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| | {{STRUCTURE_1j9n| PDB=1j9n | SCENE= }} | | {{STRUCTURE_1j9n| PDB=1j9n | SCENE= }} |
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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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| - | ==Overview==
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| - | 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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_12512075}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 12512075 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_12512075}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9N OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9N OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Covalently linked peptide-dna complex]] | | [[Category: Covalently linked peptide-dna complex]] |
| | [[Category: Tryptophan stacking]] | | [[Category: Tryptophan stacking]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:57:15 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 14:44:39 2008'' |
Revision as of 11:44, 1 July 2008
Template:STRUCTURE 1j9n
Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dGCATCG)-ALA]-[p5*dCGTAGC]
Template:ABSTRACT PUBMED 12512075
About this Structure
Full experimental 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 Tue Jul 1 14:44:39 2008
