User:Karsten Theis/overall views

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(→Types of overall views)
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==Types of overall views==
==Types of overall views==
<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='78/780454/Domains/8'>
<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='78/780454/Domains/8'>
 +
===Secondary structure===
The first view of a protein shown in a publication is often a cartoon of the <scene name='78/780454/Domains/7'>secondary structure colored by domains</scene>.
The first view of a protein shown in a publication is often a cartoon of the <scene name='78/780454/Domains/7'>secondary structure colored by domains</scene>.
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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. <scene name='78/780454/Domain3_core/3'>red domain</scene>) 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).
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. <scene name='78/780454/Domain3_core/3'>red domain</scene>) 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).
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<nowiki>
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===Surface charges===
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select protein; cartoon; color gold;
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select 415-600; color red;
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select 157-244; color blue;
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select 244-324, 349-378; color lime;
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select 91-116; color cyan;
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select not helix and not sheet; cartoon 0.3 #makes turns a bit thicker</nowiki>
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-
 
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-
 
+
-
 
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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 <scene name='78/780454/Charges/1'>color the charged side chains</scene>. (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.
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 <scene name='78/780454/Charges/1'>color the charged side chains</scene>. (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.
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<nowiki>select protein; spacefill 100%; color silver;
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===Hydrophobic side chains===
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select (arg, lys, his) AND sidechain; color blue;
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select (arg, lys, his) AND sidechain; color blue;</nowiki>
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To show <scene name='78/780454/Hydrophobic/3'>hydrophobic patches</scene> 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.
To show <scene name='78/780454/Hydrophobic/3'>hydrophobic patches</scene> 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.
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</jmol>
</jmol>
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===Degree of conservation===
To show evolutionary <jmol>
To show evolutionary <jmol>
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</jmolLink>
</jmolLink>
</jmol>, we use data from ConSurf.
</jmol>, we use data from ConSurf.
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<nowiki>
 
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select protein; define ~consurf_to_do selected
 
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consurf_initial_scene = true; script "/wiki/ConSurf/d9/1d9z_consurf.spt"
 
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select protein; isosurface ignore(solvent) sasurface MAP property color</nowiki>
 
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</jmol>
</jmol>
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157-244 blue
 
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415-600 red
 
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349 - 378 lime
 
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244 - 324 lime
 
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91 - 116 cyan
 
</StructureSection>
</StructureSection>

Revision as of 00:03, 30 August 2018

Contents

Introduction

This is a collection of how protein structures are depicted in publications. The most common views show

  • domains
  • conservation
  • charge distribution
  • contact interfaces

Standard and other views

In publications where figures are two dimensional and non-interactive, researchers have to choose a view that shows as much of the interesting features of the protein as possible. Often, when that is not possible, there will be two orthoganal views (e.g. the second rotated by 90 or 180 degrees. The protein used as an example here is the DNA repair enzyme UvrB in complex with ATP (PDB ID 1d9z). This protein not only binds to ATP, but also to DNA and to another DNA repair protein, UvrA. As you look at the various ways protein structures are depicted, you can zoom in to the different binding surfaces or zoom out to the standard view showing the entire protein with the "business" side facing you.


Types of overall views

Caption for this structure

Drag the structure with the mouse to rotate


References

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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