Keywords: Protein Dynamics, Protein Structure-Function, Protein-Inhibitor Complex, Ribonuclease, X-Ray Diffraction, Cytidylic Acid, Cytidine Derivative, Oligomer, Unclassified Drug, Article, Conformational Transition, Crystal Structure, Enzyme Binding, Enzyme Conformation, Enzyme Substrate Complex, Molecular Dynamics, Motion, Priority Journal, Protein Domain, X Ray Crystallography, Animals, Cattle, Crystallization, Cytidine Monophosphate, Ligands, Models, Protein Binding, Protein Conformation, Tertiary, Pancreatic,
Affiliations: *** IBB - CNR ***
Centro di Biocristallografia, CNR, Napoli, Italy
Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Napoli, Italy
CEINGE, Biotecnologie Avanzate Scarl, Napoli, Italy
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Rasmussen, B.F., Stock, A.M., Ringe, D., Petsko, G.A., Crystalline ribonuclease A loses function below the dynamical transition at 22 0 K (1992) Nature, 357, pp. 423-424
Triton, R.F.J., Dewan, J.C., Petsko, G.A., Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K (1992) Biochemistry, 31, pp. 2469-2481
Radha Kishan, K.V., Chandra, N.R., Sudarsanakumar, C., Suguna, K., Vijayan, M., Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme (1995) Acta Crystallogr D Biol Crystallogr, 51, pp. 703-710
Sadasivan, C., Nagendra, H.G., Vijayan, M., Plasticity, hydration and accessibility in ribonuclease A. The structure of a new crystal form and its low-humidity variant (1998) Acta Crystallogr D Biol Crystallogr, 54, pp. 1343-1352
Leonidas, D.D., Shapiro, R., Irons, L.I., Russo, N., Acharya, K.R., Crystal structures of ribonuclease A complexes with 5′-diphosphoadenosine 3′-phosphate and 5′-diphosphoadenosine 2′-phosphate at 1.7 Å resolution (1997) Biochemistry, 36, pp. 5578-5588
Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L., Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2′,5′)guanosine (2000) Protein Sci, 9, pp. 1217-1225
Otwinowsky, Z., Minor, W., Processing of X-ray diffraction data collected in oscillation mode (1997) Methods Enzymol, 276, pp. 307-326
Brunger, A.T., (1992) X-PLOR version 3.1: A system for X-ray crystallography and NMR, , New Haven, CT: Yale University Press
Jones, T.A., Zou, J.Y., Cowan, S.W., Kjeldgaard, M., Improved methods for binding protein models in electron density maps and the location of errors in these models (1991) Acta Crystallogr A, 47, pp. 110-119
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
Campbell, R.L., Petsko, G.A., Ribonuclease structure and catalysis: Crystal structure of sulfate-free native ribonuclease A at 1.5-Å resolution (1987) Biochemistry, 26, pp. 8579-8584
Wlodawer, A., Svensson, L.A., Sjolin, L., Gilliland, G.L., Structure of phosphate-free ribonuclease A refined at 1.26 Å (1988) Biochemistry, 27, pp. 2705-2717
Lisgarten, J.N., Gupta, V., Wyns, L., Structure of the crystalline complex of cytidylic acid (2′-CMP) with ribonuclease at 1.6 Å resolution. Conservation of solvent sites in RNase A high-resolution structures (1993) Acta Crystallogr D Biol Crystallogr, 49, pp. 541-547
Zegers, I., Maes, D., Dao-Thi, M.H., Poortmans, F., Palmer, R., Wyns, L., The structures of RNase A complexed with 3′-CMP and d(CpA): Active site conformation and conserved water molecules (1994) Protein Sci, 3, pp. 2322-1339
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Rossi, G.L., Biological activity in the crystalline state (1992) Curr Opin Struct Biol, 2, pp. 816-820
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Lesk, A. M., Chothia, C., Mechanisms of domain closure in proteins (1984) J Mol Biol, 174, pp. 175-19
Rasmussen, B. F., Stock, A. M., Ringe, D., Petsko, G. A., Crystalline ribonuclease A loses function below the dynamical transition at 22 0 K (1992) Nature, 357, pp. 423-424
Triton, R. F. J., Dewan, J. C., Petsko, G. A., Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K (1992) Biochemistry, 31, pp. 2469-2481
Radha Kishan, K. V., Chandra, N. R., Sudarsanakumar, C., Suguna, K., Vijayan, M., Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme (1995) Acta Crystallogr D Biol Crystallogr, 51, pp. 703-710
Leonidas, D. D., Shapiro, R., Irons, L. I., Russo, N., Acharya, K. R., Crystal structures of ribonuclease A complexes with 5 -diphosphoadenosine 3 -phosphate and 5 -diphosphoadenosine 2 -phosphate at 1. 7 resolution (1997) Biochemistry, 36, pp. 5578-5588
Brunger, A. T., (1992) X-PLOR version 3. 1: A system for X-ray crystallography and NMR, , New Haven, CT: Yale University Press
Jones, T. A., Zou, J. Y., Cowan, S. W., Kjeldgaard, M., Improved methods for binding protein models in electron density maps and the location of errors in these models (1991) Acta Crystallogr A, 47, pp. 110-119
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
Campbell, R. L., Petsko, G. A., Ribonuclease structure and catalysis: Crystal structure of sulfate-free native ribonuclease A at 1. 5- resolution (1987) Biochemistry, 26, pp. 8579-8584
Lisgarten, J. N., Gupta, V., Wyns, L., Structure of the crystalline complex of cytidylic acid (2 -CMP) with ribonuclease at 1. 6 resolution. Conservation of solvent sites in RNase A high-resolution structures (1993) Acta Crystallogr D Biol Crystallogr, 49, pp. 541-547
Richards, F. M., Kundrot, C. E., Identification of structural motifs from protein coordinate data: Secondary structure and first-level super-secondary structure (1988) Proteins, 3, pp. 71-84
Rossi, G. L., Biological activity in the crystalline state (1992) Curr Opin Struct Biol, 2, pp. 816-820
Reversible substrate-induced domain motions in ribonuclease
Despite the increasing number of successful determinations of complex protein structures the understanding of their dynamics properties is still rather limited. Using X-ray crystallography, we demonstrate that ribonuclease A (RNase A) undergoes significant domain motions upon ligand binding. In particular, when cytidine 2'-monophosphate binds to RNase A, the structure of the enzyme becomes more compact. Interestingly, our data also show that these structural alterations are fully reversible in the crystal state. These findings provide structural bases for the dynamic behavior of RNase A in the binding of the substrate shown by Petsko and coworkers (Rasmussen et al. Nature 1992; 357: 423-424). These subtle domain motions may assume functional relevance for more complex system and may play a significant role in the cooperativity of oligomeric enzymes. Proteins 2002; 46: 97-104. (C) 2001 Wiley-Liss, Inc
Reversible substrate-induced domain motions in ribonuclease
No results.
Reversible substrate-induced domain motions in ribonuclease