cryo-EM

Structural basis for inefficient G protein coupling by Frizzled receptors

The paper identifies detergent LMNG as stabilizing a weak FZD-G protein interface, revealing that FZDs inherently weakly couple to G proteins and preferentially signal through DVL.

Facilitating the identification of cryo-EM hit matter in drug discovery with Astex-Faro

Astex-Faro improves cryo-EM hit identification by detecting structural deviations and enhancing weak features across diverse datasets.

Preserving Information and Integrity in Cryo-EM: A Fourier-Space Deposition Approach

The paper identifies limitations in current cryo-EM data deposition practices and proposes an alternative approach to better preserve information and support validation.

Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation

This study introduces OpenCGChromatin, a model that simulates chromatin structure and phase separation, revealing how linker-DNA length and histone modifications affect chromatin organization.

Transition Intermediates Encode Ligand Efficacy at the μ-Opioid Receptor-Gi Protein Complex

The paper uses computational and experimental methods to identify transition intermediates in the μ-opioid receptor-Gi protein complex that encode ligand efficacy.

MxB N-Terminus Adopts a Stable α-Helix to Engage the HIV-1 Capsid Trimer Interface

The paper determines the structure of HIV-1 capsid lattice bound to MxB N-terminal fragment, revealing an alpha-helix stabilizes binding at the trimer interface.

Cryo-EM reveals patient- versus organ-specific structural diversity and bound ligands in lambda-6 light chain amyloids

The paper uses cryo-EM to analyze lambda-6 light chain amyloid structures from different organs and patients, revealing structural diversity and potential interactions with collagen-VI.

Cryo-EM structures of apo human Factor XIa reveal catalytic-domain flexibility and exposure of the Factor IX-binding site

This study uses cryo-EM to show that Factor XIa exists as a dynamic ensemble with flexible catalytic domains that expose the Factor IX-binding site.

Progressive Loosening of a Dual Autoinhibitory Interface Activates PP2A-B56δ

This paper investigates the activation mechanism of PP2A-B56δ by analyzing disease variant E198K using cryo-EM and computational methods, revealing progressive loosening of the N/C-arm interface as the activation pathway.

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.

cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle Cryo-EM

The paper introduces cFAR and Relative Signal to diagnose preferred orientation in single-particle cryo-EM, using synthetic and real datasets to validate their effectiveness.

Conformational gating at histidine junctions coordinates proton translocation in respiratory complex I

The paper presents cryo-EM structures of bovine respiratory complex I under varying protonation conditions, revealing conformational changes at histidine junctions that coordinate proton translocation.

Bovine coronavirus evolution preserves spike architecture while remodeling key functional regions

This study investigates BCoV spike protein evolution, showing preserved architecture but functional region remodeling, with implications for vaccine development.

Conformational changes underlying electromechanical transduction in prestin resemble a transport transition in pendrin

This study shows that prestin's conformational changes during electromechanical transduction resemble a transport transition in pendrin, with shared structural and functional properties.

A workflow for the identification of oligomeric structures on tilted sample planes in Cryo-SMLM

This paper introduces a workflow to identify oligomeric structures in Cryo-SMLM by accounting for tilted sample planes and demonstrates its accuracy on synthetic data.

Asynchronous structural rearrangements govern constriction of the human nuclear pore complex

The paper uses a structure-based model to study the asynchronous structural rearrangements during nuclear pore complex constriction and their energetic contributions.

Layered helical order reveals assembly states in podosome actin networks

The paper uses cryo-electron tomography and computational methods to infer the assembly states of actin networks in podosomes, revealing layered helical order and preferred orientation transitions.

BRCA2 and RAD54B FxPP motifs Bind DMC1 Filaments through Persistent and Transient Interfaces

This study identifies and characterizes P-motifs in BRCA2 and RAD54B that bind to DMC1 filaments through stable and transient interactions, revealing structural insights into their roles in meiotic recombination.

Quinoa: Efficient and Robust CTF Estimation for CryoET Tilt Series

Quinoa provides efficient and robust CTF estimation for cryoET tilt series, improving automated structural analysis of cells and tissues.

Structural Basis of Kinesin-1 Autoinhibition and Its Control of Microtubule-Based Motility

This study determines the cryo-EM structure of autoinhibited kinesin-1 and identifies mechanisms of autoinhibition and activation.

Fast prediction of acidic amino acid sidechain conformations for cryo-EM modeling

The paper develops a workflow to predict sidechain conformations of acidic amino acids in cryo-EM maps, validated through Q-score and molecular dynamics simulations.

A structural trade-off balances mechanical resilience and supramolecular adaptability in type IV pili

This study identifies a structural trade-off in type IV pili that balances mechanical resilience and supramolecular adaptability using cryo-EM, simulations, and experimental validation.

CryoROLE: describing large inter-domain rotation in single particle cryo-EM

CryoROLE extracts continuous conformational dynamics from cryo-EM data by analyzing relative domain orientations, revealing hidden protein motions relevant to function.

Where do the ligands bind? Co-folding bitter taste GPCRs with the BitterDB chemical space

The paper evaluates the Boltz-2 co-folding framework to predict ligand binding pockets in TAS2R GPCRs and identifies sequence features that determine pocket preference.

3dcon: tomogram denoising by deconvolution

This paper introduces 3dcon, a deconvolution algorithm for cryo-electron tomography to reduce structural artifacts in reconstructed 3D volumes.

Structural insights into YheS-mediated release of SecM-arrested ribosome.

The paper elucidates the mechanism by which YheS releases SecM-arrested ribosomes using cryo-EM and molecular dynamics simulations.

AlignPCA-2D: PCA-Reduced Euclidean Vector Alignment for 2D Classification in Cryo-EM

AlignPCA-2D improves 2D classification in cryo-EM by using PCA-reduced Euclidean vector alignment, achieving competitive accuracy with lower computational cost.

Mechanistic basis of teichoic acid transport by a gatekeeper flippase

The paper determines the mechanism of teichoic acid transport by the flippase TacF in Streptococcus pneumoniae using cryo-EM and computational methods.

Structural basis for the intestinal protocadherin-based intermicrovillar adhesion complex

The paper determines the Cryo-EM structure of the intestinal IMAC complex, revealing its heterotetrameric composition and structural features that enable microvilli adhesion and resilience to shear stress.

Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling

This paper introduces CRIM, a scoring function combining cryo-EM and IM-MS data to improve monomeric protein structure prediction, showing reduced RMSD and increased TM-score on both simulated and experimental datasets.