1j9n
From Proteopedia
|
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
1J9N is a Protein complex structure of sequences from [1] with ACE as ligand. 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 Sat Nov 24 23:19:32 2007
