In this tutorial, you will get a three-dimensional look at these crossover questions in a protein that contains a classic parallel beta sheet - flavodoxin from the microorganism Anabaena
Click here to show this flavodoxin as a ribbon structure:
Flavodoxin from Anabaena contains a molecule of flavin mononucleotide Now let's take a closer look: For the rest of this exercise, it will be important for you to rotate the molecule in various ways to see it from different perspectives. You may either do this with the buttons shown below or by clicking and holding the left mouse button and moving the mouse to rotate the image about the x- and y-axes. (Rotations about the z-axis are done by holding down the shift key and rotating with the right mouse button.) Rotate 5 degrees about x-axis: Rotate 10 degrees about x-axis: Rotate 5 degrees about y-axis: Rotate 10 degrees about y-axis: Rotate 5 degrees about z-axis: Rotate 10 degrees about z-axis: Now let's look at the crossovers of flavodoxin. Each crossover' is defined as consisting of a beta strand, a loop (usually consisting of a turn, a helix and another turn), and another beta strand. In the following exercise, the leading beta strand will be colored orange, the turn-helix-turn motif will be red and the following beta strand will be yellow. Now, let's look at the first crossover of flavodoxin. Click the button to color the leading beta strand orange: This beta strand is residues 4 to 9 of the protein. Notice that they constitute the second beta strand of the parallel beta sheet. Rotate the protein to confirm this point. Now let's color the turn-helix-turn motif red: This t-h-t motif includes residues 10 to 30 of the protein. Let's now color the following beta strand of the first crossover. It will be shown in yellow: Notice that this segment is actually the first beta strand of the parallel beta sheet. Now let's see the whole thing again. First, reset the first crossover to white: Click the button to see the entire first crossover of flavodoxin: It is important at this point that you see this crossover from different perspectives and that you determine its 'handedness'. Rotate the protein to several different views and repeat the two steps above. See the crossover unfold from several different views and decide whether it is right-handed or left-handed. You may wish to consult a textbook (for example, page 159 of Biochemistry, by Garrett and Grisham) for views of both types of crossovers. Nearly all crossovers in natural proteins are right-handed crossovers and the crossovers of flavodoxin are no exception. Now click to reset the first crossover to blue and we'll look at the second crossover. The second crossover in this protein involves a leading beta strand that includes residues 31 to 35 a turn-helix-turn motif including residues 36 to 48 and a following beta strand (residues 49 to 53) Notice that this second crossover involves the third and first beta strands of the parallel sheet (in that order). Rotate the protein for another view and take another look at this crossover. Click here to reset the crossover to white. and here to see the second crossover again. Notice that this crossover is also right-handed. Reset again to blue: and we'll look at crossover 3. Crossover 3 involves a leading beta strand of residues 49-53 a t-h-t motif in residues 54 to 81 and a following beta strand in residues 82 to 88 This crossover involves beta strands 3 and 4 of the parallel beta sheet and, like the others, is a right-handed crossover. Click here to reset the crossover to white. Now take another look at this crossover Now click to reset the third crossover to blue and we'll look at the fourth crossover. The fourth and final crossover in this parallel beta sheet involves the beta strand composed of residues 82 to 88, the t-h-t motif composed of residues 89 to 140 and a following beta strand composed of residues 141 to 144. Rotate the molecue to change your view and convince yourself that this also is a right-handed crossover. Click here to reset the crossover to white. Click here to see the fourth crossover again. Now reset this crossover to blue and take one last look at the parallel beta sheet of flavodoxin, with the coloring shown below: First strand: red Second strand: redorange Third strand: orange Fourth strand: yellow Fifth strand: green Reset the beta sheet to blue and you can scroll back up through this tutorial and reexamine any of the crossovers discussed above.
Now let's take a closer look:
For the rest of this exercise, it will be important for you to rotate the molecule in various ways to see it from different perspectives. You may either do this with the buttons shown below or by clicking and holding the left mouse button and moving the mouse to rotate the image about the x- and y-axes. (Rotations about the z-axis are done by holding down the shift key and rotating with the right mouse button.)
Rotate 5 degrees about x-axis: Rotate 10 degrees about x-axis: Rotate 5 degrees about y-axis: Rotate 10 degrees about y-axis: Rotate 5 degrees about z-axis: Rotate 10 degrees about z-axis:
Now let's look at the crossovers of flavodoxin. Each crossover' is defined as consisting of a beta strand, a loop (usually consisting of a turn, a helix and another turn), and another beta strand. In the following exercise, the leading beta strand will be colored orange, the turn-helix-turn motif will be red and the following beta strand will be yellow.
Now, let's look at the first crossover of flavodoxin. Click the button to color the leading beta strand orange: This beta strand is residues 4 to 9 of the protein. Notice that they constitute the second beta strand of the parallel beta sheet. Rotate the protein to confirm this point.
