User:Gregory Hoeprich/Sandbox 1: Difference between revisions
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#'''Superfamily:''' tropomyosin | #'''Superfamily:''' tropomyosin | ||
#'''Family:''' pig [[http://www.pdb.org/pdb/explore/explore.do?structureId=1C1G 1c1g]] | #'''Family:''' pig [[http://www.pdb.org/pdb/explore/explore.do?structureId=1C1G 1c1g]] | ||
<Structure load='1c1g' size='400' frame='true' align='left' caption='Tropomyosin Dimer: Click on Green Links (right) to see hydrophobic and ionic interactions between the two alpha helices' scene='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_dimer/2'/> [[Image:Helical Wheel Respresentation of Tropomyosin.jpg | thumb | right | 333x200px | alt text | '''Helical Wheel Diagram Representation of Tropopomyosin:''' The coiled-coil dimer is stabilized by hydrophobic and ionic interactions (red=hydrophobic, blue=polar & green=charged)Image Reconstructed from <ref name="Gunning"/>.]] Categorization of tropomyosin's <scene name='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_dimer/2'>coiled-coil</scene> describes a unique pattern of amino acids within the primary structure of the alpha helices that comprise the dimer interface<ref name="Gunning"/>. The unique amino acid pattern, found within all coiled-coil proteins, is a heptad repeat, which follows a similar pattern to: '''H-P-P-H-C-P-C''', where H is hydrophobic, P is polar and C is charged<ref name="Gunning"/><ref name="Whitby"/>. This heptad repeat forms a right handed alpha helical secondary structure (see right for alpha helix secondary structure)<ref name="Gunning"/>. This alpha helix is special in that it forms a hydrophobic strip along one side, which will interface with an adjacent alpha helix that also contains the heptad repeat and hydrophobic strip. These strips aid in the dimerization of tropomyosin and is important in the characteristic coiled-coil domain. | <Structure load='1c1g' size='400' frame='true' align='left' caption='Tropomyosin Dimer: Click on Green Links (right) to see hydrophobic and ionic interactions between the two alpha helices' scene='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_dimer/2'/> [[Image:Helical Wheel Respresentation of Tropomyosin.jpg | thumb | right | 333x200px | alt text | '''Helical Wheel Diagram Representation of Tropopomyosin:''' The coiled-coil dimer is stabilized by hydrophobic and ionic interactions (red=hydrophobic, blue=polar & green=charged)Image Reconstructed from <ref name="Gunning"/>.]] Categorization of tropomyosin's <scene name='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_dimer/2'>coiled-coil</scene> describes a unique pattern of amino acids within the primary structure of the alpha helices that comprise the dimer interface<ref name="Gunning"/>. The unique amino acid pattern, found within all coiled-coil proteins, is a heptad repeat, which follows a similar pattern to: '''H-P-P-H-C-P-C''', where H is hydrophobic, P is polar and C is charged<ref name="Gunning"/><ref name="Whitby"/>. This heptad repeat forms a right-handed alpha helical secondary structure (see right for alpha helix secondary structure)<ref name="Gunning"/>. This alpha helix is special in that it forms a hydrophobic strip along one side, which will interface with an adjacent alpha helix that also contains the heptad repeat and hydrophobic strip. These strips aid in the dimerization of tropomyosin and is important in the characteristic coiled-coil domain. | ||
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This coiled-coil domain is represented as a helical wheel diagram (see right), whereby the four amino acids (two from each alpha chain) that are adjacent to each other contribute to a <scene name='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_hydrophobic_aa/4'>hydrophobic interaction</scene>, represented in red, while the four amino acids (two from each alpha chain) flanking the hydrophobic core provide an <scene name='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_ionic_interaction/2'>ionic interaction</scene>, or salt-bridge represented as green. Both the hydrophobic and ionic interactions contribute to the stability of the dimer<ref name="Gunning"/><ref name="Whitby"/>. | This coiled-coil domain is represented as a helical wheel diagram (see right), whereby the four amino acids (two from each alpha chain) that are adjacent to each other contribute to a <scene name='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_hydrophobic_aa/4'>hydrophobic interaction</scene>, represented in red, while the four amino acids (two from each alpha chain) flanking the hydrophobic core provide an <scene name='User:Gregory_Hoeprich/Sandbox_1/Tropomyosin_ionic_interaction/2'>ionic interaction</scene>, or salt-bridge represented as green. Both the hydrophobic and ionic interactions contribute to the stability of the dimer<ref name="Gunning"/><ref name="Whitby"/>. | ||
