Introduction to protein structure: Difference between revisions
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--Quest #11) What is the amino acid range (i.e. from first AA to last AA number) of this alpha helix? | --Quest #11) What is the amino acid range (i.e. from first AA to last AA number) of this alpha helix? | ||
Rotate the helix so that you are looking down the helix. What does the middle of the helix look like? | Rotate the helix so that you are looking down the helix. | ||
Quest #12) What does the middle of the helix look like? | |||
Right click on the mouse, choose style, then scheme, then CPK spacefill. | Right click on the mouse, choose style, then scheme, then CPK spacefill. | ||
Quest # | Quest #13) What does the middle of the helix look like? | ||
Quest # | Quest #14) Which view is more representative of the true structure of the molecule? | ||
Let's try changing to another view. Right click on the mouse, choose style, then scheme, then ball and stick. Based upon what you know about peptide composition or by holding the mouse over the atoms determine the color scheme: | Let's try changing to another view. Right click on the mouse, choose style, then scheme, then ball and stick. Based upon what you know about peptide composition or by holding the mouse over the atoms determine the color scheme: | ||
Quest # | Quest #15a) red = | ||
Quest # | Quest #15b) black = | ||
Quest # | Quest #15c) blue = | ||
Notice that hydrogens are not shown on this model. Xray crystallography is not able to resolve hydrogens, so they are omitted from the images. This also simplifies the data set, as there are many fewer atoms to position. | Notice that hydrogens are not shown on this model. Xray crystallography is not able to resolve hydrogens, so they are omitted from the images. This also simplifies the data set, as there are many fewer atoms to position. | ||
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Jmol can be used to make measurements of various properties of the alpha helix, such as the dihedral angle. <scene name='57/575866/No_sidechains/1'>This structure</scene> has the side chains removed (though the alpha carbons show where the side chain would be). Right click in the structure box. In the Measurements menu, select "double click begins and ends measurements". Double click on one of the nitrogens, then click once on the following atoms in order: the attached Calpha, carbonyl C, and N. Record this dihedral angle (a psi angle) in a table, recording the number of the Calpha. Repeat, starting at the N you ended on. Notice each click gives a different property: the first is the bond length, the second is the bond angle, and the third is the dihedral (torsional) angle. You may need to rotate around the helix to see the atoms you want to measure; repeat for four psi angles. After you have completed it for the psi angles, repeat for the phi angles by clicking on the carbonyl C, Calpha, N and carbonyl C. If you are having problems making the measurements, here is one with the <scene name='57/575866/No_sidechains/2'>psi angles</scene> and one with the <scene name='57/575866/Phi_angles/1'>phi angles</scene>. | Jmol can be used to make measurements of various properties of the alpha helix, such as the dihedral angle. <scene name='57/575866/No_sidechains/1'>This structure</scene> has the side chains removed (though the alpha carbons show where the side chain would be). Right click in the structure box. In the Measurements menu, select "double click begins and ends measurements". Double click on one of the nitrogens, then click once on the following atoms in order: the attached Calpha, carbonyl C, and N. Record this dihedral angle (a psi angle) in a table, recording the number of the Calpha. Repeat, starting at the N you ended on. Notice each click gives a different property: the first is the bond length, the second is the bond angle, and the third is the dihedral (torsional) angle. You may need to rotate around the helix to see the atoms you want to measure; repeat for four psi angles. After you have completed it for the psi angles, repeat for the phi angles by clicking on the carbonyl C, Calpha, N and carbonyl C. If you are having problems making the measurements, here is one with the <scene name='57/575866/No_sidechains/2'>psi angles</scene> and one with the <scene name='57/575866/Phi_angles/1'>phi angles</scene>. | ||
Quest # | Quest #16a) What is the average phi angle in this alpha helix? | ||
Quest # | Quest #16b) What is the range of values? | ||
Quest # | Quest #17a) What is the average psi angle in this alpha helix? | ||
Quest # | Quest #17b) What is the range? | ||
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. | ||
Quest # | Quest #18) 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. | ||
Quest # | Quest #19) 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 # | Quest #20) Are these two strands are parallel or antiparallel. | ||
Quest # | Quest #21) Where are the side chains positioned, relative to the main direction of the strand? | ||
Quest # | Quest #22) 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 # | Quest #23) What is the average psi angle? What is the range of values? | ||
Quest # | Quest #24) What is the average phi angle? What is the range of values? | ||
Quest # | Quest #25) Which has more variability in the dihedral angles, an alpha helix or a beta sheet? | ||
Quest # | Quest #26) 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=== | ||