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

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The example structure shown to <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_highlight/1'>illustrate the motif</scene> is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_histidine/1'>histidine</scene> residues form ligands to a <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_recognition/1'>recogniton helices</scene> to bind to the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.

The example structure shown to <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_highlight/1'>illustrate the motif</scene> is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_histidine/2'>histidine</scene> residues form ligands to a <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_recognition/1'>recogniton helices</scene> to bind to the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.

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===α-helices===

In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). The α-helix is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The sidechains point outward, away from the centre of the helix, where they can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the carbonyl group of residue i ~~hydrogen~~ interacting with the amide group of residue i+4, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 310-helices and their left handed forms (see table 1 for the helix parameters).

In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alphahelix/1'>α-helix</scene> is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_sc/1'>sidechains point outward</scene>, away from the centre of the helix, where they can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_hbon/1'>carbonyl group of residue i interacting with the amide group of residue i+4</scene>, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 310-helices and their left handed forms (see table 1 for the helix parameters).

Table 1:

Table 1:

<tr>

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</tr>

<tr>

<td>3.10 helix</td>

<td>310-helix</td>

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===β-sheets===

A single beta-strand can be described as a flat helix with 2 residues per turn although this may not be initially obvious. When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a β-sheet. As the backbones need to come close together to interact and form a sheet, the sidechains are oriented away from the plane of the sheet. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in cartoon ~~form~~ as an arrowhead on beta ~~strands~~). β-sheets therefore occur in two varieties:<OL>

In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). A single <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta/1'>beta-strand</scene> can technically be described as a flat helix with 2 residues per turn although this may not be initially obvious.

<LI>Anti-parallel - here the beta strands aligned next to each other run in opposite directions. As the interacting carbonyls and amides align well, the hydrogen bonds appear to be straight.

When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betasheet/1'>β-sheet</scene>. As the backbones need to come close together to interact and form a sheet, the <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_sc/1'>sidechains are oriented away from the plane of the sheet</scene>. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in the cartoon format as an arrowhead on each beta strand). β-sheets therefore occur in two varieties:<OL>

<LI>Parallel - here the interacting strands run alongside each other and point in the same direction. In this conformation the carbonyl oxygen and the amides tend to be more staggered than in an anti-parallel sheet, therefore the hydrogen bonds tend to be angled.

<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_ap/1'>Anti-parallel</scene> - here the beta strands aligned next to each other run in opposite directions. As the interacting carbonyls and amides align well, the hydrogen bonds appear to be straight.

<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_para/1'>Parallel</scene> - here the interacting strands run alongside each other and point in the same direction. In this conformation the carbonyl oxygen and the amides tend to be more staggered than in an anti-parallel sheet, therefore the hydrogen bonds tend to be angled. Also note the rare (i, i+2) bond within the lower strand.

</OL>

===Turns and loops===

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

<LI>Beta Turns - 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>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.

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

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==

Smaller than loops and turns are some recently discovered motifs known as "nests". These are mainchain conformations where 3 successive amide groups form a positively charged concavity capable of binding one or more negatively charged atoms (Figure 1). They are characterised by alternating enantiomeric mainchain dihedral angles from the alpha and gamma regions of the Ramachandran plot, and can be of RL (right handed - left handed) or LR type. They are most commonly found as part of previously described hydrogen bonded structural motifs but are also found at functional sites.

Smaller than loops and turns are some recently discovered motifs known as "nests". These are mainchain conformations where 3 successive amide groups form a positively charged concavity capable of binding one or more negatively charged atoms (Figure 1). They are characterised by alternating enantiomeric mainchain dihedral angles from the alpha and gamma regions of the Ramachandran plot, and can be of RL (right handed - left handed) or LR type. They are most commonly found as part of previously described hydrogen bonded structural motifs but are also found at functional sites.

[[Image:Nest 1np4.gif]]

These basic units can be combined in succession to form more complex motifs and come in two categories:<OL>

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In compound nests the result is a long chain with all the overlapping nests facing a similar direction. This basically forms a much wider nest that is capable of binding a larger anionic group of atoms such as the phosphate ion, and are usually functionally important motifs. Tandem nests are not as common and, due to the greater change in the direction that adjacent nests face, only seem to perform functional roles when found in conjunction with one or more compound nests.

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).

One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop/1'>P-loop</scene> 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 <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop_nest/1'>forms a binding site for the β-phosphate of ATP or GTP</scene>. 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==

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Moving away from secondary structure elements, loop and nests, another type of structural motif is that of enzyme active sites. These structural motifs are usually more difficult to detect as they can be discontinuous, often involving elements widely spaced along the sequence. 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.

