Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain(436 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
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Otting, G., Qian, Y.Q., Billeter, M., Müller, M., Affolter, M., Gehring, W.J., Wüthrich, K., Protein-DNA contacts in the structure of a homeodomain-DNA complex determined by nuclear magnetic resonance spectroscopy in solution (1990) EMBO J., 9, pp. 3085-3092
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Pabo, C.O., Sauer, R.T., Transcription factors: Structural families and principles of DNA recognition (1992) Annu. Rev. Biochem., 61, pp. 1053-1095
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John Wiley, New York, UK
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Wüthrich, K., Sequence-specific assignments in protein (1986) NMK of Proteins and Nucleic Acids, pp. 130-161. , edited by: Wuthrich, K. Wiley, New York, USA
Wishart, D.S., Sykes, B.D., Richards, F.M., Relationship between NMR chemical shift and protein secondary structure (1991) J. Mol. Biol., 222, pp. 311-333
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Merutka, G., Dyson, H.J., Wright, P.E., Random coil 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG (1995) J. Biomol. NMR, 5, pp. 14-24
Gehring, W. J., Qian, Y. Q., Billeter, M., Furukubo-Tokunaga, K., Schier, A. F., Resendez-Perez, D., Affolter, M., W thrich, K., Homeodomain-DNA recognition (1994) Cell, 78, pp. 211-22
Gehring, W. J., M ller, M., Affolter, M., Percival-Smith, A., Billeter, M., Qian, Y. Q., Otting, G., W thrich, K., The structure of the homeodomain and its functional implications (1990) Trends Genet., 6, pp. 323-329
Kissinger, C. R., Liu, B., Martin-Blanco, E., Kornberg, T. B., Pabo, C. O., Crystal structure of an engrailed homeodomain-DNA complex at 2. 8 resolution: A framework for understanding homeodomain-DNA interactions (1990) Cell, 63, pp. 579-590
Pabo, C. O., Sauer, R. T., Transcription factors: Structural families and principles of DNA recognition (1992) Annu. Rev. Biochem., 61, pp. 1053-1095
Berlose, J. P., Convert, O., De Rossi, D., Brunissen, A., Chassaing, G., Conformational and associative behaviours of the third helix of Antennapedia homeodomain in membrane-mimetic environments (1996) Eur. J. Biochem., 242, pp. 372-386
Killian, J. A., Trouard, T. P., Greathouse, D. V., Chupin, V., Lindblom, G., A general method for the preparation of mixed micelles of hydrophobic peptides and sodium dodecyl sulphate (1994) FEBS Lett., 348, pp. 161-165
Yang, J. T., Kubota, S., Ordered conformation of poly (L-lysine) and its homologs in anionic surfactant solution (1985) Microdomains in Polymer Solutions, pp. 311-331. , (Dubin, P. L., ed.), Plenum Press, New York, USA
Rance, M., S rensen, O. W., Bodenhausen, G., Wagner, G., Ernst, R. R., W thrich, K., Improved spectral resolution in COSY1H NMR spectra of proteins via double quantum filtering (1983) Biochem. Biophys. Res. Commun., 117, pp. 479-485
Griesinger, C., S rensen, O. W., Ernst, R. R., Practical aspects of the E. COSY technique. Measurement of scalar spin-spin coupling constants in peptides (1987) J. Magn. Res., 75, pp. 474-492
W thrich, K., Billeter, M., Braun, W., Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance (1983) J. Mol. Biol., 169, pp. 949-961
Havel, T. F., (1986) DISGEO, Quantum Chemistry Exchange Program Exchange No. 507, , Indiana University, USA
Crippen, G. M., Havel, T. F., (1988) Distance Geometry and Molecular Conformation, , Research Studies Press Ltd, Somerset, England
Havel, T. F., An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by NMR spectroscopy (1991) Prog. Biophys. Mol. Biol., 56, pp. 43-78
Van Nuland, N. A. J., Gr tzinger, J., Dijkstra, K., Scheck, R. M., Robillard, G. T., Determination of the three-dimensional solution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli using multidimensional NMR spectroscopy (1992) Eur. J. Biochem., 210, pp. 881-891
Scheck, R. M., Torda, A. E., Kenmink, J., Van Gunsteren, W. F., Structure determination by NMR: The modeling of NMR parameters as ensemble averages (1991) Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance, pp. 209-217. , edited by: Hoch, J. C., Poulser, P. M., Redfield, C. Plenum Press, New York, USA
Scheck, R. M., Van Gunsteren, W. F., Kaptein, R., Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data (1989) Methods in Enzymology, 177, pp. 204-218. , (Oppenheimer, N. J. & James, T. L., eds). Academic Press, New York, USA
W thrich, K., Sequence-specific assignments in protein (1986) NMK of Proteins and Nucleic Acids, pp. 130-161. , edited by: Wuthrich, K. Wiley, New York, USA
Wishart, D. S., Sykes, B. D., Richards, F. M., Relationship between NMR chemical shift and protein secondary structure (1991) J. Mol. Biol., 222, pp. 311-333
Bundi, A., W thrich, K., Use of amide1H NMR titration shifts for studies of polypeptide conformation (1979) Biopolymers, 18, pp. 299-311
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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