Keywords: 3d Domain Swapping, Cis-Pro, Protein Mutations, Protein Structure, Structural Stability, Alanine, Asparagine, Dimer, Monomer, Pancreatic Ribonuclease, Proline, Protein Variant, Alpha Helix, Amino Acid Substitution, Amino Terminal Sequence, Article, Carboxy Terminal Sequence, Cis Trans Isomerism, Controlled Study, Crystal Structure, Female, Hydration, Molecular Interaction, Nonhuman, Nuclear Magnetic Resonance, Protein Conformation, Protein Stability, X Ray Diffraction, Animals, Cattle, Dimerization, Magnetic Resonance Spectroscopy, Protein Folding, Secondary, Tertiary, X-Ray Diffraction, Bovinae,
Affiliations: *** IBB - CNR ***
Dipartimento di Chimica, Università di Napoli Federico II, Complesso, Universitario di Monte Sant' Angelo, Via Cintia, 80126 Napoli, Italy
Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy
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Gronenborn, A. M., Protein acrobatics in pairs-dimerization via domain swapping (2009) Curr. Opin. Struct. Biol., 19, pp. 39-49
Liu, Y., Hart, P. J., Schlunegger, M. P., Eisenberg, D., The crystal structure of a 3D domain-swapped dimer of RNase A at a 2. 1-A resolution (1998) Proc. Natl. Acad. Sci. U S A, 95, pp. 3437-3442
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Schultz, D. A., Baldwin, R. L., Cis proline mutants of ribonuclease A. I. thermal stability (1992) Protein Sci., 1, pp. 910-916
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Dodge, R. W., Scheraga, H. A., Folding and unfolding kinetics of the proline-to-alanine mutants of bovine pancreatic ribonuclease A (1996) Biochemistry, 35, pp. 1548-1559
Schultz, L. W., Hargraves, S. R., Klink, T. A., Raines, R. T., Structure and stability of the P93G variant of ribonuclease A (1998) Protein Sci., 7, pp. 1620-1625
Schultz, D. A., Friedman, A. M., White, M. A., Fox, R. O., The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A (2005) Protein Sci., 14, pp. 2862-2870
Pearson, M. A., Karplus, P. A., Dodge, R. W., Laity, J. H., Scheraga, H. A., Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A (1998) Protein Sci., 7, pp. 1255-1258
Johnson, B. A., Using NMRVIEW to visualize and analyze the NMR spectra of macromolecules (2004) Methods Mol. Biol., 278, pp. 313-352
Brunger, A. T., (1996) X-PLOR Version 3. 8, , Department of Molecular Biophysics and Biochemistry, Yale University New Haven, Connecticut
Brunger, A. T., Adams, P. D., Clore, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Warren, G. L., Crystallography & NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallogr. D Biol. Crystallogr., 54 (PART 5), pp. 905-921
Jones, T. A., Bergdoll, M., Kjeldgaard, M., (1990) O: A Macromolecule Modeling Environment, Crystallogr. Model. Methods Mol. Des., [Pap. Symp.], pp. 189-199. , C. Bugg, S. Ealick, Springer-Verlag Press
Laskowski, R. A., MacArthur, M. W., Moss, M. D., Thorton, J. M., PROCHECK: A program to check the stereochemical quality of protein structure (1993) J. Appl. Crystallogr., 26, pp. 283-291
Kraulis, P. J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures (1991) J. Appl. Crystallogr, 24, pp. 946-950
Esnouf, R. M., Further additions to MolScript version 1. 4, including reading and conturing of electron-density maps (1999) Acta Crystallogr. D, 55, pp. 938-940
Lopez-Alonso, J. P., Bruix, M., Font, J., Ribo, M., Vilanova, M., Jimenez, M. A., Santoro, J., Laurents, D. V., NMR spectroscopy reveals that RNase A is chiefly denatured in 40% acetic acid: Implications for oligomer formation by 3D domain swapping (2010) J. Am. Chem. Soc., 132, pp. 1621-1630
Miller, K. H., Karr, J. R., Marqusee, S., A hinge region cis-proline in ribonuclease A acts as a conformational gatekeeper for C-terminal domain swapping (2010) J. Mol. Biol., 400, pp. 567-578
Chain termini cross-talk in the swapping process of bovine pancreatic ribonuclease
3D domain swapping is the process by which two or more protein molecules exchange part of their structure to form intertwined dimers or higher oligomers. Bovine pancreatic ribonuclease (RNase A) is able to swap the N-terminal alpha-helix (residues 1-13) and/or the C-terminal beta-strand (residues 116-124), thus forming a variety of oligomers, including two different dimers. Cis-trans isomerization of the Asn113-Pro114 peptide group was observed when the protein formed the C-terminal swapped dimer. To study the effect of the substitution of Pro114 on the swapping process of RNase A, we have prepared and characterized the P114A monomeric and dimeric variants of the enzyme. In contrast with previous reports, the crystal structure and NMR data on the monomer reveals a mixed cis-trans conformation for the Asn113-Ala114 peptide group, whereas the X-ray structure of the C-terminal swapped dimer of the variant is very close to that of the corresponding dimer of RNase A. The mutation at the C-terminus affects the capability of the N-terminal alpha-helix to swap and the stability of both dimeric forms. The present results underscore the importance of the hydration shell in determining the cross-talk between the chain termini in the swapping process of RNase A. (C) 2012 Elsevier Masson SAS. All rights reserved.
Chain termini cross-talk in the swapping process of bovine pancreatic ribonuclease