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| [[Image:1ikk.gif|left|200px]]<br /><applet load="1ikk" size="450" color="white" frame="true" align="right" spinBox="true"
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| caption="1ikk, resolution 1.60Å" />
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| '''Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts'''<br />
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| ==Overview== | | ==Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts== |
| Introduction of a T-A or pyrimidine-purine step into a straight and rigid, A-tract can cause a positive roll deformation that kinks the DNA helix at, that step. In CCTTTAAAGG, the central T-A step has an 8.6 degrees bend, toward the major groove. We report the structural analysis of CCTTTAAAGG, and a comparison with 25 other representative crystal structures from the, NDB containing at least four consecutive A or T bases. On average, more, local bending occurs at the disruptive T-A step (8.21 degrees ) than at an, A-T step (5.71 degrees ). In addition, A-tracts containing an A-T step are, more bent than are pure A-tracts, and hence A-A and A-T steps are not, equivalent. All T-A steps examined exhibit positive roll, bending towards, the major groove, while A-T steps display negative roll and bend slightly, towards the minor groove. This illustrates how inherent negative and, positive roll are, respectively, at A-T and T-A steps within A-tracts. T-A, steps are more deformable, showing larger and more variable deformations, of minor groove width, rise, cup, twist, and buckle. Standard deviations, of twist, rise, and cup for T-A steps are 6.66 degrees, 0.55 A, and 15.90, degrees, versus 2.28 degrees, 0.21 A, and 2.99 degrees for A-T steps., Packing constraints determine which local values of these helical, parameters an individual T-A step will adopt. For instance, with, CCTTTAAAGG and three isomorphous structures, CGATTAATCG, CGATATATCG, and, CGATCGATCG, crystal packing forces lead to a series of correlated changes:, widened minor groove, large slide, low twist, and large rise. The, difference in helical parameters between A-T steps lying within A-tracts, versus A-T steps within alternating AT sequences, demonstrates the, importance of neighboring steps on the conformation of a given, dinucleotide step.
| | <StructureSection load='1ikk' size='340' side='right'caption='[[1ikk]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1ikk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IKK FirstGlance]. <br> |
| 1IKK is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IKK 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]] 1.6Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| ==Reference==
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ikk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ikk OCA], [https://pdbe.org/1ikk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ikk RCSB], [https://www.ebi.ac.uk/pdbsum/1ikk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ikk ProSAT]</span></td></tr> |
| Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts., Mack DR, Chiu TK, Dickerson RE, J Mol Biol. 2001 Oct 5;312(5):1037-49. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11580248 11580248]
| | </table> |
| [[Category: Protein complex]]
| | __TOC__ |
| [[Category: Chiu, T.K.]]
| | </StructureSection> |
| [[Category: Dickerson, R.E.]] | | [[Category: Large Structures]] |
| [[Category: Mack, D.R.]] | | [[Category: Chiu TK]] |
| [[Category: MG]] | | [[Category: Dickerson RE]] |
| [[Category: a-tract containing a t-a step]] | | [[Category: Mack DR]] |
| [[Category: b-dna double helix]] | |
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| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:09:05 2007''
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