Conservation, Evolutionary: Difference between revisions
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==Locating Conserved Patches== | ==Locating Conserved Patches== | ||
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]]. | ||
==Locating Variable Patches== | |||
In some cases, patches of highly variable (rapidly mutating) residues are also functional sites. These can also be identified with the [http://consurf.tau.ac.il ConSurf Server]. For example, mutations in influenza hemagglutinin help the virus to evade host defenses. Another example is the high allelic variability of the peptide-binding groove of [[Major Histocompatibility Complex Class I]]. That variability helps the grooves of the alleles within any individual to bind a wide range of peptides, hence enabling the T lymphocyte system to defend against a wide range of pathogens, including influenza virus. | |||
==Caveat== | ==Caveat== | ||
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# Calculates a conservation score for each amino acid. | # Calculates a conservation score for each amino acid. | ||
# Displays the protein, colored by conservation, in interactive 3D, using [[FirstGlance in Jmol]], [[Chimera]], [[PyMOL]], or [[Protein Explorer]]. | # Displays the protein, colored by conservation, in interactive 3D, using [[FirstGlance in Jmol]], [[Chimera]], [[PyMOL]], or [[Protein Explorer]]. | ||
==Examples== | ==Examples== | ||
