1ikk
From Proteopedia
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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
Overview
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.
About this Structure
1IKK is a Protein complex structure of sequences from [1] with MG as ligand. Full crystallographic information is available from OCA.
Reference
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:11580248
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