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

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There are a number of small hydrogen bonded motifs and patterns which are observed regularly. These are described below:<UL>

<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betaturn/1'>Beta Turns</scene> - originally defined by the one hydrogen bond common to all (an i, i+3 hydrogen bond) but some modern descriptions do not require a hydrogen bond.

<LI>'''<scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betaturn/1'>Beta Turns</scene>''' - originally defined by the one hydrogen bond common to all (an i, i+3 hydrogen bond) but some modern descriptions do not require a hydrogen bond.

<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>'''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>'''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><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>'''<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.

<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>

<br>

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.

<br>

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. The structure to the right is that of lambda repressor bound to DNA. The helix-turn-helix motif is readily identified in green.

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 <applet load='5p21' size='350' frame='true' align='left' caption='Secondary structure - Alpha' scene='User:James_D_Watson/Structural_Templates/Secondary_structure_start/3'/>
 There are a number of small hydrogen bonded motifs and patterns which are observed regularly. These are described below:<UL>
-<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betaturn/1'>Beta Turns</scene> - originally defined by the one hydrogen bond common to all (an i, i+3 hydrogen bond) but some modern descriptions do not require a hydrogen bond.
+<LI>'''<scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betaturn/1'>Beta Turns</scene>''' - originally defined by the one hydrogen bond common to all (an i, i+3 hydrogen bond) but some modern descriptions do not require a hydrogen bond.
-<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>'''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>'''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><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>'''<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.
+<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>
+<br>
-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.
+<br>
+<br>
+{{Clear}}
+<applet load='1lmb' size='300' frame='true' align='right' caption='Lambda repressor' scene='User:James_D_Watson/Structural_Templates/Helix_t_helix/1'/>
+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. The structure to the right is that of lambda repressor bound to DNA. The helix-turn-helix motif is readily identified in green.
 {{Clear}}