1ksb
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Relationship of Solution and Protein-Bound Structures of DNA Duplexes with the Major Intrastrand Cross-Link Lesions Formed on Cisplatin Binding to DNA
OverviewOverview
DNA bases in the three-base-pair (3bp) region of duplexes with the two, major lesions of cisplatin (cis-PtCl(2)(NH(3))(2)) with DNA, namely d(XGG), and d(XAG) ( = N7-platinated base), differ in their relative positions by, as much as approximately 3.5 A in structures in the literature. Such large, differences impede drug design and assessments of the effects of protein, binding on DNA structure. One recent and several past structures based on, NMR-restrained molecular dynamics (RMD) differ significantly from the, reported X-ray structure of an HMG-bound XGG 16-mer DNA duplex (Ohndorf, U.-M.; Rould, M. A.; He, Q.; Pabo, C. O.; Lippard, S. J. Nature 1999, 399, 708). This 16-mer structure has several significant novel and unique, features (e.g., a bp step with large positive shift and slide)., Hypothesizing that novel structural features in the XGG or XAG region of, duplexes elude discovery by NMR methods (especially because of the, flexible nature of the 3bp region), we studied an oligomer with only G.C, bp's in the XGGY site by NMR methods for the first time. This 9-mer gave a, 5'-G N1H signal with a normal shift and intensity and showed clear NOE, cross-peaks to C NHb and NHe. We assigned for the first time (13)C NMR, signals of a duplex with a GG lesion. These data, by adding NMR-based, criteria to those inherent in NOESY and COSY data, have more specifically, defined the structural features that should be present in an acceptable, model. In particular, our data indicated that the sugar of the X residue, has an N pucker and that the GG cross-link should have a structure similar, to the original X-ray structure of cis-Pt(NH(3))(2)(d(pGpG)) (Sherman S., E.; Gibson, D.; Wang, A. H.-J.; Lippard, S. J. J. Am. Chem. Soc. 1988, 110, 7368). With these restrictions added to NOE restraints, an acceptable, model was obtained only when we started our modeling with the 16-mer, structural features. The new X-ray/NMR-based model accounted for the NOESY, data better than NOE-based models, was very similar in structure to the, 16-mer, and differed from solely NOE-based models. We conclude that all, XGG and XAG (X = C or T) duplexes undoubtedly have structures similar to, those of the 16-mer and our model. Thus, protein binding does not change, greatly the structure of the 3bp region. The structure of this region can, now be used in understanding structure-activity relationships needed in, the design of new carrier ligands for improving Pt anticancer drug, activity.
About this StructureAbout this Structure
1KSB is a Protein complex structure of sequences from [1] with CPT as ligand. Full crystallographic information is available from OCA.
ReferenceReference
Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA., Marzilli LG, Saad JS, Kuklenyik Z, Keating KA, Xu Y, J Am Chem Soc. 2001 Mar 28;123(12):2764-70. PMID:11456962
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