Introduction to Evolutionary Conservation: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, journal, Administrators
30,118 edits
No edit summary
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, journal, Administrators
30,118 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 104: Line 104:
<center>{{Template:ColorKey_ConSurf_NoGray}}</center>
<center>{{Template:ColorKey_ConSurf_NoGray}}</center>


====Sequence Colored by Conservation====
When ConSurf's colors are applied to the 436 amino acids in the sequence of enolase (based on a multiple sequence alignment containing 150 sequences), this is the result:
When ConSurf's colors are applied to the 436 amino acids in the sequence of enolase (based on a multiple sequence alignment containing 150 sequences), this is the result:
[[Image:4enl consurf150 sequence wb.jpg|400 px|left]]
[[Image:4enl consurf150 sequence wb.jpg|400 px|left]]
{{Clear}}
{{Clear}}
Notice that the conserved residues are scattered around the sequence with no obvious pattern. However, when the same <scene name='Introduction_to_Evolutionary_Conservation/Enolase_with_consurf_colors/1'>colors are applied to the amino acids in the 3D structure</scene>, they form a conserved patch around the catalytic site (marked with a <span style="background:black; color:#00ff00;">'''&nbsp;zinc ion colored green&nbsp;'''</span>.
Notice that the conserved residues are scattered around the sequence with no obvious pattern.
 
====3D Structure Colored by Conservation====
However, when the same <scene name='Introduction_to_Evolutionary_Conservation/Enolase_with_consurf_colors/1'>colors are applied to the amino acids in the 3D structure</scene>, they form a conserved patch around the catalytic site (marked with a <span style="background:black; color:#00ff00;">'''&nbsp;zinc ion colored green&nbsp;'''</span>.
*Show  [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/firstglance/fgij/localPDBFiles/4ENLA_ConSurf_DB_pipe.pdb.gz conservation of enolase in FirstGlance in Jmol] ([[4enl]]).
*Show  [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/firstglance/fgij/localPDBFiles/4ENLA_ConSurf_DB_pipe.pdb.gz conservation of enolase in FirstGlance in Jmol] ([[4enl]]).


Line 113: Line 117:


For instructions on how to identify conserved regions of a molecule of interest, and how to show them in Proteopedia (for example with green links), please see [[How to see conserved regions]].
For instructions on how to identify conserved regions of a molecule of interest, and how to show them in Proteopedia (for example with green links), please see [[How to see conserved regions]].
==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, 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>
<th colspan="2"><center>
Expected Evolutionary Conservation
</center>
</th></tr><tr><th>
Amino Acids
</th><th>
Reason for Conservation
</th></tr><tr><td>
Gly, Pro in turns between helices or beta strands
</td><td>
Required for [[Evolutionary_Conservation#Conservation_for_Domain_Folding|protein domain folding]]
</td></tr><tr><td>
Charged amino acid (Lys, Arg, Asp, Glu) in a salt bridge
</td><td>
Required for [[Salt bridges|protein stability]]
</td></tr><tr><td>
Cys in a disulfide bond
</td><td>
Required for protein stability
</td></tr><tr><td>
N-terminal Met
</td><td>
Start codon for protein synthesis
</td></tr><tr><td>
Amino acids in a large cluster of highly-conserved residues
</td><td>
Required for protein function, e.g. catalytic or binding site
</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}}
Line 121: Line 166:
*[[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==
Retrieved from "https://proteopedia.org/Introduction_to_Evolutionary_Conservation"