I’ve been thinking about what kind of schematic representation of the RNA might be best for solving the new “construct a 3D path” puzzle Vineet is creating. Yesterday, I was replacing a clothes drier vent, and it gave rise to the following idea.
First, here’s the type of flexible venting tube that served as an inspiration.
The idea was to represent each stem (helical segment) as a section of straight tubing, and each motif as a segment that has been bent in a way representative of that motif. The puzzle then becomes one of choosing from those pieces to build a duct between the desired end points (as well as the proper twist.) This doesn’t really change anything about the puzzle, but it might make it easier to bring one’s repertory of 3D experience to bear.
I’m not a great 3D modeler, but I did manage to put together some models in Second Life to try out various ideas. Here’s what I came up with.
For starters, I constructed a schematic representation of double stranded backbone, throwing away all the details about the nucleosides.
This is similar to the “smoothed backbone” option in Chimera.
Then I added a partially transparent cylinder, constructed so that the backbone lay on the surface of the cylinder.
An interesting thing to point out here is that in an RNA double helix, the plane roughly defined by paired nucleosides is not perpendicular to the central axis of the helix. In the image above, this shows up in the fact that at the top and bottom of the cylinder, one of the backbone strands extends beyond the end of the cylinder and the other strand falls short. I think this accounts for the fact that the current “hints” don’t work out quite like I expected them to. When I look at the hints, I expect them to show the direction a helical section will project. But I think the hints actually show the plane of the closing base pairs, which is in a somewhat different direction.
To make the direction of a helix extension clear, I added an arrow that follows the path of the center of the helix, and thus points in the direction a subsequent helical extension would take.
Finally, I added a “cap” to the cylinder.
The point where the pie shaped wedge cut out of the cap meets the outer surface of the cylinder is supposed to represent where the backbone (or its extension) meets the end of the cylinder. (The cut-out wedge thus represents what is called the helix’s major groove.) In this picture, it looks like I didn’t get the torsion angle of the cap quite right.
If I were more accomplished at 3D modeling, I would have built a model for a non-helical motif or two. But you can imagine them just as just bent versions of the above. A simple bulge or small loop could probably be represented accurately by a simple curve, i.e. the entire central axis would lie in a single plane. A larger loop would probably have to be modeled by a kink turn, where the entering and exiting end of the central axis didn’t stay in one plane.
An important point to note is that all the essential information needed to specify the path of the RNA segment is encoded in the end cap, which should be easily computed from the 3D information already encoded into the program. Calculating the “best” path for a central axis through a twisty-turny motif might be tricky (or maybe not; I just don’t know), but it really isn’t important. Any simple smooth spline between the entering and exiting cap vectors will suffice for supporting the physical intuition of the complete RNA as being equivalent to a flexible duct built out of pre-made pieces, where each section has a groove that has to line up with the next piece.
Here’s two pictures showing joining segments.
Again, it would make a better illustration if one of the segments was a curved motif, but I hope this conveys the idea.