1j9n

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[[Image:1j9n.gif|left|200px]]
[[Image:1j9n.gif|left|200px]]
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{{Structure
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|PDB= 1j9n |SIZE=350|CAPTION= <scene name='initialview01'>1j9n</scene>
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The line below this paragraph, containing "STRUCTURE_1j9n", creates the "Structure Box" on the page.
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|SITE=
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|LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=HSE:L-HOMOSERINE'>HSE</scene>, <scene name='pdbligand=PGN:2&#39;-DEOXYGUANOSINE-3&#39;,5&#39;-DIPHOSPHATE'>PGN</scene>
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{{STRUCTURE_1j9n| PDB=1j9n | SCENE= }}
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9n OCA], [http://www.ebi.ac.uk/pdbsum/1j9n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j9n RCSB]</span>
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'''Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dGCATCG)-ALA]-[p5*dCGTAGC]'''
'''Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dGCATCG)-ALA]-[p5*dCGTAGC]'''
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==About this Structure==
==About this Structure==
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1J9N is a [[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=1J9N OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9N OCA].
==Reference==
==Reference==
Solution structure and stability of tryptophan-containing nucleopeptide duplexes., Gomez-Pinto I, Marchan V, Gago F, Grandas A, Gonzalez C, Chembiochem. 2003 Jan 3;4(1):40-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12512075 12512075]
Solution structure and stability of tryptophan-containing nucleopeptide duplexes., Gomez-Pinto I, Marchan V, Gago F, Grandas A, Gonzalez C, Chembiochem. 2003 Jan 3;4(1):40-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12512075 12512075]
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[[Category: Protein complex]]
 
[[Category: Gago, F.]]
[[Category: Gago, F.]]
[[Category: Gomez-Pinto, I.]]
[[Category: Gomez-Pinto, I.]]
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[[Category: Grandas, A.]]
[[Category: Grandas, A.]]
[[Category: Marchan, V.]]
[[Category: Marchan, V.]]
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[[Category: covalently linked peptide-dna complex]]
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[[Category: Covalently linked peptide-dna complex]]
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[[Category: tryptophan stacking]]
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[[Category: Tryptophan stacking]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:57:15 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:30:31 2008''
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Revision as of 17:57, 2 May 2008

Image:1j9n.gif

Template:STRUCTURE 1j9n

Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dGCATCG)-ALA]-[p5*dCGTAGC]


Overview

Covalently linked peptide-oligonucleotide hybrids were used as models for studying tryptophan-DNA interactions. The structure and stability of several hybrids in which peptides and oligonucleotides are linked through a phosphodiester bond between the hydroxy group of a homoserine (Hse) side chain and the 3'-end of the oligonucleotide, have been studied by both NMR and CD spectroscopy and by restrained molecular dynamics methods. The three-dimensional solution structure of the complex between Ac-Lys-Trp-Lys-Hse(p3'dGCATCG)-Ala-OH (p=phosphate, Ac=acetyl) and its complementary strand 5'dCGTAGC has been determined from a set of 276 experimental NOE distances and 33 dihedral angle constraints. The oligonucleotide structure is a well-defined duplex that belongs to the B-form family of DNA structures. The covalently linked peptide adopts a folded structure in which the tryptophan side chain stacks against the 3'-terminal guanine moiety, which forms a cap at the end of the duplex. This stacking interaction, which resembles other tryptophan-nucleobase interactions observed in some protein-DNA complexes, is not observed in the single-stranded form of Ac-Lys-Trp-Lys-Hse(p3'dGCATCG)-Ala-OH, where the peptide chain is completely disordered. A comparison with the pure DNA duplex, d(5'GCTACG3')-(5'CGTAGC3'), indicates that the interaction between the peptide and the DNA contributes to the stability of the nucleopeptide duplex. The different contributions that stabilize this complex have been evaluated by studying other nucleopeptide compounds with related sequences.

About this Structure

Full crystallographic information is available from OCA.

Reference

Solution structure and stability of tryptophan-containing nucleopeptide duplexes., Gomez-Pinto I, Marchan V, Gago F, Grandas A, Gonzalez C, Chembiochem. 2003 Jan 3;4(1):40-9. PMID:12512075 Page seeded by OCA on Fri May 2 20:57:15 2008

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