title: The solution structure of the synthetic circular peptide CGVSRQGKPYC. NMR studies of the folding of a synthetic model for the DNA-binding loop of the ssDNA-binding protein encoded by gene V of phage M13.
abstract: The cyclic disulfide peptide CGVSRQGKPYC was prepared to obtain a constrained analogue of residues 17-27 of the DNA-binding loop of the gene-V-encoded sDNA-binding protein of filamentous bacteriophage M13. Amino acid sequences very similar to that of the beta-loop have been found in various phage-encoded ssDNA-binding proteins, and it has been proposed that such a loop may occur as a common motif in this class of proteins. The conformation, in aqueous solution, of the synthetic gene-V-protein binding-loop analogue has been investigated by means of two-dimensional-1H-NMR techniques. Subsequent structure calculations show that the molecule forms a beta-loop that includes a turn formed by three residues. This structure, very unusually for a cyclic disulfide peptide, is highly similar to that of the analogous part of the binding loop of the native protein. Comparison with experiments on other cyclic disulfide peptides indicates that the formation, of the beta-sheet (beta-hairpin) secondary structure is essentially governed by the amino acid composition of the 11-residue sequence. The disulfide bridge in the 11-residue sequence is essential for conformational stability, as indicated by the finding that the open peptide analogue that encompasses residues Ser17-Ser27 does not adopt a detectable secondary structure in water. The bridge replaces the role of the loop formed by residues 49-58 in the protein, which act as a scaffold to hold the N-terminal and C-terminal ends of the DNA-binding loop together.
authors.affiliation: Laboratory of Organic Chemistry, NSR Center for Molecular Structure, Design and Synthesis, Faculty of Science, University of Nijmegen, The Netherlands.
authors.forename: B H
authors.initials: BH
authors.lastname: Rietman
authors.forename: P J
authors.initials: PJ
authors.lastname: Folkers
authors.forename: R H
authors.initials: RH
authors.lastname: Folmer
authors.forename: G I
authors.initials: GI
authors.lastname: Tesser
authors.forename: C W
authors.initials: CW
authors.lastname: Hilbers
mesh_terms: D000595:Amino Acid Sequence; D017104:Bacteriophage M13 / Q000737:chemistry*; D003545:Cysteine / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D004220:Disulfides / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010456:Peptides, Cyclic / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014764:Viral Proteins / Q000737:chemistry*
chemical_list: D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D004220:Disulfides; D010456:Peptides, Cyclic; D014764:Viral Proteins; C069558:gene V protein, Enterobacteria phage f1; D003545:Cysteine