Introduction to Evolutionary Conservation: Difference between revisions
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==Finding Conservation== | ==Finding Conservation== | ||
===Simplistic Analysis of Conservation=== | |||
Evolutionary conservation in proteins is identified by aligning the amino acid sequences of proteins with the same function from different taxa (orthologs). As an example, we'll use the glycolytic enzyme '''enolase''', present in a wide range of taxa. Take a quick look to get an impression of a [[Enolase multiple sequence alignment|multiple sequence alignment for ~400 amino acids in enolase]] for taxa ranging from eubacteria and archaebacteria through yeast, insects, and humans. In the full [[Enolase multiple sequence alignment|multiple sequence alignment]] is one <span style="background:pink;"> segment highlighted in pink </span>. This segment is enlarged below. | Evolutionary conservation in proteins is identified by aligning the amino acid sequences of proteins with the same function from different taxa (orthologs). As an example, we'll use the glycolytic enzyme '''enolase''', present in a wide range of taxa. Take a quick look to get an impression of a [[Enolase multiple sequence alignment|multiple sequence alignment for ~400 amino acids in enolase]] for taxa ranging from eubacteria and archaebacteria through yeast, insects, and humans. In the full [[Enolase multiple sequence alignment|multiple sequence alignment]] is one <span style="background:pink;"> segment highlighted in pink </span>. This segment is enlarged below. | ||
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Finally, there are columns in which at least two of the amino acids are not only different, but also not members of a group of amino acids with similar properties. These are given in lower case, and there is no mark at the bottom of the column. | Finally, there are columns in which at least two of the amino acids are not only different, but also not members of a group of amino acids with similar properties. These are given in lower case, and there is no mark at the bottom of the column. | ||
===Sophisticated Analysis of Conservation: ConSurf=== | |||
The above analysis assigns each amino acid in enolase to one of three categories: conserved, similar, or different. This is very simplistic. In contrast, the analysis used in Proteopedia (and in the above image) is sophisticated, using many more sequences, and weighting each sequence in the multiple sequence alignment according to the phylogenetic tree calculated from the alignment. This sophisticated determination of conservation and variability is done by the [[ConSurfDB vs. ConSurf|ConSurf Servers]] (see also a [[ConSurfDB_vs._ConSurf#The_ConSurf-DB_Mechanism|summary of their mechanism]]. | The above analysis assigns each amino acid in enolase to one of three categories: conserved, similar, or different. This is very simplistic. In contrast, the analysis used in Proteopedia (and in the above image) is sophisticated, using many more sequences, and weighting each sequence in the multiple sequence alignment according to the phylogenetic tree calculated from the alignment. This sophisticated determination of conservation and variability is done by the [[ConSurfDB vs. ConSurf|ConSurf Servers]] (see also a [[ConSurfDB_vs._ConSurf#The_ConSurf-DB_Mechanism|summary of their mechanism]]. | ||
==Notes and References== | ==Notes and References== | ||
<references /> | <references /> | ||
