|
|
| (14 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| [[Image:167d.gif|left|200px]]<br /><applet load="167d" size="450" color="white" frame="true" align="right" spinBox="true"
| |
| caption="167d, resolution 2.300Å" />
| |
| '''THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS'''<br />
| |
|
| |
|
| ==Overview== | | ==THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS== |
| The single-crystal X-ray analysis of trigonal C-C-A-T-T-A-A-T-G-G, and its, comparison with orthorhombic C-G-A-T-T-A-A-T-C-G, have shown that the, A-T-T-A-A-T sequence has limited polymorphism under the influence of, packing forces from neighboring molecules in the crystal. The T-A step is, intrinsically variable. It is not inconsistent with a large propeller, twist, a narrow minor groove, and a single spine of hydration, as has, sometimes been claimed on theoretical grounds. The T-A step does show a, persistent positive roll, in a direction that compresses the major groove, and this may be a significant factor in macroscopic DNA curvature induced, by phased A-tracts. A-tracts, as understood in this paper, include A-A and, A-T steps, but not the T-A step, which is disruptive. Three conclusions, regarding A-tract-induced curvature can be drawn from this and other X-ray, crystal structure analyses, and from key gel retardation experiments: (1), The A-tract bending model is disqualified on two grounds: (i) tilt-wedge, bending within A-tracts is incompatible with the observed direction of, curvature; (ii) roll-wedge bending within A-tracts is contradicted by, every crystal structure analysis, and is inconsistent with gel retardation, results for (G-C-A-A-A-A-T-T-T-T)n and for (A-A-A-A-A-T-T-T-T-T)n. (2) The, junction bend model is contradicted by crystallography because: (i) the, inclination of base-pairs does not change between A-tract and non-A-tract, regions of helix; and (ii) the observed bends at GC/AT junctions are, roll-wedge bends, not tilt-wedge as the junction bend model demands. (3), The non-A-tract bending model is consistent with both gel retardation data, and with X-ray crystallography, and must be regarded as the only, consistent model for A-tract bending.
| | <StructureSection load='167d' size='340' side='right'caption='[[167d]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[167d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=167D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=167D FirstGlance]. <br> |
| 167D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=167D OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=167d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=167d OCA], [https://pdbe.org/167d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=167d RCSB], [https://www.ebi.ac.uk/pdbsum/167d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=167d ProSAT]</span></td></tr> |
| ==Reference== | | </table> |
| The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps., Goodsell DS, Kaczor-Grzeskowiak M, Dickerson RE, J Mol Biol. 1994 May 27;239(1):79-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8196049 8196049]
| | __TOC__ |
| [[Category: Protein complex]] | | </StructureSection> |
| [[Category: Dickerson, R.E.]]
| | [[Category: Large Structures]] |
| [[Category: Goodsell, D.S.]]
| | [[Category: Dickerson RE]] |
| [[Category: Kaczor-Grzeskowiak, M.]] | | [[Category: Goodsell DS]] |
| [[Category: b-dna]] | | [[Category: Kaczor-Grzeskowiak M]] |
| [[Category: double helix]] | |
| | |
| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:02:41 2007''
| |