Now let's color the turn-helix-turn motif red:
This t-h-t motif includes residues 10 to 30 of the protein. Let's now color the following beta strand of the first crossover. It will be shown in yellow: Notice that this segment is actually the first beta strand of the parallel beta sheet.
Now let's see the whole thing again. First, reset the first crossover to white: Click the button to see the entire first crossover of flavodoxin: It is important at this point that you see this crossover from different perspectives and that you determine its 'handedness'. Rotate the protein to several different views and repeat the two steps above. See the crossover unfold from several different views and decide whether it is right-handed or left-handed. You may wish to consult a textbook (for example, page 159 of Biochemistry, by Garrett and Grisham) for views of both types of crossovers. Nearly all crossovers in natural proteins are right-handed crossovers and the crossovers of flavodoxin are no exception. Now click to reset the first crossover to blue and we'll look at the second crossover. The second crossover in this protein involves a leading beta strand that includes residues 31 to 35 a turn-helix-turn motif including residues 36 to 48 and a following beta strand (residues 49 to 53) Notice that this second crossover involves the third and first beta strands of the parallel sheet (in that order). Rotate the protein for another view and take another look at this crossover. Click here to reset the crossover to white. and here to see the second crossover again. Notice that this crossover is also right-handed. Reset again to blue: and we'll look at crossover 3.
Click the button to see the entire first crossover of flavodoxin:
It is important at this point that you see this crossover from different perspectives and that you determine its 'handedness'. Rotate the protein to several different views and repeat the two steps above. See the crossover unfold from several different views and decide whether it is right-handed or left-handed. You may wish to consult a textbook (for example, page 159 of Biochemistry, by Garrett and Grisham) for views of both types of crossovers.
Nearly all crossovers in natural proteins are right-handed crossovers and the crossovers of flavodoxin are no exception.
Now click to reset the first crossover to blue and we'll look at the second crossover.
The second crossover in this protein involves a leading beta strand that includes residues 31 to 35 a turn-helix-turn motif including residues 36 to 48 and a following beta strand (residues 49 to 53)
Notice that this second crossover involves the third and first beta strands of the parallel sheet (in that order). Rotate the protein for another view and take another look at this crossover.
Click here to reset the crossover to white. and here to see the second crossover again. Notice that this crossover is also right-handed.
Crossover 3 involves a leading beta strand of residues 49-53 a t-h-t motif in residues 54 to 81 and a following beta strand in residues 82 to 88 This crossover involves beta strands 3 and 4 of the parallel beta sheet and, like the others, is a right-handed crossover. Click here to reset the crossover to white. Now take another look at this crossover Now click to reset the third crossover to blue and we'll look at the fourth crossover. The fourth and final crossover in this parallel beta sheet involves the beta strand composed of residues 82 to 88, the t-h-t motif composed of residues 89 to 140 and a following beta strand composed of residues 141 to 144. Rotate the molecue to change your view and convince yourself that this also is a right-handed crossover. Click here to reset the crossover to white. Click here to see the fourth crossover again. Now reset this crossover to blue and take one last look at the parallel beta sheet of flavodoxin, with the coloring shown below: First strand: red Second strand: redorange Third strand: orange Fourth strand: yellow Fifth strand: green Reset the beta sheet to blue and you can scroll back up through this tutorial and reexamine any of the crossovers discussed above.
Click here to reset the crossover to white.
Now take another look at this crossover Now click to reset the third crossover to blue and we'll look at the fourth crossover. The fourth and final crossover in this parallel beta sheet involves the beta strand composed of residues 82 to 88, the t-h-t motif composed of residues 89 to 140 and a following beta strand composed of residues 141 to 144. Rotate the molecue to change your view and convince yourself that this also is a right-handed crossover. Click here to reset the crossover to white. Click here to see the fourth crossover again. Now reset this crossover to blue and take one last look at the parallel beta sheet of flavodoxin, with the coloring shown below: First strand: red Second strand: redorange Third strand: orange Fourth strand: yellow Fifth strand: green Reset the beta sheet to blue and you can scroll back up through this tutorial and reexamine any of the crossovers discussed above.
Now click to reset the third crossover to blue and we'll look at the fourth crossover.
Click here to see the fourth crossover again. Now reset this crossover to blue and take one last look at the parallel beta sheet of flavodoxin, with the coloring shown below: First strand: red Second strand: redorange Third strand: orange Fourth strand: yellow Fifth strand: green Reset the beta sheet to blue and you can scroll back up through this tutorial and reexamine any of the crossovers discussed above.
Now reset this crossover to blue and take one last look at the parallel beta sheet of flavodoxin, with the coloring shown below: First strand: red Second strand: redorange Third strand: orange Fourth strand: yellow Fifth strand: green Reset the beta sheet to blue and you can scroll back up through this tutorial and reexamine any of the crossovers discussed above.
Reset the beta sheet to blue and you can scroll back up through this tutorial and reexamine any of the crossovers discussed above.