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2hmr

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Revision as of 06:30, 27 June 2018

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

Structural highlights

2hmr is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	2hli, 2hmd
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Cho YJ, Kozekov ID, Harris TM, Rizzo CJ, Stone MP. 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. Biochemistry. 2007 Mar 13;46(10):2608-21. Epub 2007 Feb 17. PMID:17305317 doi:http://dx.doi.org/10.1021/bi061381h

1 Structural highlights
2 Publication Abstract from PubMed
3 References

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Retrieved from "http://52.214.119.220/wiki/index.php/2hmr"

@@ Line 1: / Line 1: @@
 ==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==
 <StructureSection load='2hmr' size='340' side='right' caption='[[2hmr]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2EG:2-DEOXY-N-ETHYLGUANOSINE+5-PHOSPHATE'>2EG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hli|2hli]], [[2hmd|2hmd]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hmr OCA], [http://pdbe.org/2hmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hmr RCSB], [http://www.ebi.ac.uk/pdbsum/2hmr PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hmr OCA], [http://pdbe.org/2hmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hmr RCSB], [http://www.ebi.ac.uk/pdbsum/2hmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hmr ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">

2hmr

From Proteopedia

Revision as of 06:30, 27 June 2018

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

Structural highlights

Publication Abstract from PubMed

References

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