UreE and UreG.

Lenacapavir allosterically remodels the HIV-1 capsid

This study shows lenacapavir remodels HIV-1 capsid structure by altering non-covalent interactions and material properties, leading to capsid rupture and impaired viral replication.

Molecular basis of nick ligation in the nucleosome by DNA Ligase IIIα

This study investigates how DNA Ligase IIIα ligates nicks in nucleosomes using biochemical assays, molecular dynamics, and cryo-EM, revealing position-dependent efficiency and structural constraints.

Structures of LolB bound to LolA or lipoprotein resolve the final steps of bacterial lipoprotein trafficking

This study presents structures of LolB bound to LolA or lipoprotein, revealing the mechanism of bacterial lipoprotein trafficking at the outer membrane.

Structural Evolution of LEAFY Reveals DNA-Mediated Cooperativity and Dimerization Shifts at the Water-to-Land Transition

This study reveals how LEAFY transcription factors evolved DNA-binding specificity through structural changes in dimerization mechanisms during the water-to-land transition.