2hli

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Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence

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-[[Image:2hli.gif|left|200px]]<br /><applet load="2hli" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2hli" />
-'''Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence'''<br />
-==Overview==
+==Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence==
-The conformation of the crotonaldehyde-derived, N(2)-[3-oxo-1(S)-methyl-propyl]-dG adduct in the oligodeoxynucleotide, 5'-d(G(1)C(2)T(3)A(4)G(5)C(6)X(7)A(8)G(9)T(10)C(11)C(12))-3'.5'-d(G(13)G(1, 4)A(15)C(16)T(17)C(18)G(19)C(20)T(21)A(22)G(23)C(2)(4))-3', where X =, N(2)-[3-oxo-1(S)-methyl-propyl]-dG, is reported. This adduct arises from, opening of the cyclic N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG, adduct when placed opposite dC in duplex DNA. This oligodeoxynucleotide, contains the 5'-CpG-3' sequence in which the, N(2)-(R-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG but not the, N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct preferentially, formed an interstrand carbinolamine cross-link [Kozekov, I. D., Nechev, L., V., Moseley, M. S., Harris, C. M., Rizzo, C. J., Stone, M. P., and Harris, T. M. (2003) J. Am. Chem. Soc. 125, 50-61; Cho, Y.-J., Wang, H., Kozekov, I. D., Kurtz, A. J., Jacob, J., Voehler, M., Smith, J., Harris, T. M., Lloyd, R. S., Rizzo, C. J., and Stone, M. P. (2006) Chem. Res. Toxicol., 19, 195-208]. Analysis of (1)H NOE data, chemical shift perturbations, and, deoxyribose pseudorotations and backbone torsion angles suggested the, presence of a stable and ordered DNA conformation at pH 9.3 and 30 degrees, C, with minimal conformational perturbation. The spectral line widths of, the adduct protons were comparable to those of the oligodeoxynucleotide, suggesting that the correlation times of these protons were similar to, those of the overall duplex. The crotonaldehydic-derived methyl protons, showed NOEs in the 5'-direction to C(18) H1', G(19) H1', and G(19) H4' in, the complementary strand of the duplex. The aldehyde proton of the adduct, exhibited NOEs in the 3'-direction to A(8) H1' and A(8) H4' in the, modified strand. All of these NOEs involved DNA protons facing the minor, groove. Molecular dynamics calculations, restrained by distances and, torsion angles derived from the NMR data, revealed that within the minor, groove, the aldehyde of the N(2)-[3-oxo-1(S)-methyl-propyl]-dG adduct, oriented in the 3'-direction, while the 1(S) methyl group oriented in the, 5'-direction. This positioned the aldehyde distal to the G(19) exocyclic, amine and provided a rationale as to why the, N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct generated, interstrand cross-links less efficiently than did the, N(2)-(R-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct.
+<StructureSection load='2hli' size='340' side='right'caption='[[2hli]]' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2hli]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HLI FirstGlance]. <br>
-HLI 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://oca.weizmann.ac.il/oca-bin/ocashort?id=2HLI OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KAG:2-DEOXY-N-[(1S)-1-METHYL-3-OXOPROPYL]GUANOSINE+5-PHOSPHATE'>KAG</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=2hli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hli OCA], [https://pdbe.org/2hli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hli RCSB], [https://www.ebi.ac.uk/pdbsum/2hli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hli ProSAT]</span></td></tr>
-Orientation of the crotonaldehyde-derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA adduct hinders interstrand cross-link formation in the 5'-CpG-3' sequence., Cho YJ, Wang H, Kozekov ID, Kozekova A, Kurtz AJ, Jacob J, Voehler M, Smith J, Harris TM, Rizzo CJ, Lloyd RS, Stone MP, Chem Res Toxicol. 2006 Aug;19(8):1019-29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16918240 16918240]
+</table>
-[[Category: Protein complex]]
+__TOC__
-[[Category: Cho, Y.J.]]
+</StructureSection>
-[[Category: Harris, T.M.]]
+[[Category: Large Structures]]
-[[Category: Jacob, J.]]
+[[Category: Cho Y-J]]
-[[Category: Kozekov, I.D.]]
+[[Category: Harris TM]]
-[[Category: Kurtz, A.J.]]
+[[Category: Jacob J]]
-[[Category: Rizzo, C.J.]]
+[[Category: Kozekov ID]]
-[[Category: Smith, J.]]
+[[Category: Kurtz AJ]]
-[[Category: Stone, M.P.]]
+[[Category: Rizzo CJ]]
-[[Category: Voehler, M]]
+[[Category: Smith J]]
-[[Category: Wang, H.]]
+[[Category: Stone MP]]
-[[Category: interstrand dna cross-link; s-crotonaldehyde-dg adduct; 5'-cpg-3' sequence]]
+[[Category: Voehler M]]
+[[Category: Wang H]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:23:27 2008''

2hli

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Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence

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