Structure Mode ButtonEdit
Structure mode, Hotkey '2', changes the puzzle to be able to accept
changes to the structure. Each segment of a protein can have one of three structural assignments, Sheet, Helix or Loop. These structures are a reflection of the geometry the backbone segment has. Assigning a structure does not impart any forces on the segments, though, it might seem that way at times. For example, in attempting to rebuild a section as a helix, you might have no success. Then, after setting the segment section using the Structure Mode to Helices, the section zips right into a helix formation. It might seem as though the structural setting applied forces on the segments but all it did was to present the rebuild with more helical geometry points to choose from than others.
To use the Design ModeEdit
Hit HotKey '2'. Using the mouse, point to a segment you would like to
change with the cursor and click the right mouse button in windows, or click while holding down the Control key on a Mac. A pie-wheel selector appears with three choices: Loop, Helix and Sheet. Slide the cursor to one of the choices while holding down the mouse button and let it go over your choice,or similarly, on Windows, you can right-click the segment you wish to change and then left-click the structure you would like to set that segment to on the wheel. The segment you selected changes to that structural type.
You may change as many segments or as often as you would like. There is no limit or score penalty to changing the design of structures.
You may also change structures once you are in the Structure Mode by dragging the cursor from a segment whose structure you want to extend to its neighbors. Let's say that segment #1 is a loop and segments #2 through #10 are sheets and you want to extend the loop of segment #1 through segments #6. Point to #1 in the Design Mode, and without lifting your mouse button, drag the cursor to segment #6. As you move to segment #6, the structures change from the sheets of #2 through #6 to all loops of #1.
Uses of Structure ModeEdit
The Structure Mode and the ability to change segments from
loop to helix to sheet allows you to better visualize the organization of the protein. After all, good organization is what protein design is all about. It is often times difficult to visualize the overall organization of the protein without these organizing shortcuts.
For example, in one puzzle the protein's over design might be described as a saddle shape with a group of sheets aligned to form one large sheet that is warped in two directions like a saddle shape. IF the entire protein is left as loops, and the sidechains are shown in that view mode, it would be very difficult to see that the overall design should look like a saddle shape and that your best score is going to come from helping it to conform to that shape. However by using the Structure Mode, applying sheets to segments in the right places, the smooth contour of a saddle might be easer to visualize.
Rebuilding is a great way to change the configuration of the protein's backbone. Often, it is easy to see that one structure will work better for a certain section than another; e.g. a helix might fit where a sheet would not. But using 'rebuild' as a tool is difficult to master without understanding the technique. Rebuild, when directed at a section of segments, chooses at random known geometries and attempts to reposition the section in between those new locations. If the geometry does not work for some reason, e.g. it doesn't fit, the attempt is abandoned and rebuild goes on to try another geometry. By setting the section to a certain structure, rebuild will try more of that structure's possible geometries than any others in its random attempts to find new positions. Therefore, it may be much more effective to set the section to the new structure you wish to achieve before attempting a rebuild. The selected structure helpes guide the rebuild.
Perhaps the most important aspect of protein folding is the execution of an original design concept. For example, after looking at the protein you have a notion that it should be shaped, more or less, like a basket, or a fruit, or a marching band! Whatever the design concept, it is then useful to be able to quickly design and layout how that concept might take shape. To do that the Structure Mode is very useful. Each of the different design structures have important chracteristics. Sheets are flat and extend further in distance than the other two states. Helices allow more segments to occupy the most compact space of the three. Loops allow sudden and extreme changes in direction. By using the Structure Mode, you can visualize how each of these three structures might influence your overall design.
More on structure:Edit
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