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 (PDB entry [[1ab9]]) these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin (PDB entry [[1st2]]) 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 using structural comparison, particularly the template-based motif detection algorithms (some of which are listed in table 2 below). 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 using such methods.

~~==QUESTIONS==~~

The following interactive question(s) require you to interact with the structure to arrive at the correct answer. You may use any of the visualization controls or the dropdown menus to help you to answer the questions - direct manipulation of the structure may be required.

~~Question 1- Load structure~~

The α helix and β sheets we've been looking at are parts of the ribosomal protein L9. It is composed of two globular domains with a very long α-helix between them. Given this image of L9 in spacefill, colored by element, use the Jmol menu to change the display to so that you can clearly see both (1) the pattern of the protein chain and (2) the default colors for secondary structure.

~~<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />~~

~~View Answer~~

~~Question 2 - Load structure~~

~~Explore the Jmol menu to find commands relating to hydrogen bonds. Given this display of the backbone of ribosomal L9, display the hydrogen bonds that stabilize secondary structres.~~

~~View Answer~~

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 using structural comparison, particularly template-based motif detection algorithms. The subtilisin and chymotrypsin structures are shown side by side - note that the global folds of these two proteins are very different so the site could not have been detected using such methods. Click to see the catalytic triad in <scene name='User:James_D_Watson/Structural_Templates/Subtilisin_startpoint_catalyti/1' target='subtilisin'>subtilisin</scene> and <scene name='User:James_D_Watson/Structural_Templates/Chymotrypsin_start_triad/1' target='chymotrypsin'>chymotrypsin</scene> respectively.

