D. Lyumkis

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.