[Proteopedia] Virus capsids and other large protein assemblies visualized easily

[Eric Martz]

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 
<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, orhttp://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).

To clear the old FirstGlance out of your browser cache:

http://firstglance.jmol.org/fg.htm?mol=7mgp

Regardless of whether the molecule is displayed, hold down the Shift key 
while clicking Reload. *Shift-Reload* forces the browser to get all 
files from the server. In the 7mgp tab of FirstGlance, click on 
"Biological Unit 1" to find out that the hexamer displayed has been 
constructed from a single chain in the asymmetric unit.

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 <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 
<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 
<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 
<https://proteopedia.org/w/Electron_density_maps>

New color schemes for simplified models:

http://firstglance.jmol.org/notes.htm#bucolors 
<http://firstglance.jmol.org/notes.htm#bucolors>

*"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 
<http://firstglance.jmol.org/notes.htm#simplification>

Hope you enjoy!

Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his)
Univ. Massachusetts, Amherst-- Martz.MolviZ.Org <http://martz.molviz.org/>

  * Guided Exploration of Macromolecules with Powerpoint-Ready
    Animations: FirstGlance.Jmol.Org <http://firstglance.jmol.org/>
  * Make Custom Interactive Molecular Scenes EASILY: Proteopedia.Org
    <http://proteopedia.org/>
  * DNA, Hemoglobin, etc. Tutorials: MolviZ.Org <http://molviz.org/>
  * Find Functional Patches in Proteins with ConSurf
    <http://consurf.tau.ac.il/>
  * Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.molviz.org/>
  * See multiple protein sequence alignments clearly: MSAReveal.Org
    <http://msareveal.org/>
  * Pockets And Cavities Using Pseudoatoms in Proteins: PACUPP
    <http://molviz.org/pacupp>
  * Interactive Molecules in Architectural Spaces:
    MolecularPlayground.Org <http://molecularplayground.org/>
  * Teaching Plans: Workshops.MolviZ.Org <http://workshops.molviz.org/>

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