Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain(607 views) Saviano M, Isernia C, Bassarello C, Di Lello P, Galdiero S, Mierke DF, Benedetti E, Pedone C
J Pept Res (ISSN: 1397-002x), 2005 Feb; 65(2): 200-208.
Keywords: Antennapedia, Circular Dichroism, Distance Geometry, Linear Peptides, Nuclear Magnetic Resonance, Antennapedia Protein, Dna Binding Protein, Homeodomain Protein, Unclassified Drug, Article, Nonhuman, Nuclear Magnetic Resonance Spectroscopy, Peptide Analysis, Priority Journal, Protein Analysis, Protein Conformation, Protein Dna Binding, Reversed Phase High Performance Liquid Chromatography, Animals, Antennapedia Homeodomain Protein, Nuclear Proteins, Protein Structure, Secondary, Solvents, Transcription Factors, Trifluoroethanol,
Affiliations: *** IBB - CNR ***
Inst. Biostructures and Bioimaging, CNR, via Mezzocannone 16, I-80134 Napoli, Italy
Environmental Sciences Department, Second University of Naples, via Vivaldi 43, 81100 Caserta, Italy
Dipto. di Scienze Farmaceutiche, Università di Salerno, 84084 Fisciano, SA, Italy
Department of Molecular Pharmacology, Box B-G4, Brown University, 171 Meeting Street, Providence, RI 02912, United States
References: Not available.
Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain
The Antennapedia homeodomain structure consists of four helices. The helices II and III are connected by a tripeptide that forms a turn, and constitute the well-known helix-turn-helix motif. The recognition helix penetrates the DNA major groove, gives specific protein-DNA contacts and forms direct, or water-mediated, intermolecular hydrogen bonds. It was suggested that helix III (and perhaps also helix IV) might represent the recognition helix of Antennapedia homeodomain, which makes contact with the surface of the major groove of the DNA. In an attempt to clarify the helix III capabilities of assuming an helical conformation when separated from the rest of the protein, we carried out the structural determination of the recognition helix III in different solvent media. The conformational study of fragments 42-53, where residues W48 and F49, not involved in the protein-DNA interaction, were substituted by two alanines, was conducted in sodium dodecyl sulfate (SDS), trifluoroethanol (TFE) and TFE/ water, using circular dichroism, nuclear magnetic resonance (NMR) and distance geometry (DG) techniques. The fragment assumes a well-defined secondary structure in TFE and in TFE/water (90/10, v/v) with an α-helix encompassing residues 4-9, while in TFE/water (70/30, v/v) a less regular structure was found. The DG results in the micellar system evidence the presence of a distorted α-helical conformation involving residues 4-8. Our results reveal that the isolated Antennapedia recognition helix III tend to preserve in solution the α-helical conformation even if separated from the rest of the molecule. Copyright Blackwell Munksgaard, 2005.
Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain
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