matav3

matav3 computes the history tree of nucleocapsid (NC) structures in bacteriophage φ6 by applying component tree analysis to cryo-electron microscopy single-particle reconstruction density maps to elucidate 3-dimensional architecture and protein occupancy.

Key Features:

• Component Tree Analysis: Uses component trees as a topological and geometric image descriptor to map structural elements within NCs.
• Density Map Integration: Processes cryo-electron microscopy single-particle reconstruction density maps to derive accurate 3D representations of the nucleocapsid.
• Occupancy Analysis: Determines positions and occupancy of hexameric nucleotide triphosphorylase (P4) and RNA polymerase (P2), indicating these proteins are essentially fully occupied within the NC.
• Dynamic Structural Modeling: Models the procapsid (PC) as a dynamic intermediate in which P4 and P2 can transiently attach and detach until stabilization in mature NCs.
• Expansion and Translation Tracking: Tracks PC expansion during RNA packaging and the translation of P2 from the inner 3-fold axis (20 sites) to the inner 5-fold axis (12 sites), with excess P2 positioned in the central NC region.

Scientific Applications:

• Viral Assembly Studies: Provides structural information to investigate assembly and maturation processes of bacteriophage φ6.
• RNA Packaging Mechanisms: Supports analysis of protein occupancy and positioning relevant to RNA packaging within viral capsids.
• Structural Biology Research: Facilitates investigation of geometric and topological properties of viral nucleocapsids for virology and related studies.

Methodology:

matav3 applies component tree analysis to interpret cryo-electron microscopy single-particle reconstruction density maps to determine protein occupancy and spatial configuration within bacteriophage φ6 nucleocapsids.