Dmitry Lyumkis

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.

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.

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.

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.

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.

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.

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

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.

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

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

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

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

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

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.