@@ Line 13: / Line 13: @@
-The example structure shown to <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_highlight/1'>illustrate the motif</scene> is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_histidine/1'>histidine</scene> residues form ligands to a <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_recognition/1'>recogniton helices</scene> to bind to the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.
+The example structure shown to <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_highlight/1'>illustrate the motif</scene> is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_histidine/2'>histidine</scene> residues form ligands to a <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_recognition/1'>recogniton helices</scene> to bind to the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.
 {{Clear}}
@@ Line 24: / Line 24: @@
 ===α-helices===
 <applet load='5p21' size='350' frame='true' align='right' caption='Secondary structure - Alpha' scene='User:James_D_Watson/Structural_Templates/Secondary_structure_start/1'/>
-In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). The α-helix is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The sidechains point outward, away from the centre of the helix, where they can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the carbonyl group of residue i hydrogen interacting with the amide group of residue i+4, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 3<sub>10</sub>-helices and their left handed forms (see table 1 for the helix parameters).</br>
+In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alphahelix/1'>α-helix</scene> is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_sc/1'>sidechains point outward</scene>, away from the centre of the helix, where they can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_hbon/1'>carbonyl group of residue i interacting with the amide group of residue i+4</scene>, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 3<sub>10</sub>-helices and their left handed forms (see table 1 for the helix parameters).<br>
-</br>
+<br>
-Table 1:</br>
+Table 1:<br>
 <table border=1>
 <tr>
@@ Line 36: / Line 36: @@
 </tr>
 <tr>
-<td>3.10 helix</td>
+<td>3<sub>10</sub>-helix</td>
 <td>(i, i+3)</td>
 <td>3.0</td>
@@ Line 60: / Line 60: @@
 ===β-sheets===
-<applet load='1vkp' size='350' frame='true' align='right' caption='Secondary structure - Beta'/>
+<applet load='5p21' size='350' frame='true' align='right' caption='Secondary structure - Alpha' scene='User:James_D_Watson/Structural_Templates/Secondary_structure_start/2'/>
-A single beta-strand can be described as a flat helix with 2 residues per turn although this may not be initially obvious. When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a β-sheet. As the backbones need to come close together to interact and form a sheet, the sidechains are oriented away from the plane of the sheet. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in cartoon form as an arrowhead on beta strands). β-sheets therefore occur in two varieties:<OL>
+In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). A single <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta/1'>beta-strand</scene> can technically be described as a flat helix with 2 residues per turn although this may not be initially obvious. <br>
-<LI>Anti-parallel - here the beta strands aligned next to each other run in opposite directions. As the interacting carbonyls and amides align well, the hydrogen bonds appear to be straight.
+When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betasheet/1'>β-sheet</scene>. As the backbones need to come close together to interact and form a sheet, the <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_sc/1'>sidechains are oriented away from the plane of the sheet</scene>. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in the cartoon format as an arrowhead on each beta strand). β-sheets therefore occur in two varieties:<OL>
-<LI>Parallel - here the interacting strands run alongside each other and point in the same direction. In this conformation the carbonyl oxygen and the amides tend to be more staggered than in an anti-parallel sheet, therefore the hydrogen bonds tend to be angled.
+<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_ap/1'>Anti-parallel</scene> - here the beta strands aligned next to each other run in opposite directions. As the interacting carbonyls and amides align well, the hydrogen bonds appear to be straight.
+<LI><scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_para/1'>Parallel</scene> - here the interacting strands run alongside each other and point in the same direction. In this conformation the carbonyl oxygen and the amides tend to be more staggered than in an anti-parallel sheet, therefore the hydrogen bonds tend to be angled. Also note the rare (i, i+2) bond within the lower strand.
 </OL>
 {{Clear}}
 ===Turns and loops===
+<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>Beta Turns - 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>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.
+<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>
+<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.
-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==
+Smaller than loops and turns are some recently discovered motifs known as "nests". These are mainchain conformations where 3 successive amide groups form a positively charged concavity capable of binding one or more negatively charged atoms (Figure 1). They are characterised by alternating enantiomeric mainchain dihedral angles from the alpha and gamma regions of the Ramachandran plot, and can be of RL (right handed - left handed) or LR type. They are most commonly found as part of previously described hydrogen bonded structural motifs but are also found at functional sites.<br>
-Smaller than loops and turns are some recently discovered motifs known as "nests". These are mainchain conformations where 3 successive amide groups form a positively charged concavity capable of binding one or more negatively charged atoms (Figure 1). They are characterised by alternating enantiomeric mainchain dihedral angles from the alpha and gamma regions of the Ramachandran plot, and can be of RL (right handed - left handed) or LR type. They are most commonly found as part of previously described hydrogen bonded structural motifs but are also found at functional sites.
+<br>
+[[Image:Nest 1np4.gif]]
 These basic units can be combined in succession to form more complex motifs and come in two categories:<OL>
@@ Line 89: / Line 98: @@
 In compound nests the result is a long chain with all the overlapping nests facing a similar direction.  This basically forms a much wider nest that is capable of binding a larger anionic group of atoms such as the phosphate ion, and are usually functionally important motifs. Tandem nests are not as common and, due to the greater change in the direction that adjacent nests face, only seem to perform functional roles when found in conjunction with one or more compound nests.
-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).
+<applet load='1lmb' size='300' frame='true' align='left' caption='Nest in PDB entry 5p21' scene='User:James_D_Watson/Structural_Templates/Secondary_structure_start/4'/>
+One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop/1'>P-loop</scene> 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 <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop_nest/1'>forms a binding site for the β-phosphate of ATP or GTP</scene>. 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==
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 Moving away from secondary structure elements, loop and nests, another type of structural motif is that of enzyme active sites. These structural motifs are usually more difficult to detect as they can be discontinuous, often involving elements widely spaced along the sequence. 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.
+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 (PDB entry [[1ab9]]) these residues are (Ser-195, His-57 and Asp-102) whereas in the bacterial subtilisin (PDB entry [[1st2]]) 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 using structural comparison, particularly the template-based motif detection algorithms (some of which are listed in table 2 below). 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 using such methods.
-==QUESTIONS==
-The following interactive question(s) require you to interact with the structure to arrive at the correct answer. You may use any of the visualization controls or the dropdown menus to help you to answer the questions - direct manipulation of the structure may be required.
-Question 1- Load structure
-The α helix and β sheets we've been looking at are parts of the ribosomal protein L9. It is composed of two globular domains with a very long α-helix between them. Given this image of L9 in spacefill, colored by element, use the Jmol menu to change the display to so that you can clearly see both (1) the pattern of the protein chain and (2) the default colors for secondary structure.
-<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />
-View Answer
-Question 2 - Load structure
-Explore the Jmol menu to find commands relating to hydrogen bonds. Given this display of the backbone of ribosomal L9, display the hydrogen bonds that stabilize secondary structres.
-View Answer
-<applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />
+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 using structural comparison, particularly template-based motif detection algorithms. The subtilisin and chymotrypsin structures are shown side by side - note that the global folds of these two proteins are very different so the site could not have been detected using such methods. Click to see the catalytic triad in <scene name='User:James_D_Watson/Structural_Templates/Subtilisin_startpoint_catalyti/1' target='subtilisin'>subtilisin</scene> and <scene name='User:James_D_Watson/Structural_Templates/Chymotrypsin_start_triad/1' target='chymotrypsin'>chymotrypsin</scene> respectively.
+<applet load='1st2' size='300' frame='true' align='left' caption='Subtilisin 1st2' scene='User:James_D_Watson/Structural_Templates/Subtilisin_startpoint/1' name='subtilisin' />
+<applet load='1st2' size='300' frame='true' align='right' caption='Chymotrypsin 1ab9' scene='User:James_D_Watson/Structural_Templates/Chymotrypsin_start/1' name='chymotrypsin' />