D. Lyumkis

Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing

The paper uses anti-sense oligonucleotides to disrupt RNA interactions in bacterial ribosome assembly, revealing intermediate structures and domain consolidation during RNP formation.

Two-Metal Ion Mechanism of DNA Cleavage by Activated, Filamentous SgrAI

The paper presents two cryo-EM structures of filamentous SgrAI to elucidate the two-metal ion mechanism of DNA cleavage during enzymatic activity.

Assembly of the Bacterial Ribosome with Circularly Permuted rRNA

This study investigates bacterial ribosome assembly using circularly permuted rRNAs, revealing conserved assembly routes and domain association order.

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

This study determines cryo-EM structures of HIV-1 integrase tetramers and intasome hexadecamers, revealing structural plasticity and functional roles in viral integration and RNA binding.

Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization

This study identifies molecular determinants of binding modes for a third-generation HIV-1 integrase inhibitor, showing that side chain and solvent reorganization, along with conformational entropy, influence ligand binding preferences in closely related viral intasomes.

Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection

This study improves cryo-EM data collection by reducing resolution attenuation during stage tilt, enabling isotropic map reconstruction of specimens with preferred orientations.

Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants

The paper investigates mechanisms of HIV-1 integrase resistance to Dolutegravir and shows that 4d is more effective against resistant variants.

Kinetic co-evolutionary models predict the temporal emergence of HIV resistance mutations under drug selection pressure

This paper uses kinetic co-evolutionary models to predict the temporal emergence of HIV resistance mutations under drug selection pressure, showing that epistasis determines DRM acquisition rates.

Near-Physiological in vitro Assembly of 50S Ribosomes Involves Parallel Pathways

The paper reports the assembly of 50S ribosome intermediates using in vitro reconstitution and cryo-EM, revealing parallel assembly pathways and cooperative blocks.

Unsupervised Voxel-based Segmentation reveals a Landscape of Bacterial Ribosome Large Subunit Early Assembly

The paper uses cryo-EM and a new segmentation method to reveal the early assembly pathway of bacterial ribosome large subunit, identifying cooperative blocks and a unified maturation landscape.

Multivalent interactions essential for lentiviral integrase function

This study reports cryo-EM structures of the lentiviral intasome and shows that multivalent interactions are essential for integrase function and virus infectivity.

Cryo-EM Structure of the Pol Polyprotein Provides Insights into HIV Maturation

The paper determines the cryo-EM structure of the HIV-1 Pol polyprotein intermediate, revealing how RT dimerization activates proteolytic processing by bringing PR monomers together.

Quantitative Mining of Compositional Heterogeneity in Cryo-EM Datasets of Ribosome Assembly Intermediates

The paper develops a workflow to quantitatively analyze structural heterogeneity in cryo-EM datasets, applied to E. coli ribosome assembly intermediates to identify new branch points and interactions.

Tools for Visualizing and Analyzing Fourier Space Sampling in Cryo-EM

The paper introduces a GUI tool to analyze Fourier space sampling in cryo-EM by evaluating orientation distributions and their impact on resolution.

Non-Uniformity of Projection Distributions Attenuates Resolution in Cryo-EM

This paper quantifies how non-uniform projection distributions in cryo-EM reduce resolution by introducing the sampling compensation factor (SCF) and demonstrating its impact on Fourier Shell Correlation (FSC).

Indirect Readout of DNA Controls Filamentation and Activation of a Sequence-Specific Endonuclease

This study reveals how SgrAI's filamentation and indirect DNA readout enhance its DNA cleavage activity and sequence specificity.

Sub-2 A Ewald Curvature Corrected Single-Particle Cryo-EM

The paper improves cryo-EM resolution by correcting Ewald sphere curvature, achieving 1.86 Å resolution for an AAV2 variant.

Analysis of Local Variability and Allostery in Macromolecular Assemblies using Cryo-EM and Focused Classification

The paper develops focused classification strategies for single-particle cryo-EM to analyze structural variability and allostery, applying them to an HIV-1 TAR element RNA dataset.

Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d

The paper determines the structural basis of CRISPR-Cas13d's RNA-guided ribonuclease activity through cryo-EM and biochemical analysis, revealing its molecular architecture and activation mechanisms.