Sandbox 50: Difference between revisions
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The <scene name='Sandbox_50/Helix/2'>secondary structure</scene> of HPL contains 13 alpha helices and 28 strands of beta sheets, representing 22% and 30%, respectively, of the protein's residues. Hydrophic collapse contributes to much of the secondary and tertiary structures, as the <scene name='Sandbox_50/Hphobic_residues/2'>hydrophobic residues</scene> shown in grey are mostly facing towards the interior of the protein. Conversely, the <scene name='Sandbox_50/Polar_residues/2'>polar residues</scene> in pink point congregate more on the exterior and point outwards. | The <scene name='Sandbox_50/Helix/2'>secondary structure</scene> of HPL contains 13 alpha helices and 28 strands of beta sheets, representing 22% and 30%, respectively, of the protein's residues. Hydrophic collapse contributes to much of the secondary and tertiary structures, as the <scene name='Sandbox_50/Hphobic_residues/2'>hydrophobic residues</scene> shown in grey are mostly facing towards the interior of the protein. Conversely, the <scene name='Sandbox_50/Polar_residues/2'>polar residues</scene> in pink point congregate more on the exterior and point outwards. | ||
=== Disulfide Bonds === | |||
Additional tertiary stability is provided by <scene name='Sandbox_50/Disulfide_bonds/1'>disulfide bonds</scene> between cysteine residues shown in yellow linkages. Cysteine residues not involved in disulfide bonds are shown as spheres. | Additional tertiary stability is provided by <scene name='Sandbox_50/Disulfide_bonds/1'>disulfide bonds</scene> between cysteine residues shown in yellow linkages. Cysteine residues not involved in disulfide bonds are shown as spheres. | ||
=== Chain Contacts === | |||
The two chains of HPL are connected through <scene name='Sandbox_50/Hydrophobic_chain_interactions/2'>hydrophobic interactions</scene>, <scene name='Sandbox_50/Hydrogen_bonds_non_water/1'>hydrogen bonds</scene>, <scene name='Sandbox_50/Salt_bridges/1'>salt bridges</scene>, and <scene name='Sandbox_50/Putative_water_bridges/1'>putative water bridges</scene>. In the last scene, water molecules are shown as pink spheres. | The two chains of HPL are connected through <scene name='Sandbox_50/Hydrophobic_chain_interactions/2'>hydrophobic interactions</scene>, <scene name='Sandbox_50/Hydrogen_bonds_non_water/1'>hydrogen bonds</scene>, <scene name='Sandbox_50/Salt_bridges/1'>salt bridges</scene>, and <scene name='Sandbox_50/Putative_water_bridges/1'>putative water bridges</scene>. In the last scene, water molecules are shown as pink spheres. | ||
=== Calcium Ions === | |||
Two calcium ions are also present in the protein to further <scene name='Sandbox_50/Calcium_coordination_no_bb/2'>coordinate</scene> the structure of HPL. Each chain contains one calcium ion, each bound by the same residues. While the calcium ligands are no involved in the manipulating the substrate in the active site, enzymatic activity has been shown to be related to free calcium concentration. At lower calcium concentrations, lipases show reduced activity.<ref>http://www.springerlink.com/content/g5h1613440115701/fulltext.pdf</ref> This is most likely due to reduced structural coordination. A more detailed view of the calcium coordination can be seen here: | Two calcium ions are also present in the protein to further <scene name='Sandbox_50/Calcium_coordination_no_bb/2'>coordinate</scene> the structure of HPL. Each chain contains one calcium ion, each bound by the same residues. While the calcium ligands are no involved in the manipulating the substrate in the active site, enzymatic activity has been shown to be related to free calcium concentration. At lower calcium concentrations, lipases show reduced activity.<ref>http://www.springerlink.com/content/g5h1613440115701/fulltext.pdf</ref> This is most likely due to reduced structural coordination. A more detailed view of the calcium coordination can be seen here: | ||