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Software: Virus capsids and other large protein assemblies visualized easily
Submitted by Eric Martz; posted on Friday, August 19, 2022
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Would you like to see an interactive virus capsid model quickly and easily? Slab it or cut it in half? A clathrin coat? A bacterial gas vesicle? The mysterious "vault" eukaryotic nanocompartment?
https://proteopedia.org/w/FirstGlance/Virus_Capsids_and_Other_Large_Assemblies
The views at the above link were obtained with Version 4.0 of FirstGlance in Jmol released August 15, 2022 (free and open source; google "firstglance" as one word, or http://firstglance.jmol.org). Newly, it automatically constructs "biological assemblies" and shows "biomolecule 1" in its initial view. Exploring the asymmetric unit is then an option.
Very large assemblies+++ are automatically simplified to alpha carbons, or a subset of alpha carbons; see examples at the above link. What are such simplified models good for? They can be measured, colored by secondary structure, hydrophobic/polar, charge, amino-to-carboxy rainbow, or evolutionary conservation (if pre-processed by the ConSurf Server). Each group of sequence-identical chains can be assigned a distinct color (under Solid in the Views tab).
You can make an animation, ready to drop into a presentation slide, from any view in FirstGlance. It takes just a few mouse clicks. Examples in Google Slides:
http://tinyurl.com/movingmolecules
A small assembly, 2acz, has 4 chains in its asymmetric unit, and 12 chains in its biomolecule 1. You will be offered the option to simplify, so you can try it both ways. Even simplified to alpha carbons, the transmembrane helices stand out with the hydrophobic/polar and charge views. Its construction can be understood by giving a distinct color to each of the 4 sequence-distinct protein chains (Solid in the Views tab).
http://firstglance.jmol.org/fg.htm?mol=2acz
Structural biologists: With FirstGlance, you can't miss (after clicking "Show more details") incomplete sidechains, missing residues, alternate locations (can be animated), occupancy < 1.0 (all exemplified in 1ijw). All salt bridges can be displayed with one click (Tools tab), and a spreadsheet-ready list is reported with one more click. A "Contacts & Non-Covalent Interactions" tool makes it easy to visualize the interactions with any moiety you specify. Protein crosslinks are automatically detected and highlighted/zoomed with a few clicks: isopeptides, thioesters, thioethers, his-tyr, lys-cys NOS as well as, of course, disulfides. Step by step:
https://proteopedia.org/w/FirstGlance/Evaluating_Protein_Crosslinks
Electron density maps (or EM density maps) can be displayed for anything selected with the Find.. dialog, as well as crosslinks and ends of chains. See examples from FirstGlance here:
https://proteopedia.org/w/Electron_density_maps
New color schemes for simplified models:
http://firstglance.jmol.org/notes.htm#bucolors
New color schemes for simplified models:
http://firstglance.jmol.org/notes.htm#bucolors
To clear the old version of FirstGlance out of your browser's cache, go to
http://firstglance.jmol.org/fg.htm?mol=1ijw
Then regardless of whether the molecule displays, hold down the Shift key while you Reload.
+++"Very large assemblies" means >25,000 non-hydrogen atoms. Only about 3% of entries in the World-Wide Protein Data Bank have biological assemblies that large. However, these include very important structures, such as virus capsids. Simplification rules:
http://firstglance.jmol.org/notes.htm#simplification
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