The first view of a protein shown in a publication is often a cartoon of the .
Looking at the diagram, and using the view buttons and the buttons to turns things on and off, you can answer questions like:
- Which secondary structures do you see in the different domains?
- Which domains potentially interact with the bound ATP molecule?
- How big is this molecule?
- What shape is this molecule?
- Zooming in using the views provided above, which domains might be involved in binding UvrA?
- Zooming in using the views provided above, which domains might be involved in binding DNA?
- What kinds of beta sheets are found in the different domains (parallel/antiparallel/mixed)?
- What parts of the molecule might be flexible (do you see any potential hinges)?
- In the beta sheets, how are beta strands connected (by which secondary structure element, on which side of the sheet?
- Are the beta sheets flat or twisted?
- What is the central domain (i.e. the one directly connected to everything)?
- How are the other domains connected to the central domain, by one or more connector?
- How many residues in a typical strand or helix (hover over ends to see residue numbers)?
Domains are whatever the authors define them as. In the case of UvrB, we highlighted the parts similar to other helicases in yellow and red, while the green, blue and cyan elements were novel. We did try to separate the protein into parts with separate hydrophobic cores (e.g. ) along sensible boundaries, but there is mostly no experimental evidence. However, the blue domain is a real domain in the sense that it was deleted in a protein variant that retained function (except UvrA-binding, which is through the blue domain). In a different study, the cyan element was deleted, and again, the remainder of the protein folded properly as it still hydrolyzed ATP (but no longer bound tightly to DNA, which is via the cyan hairpin loop).
select protein; cartoon; color gold;
select 415-600; color red;
select 157-244; color blue;
select 244-324, 349-378; color lime;
select 91-116; color cyan;
select not helix and not sheet; cartoon 0.3 #makes turns a bit thicker
To show where negatively or positively charged molecules are bound, 2D-figures sometimes show surfaces colored by an electrostatic potential calculated from the point charges on Asp, Glu, Arg, Lys and - if the charge state is known - His. The common color scheme is blue for positive and red for negative potential (corresponding nicely to the CPK color scheme with blue nitrogen atoms - carrying a positive formal charge - and red oxygen atoms - carrying a negative formal charge). A quick and simple approximation in Jmol is to show the molecule as spacefill, and . (You could also just color the side chain oxygen and nitrogen atoms, but you then ignore charges of disordered atoms missing in the model but present in the protein.) The UvrB protein shown does not exhibit any obvious regions of positive or negative charges.
select protein; spacefill 100%; color silver;
select (arg, lys, his) AND sidechain; color blue;
select (arg, lys, his) AND sidechain; color blue;
To show on the surface of the protein, we can color the carbons on the side chains of Met, Ile, Leu, Val, Phe, Tyr and Trp gray while all other side chain atoms are the color orchid and the backbone is white (the OH group of Tyr is also shown in purple.
Looking at the diagram, and using the view buttons and the buttons to turns things on and off, you can answer questions like:
- Comparing hydrophobic and hydrophilic side chains, which tend to be on the inside and which on the outside?
- Are the hydrophilic side chains clumped or distributed?
- Are the hydrophobic side chains clumped or distributed?
- Is there one hydrophobic core or multiple?
- How are domains related to hydrophobic cores (you might have to go back to the first figure)?
- Does domain 2 behave differently than the others (it is the most disordered domain, is missing several sidechains and its connectivity was updated in later models where the domain was more ordered, e.g. PDBID 1T5L and 2NMV.
- Where are the OH-groups of tyrosines (shown in orchid)?
- What would happen if we place this molecule into a nonpolar solvent such as cyclohexane?
If we want to, we can color the sulfur atoms of Cys and Met in a different color like darkgreen. One exposed hydrophobic side chain of known function is tyrosine 11, which stacks with the adenine ring of bound ATP (shown as ball-and-stick in color).
This might look like there are a lot hydrophobic side chain on the surface, but if you look inside the protein, it is much more hydrophobic in the hydrophobic cores of the various domains.
To show evolutionary , we use data from ConSurf.
select protein; define ~consurf_to_do selected
consurf_initial_scene = true; script "/wiki/ConSurf/d9/1d9z_consurf.spt"
select protein; isosurface ignore(solvent) sasurface MAP property color
157-244 blue
415-600 red
349 - 378 lime
244 - 324 lime
91 - 116 cyan
