Introduction to protein structure: Difference between revisions
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Since hemoglobin doesn't have any beta sheets, we will switch to another protein: <scene name='57/575866/1cyo_rainbow/1'>cytochrome B5</scene>, PDB code 1CYO. | Since hemoglobin doesn't have any beta sheets, we will switch to another protein: <scene name='57/575866/1cyo_rainbow/1'>cytochrome B5</scene>, PDB code 1CYO. | ||
Which rendering (spacefill, ball and stick, etc) is presented in this scene? | Quest #17) Which rendering (spacefill, ball and stick, etc) is presented in this scene? | ||
The coloring in this view is a N-->C rainbow, with the N terminus being blue and the C terminus red. | The coloring in this view is a N-->C rainbow, with the N terminus being blue and the C terminus red. | ||
Describe the relative positioning of the alpha helices and beta sheets. | Quest #18) Describe the relative positioning of the alpha helices and beta sheets, i.e. are all the alpha helices clustered with the beta sheets in another portion of the sequence, or are they interspersed? | ||
Next, we will look at two of the <scene name='57/575866/1cyo_20_32_transparent/1'>beta strands</scene>. The side chains have been faded out to make the backbone more obvious. | Next, we will look at two of the <scene name='57/575866/1cyo_20_32_transparent/1'>beta strands</scene>. The side chains have been faded out to make the backbone more obvious. | ||
Quest #19) Are these two strands are parallel or antiparallel. | |||
Where are the side chains positioned, relative to the main direction of the strand? | Quest #20) Where are the side chains positioned, relative to the main direction of the strand? | ||
Like before, measure four <scene name='57/575866/1cyo_20_32_psi/1'>psi</scene> and four <scene name='57/575866/1cyo_20_32_phi/1'>phi</scene> angles. Record these values in a table. | Quest #21) Like before, measure four <scene name='57/575866/1cyo_20_32_psi/1'>psi</scene> and four <scene name='57/575866/1cyo_20_32_phi/1'>phi</scene> angles. '''Record these values in a table.''' | ||
What is the average psi angle? What is the range of values? | Quest #22) What is the average psi angle? What is the range of values? | ||
What is the average phi angle? What is the range of values? | Quest #23) What is the average phi angle? What is the range of values? | ||
Which has more variability in the dihedral angles, an alpha helix or a beta sheet? | Quest #24) Which has more variability in the dihedral angles, an alpha helix or a beta sheet? | ||
The overall dihedral angles in a protein can be displayed in a <scene name='57/575866/Ramachandran/1'>Ramachandran plot</scene>, which graphs the interrelationship between phi and psi angles. Pink dots are angles found in alpha helices; yellow dots are found in beta sheets, and white dots are found in other regions (either disordered or turns). Mouse over the white dots on the right sides; what amino acids tend to have atypical phi and psi angles? | Quest #25) The overall dihedral angles in a protein can be displayed in a <scene name='57/575866/Ramachandran/1'>Ramachandran plot</scene>, which graphs the interrelationship between phi and psi angles. Pink dots are angles found in alpha helices; yellow dots are found in beta sheets, and white dots are found in other regions (either disordered or turns). Mouse over the white dots on the right sides; '''what amino acids tend to have atypical phi and psi angles?''' | ||
===Turns and loops=== | ===Turns and loops=== | ||