Introduction to protein structure: Difference between revisions
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Secondary structures are often connected by turns and loops, such as:<UL> | Secondary structures are often connected by turns and loops, such as:<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>'''Alpha turns''' - the simplest of all motifs and is | <LI>'''Alpha turns''' - the simplest of all motifs and is characterized 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 | <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 characterized by the presence of a left handed residue and two hydrogen bonds: an i, i+3 bond and an i, i+5 bond. | ||
</UL> | </UL> | ||
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==Motifs In Proteins== | ==Motifs In Proteins== | ||
A motif is a super-secondary structure; it describes a set of secondary structures that plays a functional or structural role in a protein. The term is also used to describe a conserved amino acid sequence that characterizes a biochemical function. | A motif is a super-secondary structure; it describes a set of secondary structures that plays a functional or structural role in a protein. The term is also used to describe a conserved amino acid sequence that characterizes a biochemical function. | ||
One of the most common and widely distributed motifs is the [[Rossmann fold]] that appears in dinucleotide binding proteins. | |||
Another example is the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_highlight/1'>zinc finger motif</scene> that is readily identified by the following consensus sequence pattern (where "X" represents ''any'' amino acid):<br/> | |||
'''Cys''' - X<sub>(2-4)</sub> - '''Cys''' - X<sub>(3)</sub> - Phe - X<sub>(5)</sub> - Leu - X<sub>(2)</sub> - '''His''' - X<sub>(3)</sub> - '''His''' | |||
The example structure shown 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'>recognition 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 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'>recognition 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}} | {{Clear}} | ||
