From owner-biophysics@net.bio.net Thu Jan 28 22:00:00 1999 From: "Clive Delmonte" Newsgroups: bionet.biophysics,bionet.xtallography Subject: DNA Structure: An Age of Refinement Part 3 of 6 Date: Fri, 29 Jan 1999 11:23:49 -0000 Lines: 97 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 195.7.225.194 Message-ID: <36b194e5.0@news.netdirect.net.uk> X-Trace: 29 Jan 1999 11:00:53 GMT, 195.7.225.194 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!194.72.7.126!btnet-peer!btnet-feed2!btnet!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.194 Xref: biosci bionet.biophysics:4746 bionet.xtallography:4571 Stereochemically Restrained Crystallographic Least-Squares Refinement of Macromolecular Structures Readers may recall that the DNA Structure Puzzles focussed attention upon those published, experimental results for which a plectonaemically wound DNA duplex would not seem to offer an explanation. Aside from the adoption by Watson & Crick of Pauling & Corey's first use of plectonaemic winding in DNA (and in many other biological macromolecules also) (66,67), there is the complex question of the precise computational origin of the proposed plectonaemic winding deduced from the deconvoluted structure factors derived from the x-ray diffraction from true crystals of short, synthetic oligonucleotides. The well-known paper of Hendrickson & Konnert (68) has been adapted to serve the specific needs of oligonucleotide refinement by at least two groups (69a,b). For example, Westhof et al. (69a) report "The adaptation of the restrained least-squares program for nucleic acids..." and "...we developed an extended version of restrained least-squares programs specifically for the refinement of nucleic acids (NUCLIN and NUCLSQ)." (Page 120) It would not seem to be explicit in this paper whether or not plectonaemic winding of the strands was incorporated as part of the "adaptation". However, bond lengths, bond angles, torsion angles and other data were incorporated as restraints, and, inasmuch as this data may have been taken, at least in part, "from small molecule crystallography" (page 121) which could have included studies of short oligonucleotides, the data may carry within it the implication of plectonaemic winding. While that of itself could be perfectly satisfactory, we may wish to keep in mind that there has never been a direct demonstration of any kind to show that oligonucleotide structures formed in vitro by low polymers, and then determined by crystallography, are actually the same as those to be found in high polymer DNA formed by proteins in vivo. There would be, therefore, a philosophical distinction between, on the one hand, arriving at a satisfactory small oligonucleotide structure through crystallography, and, on the other, to merely suppose that data taken from such short chain structures, such as torsion angles, sugar puckers and pseudorotation angles, for example, can be properly incorporated into the proposed structures of high polymer nucleic acids found in vivo. Moreover, there is a further level of ambiguity to be considered. Some of the earlier reports on dinucleotide crystal structures are the synopses of the work of Seeman et al. and Rosenberg et al. (70, 71). The synopses respectively contain the phrases "...The best fit to a double helix.." and "...The best double helical fit..." These phrases might mean that the data had been fitted to a double helix by the investigators, or they might mean that the deconvoluted data fell out naturally of itself into a good fit to a double helical structure. Evidently, if it transpires that the investigators in refs. 70 & 71 themselves fitted the data to a double helix, the consequent determinations of bond angles, torsion angles, rotation angles, etc., could have been carried forward into the libraries upon which later studies were based. In Part 4 of 6, we shall reflect on the context of the use of the refinement program ULTIMA. ------------------------------------------------------------------ 66 Structure of the Nucleic Acids; L. Pauling & R. Corey; Nature Vol 171 (1953) 346 67 L. Pauling & R. Corey in Proc Nat Acad Sci Vol 37 (1951) 235 - 271 (Helical Configuration of Polypeptide Chains, The Pleated Sheet, Feather Rachis Keratin, Hair, Muscle & Related Proteins) 68 Stereochemically Restrained Crystallographic Least-Squares Refinement of Macromolecule Structures by W.A. Hendrickson & J.H. Konnert, pages 43 - 82 in Biomolecular Structure, Conformation, Function and Evolution, Volume 1, Editor: R. Srinivasan, Pergamon Press, 1981, ISBN 0-08-023187-X 69a Crystallographic Refinement of Yeast Aspartic Acid Transfer RNA; E. Westhof, P. Dumas & D. Moras; J Mol Biol Vol 184 (1985) 119 - 145 69b Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA; G.J. Quigley, M.M. Teeter & A. Rich; Proc Nat Acad Sci Vol 75 (1978) 64 - 68 70 The Double Helix at Atomic Resolution I (ApU); N.C. Seeman et al.; Amer. Cryst. Assoc. Meeting, Vol 1, Ser 2, C6 (1973) 130 71 The Double Helix at Atomic Resolution II (GpC); J.M. Rosenberg et al.; ibid, C7 (1973) 130 --------------------------------------------------------------------- Clive Delmonte .