Most proteins operate as part of molecular assemblies -- few act alone. Human cells contain thousands of distinct assemblies built from a few to thousands of proteins. Examples are ribosomes (synthesize proteins), polymerases (transcribe DNA to RNA), nucleosomes (spool DNA), nuclear pores (portals for all traffic into and out of the cell nucleus), microtubules (used in cell division, motility and other processes), proteasomes (degrade unneeded proteins), chaperonins (enclosures for folding proteins), clathrin cages (transport in/out of cell), spliceosomes (remove introns from mRNA), and topoisomerases (unwind DNA). Hundreds of assemblies are known and thousands remain to be discovered and studied.
This project develops interactive software used to determine the structure and function of assemblies, especially through analysis of 3-dimensional electron microscopy density maps. Specifically we develop improved capabilities for
- display and manipulation of atomic models comprised of tens to thousands of macromolecules.
- creating animations of assemblies that elucidate structural organization and conformational changes.
- fitting of electron microscopy single particle reconstructions.
- analysis of structurally heterogeneous assemblies, for example polymorphic viruses such as HIV, imaged by electron microscope tomography.
Fitting in Electron Microscopy Maps
Myosin thick filament density map (Woodhead, 2005) fit using a smooth muscle myosin crystal structure (PDB 1i84) containing two heavy chains, two essential light chains, and two regulatory light chains. Copies of the myosin subunit are automatically reoriented to maintain helical symmetry during fitting so that steric clashes are apparent.
Some relevant Chimera tools:
- Volume Viewer - display contour surfaces of density maps.
- Fit in Map - fit atomic models into density maps.
- Multiscale Models - replicate atomic models using symmetry. Also sym command to maintain symmetry during fitting.
- Find Clashes - find atomic contacts between neighboring molecules.
- Movie Recorder - record movies. Also movie command.
- Surface Color - color surfaces radially.
Molecular Assemblies in Cellular Environments
Microtubules (red), a centriole (yellow), lysosomes (blue), Golgi (green) and cell membrane (orange) are shown traced in an electron tomography density map of a human cytotoxic T-cell. Lysosome are towed along microtubules to deliver a lethal dose of serine proteases to an infected adjacent cell.
Additional tools for analyzing density maps are described in the Guide to Volume Data Display
More animations of molecular assemblies can be found in the animation gallery.
Further demonstrations of Chimera capabilities for elucidating molecular assemblies are given on the Demonstrations, Talks and Posters web page.
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