DOPA decarboxylase: Difference between revisions
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The formation of secondary structural elements (like α helices and β sheets) arise in response to the hydrophobic effect and the need to neutralize main-chain polar groups by '''hydrogen bonding'''. Each polypeptide chain of DOPA decarboxylase is composed of a seven-stranded mixed <scene name='DOPA_decarboxylase/Beta-sheet/1'>β sheet</scene>, a four-stranded anti-parallel <scene name='DOPA_decarboxylase/Beta-sheet2/1'>β sheet</scene>, several <scene name='DOPA_decarboxylase/Alpha_helices/1'>α helices</scene>, and other, lesser known, secondary structural elements (like loops and the extended strand). Another common secondary structure is the β-turn, or reverse turn. Depicted below is an example of a '''Type 1 β-turn''' of DOPA decarboxylase. This β-turn is comprised of residues Leu-440, Arg-441, Gly-442, and Gln-443. The distance between Cαi and Cαi+3 is 5.1Å, within the acceptable limit of 7Å. As in most β-turns, there is a hydrogen bond between the C=O of Leu-440 and the NH of Gln-443. The phi and psi angles of residues i+1 (Arg-441) and i+2 (Gly-442) are indicated in the diagram. | The formation of secondary structural elements (like α helices and β sheets) arise in response to the hydrophobic effect and the need to neutralize main-chain polar groups by '''hydrogen bonding'''. Each polypeptide chain of DOPA decarboxylase is composed of a seven-stranded mixed <scene name='DOPA_decarboxylase/Beta-sheet/1'>β sheet</scene>, a four-stranded anti-parallel <scene name='DOPA_decarboxylase/Beta-sheet2/1'>β sheet</scene>, several <scene name='DOPA_decarboxylase/Alpha_helices/1'>α helices</scene>, and other, lesser known, secondary structural elements (like loops and the extended strand). Another common secondary structure is the β-turn, or reverse turn. Depicted below is an example of a '''Type 1 β-turn''' of DOPA decarboxylase. This β-turn is comprised of residues Leu-440, Arg-441, Gly-442, and Gln-443. The distance between Cαi and Cαi+3 is 5.1Å, within the acceptable limit of 7Å. As in most β-turns, there is a hydrogen bond between the C=O of Leu-440 and the NH of Gln-443. The phi and psi angles of residues i+1 (Arg-441) and i+2 (Gly-442) are indicated in the diagram. | ||
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[[image:secondary.png | [[image:secondary.png|center|600px|''' β turn (left) and capping-box (right) ''']] | ||
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The α helix is characterized by main chain hydrogen bonds between the C=O of residue n and the NH of residue n+4. All residues in the helix participate in this type of hydrogen bonding except the first NH groups and the last C=O groups at the ends of the helix. '''Helix-capping motifs''' are specific hydrogen bonding and hydrophobic interactions found at the ends of helices. Seven distinct capping motifs have been identified; three at the N-terminus and four at the C-terminus. Shown above is the '''capping-box''' motif found at the end of the helix composed of residues 147-171. This form of special capping satisfies two of the four non hydrogen-bonded helix N-terminal amides. The side-chain capping apparent here is typical at the N-terminus. | The α helix is characterized by main chain hydrogen bonds between the C=O of residue n and the NH of residue n+4. All residues in the helix participate in this type of hydrogen bonding except the first NH groups and the last C=O groups at the ends of the helix. '''Helix-capping motifs''' are specific hydrogen bonding and hydrophobic interactions found at the ends of helices. Seven distinct capping motifs have been identified; three at the N-terminus and four at the C-terminus. Shown above is the '''capping-box''' motif found at the end of the helix composed of residues 147-171. This form of special capping satisfies two of the four non hydrogen-bonded helix N-terminal amides. The side-chain capping apparent here is typical at the N-terminus. | ||
