Saturday, November 14, 2009

How shear affects twist angle of a dinucleotide step?

A recent post in the 3DNA forum, titled "NUPARM vs X3DNA twist values", made me to rethink the issue of how or why shear affects twist angle of a dinucleotide step.

To me, this problem has long been solved as demonstrated by the following two well-cited publications:
  1. The Tsukuba report, a.k.a., "A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry". When Dr. Olson and I were drafting this report, I felt clearly the need to caution the community of the intrinsic correlations between base-pair parameters and the associated step parameters (Figure 3 there) to avoid possible mis-interpretations in structural analysis. This is specially the case for the effect of shear on twist, since the G–U wobble base-pair is common in RNA and it has a ~2.0 A shear.

  2. The 3DNA 2003 NAR paper. There is a subsection on the "Treatment of non-Watson–Crick base pairing motifs", and Figure 3 addressed specially on the issue:
    "Large Shear of the G–U wobble base pair influences the calculated but not the ‘observed’ Twist. The 3DNA numerical values of Twist, 20° (top) and 43° (bottom), differ from the visualization of nearly equivalent Twist suggested by the angle between successive C1'···C1' vectors (finely dotted lines)."
It was thus a bit surprising that such question still popping up. On second thought, however, it is quite understandable: one cannot expect everyone to read that two papers; not to mention remembering such details. So I am glad that this question was brought up to my attention, and it made me thinking possible ways to document more thoroughly the many 3DNA-related "technical details" that are crucial for better understanding of nucleic acid structures.

Coming back to the shear on twist angle issue, the figure at the left shows a G–U wobble pair example (top), and a simple rationale: the base-pair is approximately of 10Å-by-5Å (as defined in SCHNArP/3DNA), so a 2Å shift will lead to an angle:
atan2(2, 10) * 180 / pi = 11.3 degrees
(i.e., the red dotted line relative to the bottom horizontal line).

To a first order approximation, that is the difference between RC8–YC6 (or C1'–C1') vs. the base-centered mean y-axis of the pair for calculating twist angle. So whenever one has a G–U wobble pair next to a normal Watson-Crick pair, there would be ~11 degrees difference in "calculated" twist angle between the two approaches (NewHelix/CEHS/SCHNAaP/NUPARM vs 3DNA/Curve+). Moreover, when a G–U wobble is next to a U–G wobble pair, the difference would be doubled to ~23 degrees!

It is worth mentioning that the issue here (as in other similar cases) is not which number is "correct" or which is "wrong": a number is a number. It is its interpretation that matters, and it is here that "details" do count.

Sunday, November 8, 2009

It's sad to hear that Warren DeLano, author of PyMOL, passed away

From a couple of mailing lists, I heard the sad news that Warren DeLano, author of PyMOL, passed away on Tuesday morning, November 3rd. He was only 37!

I have never met Dr. DeLano personally, nor even I communicated with him by email, but I am very aware of PyMol, the de facto standard nowadays for molecular graphics. In writing 3DNA Nature Protocols paper, I dug more deeply into PyMol. I was impressed by its interactive interface to .r3d files (Raster3D) and the high quality ray-traced images it produced. So I came up with a Perl script (x3dna_r3d2png) to convert automatically from a 3DNA generated .r3d file to a PNG image through the PyMol engine.

Through his seminal contributions to PyMol, Dr. DeLano achieved something very few others in computational chemistry/biology can match: he successfully mobilized literately thousands of software programmers and ordinary users from multi-disciplines to join him to produce phenomenal pictures, each of which is worth a thousand words!

It was due to Dr. DeLano's vision that he made PyMol open source so the community now has the possibility/opportunity to continue support and further improve the software. At this stage, however, no one is likely to knows PyMol code to the depth Dr. DeLano did, not to mention the leadership and enthusiasm that he brought to the project. Whatever the case, the community undoubtedly would appreciate Dr. DeLano's valuable contributions.

Thanks, Dr. DeLano, for bring PyMol to the world!