structural biology

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.

Structural mechanism defining product specificity in glycoside hydrolase family 66 cycloisomaltotetraose glucanotransferase

This study identifies a molecular mechanism in CI4Tase that enforces strict DP4 specificity for cycloisomaltotetraose synthesis through structural and mutational analysis.

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.

Structure of an RNA polymerase ribozyme replication complex

The paper presents the structure of an RNA polymerase ribozyme complex bound to RNA substrates, revealing its catalytic mechanism and structural similarity to polymerase proteins.

Structural and biochemical analysis of the IBV nsp15 endoribonuclease reveals the necessity of peripheral site residues for activity

This study analyzes IBV nsp15 endoribonuclease structure and function, showing peripheral residues are critical for RNA cleavage and revealing species-specific RNA engagement mechanisms.

Isoprenoid Binding and Substrate Channeling in Drimenol Synthase, a Bifunctional Class II Terpene Cyclase-Phosphatase

This paper reports crystal structures of a bifunctional terpene cyclase-phosphatase enzyme and provides kinetic evidence for substrate channeling in its wild-type form.

Cryptic RNA binding sites are energetically accessible and chemically addressable

The paper investigates cryptic RNA binding sites in the env8 Cbl riboswitch, showing they are energetically accessible and chemically addressable through base displacement and ligand binding.

RPDynaFlow: Generating RNA-Protein Conformational Ensembles by Atomic Conditional Flow Matching

RPDynaFlow generates RNA-protein conformational ensembles using flow-matching, expanding phase space sampling beyond MD simulations for studying interactions.

Structural insights into fosfomycin efflux by a streptococcal ABC transporter

This study identifies and characterizes FoeAB, a type IV ABC transporter in Streptococcus pneumoniae that exports fosfomycin, using functional assays and cryo-EM structures.

Structural and mechanistic analyses reveal collaborative regulation of HSF1 by the Hsp70-Hsp90 chaperone systems

This study reveals how HSF1 is regulated by Hsp70 and Hsp90 chaperones through structural and mechanistic analyses, showing Hsp90's role in maintaining HSF1 in a pre-activated state.

Structural basis for covalent inhibition of sulfatases by sulfamate warheads

This paper investigates why aryl sulfatases are inhibited by sulfamate warheads while carbohydrate sulfatases are not, using structural and computational analyses.

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.

Enzymatic formation of a conserved isoaspartate in ribosomal protein uS11

The paper identifies an enzymatic pathway for isoaspartate formation in bacterial ribosomal protein uS11, showing its conservation and structural importance.

Effect of Glycosylation on the Free Energy Landscape of the Catalytic Domain of Human Carbonic Anhydrase IX

This study uses molecular dynamics simulations to analyze how glycosylation affects the free energy landscape of HCA IX's catalytic domain in monomeric and dimeric forms, revealing increased landscape complexity with glycosylation.

Conformational ensembles of flexible multidomain proteins: How close are we to accurate and reliable predictions?

This study evaluates five computational methods for modeling conformational ensembles of flexible multidomain proteins using SAXS data, highlighting discrepancies and biases in their predictions.

How Phosphorylation of alpha/beta-Tubulin Perturbs Microtubule Structure: A Computational Study

This study uses molecular dynamics simulations to show how phosphorylation of alpha or beta-tubulin alters microtubule structure and affects GTP hydrolysis and dynamic instability.

Avs2 drives non-canonical tetrameric assembly of trypsin-like domain for anti-phage defense

The paper elucidates the molecular mechanism of the Avs2-trypsin-MBL system, revealing how phage terminase recognition triggers tetramerization and activation of the system for anti-phage defense.

Alternative splicing expands and remodels the breast cancer proteoform landscape

The paper develops 3DisoGalaxy to study alternative splicing in breast cancer, finding that many transcripts produce translation-supported proteins and that functional divergence is concentrated in specific regions.

Structural basis of sulfide production in dissimilatory sulfur metabolism

This study reveals the structural basis of sulfide production in dissimilatory sulfur metabolism through cryo-EM structures of the DsrMKJOP complex from Archaeoglobus fulgidus.

Site-specific processing of phosphoethanolamine cellulose by the BcsZ cellulase reveals stochastic biofilm cellulose modification

This study identifies how BcsZ cellulase processes phosphoethanolamine-modified cellulose in the periplasm, revealing stochastic pEtN distribution and independent BcsZ function.

Enhanced-Sampling Molecular Dynamics Recovers Rare Functional RNA Conformations Across Diverse Structural Contexts

This study compares enhanced sampling methods for RNA conformational sampling, finding T-REMD provides the most accurate ensembles and improves virtual screening.

Transposon end recognition and excision mechanisms of type I-F CRISPR-associated transposases

This study investigates the mechanism of transposon excision by type I-F CRISPR-associated transposases using structural and biochemical analyses.

MOLECULAR BASIS FOR PINK1 MATURATION

This study identifies the structural basis for PINK1 maturation by the HSP90/CDC37/FKBP51 chaperone complex and shows FKBP51 negatively regulates PINK1 function in mitophagy.

Comparative electrostatic mapping of ATP synthase reveals species-dependent axial asymmetry

The paper compares electrostatic properties of ATP synthase across species using crystallographic and cryo-EM structures, revealing species-dependent axial asymmetry in electrostatic potential.

An intact primordial interferon antiviral signalling network in amphioxus illuminates the basal chordate origin of vertebrate IFN immunity

This paper identifies an intact primordial interferon signaling network in amphioxus, showing that IFN immunity originated in basal chordates before vertebrates.

Secondary nucleation drives polymorph diversity in hIAPP amyloids

This study shows that secondary nucleation increases polymorphic diversity in hIAPP amyloids, and molecular chaperones can steer aggregation toward a monomorphic state.

Graphene Device for High-Temperature Crystallography Visualizes How Enzymatic Reactivity is Rooted in Ensemble Probability

The paper develops a graphene device for high-temperature crystallography to study enzymatic reactivity across temperature ranges, revealing how transition state ensembles relate to catalytic rates.