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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.

Kishan RV, Chandra NR, Sudarsanakumar C, Suguna K, Vijayan M
Acta Crystallogr D Biol Crystallogr 51 703-10 (1995)
Cited: 15 times
EuropePMC logo PMID: 15299799

Abstract

The crystal structures of 88 and 79% relative humidity forms of ribonuclease A, resulting from water-mediated transformations, have been refined employing the restrained least-squares method using X-ray data collected on an area detector to R = 0.173 for 15 326 observed reflections in the 10-1.5 A resolution shell and R = 0.176 for 8534 observed reflections in the 10-1.8 A shell, respectively. The comparison of these structures with those of the native, the phosphate-bound and the sulfate-bound forms demonstrates that the mobility of the ribonuclease A molecule involves hinge-bending movement of the two domains and local flexibility within them, particularly at the termini of regular secondary structures and in loops. The comparison also leads to the identification of 31 invariant water molecules in the hydration shell of the enzyme, many of which are involved in holding different parts of the molecule together and in stabilizing local structure. The conformational changes that accompany the partial removal of the surrounding water, particularly those observed in the 79% form, could be similar to those that occur during enzyme action.

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  1. NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. Alexandrescu AT, Snyder DR, Abildgaard F. Protein Sci 10 1856-1868 (2001)


Reviews citing this publication (1)

  1. Structural and functional importance of local and global conformational fluctuations in the RNase A superfamily. Gagné D, Doucet N. FEBS J 280 5596-5607 (2013)

Articles citing this publication (13)

  1. Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. Tahirov TH, Oki H, Tsukihara T, Ogasahara K, Yutani K, Ogata K, Izu Y, Tsunasawa S, Kato I. J Mol Biol 284 101-124 (1998)
  2. Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin. Merlino A, Vitagliano L, Ceruso MA, Mazzarella L. Proteins 53 101-110 (2003)
  3. Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution. Prabu MM, Sankaranarayanan R, Puri KD, Sharma V, Surolia A, Vijayan M, Suguna K. J Mol Biol 276 787-796 (1998)
  4. Reversible substrate-induced domain motions in ribonuclease A. Vitagliano L, Merlino A, Zagari A, Mazzarella L. Proteins 46 97-104 (2002)
  5. Global and local motions in ribonuclease A: a molecular dynamics study. Merlino A, Vitagliano L, Ceruso MA, Di Nola A, Mazzarella L. Biopolymers 65 274-283 (2002)
  6. Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA. Krishna R, Prabu JR, Manjunath GP, Datta S, Chandra NR, Muniyappa K, Vijayan M. J Mol Biol 367 1130-1144 (2007)
  7. Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies. Sharma A, Sekar K, Vijayan M. Proteins 77 760-777 (2009)
  8. An asymmetric dimer of beta-lactoglobulin in a low humidity crystal form--structural changes that accompany partial dehydration and protein action. Vijayalakshmi L, Krishna R, Sankaranarayanan R, Vijayan M. Proteins 71 241-249 (2008)
  9. Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer. Merlino A, Vitagliano L, Sica F, Zagari A, Mazzarella L. Biopolymers 73 689-695 (2004)
  10. Stereochemical metrics of lectin-carbohydrate interactions: comparison with protein-protein interfaces. García-Hernández E, Zubillaga RA, Rodríguez-Romero A, Hernández-Arana A. Glycobiology 10 993-1000 (2000)
  11. Crystal structure of Onconase at 1.1 Å resolution--insights into substrate binding and collective motion. Holloway DE, Singh UP, Shogen K, Acharya KR. FEBS J 278 4136-4149 (2011)
  12. Complexity of protein energy landscapes studied by solution NMR relaxation dispersion experiments. Khirich G, Loria JP. J Phys Chem B 119 3743-3754 (2015)
  13. X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability. Kurpiewska K, Font J, Ribó M, Vilanova M, Lewiński K. Proteins 77 658-669 (2009)


Related citations provided by authors (5)

  1. Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content. Madhusudan, Kodandapani R, Vijayan M Acta Crystallogr. D Biol. Crystallogr. 49 234- (1993)
  2. Rigid and Flexible Regions in Lysozyme and the Invariant Features in its Hydration Shell. Madhusudan, Vijayan M Curr. Sci. 60 165- (1991)
  3. Crystal Structure of Low Humidity Tetragonal Lysozyme at at 2.1 Angstroms Resolution; Variability in Hydration Shell and its Structural Consequences. Kodandapani R, Suresh CG, Vijayan M J. Biol. Chem. 265 16126- (1990)
  4. Water-Mediated Transformations in Protein Crystals. Salunke DM, Veerapandian B, Kodandapani R, Vijayan M Acta Crystallogr., B 41 431- (1985)
  5. Water-Mediated Structural Transformations in a New Crystal Form of Ribonuclease A and Tetragonal Lysozyme. Salunke DM, Veerapandian B, Vijayan M Curr. Sci. 53 231- (1984)

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