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A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core.

Consonni R, Santomo L, Fusi P, Tortora P, Zetta L
Biochemistry 38 12709-17 (1999)
Cited: 19 times
EuropePMC logo PMID: 10504241

Abstract

Sso7d is a basic 7-kDa DNA-binding protein from Sulfolobus solfataricus, also endowed with ribonuclease activity. The protein consists of a double-stranded antiparallel beta-sheet, onto which an orthogonal triple-stranded antiparallel beta-sheet is packed, and of a small helical stretch at the C-terminus. Furthermore, the two beta-sheets enclose an aromatic cluster displaying a fishbone geometry. We previously cloned the Sso7d-encoding gene, expressed it in Escherichia coli, and produced several single-point mutants, either of residues located in the hydrophobic core or of Trp23, which is exposed to the solvent and plays a major role in DNA binding. The mutation F31A was dramatically destabilizing, with a loss in thermo- and piezostabilities by at least 27 K and 10 kbar, respectively. Here, we report the solution structure of the F31A mutant, which was determined by NMR spectroscopy using 744 distance constraints obtained from analysis of multidimensional spectra in conjunction with simulated annealing protocols. The most remarkable finding is the change in orientation of the Trp23 side chain, which in the wild type is completely exposed to the solvent, whereas in the mutant is largely buried in the aromatic cluster. This prevents the formation of a cavity in the hydrophobic core of the mutant, which would arise in the absence of structural rearrangements. We found additional changes produced by the mutation, notably a strong distortion in the beta-sheets with loss in several hydrogen bonds, increased flexibility of some stretches of the backbone, and some local strains. On one hand, these features may justify the dramatic destabilization provoked by the mutation; on the other hand, they highlight the crucial role of the hydrophobic core in protein stability. To the best of our knowledge, no similar rearrangement has been so far described as a result of a single-point mutation.

Reviews - 1jic mentioned but not cited (1)

  1. Advances in Human Immune System Mouse Models for Studying Human Hematopoiesis and Cancer Immunotherapy. Mian SA, Anjos-Afonso F, Bonnet D. Front Immunol 11 619236 (2020)

Articles - 1jic mentioned but not cited (2)

  1. MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling. Song Y, Mao J, Gunner MR. J Comput Chem 30 2231-2247 (2009)
  2. Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations. Bernini A, Spiga O, Consonni R, Arosio I, Fusi P, Cirri S, Guagliardi A, Niccolai N. BMC Struct. Biol. 11 44 (2011)


Reviews citing this publication (2)

  1. Protein adaptations in archaeal extremophiles. Reed CJ, Lewis H, Trejo E, Winston V, Evilia C. Archaea 2013 373275 (2013)
  2. Modulation of allosteric coupling by mutations: from protein dynamics and packing to altered native ensembles and function. Naganathan AN. Curr. Opin. Struct. Biol. 54 1-9 (2019)

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  1. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. Guerois R, Nielsen JE, Serrano L. J. Mol. Biol. 320 369-387 (2002)
  2. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Kellogg EH, Leaver-Fay A, Baker D. Proteins 79 830-838 (2011)
  3. Structural and dynamic effects of alpha-helix deletion in Sso7d: implications for protein thermal stability. Merlino A, Graziano G, Mazzarella L. Proteins 57 692-701 (2004)
  4. Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. Xu X, Su J, Chen W, Wang C. J. Biomol. Struct. Dyn. 28 717-727 (2011)
  5. Two amino acid substitutions within the first external loop of CCR5 induce human immunodeficiency virus-blocking antibodies in mice and chickens. Pastori C, Clivio A, Diomede L, Consonni R, De Mori GM, Longhi R, Colombo G, Lopalco L. J. Virol. 82 4125-4134 (2008)
  6. Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa. Ceruso MA, Grottesi A, Di Nola A. Proteins 50 222-229 (2003)
  7. Pressure denaturation of beta-lactoglobulin. Different stabilities of isoforms A and B, and an investigation of the Tanford transition. Botelho MM, Valente-Mesquita VL, Oliveira KM, Polikarpov I, Ferreira ST. Eur. J. Biochem. 267 2235-2241 (2000)
  8. Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations. Roche J, Caro JA, Dellarole M, Guca E, Royer CA, García-Moreno BE, Garcia AE, Roumestand C. Proteins 81 1069-1080 (2013)
  9. Role of hydrophobic core on the thermal stability of proteins - molecular dynamics simulations on a single point mutant of Sso7d abstract. Priyakumar UD. J. Biomol. Struct. Dyn. 29 961-971 (2012)
  10. Structural determinants responsible for the thermostability of Sso7d and its single point mutants. Consonni R, Arosio I, Recca T, Fusi P, Zetta L. Proteins 67 766-775 (2007)
  11. Guanidine-induced unfolding of the Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus. Granata V, Vecchio PD, Barone G, Shehi E, Fusi P, Tortora P, Graziano G. Int. J. Biol. Macromol. 34 195-201 (2004)
  12. Study of conformational properties of a biologically active peptide of fibronectin by circular dichroism, NMR and molecular dynamics simulation. Abbate S, Barlati S, Colombi M, Fornili SL, Francescato P, Gangemi F, Lebon F, Longhi G, Manitto P, Recca T, Speranza G, Zoppi N. Phys Chem Chem Phys 8 4668-4677 (2006)
  13. The cytochrome b Zn binding amino acid residue histidine 291 is essential for ubihydroquinone oxidation at the Qo site of bacterial cytochrome bc1. Francia F, Malferrari M, Lanciano P, Steimle S, Daldal F, Venturoli G. Biochim. Biophys. Acta 1857 1796-1806 (2016)
  14. Ensemble origins and distance-dependence of long-range mutational effects in proteins. Kannan A, Naganathan AN. iScience 25 105181 (2022)


Related citations provided by authors (2)

  1. Extreme heat- and pressure-resistant 7-kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single-point amino acid substitution.. Fusi P, Goossens K, Consonni R, Grisa M, Puricelli P, Vecchio G, Vanoni M, Zetta L, Heremans K, Tortora P Proteins 29 381-90 (1997)
  2. 1H-NMR and photo-CIDNP spectroscopies show a possible role for Trp23 and Phe31 in nucleic acid binding by P2 ribonuclease from the archaeon Sulfolobus solfataricus.. Consonni R, Limiroli R, Molinari H, Fusi P, Grisa M, Vanoni M, Tortora P FEBS Lett 372 135-9 (1995)

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