FirstGlance/Visualizing Conservation: Difference between revisions
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[[FirstGlance/Index|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 | [[FirstGlance/Index|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 an '''animation (GIF file) ready to drop into a Powerpoint Slide''' -- see examples below, and [http://tinyurl.com/movingmolecules tinyurl.com/movingmolecules]. | ||
Among many conveniences offered by FirstGlance, it is easy to see the levels of [[ConSurf/Index|evolutionary conservation determined by ConSurf]] for '''amino acids of special interest'''. Below is an overview with some illustrated examples. | Among many conveniences offered by FirstGlance, it is easy to see the levels of [[ConSurf/Index|evolutionary conservation determined by the ConSurf Server]] for '''amino acids of special interest'''. Below is an overview with some illustrated examples. Here are [[ConSurf/Index|instructions for running the ConSurf Server]] on proteins of interest. ''Note that you '''cannot''' use FirstGlance to visualize results from the ConSurf Database, ConSurfDB. Unfortunately, the interface to FirstGlance was removed from ConSurfDB PDB files in 2022.'' | ||
There are 2 ways to analyzie your own ConSurf Server results in FirstGlance: | |||
:1. At the ConSurf Server results page, open ''High Resolution Figures and PDB Files'', and then click ''Download ConSurf PDB File for FirstGlance in Jmol''. Now, you can [http://firstglance.jmol.org/where.htm#u upload the downloaded file to FirstGlance]. By downloading the PDB file, you will have it after the results '''disappear''' from the ConSurf Server. | |||
:2. At the ConSurf results page, '''Right''' click the link ''Download ConSurf PDB File for FirstGlance in Jmol'', and select '''Copy Link'''. Then, at FirstGlance, click [http://firstglance.jmol.org/where.htm#u enter a molecule's URL], paste the address into the slot, and click Submit. | |||
==Initial View of Conservation== | ==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). | 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). | ||
===Biological Unit 1 Shown Initially=== | |||
FirstGlance automatically constructs and displays [[Biological Unit]] 1 (believed to be the major functional quaternary assembly) in its initial view. If the protein chain processed by ConSurf is duplicated, you | |||
will have the option of applying conservation colors to all chains that are identical in sequence with | |||
the ConSurf-processed chain (see snapshot in next section). | |||
To find out whether any other biological units that are specified, and to display each, or to display the [[asymmetric unit]], you will need to go to the FirstGlance Control Panel: see [[#Go_To_The_FirstGlance_Control_Panel|instructions below]]. | |||
===Multiple Chains=== | ===Multiple Chains=== | ||
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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 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]). | 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 (see [https://pdb101.rcsb.org/motm/242 Coronavirus Proteases]). | ||
:[ | :[http://firstglance.jmol.org/fg.htm?mol=7bak_consurf1641000454_pipe.pdb Display 7BAK ConSurf Result in FirstGlance] | ||
A ConSurf run with all default settings left 10% of the residues with insufficient data<ref name="insufficientdata">When the confidence interval for a conservation value of an amino acid is too large, ConSurf reports "insufficient data" (uncertainty: yellow color). See [https://consurf.tau.ac.il/quick_help.php#RELIABILITY Position Specific Quality] and [https://consurf.tau.ac.il/overview.php#_Toc311131298 Confidence Interval] in the ConSurf documentation.</ref> (yellow color), and the diversity in the multiple sequence alignment (MSA) was too low ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance. | A ConSurf run with all default settings left 10% of the residues with insufficient data<ref name="insufficientdata">When the confidence interval for a conservation value of an amino acid is too large, ConSurf reports "insufficient data" (uncertainty: yellow color). See [https://consurf.tau.ac.il/quick_help.php#RELIABILITY Position Specific Quality] and [https://consurf.tau.ac.il/overview.php#_Toc311131298 Confidence Interval] in the ConSurf documentation.</ref> (yellow color), and the diversity in the multiple sequence alignment (MSA) was too low ([[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] 0.34), leaving conservation grades 2 and 3 almost unoccupied. These inadequacies are highlighted by a distribution report displayed by FirstGlance. | ||
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[[Image:7bak-consurf.gif]] | [[Image:7bak-consurf.gif]] | ||
</td></tr></table> | </td></tr></table> | ||
===Animations for Slides=== | |||
It is very easy to save any molecular view in FirstGlance as a GIF animation, ready to drop into a slide in Powerpoint (or other presentation software): [http://firstglance.jmol.org/slides.htm Instructions]. The animation above is one example. More examples: [http://tinyurl.com/movingmolecules tinyurl.com/MovingMolecules]. | |||
==Go To The FirstGlance Control Panel== | ==Go To The FirstGlance Control Panel== | ||
<table><tr><td valign="top"> | |||
