User:James D Watson/Structural Templates: Difference between revisions
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Proteins are formed from linear chains of amino acids joined together by peptide bonds. These chains then fold up to form the three dimensional shape. However, the relative rigidity of the peptide bond combined with the presence of amino acid sidechains, means that not all conformations are acceptable and there are many cases where the various atoms in the chain start to collide with one another. Two of the most stable (and therefore most commonly observed) conformations are the '''α-helix''' and the '''β-pleated sheet'''. These along with a number of small turns in the chain and random coil (folds that do not fit into a classification) are known as secondary structures. <br/> | Proteins are formed from linear chains of amino acids joined together by peptide bonds. These chains then fold up to form the three dimensional shape. However, the relative rigidity of the peptide bond combined with the presence of amino acid sidechains, means that not all conformations are acceptable and there are many cases where the various atoms in the chain start to collide with one another. Two of the most stable (and therefore most commonly observed) conformations are the '''α-helix''' and the '''β-pleated sheet'''. These along with a number of small turns in the chain and random coil (folds that do not fit into a classification) are known as secondary structures. <br/> | ||
α-helices | ===α-helices=== | ||
<applet load='5p21' size='350' frame='true' align='right' caption='Secondary structure'/> | |||
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 athey 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) | 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 athey 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) | ||
