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| - | [[Image:1b6y.gif|left|200px]] | |
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| + | ==3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES== |
| - | The line below this paragraph, containing "STRUCTURE_1b6y", creates the "Structure Box" on the page.
| + | <StructureSection load='1b6y' size='340' side='right'caption='[[1b6y]]' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1b6y]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B6Y FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </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=EDC:N3,N4-ETHENO-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>EDC</scene></td></tr> |
| - | {{STRUCTURE_1b6y| PDB=1b6y | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6y OCA], [https://pdbe.org/1b6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b6y RCSB], [https://www.ebi.ac.uk/pdbsum/1b6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6y ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Cosman M]] |
| - | The d(C-G-T-A-C-epsilon C-C-A-T-G-C).d(G-C-A-T-G-A-G-T-A-C-G) oligodeoxynucleotide duplex containing the 3, N4-etheno-2'-deoxycytidine adduct positioned opposite 2'-deoxyadenosine in the center of the helix has been analyzed by proton NMR spectroscopy and restrained molecular dynamics. The spectroscopic data establish a right-handed duplex, with sugar puckers in the C2'-endo/C3'-exo range, residues adopting an anti conformation around the glycosidic torsion angle and, with the exception of epsilon C.dA, Watson-Crick hydrogen bond alignment for all base pairs. Molecular dynamics simulations, restrained by the full relaxation matrix approach, produced a three-dimensional model with an NMR R-factor of 7%. The duplex structure shows no significant perturbation of the sugar-phosphate backbone, which remains in B-form. The exocyclic adduct and its partner dA are incorporated into the helix without producing a noticeable kink. The epsilon C.dA alignment adopts a staggered conformation with each residue displaced toward the 5'-terminus and intercalated between bases on the opposite strand, without increase of inter-phosphate distances. The partial intercalation of the epsilon C (anti).dA(anti) alignment allows stacking between the aromatic rings of epsilon C and dA and with base pairs adjacent to the lesion, suggesting an important role played by hydrophobic forces in the stabilization of the solution structure.
| + | [[Category: Cullinan D]] |
| - | | + | [[Category: De Los Santos C]] |
| - | ==About this Structure== | + | [[Category: Eisenberg M]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6Y OCA]. | + | [[Category: Grollman AP]] |
| - | | + | [[Category: Korobka A]] |
| - | ==Reference== | + | [[Category: Patel DJ]] |
| - | Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics., Korobka A, Cullinan D, Cosman M, Grollman AP, Patel DJ, Eisenberg M, de los Santos C, Biochemistry. 1996 Oct 15;35(41):13310-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873597 8873597] | + | |
| - | [[Category: Cosman, M.]] | + | |
| - | [[Category: Cullinan, D.]] | + | |
| - | [[Category: Eisenberg, M.]] | + | |
| - | [[Category: Grollman, A P.]] | + | |
| - | [[Category: Korobka, A.]] | + | |
| - | [[Category: Patel, D J.]] | + | |
| - | [[Category: Santos, C De Los.]] | + | |
| - | [[Category: Deoxyribonucleic acid]] | + | |
| - | [[Category: Edc]] | + | |
| - | [[Category: Ethenodc]] | + | |
| - | [[Category: Exocyclic lesion]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 11:08:55 2008''
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