structural biology

Transposon end recognition and pairing by I-F3 CRISPR-associated transposase

This study determines how the I-F3 CRISPR-associated transposase recognizes and pairs transposon ends for transposition using cryo-EM and biochemical analyses.

Mechanistic insights into chromatin modulation by the orphan remodeler ATRX

This study reveals how ATRX modulates chromatin by unwrapping nucleosomal DNA through a unique 'pin-like' structure and other features, proposing a 'climbing' mechanism for DNA translocation.

Decoding the Conformational Dynamics and Hyperactivity of Histone H3K36 N-Methyltransferase in Oncogenic Mutations via tICA and Markov State Modeling

This study uses molecular dynamics simulations to show that oncogenic NSD2 mutations enhance catalytic efficiency by reorganizing conformational dynamics rather than destabilizing the enzyme.

Substrates Coupling and Inhibition of the human Na+- dependent Cl-/HCO3-exchanger

This study determines cryo-EM structures of NCBE, revealing ion binding sites and an inhibitor mechanism, and proposes an elevator-like transport mechanism for Na+-coupled HCO3- transporters.

Structural basis of directionality control in large serine integrases

The paper reports structural insights into how large serine integrases control directionality during DNA integration and excision using recombination directionality factors.

MrtR of Mesorhizobium tianshanense reveals both activation and inhibition mechanisms of a LuxR-type quorum sensing receptor

This study defines how ligand structure controls function in a LuxR-type quorum sensing receptor by presenting full-length structures bound to agonist and antagonist ligands.

Mechanism of substrate recognition and catalysis in a mammalian phosphatidylserine synthase 2

The paper determines the structure of PTDSS2 from Equus caballus in complex with PE or serine substrates, revealing substrate binding sites and PLD activity.

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.

Dengue virus 2 lacking N153 glycosylation displayed enhanced recognition by neutralizing antibodies

The paper shows a dengue virus mutant lacking N153 glycosylation is more susceptible to neutralizing antibodies, as evidenced by increased Fab occupancy and slower dissociation rates.

Bifunctional Architecture Enables Substrate Catalysis and Channeling in Paracoccus TMAO Demethylase

This study reveals a bifunctional mechanism in TMAO demethylase where HCHO is channeled from a catalytic core to a THF-binding site, linking TMAO demethylation with one-carbon transfer.

DSSNA: Automated Nucleic Acid Structure Analysis in Molecular Dynamics

DSSNA v2026 analyzes nucleic acid structures in MD simulations, identifying base pairs, hydrogen bonds, and stacking interactions, showing that canonical pairs are stable while non-canonical ones are transient.

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.

Host membrane cholesterol constrains constitutive signaling of the oncogenic KSHV GPCR ORF74

This study identifies a cholesterol-dependent mechanism by which the KSHV GPCR ORF74 regulates its constitutive activity through structural and functional analysis.

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.

The Structural Basis of Malodorant Skatole Formation by the Glycyl Radical Enzyme Indoleacetate Decarboxylase

This paper determines the structure of indoleacetate decarboxylase and challenges the proposed mechanism of skatole formation by showing it may follow a Kolbe-type decarboxylation rather than hydrogen atom transfer.

Interrogating contrastive learning embeddings for structure-based virtual screening: a case study on DrugCLIP

This paper evaluates DrugCLIP's contrastive learning embeddings for virtual screening, showing strong performance but limitations under realistic conditions.

Structures of the Tilapia Lake Virus replication complex show that ANP32 is a host factor for replication across the Articulavirales order

This study shows that ANP32 is a conserved host factor for viral replication in the Articulavirales order, using structural and biochemical analyses of TiLV and its interaction with ANP32.

Structural conservation of the gabapentinoid binding site in human and Caenorhabditis elegans α2δ subunits: a docking and molecular dynamics perspective

This study compares the structural features of human and C. elegans alpha2delta subunits to assess gabapentinoid binding site conservation using docking and molecular dynamics simulations.

Structural framework for the assembly of the human tRNA ligase complex

This study determines the atomic structure of the human tRNA-ligase complex and reveals its assembly mechanism and functional implications.

Adenylyl cyclase 9 as a molecular scaffold to dissect the regulatory mechanisms of membrane adenylyl cyclases

This study designs a chimeric adenylyl cyclase (AC95) to investigate isoform-specific regulation, revealing structural insights and drug target possibilities.

Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity

This study identifies and characterizes human monoclonal antibodies targeting conserved coronavirus spike S2 epitopes, revealing distinct antiviral functions and Fc-dependent protective mechanisms.

Mechanistic Dissection of Conformational Transition of Bicyclic Peptide via Molecular Modeling and Deep Learning

This study introduces a deep learning model to analyze conformational transitions in cyclic peptides, revealing key residues and nonlinear torsional motions that govern structural changes.

Best practices for cryo-trapping time-resolvedcrystallography with the Spitrobot crystal plunger

This paper describes a protocol for cryo-trapping time-resolved crystallography using automated crystal plungers to study enzyme reaction pathways at millisecond resolution.

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.

Stereospecific GPG acylation by CLN8 drives BMP biosynthesis and its loss leads to Batten disease

This study identifies CLN8 as a stereospecific GPG acyltransferase critical for BMP biosynthesis, showing its loss causes Batten disease and that S,S-LPG supplementation can restore BMP and improve neurological symptoms.

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.

Mechanistical and structural basis of Kv channel inhibition by 4 aminopyridine

This study determines the structure of Kv channels bound to 4AP, showing it binds the closed state and enters via membrane-facing fenestrations, explaining its inhibitory mechanism.

The cytokine structural homologs IL-1β and IL-1Ra have distinct dynamical character that potentially influence their roles in allosteric regulation of the IL-1 receptor.

This study compares the dynamic properties of IL-1β and IL-1Ra using NMR relaxation to show that their distinct functional roles in IL-1R signaling arise from differences in conformational entropy at the receptor interface.

Plasmodium falciparum Myosin B is a slow motor optimized for force generation

This study determines the structure of Plasmodium falciparum MyoB, shows it is a slow motor optimized for force generation during invasion, and identifies its light chain as shared with MyoA.