1ey5 Citations

Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability.

J Mol Biol 303 125-30 (2000)
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Cited: 68 times
EuropePMC logo PMID: 11023780

Abstract

Seven hyper-stable multiple mutants have been constructed in staphylococcal nuclease by various combinations of eight different stabilizing single mutants. The stabilities of these multiple mutants determined by guanidine hydrochloride denaturation were 3.4 to 5.6 kcal/mol higher than that of the wild-type. Their thermal denaturation midpoint temperatures were 12.6 to 22.9 deg. C higher than that of the wild-type. These are among the greatest increases in protein stability and thermal denaturation midpoint temperature relative to the wild-type yet attained. There has been great interest in understanding how proteins found in thermophilic organisms are stabilized. One frequently cited theory is that the packing of hydrophobic side-chains is improved in the cores of proteins isolated from thermophiles when compared to proteins from mesophiles. The crystal structures of four single and five multiple stabilizing mutants of staphylococcal nuclease were solved to high resolution. No large overall structural change was found, with most changes localized around the sites of mutation. Rearrangements were observed in the packing of side-chains in the major hydrophobic core, although none of the mutations was in the core. It is surprising that detailed structural analysis showed that packing had improved, with the volume of the mutant protein's hydrophobic cores decreasing as protein stability increased. Further, the number of van der Waals interactions in the entire protein showed an experimentally significant increase correlated with increasing stability. These results indicate that optimization of packing follows as a natural consequence of increased protein thermostability and that good packing is not necessarily the proximate cause of high stability. Another popular theory is that thermostable proteins have more electrostatic and hydrogen bonding interactions and these are responsible for the high stabilities. The mutants here show that increased numbers of electrostatic and hydrogen bonding interactions are not obligatory for large increases in protein stability.

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  1. Energetics of protein folding. Baldwin RL. J Mol Biol 371 283-301 (2007)
  2. Physical and molecular bases of protein thermal stability and cold adaptation. Pucci F, Rooman M. Curr Opin Struct Biol 42 117-128 (2017)
  3. Condensed genome structure. Black LW, Thomas JA. Adv Exp Med Biol 726 469-487 (2012)
  4. An overview of tools for the validation of protein NMR structures. Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A. J Biomol NMR 58 259-285 (2014)

