Biology subjects

Mikirtumov, V.

Publications and source records attributed to Mikirtumov, V..

3 recordsLinked to original sources

bioRxiv2025

Integrative structural interactomics reveals protein organization and structure in a giant virus

Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrated cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocated 88 viral proteins to different virion sub-compartments and proposed topologies of 25 inner membrane proteins. We assigned eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.

biochemistry↗

bioRxiv2025

Structures of EHD2 filaments on curved membranes provide a model for caveolar neck stabilization

Caveolae are flask-shaped invaginations of the plasma membrane serving critical functions in mechano-protection and signal transduction. Caveolar dynamics, such as movement within the plasma membrane or endocytosis, relies on precise shaping of the highly curved caveolar necks. The dynamin-like EHD2 ATPase is proposed to form an oligomeric scaffold around the caveolar neck, but its detailed molecular action is poorly understood. Here, we employed cryo-electron tomography to elucidate structures of EHD2 filaments oligomerized on tubulated liposomes. EHD2 filaments form a highly curved membrane scaffold which stabilizes a sophisticated tubular membrane geometry with undulations along the tubes axis. An amino-terminal sequence facilitates this geometry by inserting into the membrane, thereby acting as a spacer between adjacent filaments. Moreover, in endothelial cells lacking EHD2, caveolar necks become narrower and elongated. Our structural work provides the molecular framework for understanding EHD2 scaffold formation and its cellular function in caveolar dynamics.

molecular biology↗

bioRxiv2023

Streamlined Structure Determination by Cryo-Electron Tomography and Subtomogram Averaging using TomoBEAR

Structures of macromolecules in their native state provide unique unambiguous insights into their functions. Cryo-electron tomography combined with subtomogram averaging demonstrated the power to solve such structures in situ at resolutions in the range of 3 Angstrom for some macromolecules. In order to be applicable to structural determination of the majority of macromolecules observable in cells in limited amounts, processing of tomographic data has to be performed in a high-throughput manner. Here we present TomoBEAR - a modular configurable workflow engine for streamlined processing of cryo-electron tomographic data for subtomogram averaging. TomoBEAR combines commonly used cryo-EM packages and reasonable presets to provide a transparent "white box" for data management and processing. We demonstrate applications of TomoBEAR to two datasets of purified proteins and to a membrane protein RyR1 in a membrane and demonstrate the ability to produce high resolution with minimal human intervention. TomoBEAR is an open-source and extendable package, it will accelerate the adoption of in situ structural biology by cryo-ET.

biophysics↗