Conservation, Evolutionary: Difference between revisions
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Eric Martz (talk | contribs) →Locating Variable Patches: added a new section with example on this page |
Eric Martz (talk | contribs) explained the ConSurf process |
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Patches of highly conserved residues on the surface of a protein molecular structure are good candidates for [[Site | functional sites]]. These can be readily identified and visualized automatically with the [http://consurf.tau.ac.il ConSurf Server], provided a sufficient number of related protein sequences are in the Uniprot database. Before submitting a custom job request to the [http://consurf.tau.ac.il ConSurf Server], check out your [[PDB code]] at [http://consurfdb.tau.ac.il ConSurfDB], a database of precalculated conservation levels for most chains in the [[Protein Data Bank]]. | Patches of highly conserved residues on the surface of a protein molecular structure are good candidates for [[Site | functional sites]]. These can be readily identified and visualized automatically with the [http://consurf.tau.ac.il ConSurf Server], provided a sufficient number of related protein sequences are in the Uniprot database. Before submitting a custom job request to the [http://consurf.tau.ac.il ConSurf Server], check out your [[PDB code]] at [http://consurfdb.tau.ac.il ConSurfDB], a database of precalculated conservation levels for most chains in the [[Protein Data Bank]]. | ||
==The ConSurf Server== | |||
In brief, the [http://consurf.tau.ac.il ConSurf Server] can do the following automatically: | |||
# Obtains the protein sequence for the specified PDB code and chain. | |||
# Gathers closely related sequences from Swiss-Prot (or Uniprot) with a PSI-BLAST search. | |||
# Does a multiple sequence alignment. | |||
# Constructs a phylogenetic tree. | |||
# Calculates a conservation score for each amino acid. | |||
# Displays the protein in interactive 3D, using [[FirstGlance in Jmol]], [[Chimera]], [[PyMOL]], or [[Protein Explorer]]. | |||
The [http://consurf.tau.ac.il ConSurf Server] can calculate and display the conservation pattern for 3D structures '''completely automatically'''. It uses state-of-the-art methods, all of which are published in peer-reviewed journal articles. It also permits considerable customization. For example, the user may submit their own multiple sequence alignment, or phylogenetic tree. I<ref>[[User:Eric Martz]] in January, 2009.</ref> know of no other server with these advantages. | |||
==Locating Variable Patches== | ==Locating Variable Patches== | ||
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<applet load='2vaa' size='400' frame='true' align='right' caption='Evolutionary conservation reported by ConSurfDB for Major Histocompatibility Class I alpha chain in [[2vaa]].'/> | <applet load='2vaa' size='400' frame='true' align='right' caption='Evolutionary conservation reported by ConSurfDB for Major Histocompatibility Class I alpha chain in [[2vaa]].'/> | ||
At right is the pattern of evolutionary conservation and variability reported by [http://consurfdb.tau.ac.il ConSurfDB] for the alpha chain of [[Major Histocompatibility Complex Class I]] (chain A of [[2vaa]]). Below are instructions for how to insert a ConSurf result into a Proteopedia scene. | At right is the pattern of evolutionary conservation and variability reported by [http://consurfdb.tau.ac.il ConSurfDB] for the alpha chain of [[Major Histocompatibility Complex Class I]] (chain A of [[2vaa]]). Below are instructions for how to insert a ConSurf result into a Proteopedia scene. | ||
Examples of conserved patches revealed by ConSurf will be found in the articles on | |||
*[[Lac repressor]] | |||
*[[Avian Influenza Neuraminidase, Tamiflu and Relenza]] | |||
==Conservation for Domain Folding== | ==Conservation for Domain Folding== | ||
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Every structure in ''Proteopedia'' has a link to be displayed in [http://firstglance.jmol.org FirstGlance in Jmol]. There, you can use the ''Find'' dialog to enter the name of an amino acid, e.g. ''glycine'' or ''proline'', and the positions of all of the specified amino acids will be highlighted. You can then visualize their distribution in the 3D structure. | Every structure in ''Proteopedia'' has a link to be displayed in [http://firstglance.jmol.org FirstGlance in Jmol]. There, you can use the ''Find'' dialog to enter the name of an amino acid, e.g. ''glycine'' or ''proline'', and the positions of all of the specified amino acids will be highlighted. You can then visualize their distribution in the 3D structure. | ||
==Notes== | |||
<references /> | |||