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  1. Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability. Hakulinen N, Turunen O, Jänis J, Leisola M, Rouvinen J. Eur J Biochem 270 1399-1412 (2003)
  2. Some thermodynamic implications for the thermostability of proteins. Rees DC, Robertson AD. Protein Sci 10 1187-1194 (2001)
  3. Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing. Li CL, Yang WZ, Chen YP, Yuan HS. Nucleic Acids Res 36 3579-3589 (2008)
  4. Geometry-based sampling of conformational transitions in proteins. Seeliger D, Haas J, de Groot BL. Structure 15 1482-1492 (2007)
  5. The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors. Harms MJ, Castañeda CA, Schlessman JL, Sue GR, Isom DG, Cannon BR, García-Moreno E B. J Mol Biol 389 34-47 (2009)
  6. Dry molten globule intermediates and the mechanism of protein unfolding. Baldwin RL, Frieden C, Rose GD. Proteins 78 2725-2737 (2010)
  7. Topological determinants of protein domain swapping. Ding F, Prutzman KC, Campbell SL, Dokholyan NV. Structure 14 5-14 (2006)
  8. Entropic stabilization of proteins and its proteomic consequences. Berezovsky IN, Chen WW, Choi PJ, Shakhnovich EI. PLoS Comput Biol 1 e47 (2005)
  9. A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values. Harms MJ, Schlessman JL, Chimenti MS, Sue GR, Damjanović A, García-Moreno B. Protein Sci 17 833-845 (2008)
  10. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations. Li H, Fajer M, Yang W. J Chem Phys 126 024106 (2007)
  11. Effect of osmolytes on pressure-induced unfolding of proteins: a high-pressure SAXS study. Krywka C, Sternemann C, Paulus M, Tolan M, Royer C, Winter R. Chemphyschem 9 2809-2815 (2008)
  12. Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles. Greaves RB, Warwicker J. BMC Struct Biol 7 18 (2007)
  13. Staphylococcus aureus Nuc2 is a functional, surface-attached extracellular nuclease. Kiedrowski MR, Crosby HA, Hernandez FJ, Malone CL, McNamara JO, Horswill AR. PLoS One 9 e95574 (2014)
  14. Stabilization of internal charges in a protein: water penetration or conformational change? Denisov VP, Schlessman JL, García-Moreno E B, Halle B. Biophys J 87 3982-3994 (2004)
  15. Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins. Gromiha MM. Biophys Chem 91 71-77 (2001)
  16. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy. Wallace JA, Wang Y, Shi C, Pastoor KJ, Nguyen BL, Xia K, Shen JK. Proteins 79 3364-3373 (2011)
  17. Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease. Baran KL, Chimenti MS, Schlessman JL, Fitch CA, Herbst KJ, Garcia-Moreno BE. J Mol Biol 379 1045-1062 (2008)
  18. Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus. Appleby TC, Mathews II, Porcelli M, Cacciapuoti G, Ealick SE. J Biol Chem 276 39232-39242 (2001)
  19. A single proline substitution is critical for the thermostabilization of Clostridium beijerinckii alcohol dehydrogenase. Goihberg E, Dym O, Tel-Or S, Levin I, Peretz M, Burstein Y. Proteins 66 196-204 (2007)
  20. Probing protein mechanics: residue-level properties and their use in defining domains. Navizet I, Cailliez F, Lavery R. Biophys J 87 1426-1435 (2004)
  21. How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin. Permyakov SE, Makhatadze GI, Owenius R, Uversky VN, Brooks CL, Permyakov EA, Berliner LJ. Protein Eng Des Sel 18 425-433 (2005)
  22. Studying pressure denaturation of a protein by molecular dynamics simulations. Sarupria S, Ghosh T, García AE, Garde S. Proteins 78 1641-1651 (2010)
  23. Hydration of the folding transition state ensemble of a protein. Brun L, Isom DG, Velu P, García-Moreno B, Royer CA. Biochemistry 45 3473-3480 (2006)
  24. A simple electrostatic criterion for predicting the thermal stability of proteins. Mozo-Villarías A, Cedano J, Querol E. Protein Eng 16 279-286 (2003)
  25. Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups. Schlessman JL, Abe C, Gittis A, Karp DA, Dolan MA, García-Moreno E B. Biophys J 94 3208-3216 (2008)
  26. Stabilization of immobilized glucose oxidase against thermal inactivation by silanization for biosensor applications. Sarath Babu VR, Kumar MA, Karanth NG, Thakur MS. Biosens Bioelectron 19 1337-1341 (2004)
  27. Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: a structural and dynamic analysis. Motono C, Gromiha MM, Kumar S. Proteins 71 655-669 (2008)
  28. Replacement of staphylococcal nuclease hydrophobic core residues with those from thermophilic homologues indicates packing is improved in some thermostable proteins. Chen J, Stites WE. J Mol Biol 344 271-280 (2004)
  29. Impacts of the G145R Mutation on the Structure and Immunogenic Activity of the Hepatitis B Surface Antigen: A Computational Analysis. Rezaee R, Poorebrahim M, Najafi S, Sadeghi S, Pourdast A, Alavian SM, Alavian SE, Poortahmasebi V. Hepat Mon 16 e39097 (2016)
  30. Kinetic and thermodynamic study of cloned thermostable endo-1,4-β-xylanase from Thermotoga petrophila in mesophilic host. ul Haq I, Hussain Z, Khan MA, Muneer B, Afzal S, Majeed S, Akram F. Mol Biol Rep 39 7251-7261 (2012)
  31. Prediction of Residue-specific Contributions to Binding and Thermal Stability Using Yeast Surface Display. Ahmed S, Bhasin M, Manjunath K, Varadarajan R. Front Mol Biosci 8 800819 (2021)
  32. Heterologous expression of a gene for thermostable xylanase from Chaetomium thermophilum in Pichia pastoris GS115. Ghaffar A, Khan SA, Mukhtar Z, Rajoka MI, Latif F. Mol Biol Rep 38 3227-3233 (2011)
  33. Kinetic proofreading by the cavity system of myoglobin: protection from poisoning. Radding W, Phillips GN. Bioessays 26 422-433 (2004)
