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

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<LI>Beta Bulge Loops - often associated with beta sheets and result from an additional residue being found in one strand. This interrupts the regular hydrogen bonding and causes a distinctive bulge.

<LI>Alpha turns - the simplest of all motifs and is characterised by one (i, i+4) hydrogen bond. It is found as part of the hydrogen bonding network of alpha helices as well as occurring on its own.

<LI>Paperclip/Schellman Motifs - a common motif found at the C-termini of alpha helices which is essentially a reverse turn that breaks the alpha helix out of its cycle. It is characterised by the presence of a left handed residue and two hydrogen bonds: an i, i+3 bond and an i, i+5 bond.

<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_paperclip/1'>Paperclip/Schellman Motifs</scene> - a common motif found at the C-termini of alpha helices which is essentially a reverse turn that breaks the alpha helix out of its cycle. It is characterised by the presence of a left handed residue and two hydrogen bonds: an i, i+3 bond and an i, i+5 bond.

<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.

==Nests==

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One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The P-loop is a well described ATP- or GTP-binding loop present in a large superfamily of important proteins which includes G-proteins and kinases. The main feature of the P-loop is a long compound LRLR nest that forms a binding site for the β-phosphate of ATP or GTP. However, this is an example of a motif where the ligand also binds to the free main chain NH groups at the N-terminus of an alpha helix. On closer inspection it becomes evident that this interaction is in addition to the compound nest and does not interfere with it. Therefore the P-loop is actually more accurately described as a compound LRLR nest and an adjacent helical N-terminus that collectively bind to the α- and β-phosphates of the GDP substrate. The P-loop, which is retained throughout the superfamily, has a highly conserved GxxxxGKS/T consensus sequence (where the xxGK section forms the LRLR compound nest).

==Templates and Active Sites==

@@ Line 74: / Line 74: @@
 <LI>Beta Bulge Loops - often associated with beta sheets and result from an additional residue being found in one strand. This interrupts the regular hydrogen bonding and causes a distinctive bulge.
 <LI>Alpha turns - the simplest of all motifs and is characterised by one (i, i+4) hydrogen bond. It is found as part of the hydrogen bonding network of alpha helices as well as occurring on its own.
-<LI>Paperclip/Schellman Motifs - a common motif found at the C-termini of alpha helices which is essentially a reverse turn that breaks the alpha helix out of its cycle. It is characterised by the presence of a left handed residue and two hydrogen bonds: an i, i+3 bond and an i, i+5 bond.
+<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_paperclip/1'>Paperclip/Schellman Motifs</scene> - a common motif found at the C-termini of alpha helices which is essentially a reverse turn that breaks the alpha helix out of its cycle. It is characterised by the presence of a left handed residue and two hydrogen bonds: an i, i+3 bond and an i, i+5 bond.
 <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.
+{{Clear}}
 ==Nests==
@@ Line 92: / Line 94: @@
 One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The P-loop is a well described ATP- or GTP-binding loop present in a large superfamily of important proteins which includes G-proteins and kinases. The main feature of the P-loop is a long compound LRLR nest that forms a binding site for the β-phosphate of ATP or GTP. However, this is an example of a motif where the ligand also binds to the free main chain NH groups at the N-terminus of an alpha helix. On closer inspection it becomes evident that this interaction is in addition to the compound nest and does not interfere with it. Therefore the P-loop is actually more accurately described as a compound LRLR nest and an adjacent helical N-terminus that collectively bind to the α- and β-phosphates of the GDP substrate. The P-loop, which is retained throughout the superfamily, has a highly conserved GxxxxGKS/T consensus sequence (where the xxGK section forms the LRLR compound nest).
+{{Clear}}
 ==Templates and Active Sites==