Introduction to Evolutionary Conservation: Difference between revisions
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==Expected vs. Unexpected Conservation== | ==Expected vs. Unexpected Conservation== | ||
Conservation is '''expected''' for those amino acids that support the 3D structure and functions of a protein. Common examples are listed in the table below. When there is no known structural or functional explanation for conservation of an amino acid, or a cluster of amino acids, | Conservation is '''expected''' for those amino acids that support the 3D structure and functions of a protein. Common examples are listed in the table below. When there is no known structural or functional explanation for conservation of an amino acid, or a cluster of amino acids, the conservation is '''unexpected'''. Unexpected conservation may provide clues for discovering new functions or structural features, e.g. through functional analysis of mutants. | ||
<table class="wikitable"><tr> | <table class="wikitable"><tr> | ||
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Charged amino acid (Lys, Arg, Asp, Glu) in a salt bridge | Charged amino acid (Lys, Arg, Asp, Glu) in a salt bridge | ||
</td><td> | </td><td> | ||
Required for protein stability | Required for [[Salt bridges|protein stability]] | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
Cys in a disulfide bond | Cys in a disulfide bond | ||
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Required for protein function, e.g. catalytic or binding site | Required for protein function, e.g. catalytic or binding site | ||
</td></tr></table> | </td></tr></table> | ||
[http://FirstGlance.Jmol.Org FirstGlance in Jmol] makes it easy to locate turns, salt bridges, disulfide bonds, or the N-teminus. In FirstGlance: | |||
* Touch the conserved residue of interest to get its name and sequence number, e.g. Gly236 (in enolase 4enl). | |||
* Use ''Find'' to put yellow halos around the residue of interest, e.g. enter ''Gly236'' in the ''Find'' slot. | |||
** Turns: Views tab, Secondary Structure. | |||
** Salt bridges: Tools tab, Salt Bridges. | |||
** Disulfide bonds: Tools tab, Disulfide Bonds. | |||
** N terminus: Views tab, N->C Rainbow. You may also wish to check ''Sequence Numbers'' and/or ''Residue Names'' near the bottom of the control panel (upper left panel). | |||
{{Clear}} | {{Clear}} | ||
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*[[Evolutionary Conservation]] | *[[Evolutionary Conservation]] | ||
*[[ConSurfDB_vs._ConSurf]] | *[[ConSurfDB_vs._ConSurf]] | ||
*[[ConSurf/Index]]: links to all Proteopedia pages about ConSurf and evolutionary conservation. | |||
==Notes and References== | ==Notes and References== | ||
