FirstGlance/Visualizing Conservation
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| - | The initial view utilizes the "ConSurf Control Panel" (labeled ''ConSurf View''). | + | The initial view utilizes the "ConSurf Control Panel" (labeled ''ConSurf View''). One side of the molecule is more conserved than the opposite side. The more conserved face includes the catalytic site, as we shall see. |
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Revision as of 21:08, 2 January 2022
This page is under construction. It is incomplete. Eric Martz 01:22, 1 January 2022 (UTC)
FirstGlance in Jmol is the easiest-to-use tool for visualizing, understanding, and sharing protein molecular structure. It offers guided exploration with extensive explanations and examples, yet provides ample power for advanced users. With a few mouse clicks, any molecular scene can be saved as a slide presentation-ready animation (GIF file) -- see examples below, and tinyurl.com/movingmolecules.
Among many conveniences offered by FirstGlance, it is easy to see the levels of evolutionary conservation determined by ConSurf for amino acids of special interest. Below is an overview with some illustrated examples. Elsewhere you will find instructions for running ConSurf on proteins of interest.
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IMPORTANT (January, 2022): Use the unreleased beta-test version FirstGlance 3.8 Beta2 which has many improvements for ConSurf results beyond the publicly available version 3.7. Some of the features shown below are absent in version 3.7.
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Contents |
Initial View of Conservation
Initially, FirstGlance colors each amino acid in the protein chain processed by ConSurf according to its level of conservation. This gives you an overview, enabling you to see patches of highly conserved residues (functional sites).
Multiple Chains
If the model has more than one copy of the chain processed by ConSurf, you can apply conservation colors to all of those sequence-identical chains. Here, for example, is a potassium channel homotetramer:
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Optimization
Before going further, it is good to decide whether the results are satisfactory, or need optimization. Lets consider 7bak, a drug-target protease of SARS-CoV-2. A ConSurf run with all default settings left 10% of the residues with insufficient data[1] (yellow color), and the diversity in the multiple sequence alignment (MSA) was too low (average pairwise distance 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance.
To improve the results, a new ConSurf job for 7bak was submitted, increasing the HMMER search iterations from 1 to 2, and increasing the maximum number of sequences in the MSA from 150 to 300. The results were satisfactory, although the APD of 0.77 was still perhaps a bit low.
Change Control Panels
The initial view utilizes the "ConSurf Control Panel" (labeled ConSurf View). One side of the molecule is more conserved than the opposite side. The more conserved face includes the catalytic site, as we shall see.
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Conservation of Salt Bridges
In the Tools tab is Salt Bridges/Cation-Pi... This shows all the salt bridges in the model where Negative (Asp, Glu) charges are within 4.0 Å of Positive (Arg, Lys) charges.
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Conservation of Protein Crosslinks
Conservation of Specified Residues
See Also
References
- ↑ When the confidence interval for a conservation value of an amino acid is too large, ConSurf reports "insufficient data" (uncertainty: yellow color). See Position Specific Quality and Confidence Interval in the ConSurf documentation.
