User:James D Watson/Structural Templates: Difference between revisions

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<LI>Gamma Turns - these rarer type of turns are characterised by an (i, i+2) hydrogen bond, which is rather weak because of the bent geometry involved.

</UL>

These secondary structure motifs can be combined to form functional motifs, the most well known of which is the helix-turn-helix motif found in a number of DNA-binding proteins. The computational identification of these motifs is straightforward but made complicated by the fact that not all helix-turn-helix motifs bind DNA. The problem faced here is therefore one involving the distinguishing between true and false positives.

==Templates and Active Sites==

Moving away from large scale secondary structure elements, other structural motifs are more difficult to detect as they are discontinuous and involve elements separated by spacing of various lengths. One such example is that of the "catalytic triad" of the serine proteases.

Serine proteases are found in a number of organisms but common to their function is the hydrolysis of peptide bonds. These enzymes catalyse the reaction using a highly reactive serine residue to attack the carbonyl group of the backbone to be hydrolysed. The chemistry of this reaction and the regeneration of the active site, requires the presence of the Ser-His-Asp catalytic triad. In chymotrypsin these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin the site is formed by (Ser-221, His-64 and Asp-32). These two proteins are evolutionary unrelated and this is the classic example of convergent evolution to solve the problem of peptide bond hydrolysis.

The detection of these types of motif is almost impossible by looking at the amino acid sequence: there is no evolutionary relationship to detect, the residues are ordered differently in the sequence, and the spacing between the residues also varies. These motifs can be detected relativeley easily however if one uses structural comparisons. The subtilisin and chymotrypsin catalytic triads are shown superposed here - note that the global folds of these two proteins are very different so the site could not have been detected that way.

This is the principle that guides template

@@ Line 39: / Line 39: @@
 <LI>Gamma Turns - these rarer type of turns are characterised by an (i, i+2) hydrogen bond, which is rather weak because of the bent geometry involved.
 </UL>
+These secondary structure motifs can be combined to form functional motifs, the most well known of which is the helix-turn-helix motif found in a number of DNA-binding proteins. The computational identification of these motifs is straightforward but made complicated by the fact that not all helix-turn-helix motifs bind DNA. The problem faced here is therefore one involving the distinguishing between true and false positives.
 ==Templates and Active Sites==
+Moving away from large scale secondary structure elements, other structural motifs are more difficult to detect as they are discontinuous and involve elements separated by spacing of various lengths. One such example is that of the "catalytic triad" of the serine proteases.
+Serine proteases are found in a number of organisms but common to their function is the hydrolysis of peptide bonds. These enzymes catalyse the reaction using a highly reactive serine residue to attack the carbonyl group of the backbone to be hydrolysed. The chemistry of this reaction and the regeneration of the active site, requires the presence of the Ser-His-Asp catalytic triad. In chymotrypsin these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin the site is formed by (Ser-221, His-64 and Asp-32). These two proteins are evolutionary unrelated and this is the classic example of convergent evolution to solve the problem of peptide bond hydrolysis.
+The detection of these types of motif is almost impossible by looking at the amino acid sequence: there is no evolutionary relationship to detect, the residues are ordered differently in the sequence, and the spacing between the residues also varies. These motifs can be detected relativeley easily however if one uses structural comparisons. The subtilisin and chymotrypsin catalytic triads are shown superposed here - note that the global folds of these two proteins are very different so the site could not have been detected that way.
+This is the principle that guides template