2hmr

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(New page: 200px<br /><applet load="2hmr" size="350" color="white" frame="true" align="right" spinBox="true" caption="2hmr" /> '''Solution structure of reduced interstrand cr...)
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[[Image:2hmr.gif|left|200px]]<br /><applet load="2hmr" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2hmr" />
 
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'''Solution structure of reduced interstrand cross-link arising from S-alpha-methyl-gamma-OH-1,N2-propano-2'-deoxyguanosine in the 5'-CpG-3' DNA sequence'''<br />
 
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==Overview==
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==Solution structure of reduced interstrand cross-link arising from S-alpha-methyl-gamma-OH-1,N2-propano-2'-deoxyguanosine in the 5'-CpG-3' DNA sequence==
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The solution structures of, 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' and, 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' interstrand DNA, cross-links in the 5'-CpG-3' sequence were determined by NMR spectroscopy., These were utilized as chemically stable surrogates for the corresponding, carbinolamine interstrand cross-links arising from the crotonaldehyde- and, acetaldehyde-derived R- and, S-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adducts. The results, provide an explanation for the observation that interstrand cross-link, formation in the 5'-CpG-3' sequence by the R- and, S-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adducts is dependent upon, stereochemistry, favoring the, R-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adduct [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]. Molecular dynamics, calculations, restrained by NOE-based distances and empirical restraints, revealed that both the 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3', and 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-links were, located in the minor groove and retained Watson-Crick hydrogen bonds at, the tandem cross-linked C.G base pairs. However, for the, 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link, the, (alpha)-CH3 group was positioned in the center of the minor groove, whereas for the 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3', cross-link, the (alpha)-CH3 group was positioned in the 3' direction, showing steric interference with the DNA helix. The, 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link exhibited a, lower thermal stability as evidenced by NMR spectroscopy as a function of, temperature. The two cross-links also exhibited apparent differences in, the conformation of the interstrand three-carbon cross-link, which may, also contribute to the lower apparent thermodynamic stability of the, 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link.
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<StructureSection load='2hmr' size='340' side='right'caption='[[2hmr]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2hmr]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HMR FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2EG:2-DEOXY-N-ETHYLGUANOSINE+5-PHOSPHATE'>2EG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hmr OCA], [https://pdbe.org/2hmr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hmr RCSB], [https://www.ebi.ac.uk/pdbsum/2hmr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hmr ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The solution structures of 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' and 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' interstrand DNA cross-links in the 5'-CpG-3' sequence were determined by NMR spectroscopy. These were utilized as chemically stable surrogates for the corresponding carbinolamine interstrand cross-links arising from the crotonaldehyde- and acetaldehyde-derived R- and S-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adducts. The results provide an explanation for the observation that interstrand cross-link formation in the 5'-CpG-3' sequence by the R- and S-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adducts is dependent upon stereochemistry, favoring the R-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adduct [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]. Molecular dynamics calculations, restrained by NOE-based distances and empirical restraints, revealed that both the 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' and 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-links were located in the minor groove and retained Watson-Crick hydrogen bonds at the tandem cross-linked C.G base pairs. However, for the 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link, the (alpha)-CH3 group was positioned in the center of the minor groove, whereas for the 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link, the (alpha)-CH3 group was positioned in the 3' direction, showing steric interference with the DNA helix. The 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link exhibited a lower thermal stability as evidenced by NMR spectroscopy as a function of temperature. The two cross-links also exhibited apparent differences in the conformation of the interstrand three-carbon cross-link, which may also contribute to the lower apparent thermodynamic stability of the 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link.
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==About this Structure==
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Stereochemistry modulates the stability of reduced interstrand cross-links arising from R- and S-alpha-CH3-gamma-OH-1,N2-propano-2'-deoxyguanosine in the 5'-CpG-3' DNA sequence.,Cho YJ, Kozekov ID, Harris TM, Rizzo CJ, Stone MP Biochemistry. 2007 Mar 13;46(10):2608-21. Epub 2007 Feb 17. PMID:17305317<ref>PMID:17305317</ref>
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2HMR 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=2HMR OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Stereochemistry Modulates the Stability of Reduced Interstrand Cross-Links Arising from R- and S-alpha-CH(3)-gamma-OH-1,N(2)-Propano-2'-deoxyguanosine in the 5'-CpG-3' DNA Sequence., Cho YJ, Kozekov ID, Harris TM, Rizzo CJ, Stone MP, Biochemistry. 2007 Mar 13;46(10):2608-21. Epub 2007 Feb 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17305317 17305317]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 2hmr" style="background-color:#fffaf0;"></div>
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[[Category: Cho, Y.J.]]
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== References ==
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[[Category: Harris, T.M.]]
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<references/>
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[[Category: Kozekov, I.D.]]
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__TOC__
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[[Category: Rizzo, C.J.]]
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</StructureSection>
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[[Category: Stone, M.P.]]
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[[Category: Large Structures]]
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[[Category: crotonaldehyde interstrand dna cross-link]]
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[[Category: Cho Y-J]]
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[[Category: Harris TM]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:24:15 2008''
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[[Category: Kozekov ID]]
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[[Category: Rizzo CJ]]
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[[Category: Stone MP]]

Current revision

Solution structure of reduced interstrand cross-link arising from S-alpha-methyl-gamma-OH-1,N2-propano-2'-deoxyguanosine in the 5'-CpG-3' DNA sequence

PDB ID 2hmr

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