Dmitry Lyumkis

HIV-1 Ribonucleoprotein Complex Organization Facilitates Assembly of the Mature HIV-1 Capsid

This study uses molecular dynamics simulations to show that IN-RNA filaments guide HIV-1 capsid assembly and shape, with octameric filaments forming more conical capsids than tetrameric ones.

Structural Mechanism of Filamentation Induced Dampening of GTP Inhibition of Glutamate Dehydrogenase

This study uses cryo-EM to show how filamentation in bovine GDH alters its allosteric response to GTP inhibition, revealing structural mechanisms with implications for disease treatment.

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.

Cryoelectron tomography of HIV-1 cell-cell transmission conjugates reveals a secluded environment for viral assembly and transfer

This study uses cryoET to reveal that HIV-1 cell-cell transmission occurs in secluded intercellular spaces, and develops flow cytometry to show CD4 partially mediates conjugate formation but not entry.

Using phage display for rational engineering of a higher affinity humanized 3-phosphohistidine-specific antibody

This paper describes the engineering of high-affinity 3-phosphohistidine-specific antibodies using phage display and validates their utility in detecting pHis proteins in mammalian cells.

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.

De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential

This paper introduces a method using molecular dynamics simulations to predict water positions in cryo-EM maps by analyzing excess chemical potential, showing high agreement with experimental data.

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

This study identifies the structural and sequence basis of epistatic interactions driving drug resistance in HIV by combining sequence models and molecular dynamics simulations.

Structural basis of context-dependent RORγt target gene activation on chromatin

This study identifies how RORγt mutations affect gene activation by altering chromatin binding modes, explaining context-dependent autoimmunity and host defense outcomes.

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.

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks

This paper introduces an unsupervised learning approach using coordinate networks to address the missing wedge problem in cryoET, improving reconstruction quality and reducing runtime.