Probing the residual structure in avian prion hexarepeats by CD, NMR and MD techniques(418 views) Russo L, Raiola L, Campitiello MA, Magrì A, Fattorusso R, Malgieri G, Pappalardo G, La Mendola D, Isernia C
Keywords: Avian Prion Repeats, Conformational Ensemble, Polyproline Ii, Peptide Fragment, Amino Acid Sequence, Animal, Article, Chemistry, Chicken, Circular Dichroism, Molecular Dynamics, Nuclear Magnetic Resonance, Protein Secondary Structure, Molecular Dynamics Simulation, Biomolecular, Protein Structure,
Affiliations: *** IBB - CNR ***
Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy
CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy
Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli Federico II, Via Mezzocannone 16, 80134 Napoli, Italy
Dipartimento di Farmacia, Università di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy
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Hornshaw, M. P., McDermott, J. R., Candy, J. M., Copper binding to the N-terminal tandem repeat regions of mammalian and avian prion protein (1995) Biochem. Biophys. Res. Commun., 207, pp. 621-629
Bienkiewicz, E. A., Moon Woody, A., Woody, R. W., Conformation of the RNA polymerase II C-terminal domain: Circular dichroism of long and short fragments (2000) J. Mol. Biol., 297, pp. 119-133
Tong, A. H. Y., Drees, B., Nardelli, G., Bader, G. D., Brannetti, B., Castagnoli, L., Evangelista, M., Cesareni, G., A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules (2002) Science, 295 (5553), pp. 321-324. , DOI 10. 1126/science. 1064987
Woody, R. W., Theory of circular dichroism of proteins (1996) Circular Dichroism and the Conformational Analysis of Biomolecules, pp. 25-68. , Fasman, G. D., Ed.
W thrich, K., (1986) NMR of Proteins and Nucleic Acids, , Wiley: New York, NY, USA
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Wishart, D. S., Sykes, B. D., The 13C chemical-shift index: A simple method for the identification of protein secondary structure using 13C chemical-shift data (1994) J. Biomol. NMR, 4, pp. 171-180
Lam, S. L., Hsu, V. L., NMR identification of left-handed polyproline type II helices (2003) Biopolymers, 69 (2), pp. 270-281. , DOI 10. 1002/bip. 10354
Andersen, N. H., Neidigh, J. W., Harris, S. M., Lee, G. M., Liu, Z., Tong, H., Extracting information from the temperature gradients of polypeptide NH chemical shifts. 1. The importance of conformational averaging (1997) Journal of the American Chemical Society, 119 (36), pp. 8547-8561. , DOI 10. 1021/ja963250h
Ramachandran, G. N., Ramadrishnan, C., Sasisekharan, V., Stereochemistry of polypeptide chain configurations (1963) J. Mol. Biol., 7, pp. 95-99
Dyson, H. J., Wright, P. E., Defining solution conformations of small linear peptides (1991) Annu. Rev Biophys. Biophys. Chem., 20, pp. 519-538
Vuister, G. W., Bax, A., Quantitative J correlation - A new approach for measuring homonuclear 3-bond J (H (N) H (Alpha) coupling-constants in N-15-enriched proteins (1993) J. Am. Chem. Soc., 115, pp. 7772-7777
Fiebig, K. M., Schwalbe, H., Buck, M., Smith, L. J., Dobson, C. M., Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements (1996) Journal of Physical Chemistry, 100 (7), pp. 2661-2666
Hinck, A. P., Eberhardt, E. S., Markley, J. L., NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: Mutants of staphylococcal nuclease with altered configuration at proline-117 (1993) Biochemistry, 32 (44), pp. 11810-11818. , DOI 10. 1021/bi00095a009
Choy, W. -Y., Forman-Kay, J. D., Calculation of ensembles of structures representing the unfolded state of an SH3 domain (2001) Journal of Molecular Biology, 308 (5), pp. 1011-1032. , DOI 10. 1006/jmbi. 2001. 4750
Marsh, J. A., Neale, C., Jack, F. E., Choy, W. -Y., Lee, A. Y., Crowhurst, K. A., Forman-Kay, J. D., Improved Structural Characterizations of the drkN SH3 Domain Unfolded State Suggest a Compact Ensemble with Native-like and Non-native Structure (2007) Journal of Molecular Biology, 367 (5), pp. 1494-1510. , DOI 10. 1016/j. jmb. 2007. 01. 038, PII S0022283607000782
Marsh, J. A., Forman-Kay, J. D., Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints (2009) J. Mol. Biol., 391, pp. 359-374
Feldman, H. J., Hogue, C. W. V., A fast method to sample real protein conformational space (2000) Proteins: Structure, Function and Genetics, 39 (2), pp. 112-131. , DOI 10. 1002/ (SICI) 1097-0134 (20000501) 39: 2<112:: AID-PROT2>
3. 0. CO
Garc a De La Torre, J., Huertas, M. L., Carrasco, B., HYDRONMR: Prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations (2000) J. Magn. Reson., 147, pp. 138-146
Ortega, A., Amor s, D., Garc a De La Torre, J., Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models (2011) Biophys J., 101, pp. 892-898
Kelley, L. A., Gardner, S. P., Sutcliffe, M. J., An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies (1996) Protein Engineering, 9 (11), pp. 1063-1065
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Keller, R. L. J., (2004) Optimizing the Process of Nuclear Magnetic Resonance Spectrum Analysis and Computer Aided Resonance Assignment, , PhD Thesis, Swiss Federal Institute of Technology, Z rich
Delano, W. L., (2002) The PyMOL Molecular Graphics System
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., Ferrin, T. E., UCSF Chimera a visualization system for exploratory research and analysis (2004) J. Comput. Chem., 25, pp. 1605-1612
Gibbs, S. J., Johnson Jr., C. S., PFG NMR experiment for accurate diffusion and flow studies in the presence of eddy currents (1991) J. Magn. Reson., 93, pp. 395-402
Wilkins, D. K., Grimshaw, S. B., Receveur, V., Dobson, C. M., Jones, J. A., Smith, L. J., Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques (1999) Biochemistry, 38, pp. 16424-16431
Boehr, D. D., Nussinov, R., Wright, P. E., The role of dynamic conformational ensembles in biomolecular recognition (2009) Nat. Chem. Biol., 5, pp. 789-796
Lange, O. F., Lakomek, N. -A., Fares, C., Schroder, G. F., Walter, K. F. A., Becker, S., Meiler, J., De Groot, B. L., Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution (2008) Science, 320 (5882), pp. 1471-1475. , DOI 10. 1126/science. 1157092
Probing the residual structure in avian prion hexarepeats by CD, NMR and MD techniques
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