User:Michael Roberts/BIOL115 CaM: Difference between revisions
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Let's start with a sinmple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein. | Let's start with a sinmple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein. | ||
The wireframe view shows us all the atoms, but this can be too much detail if we're mainly interested ion the overall structure of the protein. This next veiw takes us right doewn to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the a-carbon atoms to which R-groups are attached. | '''BACKBONE''': The wireframe view shows us all the atoms, but this can be too much detail if we're mainly interested ion the overall structure of the protein. This next veiw takes us right doewn to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the a-carbon atoms to which R-groups are attached. Notice that helical regions can now be seen. | ||
'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them as ribbons. | |||
The a-helical region is now clearly defined, and there are also regions of b-structure. | |||
The short anti-parallel b-sheet between the adjacent EF hand loops are observed in calmodulins from various species. | |||
'''CALCIUM IONS''': In each EF hand loop, the Ca2+ ions are bound by residues in and near the loops. | |||
The structure shown has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>Ca2+ ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain. | |||
Let us color the two main forms of regular <scene name='Sandbox_LUBIOL115/Structure_plus_ca/1'>secondary structure</scene> in this protein. Alpha helix appears in red, beta sheet in yellow. | Let us color the two main forms of regular <scene name='Sandbox_LUBIOL115/Structure_plus_ca/1'>secondary structure</scene> in this protein. Alpha helix appears in red, beta sheet in yellow. | ||