To further explore the pattern of conservation, we need to change from the ''ConSurf View'' to the ''FirstGlance Control Panel''. Click the link indicated by the red arrow in the above snapshot. | To further explore the pattern of conservation, we need to change from the ''ConSurf View'' to the ''FirstGlance Control Panel''. Click the link indicated by the red arrow in the above snapshot. | ||
The ''FirstGlance Control Panel'' has 5 tabs. The ''Molecule Information Tab'' and the ''Views'' tab provide a wealth of information | The ''FirstGlance Control Panel'' has 5 tabs (see snapshot at right). The ''Molecule Information Tab'' and the ''Views'' tab each provide a wealth of information. | ||
Notice that you can move freely back and forth between the ''ConSurf Controls'' and the ''FirstGlance Controls'' using the link '''ConSurf Controls''' in the middle of the left side of FirstGlance. | |||
===Biological Units=== | |||
Note the link ''Showing Biological Unit 1'' in the ''Molecule Information Tab''. Clicking this will show a report in the lower left panel of FirstGlance listing any other biological units that are specified. Links are provided to display any of these, or the asymmetric unit, in a separate section. | |||
Example: Bacterial gas vesicle [[7r1c]].<br> | |||
[http://firstglance.jmol.org/fg.htm?mol=7r1c_N_consurf_APD0.59.pdb Display ConSurf-Processed 7r1c in FirstGlance]. | |||
</td><td> | |||
[[Image:7r1c-consurf-fg-biounits.png]] | |||
</td></tr></table> | |||
==Conservation of Salt Bridges== | ==Conservation of Salt Bridges== | ||
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===Color by Conservation=== | ===Color by Conservation=== | ||
To see how well the salt-bridged residues are conserved, click the checkbox ''ConSurf Colors'' (red arrow below). Declutter the view by unchecking ''Show Backbones'' (green arrow below). | To see how well the salt-bridged residues are conserved, click the checkbox ''ConSurf Colors'' (red arrow below). Declutter the view by unchecking ''Show Backbones'' (green arrow below). Scroll down in the lower left panel and click {{Yelspan|List All}} to get a spreadsheet-ready list that includes conservation values for each pair of salt-bridged atoms. | ||
<br> | <br> | ||
<table class="wikitable"><tr><td> | <table class="wikitable"><tr><td> | ||
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FirstGlance provides an easy and powerful tool to explore residues contacting any specified portion of the model. For this example, we'll use [[acetylcholinesterase]] complexed to the [https://en.wikipedia.org/wiki/VX_(nerve_agent) inhibitor VX], crystal structure [[6cqz]]. | FirstGlance provides an easy and powerful tool to explore residues contacting any specified portion of the model. For this example, we'll use [[acetylcholinesterase]] complexed to the [https://en.wikipedia.org/wiki/VX_(nerve_agent) inhibitor VX], crystal structure [[6cqz]]. | ||
:[ | :[http://firstglance.jmol.org/fg.htm?mol=6cqz_consurf1641072297_pipe.pdb Display 6CQZ ConSurf Result in FirstGlance] | ||
We'll look at the conservation of the residues that contact the ligand/inhibitor VX. From the ''ConSurf View'', go to the FirstGlance Control Panel. | We'll look at the conservation of the residues that contact the ligand/inhibitor VX. From the ''ConSurf View'', go to the FirstGlance Control Panel. | ||
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and Astrid Walrant. ''Crystals'', 2021, '''11'''(9), 1032; [https://doi.org/10.3390/cryst11091032 doi.org/10.3390/cryst11091032].</ref>. Let's see which Trps are conserved in the potassium channel [[1bl8]] (a [[Nobel_Prizes_for_3D_Molecular_Structure#2000-2009|Nobel Prize-winning structure]]!). | and Astrid Walrant. ''Crystals'', 2021, '''11'''(9), 1032; [https://doi.org/10.3390/cryst11091032 doi.org/10.3390/cryst11091032].</ref>. Let's see which Trps are conserved in the potassium channel [[1bl8]] (a [[Nobel_Prizes_for_3D_Molecular_Structure#2000-2009|Nobel Prize-winning structure]]!). | ||
:[ | :[http://firstglance.jmol.org/fg.htm?mol=1bl8_consurf1640894833_pipe.pdb Display 1BL8 ConSurf Result FirstGlance] | ||
<table class="wikitable"><tr><td colspan=3><center> | <table class="wikitable"><tr><td colspan=3><center> | ||
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An example is isopeptide bond-linked chains of ubiquitin. [[7cap]] is an isopeptide-linked trimer of ubiquitin. The carboxy-terminal Gly76 forms an isopeptide bond with Lys48. Here is one ConSurf result (300 sequences in the multiple sequence alignment (MSA), sampled from 10,122 unique similar sequences. The MSA had an [[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] of 1.15): | An example is isopeptide bond-linked chains of ubiquitin. [[7cap]] is an isopeptide-linked trimer of ubiquitin. The carboxy-terminal Gly76 forms an isopeptide bond with Lys48. Here is one ConSurf result (300 sequences in the multiple sequence alignment (MSA), sampled from 10,122 unique similar sequences. The MSA had an [[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] of 1.15): | ||
:[http:// | :[http://firstglance.jmol.org/fg.htm?mol=7cap_consurf1639680092_pipe.pdb 7CAP Conservation in FirstGlance] | ||
First, follow the [[FirstGlance/Evaluating_Protein_Crosslinks#Instructions_for_an_Isopeptide_Bond|instructions for getting a list of the isopeptide crosslinks]]. | First, follow the [[FirstGlance/Evaluating_Protein_Crosslinks#Instructions_for_an_Isopeptide_Bond|instructions for getting a list of the isopeptide crosslinks]]. | ||