From zhurkinv@exchange.nih.gov Date: Thu, 5 Jun 2003 15:28:17 -0400 From: "Zhurkin, Victor (NIH/NCI)" To: 'Heinz Sklenar' , David Beveridge , Zippi Shakked , Remo Rohs , Thomas Cheatham , Stephen Neidle , martin.egli , ponzy , Juan.A.Subirana , Karolin.Luger , schlick , loren.williams , e.westhof , xiangjun , Krystyna.Zakrzewska , sponer , m.zacharias , agor , heinemann , olson , haim.rozenberg , Manju Bansal Cc: Richard Lavery , Rama Sarma , Richard E. Dickerson Subject: RE: Albany workshop Attached is the same text in MS WORD format ["Olson-Zhurkin-letter.doc"] Dear Colleagues, We wish to draw your attention to the following considerations regarding the topics to be discussed at the forthcoming Albany Workshop on DNA Structural Parameters. 1. It was our initial understanding that the main purpose of the Workshop is the exchange of ideas and opinions on both the parameters used to characterize nucleic acid structures and the procedures used to calculate these values, with the aim of approaching a "common denominator." We hoped that the Workshop would help to "close the gap" between various programs now in common use, such as Curves, 3DNA, CEHS/SCHNAaP, CompDNA. One of our particular concerns was the RISE values calculated by Curves, which, as mentioned in the literature are substantially higher than the values obtained with the other software packages, especially if the duplex is locally distorted (for example, kinked). 2. The recent communications from Heinz Sklenar propose a shift in the emphasis of the Workshop to a discussion of the definition of the best "mean frame." In our opinion, this is not an adequate "remedy" because the difference between Curves and other packages is not only the selection of the "mean frame" but also the geometrical procedures used to calculate the translational parameters, including RISE. The two "mean frames" H and R introduced in Dr. Sklenar's letter, are not new - the same (or very similar) mean frames have been used in our CompDNA and 3DNA procedures, as well as in CEHS. The main difference between the published equations and those suggested by Dr. Sklenar is the number of consecutive rotations introduced to get from one frame to another: we have been using three Euler angles, whereas there are five angles in the Sklenar scheme. We note that Euler angles have been used intensively for more than 200 years, and that practically all the scientists with a physics-math education know what these angles are and how to use them. So, if our "DNA community" wants to be understood by others interested in DNA and RNA, we think it would be best to stay with something well known. In the case of base pairs, the question of the frame selection was thoroughly addressed at the recent Tsukuba Workshop, where Dr. Sklenar was a participant. Moreover, the specific selection of the coordinate frame has practically no influence on the resulting parameter values. As follows from the tables available at URL http://rutchem.rutgers.edu/~olson/Tsukuba/cf_7methods.par, only the RISE values from Curves differ noticeably from the RISE values obtained with other packages; all other parameters are identical with precision higher than necessary for adequate interpretation of X-ray and NMR structures. In our opinion, these arguments are sufficient to conclude that there is no need to discuss the "mean frame" issue at the present time. 3. Instead, we would rather concentrate on the issue of "local" and "global" parameters. At present, there is a lot of confusion in the literature as to the correct Twist angle to use in addressing to the Linking Number Problem, medium- and long-scale packaging of DNA, etc., and there is need for a consistent way to describe the degree of global bending. We believe that the major emphasis of the Workshop should be shifted in this direction. Such a discussion would be much more useful and productive than re-defining again and again the coordinate frames and the order of consecutive rotations around the X, Y and Z axes. Wilma K. Olson [Olson@rutchem.rutgers.edu] Victor B. Zhurkin [Zhurkin@nih.gov] June 5, 2003 [ Part 2, Application/MSWORD 8.4KB. ] [ Unable to print this part. ]