  34. Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Watson E, Matousek WM, Irimies EL, Alexandrescu AT. Biochemistry 46 9484-9494 (2007)
  35. Analysis of the thermostability determinants of hyperthermophilic esterase EstE1 based on its predicted three-dimensional structure. Rhee JK, Kim DY, Ahn DG, Yun JH, Jang SH, Shin HC, Cho HS, Pan JG, Oh JW. Appl Environ Microbiol 72 3021-3025 (2006)
  36. Electrostatic pKa computations in proteins: role of internal cavities. Meyer T, Kieseritzky G, Knapp EW. Proteins 79 3320-3332 (2011)
  37. Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins. Saraboji K, Gromiha MM, Ponnuswamy MN. Int J Biol Macromol 35 211-220 (2005)
  38. Relationship between protein stabilization and protein rigidification induced by mannosylglycerate. Pais TM, Lamosa P, Garcia-Moreno B, Turner DL, Santos H. J Mol Biol 394 237-250 (2009)
  39. "Hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms. Paiardini A, Sali R, Bossa F, Pascarella S. BMC Struct Biol 8 14 (2008)
  40. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms. Sammond DW, Kastelowitz N, Himmel ME, Yin H, Crowley MF, Bomble YJ. PLoS One 11 e0145848 (2016)
  41. In silico enhancement of the stability and activity of keratinocyte growth factor. Poorebrahim M, Sadeghi S, Ghorbani R, Asghari M, Abazari MF, Kalhor H, Rahimi H. J Theor Biol 418 111-121 (2017)
  42. Kinetic parameters and thermodynamic values of beta-xylosidase production by Kluyveromyces marxianus. Rajoka MI. Bioresour Technol 98 2212-2219 (2007)
  43. Conformational flexibility of avidin: the influence of biotin binding. Celej MS, Montich GG, Fidelio GD. Biochem Biophys Res Commun 325 922-927 (2004)
  44. Local stability identification and the role of a key aromatic amino acid residue in staphylococcal nuclease refolding. Su Z, Wu JM, Fang HJ, Tsong TY, Chen HM. FEBS J 272 3960-3966 (2005)
  45. Local stability identification and the role of key acidic amino acid residues in staphylococcal nuclease unfolding. Chen HM, Chan SC, Leung KW, Wu JM, Fang HJ, Tsong TY. FEBS J 272 3967-3974 (2005)
  46. Proteins with simplified hydrophobic cores compared to other packing mutants. Chen J, Lu Z, Sakon J, Stites WE. Biophys Chem 110 239-248 (2004)
  47. Beta-hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease. Patel S, Sista P, Balaji PV, Sasidhar YU. J Mol Graph Model 25 103-115 (2006)
  48. Comparison of Two ESI MS Based H/D Exchange Methods for Extracting Protein Folding Energies. Liyanage R, Devarapalli N, Puckett LM, Phan NH, Gidden J, Stites WE, Lay JO. Int J Mass Spectrom 287 96-104 (2009)
  49. Mannosylglycerate stabilizes staphylococcal nuclease with restriction of slow β-sheet motions. Pais TM, Lamosa P, Matzapetakis M, Turner DL, Santos H. Protein Sci 21 1126-1137 (2012)
  50. RosettaDDGPrediction for high-throughput mutational scans: From stability to binding. Sora V, Laspiur AO, Degn K, Arnaudi M, Utichi M, Beltrame L, De Menezes D, Orlandi M, Stoltze UK, Rigina O, Sackett PW, Wadt K, Schmiegelow K, Tiberti M, Papaleo E. Protein Sci 32 e4527 (2023)
  51. Thermodynamic principles for the engineering of pH-driven conformational switches and acid insensitive proteins. Bell-Upp P, Robinson AC, Whitten ST, Wheeler EL, Lin J, Stites WE, E BG. Biophys Chem 159 217-226 (2011)
  52. Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator. Bahia MS, Khazanov N, Zhou Q, Yang Z, Wang C, Hong JS, Rab A, Sorscher EJ, Brouillette CG, Hunt JF, Senderowitz H. J Chem Inf Model 61 1762-1777 (2021)
  53. The role of tryptophan in staphylococcal nuclease stability. Hu HY, Wu MC, Fang HJ, Forrest MD, Hu CK, Tsong TY, Chen HM. Biophys Chem 151 170-177 (2010)
  54. What is the protein design alphabet? Dokholyan NV. Proteins 54 622-628 (2004)
  55. Kinetic and thermodynamic characterization of lysine production process in Brevibacterium lactofermentum. Ahmed S, Afzal M, Rajoka MI. Appl Biochem Biotechnol 170 81-90 (2013)
  56. On the physics of thermal-stability changes upon mutations of a protein. Murakami S, Oshima H, Hayashi T, Kinoshita M. J Chem Phys 143 125102 (2015)
  57. A study of the influence of the hydrophobic core residues of yeast iso-2-cytochrome c on phosphate binding: a probe of the hydrophobic core-surface charge interactions. Taniuchi H, Shi Y, San Miguel GI, Ferretti JA, Mack JW, Fisher A, Shah M, Schechter AN, Shiloach J. J Protein Chem 20 203-215 (2001)
  58. Structure, Function, and Thermodynamics of Lactate Dehydrogenases from Humans and the Malaria Parasite P. falciparum. Khrapunov S, Waterman A, Persaud R, Chang EP. Biochemistry 60 3582-3595 (2021)
  59. The effects of amino acid replacements of glycine 20 on conformational stability and catalysis of staphylococcal nuclease. Feng Y, Huang S, Zhang W, Zeng Z, Zou X, Zhong L, Peng J, Jing G. Biochimie 86 893-901 (2004)
  60. The pH dependence of staphylococcal nuclease stability is incompatible with a three-state denaturation model. Spencer D, Bertrand GM, Stites WE. Biophys Chem 180-181 86-94 (2013)
  61. Yeast hexokinase isoenzyme ScHxk2: stability of a two-domain protein with discontinuous domains. Lilie H, Bär D, Kettner K, Weininger U, Balbach J, Naumann M, Müller EC, Otto A, Gast K, Golbik R, Kriegel T. Protein Eng Des Sel 24 79-87 (2011)
  62. Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. Wilson CJ, Karttunen M, de Groot BL, Gapsys V. J Chem Theory Comput 19 7833-7845 (2023)
  63. Compact dimension of denatured states of staphylococcal nuclease. Chow CY, Wu MC, Fang HJ, Hu CK, Chen HM, Tsong TY. Proteins 72 901-909 (2008)


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