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. 2002 Dec;83(6):3126–3133. doi: 10.1016/S0006-3495(02)75316-2

Toward the physical basis of thermophilic proteins: linking of enriched polar interactions and reduced heat capacity of unfolding.

Huan-Xiang Zhou 1
PMCID: PMC1302391  PMID: 12496083

Abstract

The enrichment of salt bridges and hydrogen bonding in thermophilic proteins has long been recognized. Another tendency, featuring lower heat capacity of unfolding (DeltaC(p)) than found in mesophilic proteins, is emerging from the recent literature. Here we present a simple electrostatic model to illustrate that formation of a salt-bridge or hydrogen-bonding network around an ionized group in the folded state leads to increased folding stability and decreased DeltaC(p). We thus suggest that the reduced DeltaC(p) of thermophilic proteins could partly be attributed to enriched polar interactions. A reduced DeltaC(p) might serve as an indicator for the contribution of polar interactions to folding stability.

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Selected References

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  1. Backmann J., Schäfer G., Wyns L., Bönisch H. Thermodynamics and kinetics of unfolding of the thermostable trimeric adenylate kinase from the archaeon Sulfolobus acidocaldarius. J Mol Biol. 1998 Dec 4;284(3):817–833. doi: 10.1006/jmbi.1998.2216. [DOI] [PubMed] [Google Scholar]
  2. Baldwin R. L. Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci U S A. 1986 Nov;83(21):8069–8072. doi: 10.1073/pnas.83.21.8069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Delbrück H., Mueller U., Perl D., Schmid F. X., Heinemann U. Crystal structures of mutant forms of the Bacillus caldolyticus cold shock protein differing in thermal stability. J Mol Biol. 2001 Oct 19;313(2):359–369. doi: 10.1006/jmbi.2001.5051. [DOI] [PubMed] [Google Scholar]
  4. Deutschman W. A., Dahlquist F. W. Thermodynamic basis for the increased thermostability of CheY from the hyperthermophile Thermotoga maritima. Biochemistry. 2001 Oct 30;40(43):13107–13113. doi: 10.1021/bi010665t. [DOI] [PubMed] [Google Scholar]
  5. Dominy Brian N., Perl Dieter, Schmid Franz X., Brooks Charles L., 3rd The effects of ionic strength on protein stability: the cold shock protein family. J Mol Biol. 2002 May 31;319(2):541–554. doi: 10.1016/S0022-2836(02)00259-0. [DOI] [PubMed] [Google Scholar]
  6. Elcock A. H. The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins. J Mol Biol. 1998 Nov 27;284(2):489–502. doi: 10.1006/jmbi.1998.2159. [DOI] [PubMed] [Google Scholar]
  7. Filimonov V. V., Azuaga A. I., Viguera A. R., Serrano L., Mateo P. L. A thermodynamic analysis of a family of small globular proteins: SH3 domains. Biophys Chem. 1999 Mar 29;77(2-3):195–208. doi: 10.1016/s0301-4622(99)00025-3. [DOI] [PubMed] [Google Scholar]
  8. Gallagher K., Sharp K. Electrostatic contributions to heat capacity changes of DNA-ligand binding. Biophys J. 1998 Aug;75(2):769–776. doi: 10.1016/S0006-3495(98)77566-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Goedken E. R., Keck J. L., Berger J. M., Marqusee S. Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI. Protein Sci. 2000 Oct;9(10):1914–1921. doi: 10.1110/ps.9.10.1914. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hollien J., Marqusee S. A thermodynamic comparison of mesophilic and thermophilic ribonucleases H. Biochemistry. 1999 Mar 23;38(12):3831–3836. doi: 10.1021/bi982684h. [DOI] [PubMed] [Google Scholar]
  11. Ishikawa K., Okumura M., Katayanagi K., Kimura S., Kanaya S., Nakamura H., Morikawa K. Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 A resolution. J Mol Biol. 1993 Mar 20;230(2):529–542. doi: 10.1006/jmbi.1993.1169. [DOI] [PubMed] [Google Scholar]
  12. Jaenicke R., Böhm G. The stability of proteins in extreme environments. Curr Opin Struct Biol. 1998 Dec;8(6):738–748. doi: 10.1016/s0959-440x(98)80094-8. [DOI] [PubMed] [Google Scholar]
  13. Knapp S., Karshikoff A., Berndt K. D., Christova P., Atanasov B., Ladenstein R. Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile Sulfolobus solfataricus. J Mol Biol. 1996 Dec 20;264(5):1132–1144. doi: 10.1006/jmbi.1996.0701. [DOI] [PubMed] [Google Scholar]
  14. Knapp S., Mattson P. T., Christova P., Berndt K. D., Karshikoff A., Vihinen M., Smith C. I., Ladenstein R. Thermal unfolding of small proteins with SH3 domain folding pattern. Proteins. 1998 May 15;31(3):309–319. doi: 10.1002/(sici)1097-0134(19980515)31:3<309::aid-prot7>3.0.co;2-d. [DOI] [PubMed] [Google Scholar]
  15. Li W. T., Grayling R. A., Sandman K., Edmondson S., Shriver J. W., Reeve J. N. Thermodynamic stability of archaeal histones. Biochemistry. 1998 Jul 28;37(30):10563–10572. doi: 10.1021/bi973006i. [DOI] [PubMed] [Google Scholar]
  16. Livingstone J. R., Spolar R. S., Record M. T., Jr Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry. 1991 Apr 30;30(17):4237–4244. doi: 10.1021/bi00231a019. [DOI] [PubMed] [Google Scholar]
  17. Loladze V. V., Ermolenko D. N., Makhatadze G. I. Heat capacity changes upon burial of polar and nonpolar groups in proteins. Protein Sci. 2001 Jul;10(7):1343–1352. doi: 10.1110/ps.370101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Madan B., Sharp K. A. Hydration heat capacity of nucleic acid constituents determined from the random network model. Biophys J. 2001 Oct;81(4):1881–1887. doi: 10.1016/S0006-3495(01)75839-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Makhatadze G. I., Privalov P. L. Energetics of protein structure. Adv Protein Chem. 1995;47:307–425. doi: 10.1016/s0065-3233(08)60548-3. [DOI] [PubMed] [Google Scholar]
  20. McCrary B. S., Edmondson S. P., Shriver J. W. Hyperthermophile protein folding thermodynamics: differential scanning calorimetry and chemical denaturation of Sac7d. J Mol Biol. 1996 Dec 13;264(4):784–805. doi: 10.1006/jmbi.1996.0677. [DOI] [PubMed] [Google Scholar]
  21. Moczygemba C., Guidry J., Jones K. L., Gomes C. M., Teixeira M., Wittung-Stafshede P. High stability of a ferredoxin from the hyperthermophilic archaeon A. ambivalens: involvement of electrostatic interactions and cofactors. Protein Sci. 2001 Aug;10(8):1539–1548. doi: 10.1110/ps.49401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Motono C., Oshima T., Yamagishi A. High thermal stability of 3-isopropylmalate dehydrogenase from Thermus thermophilus resulting from low DeltaC(p) of unfolding. Protein Eng. 2001 Dec;14(12):961–966. doi: 10.1093/protein/14.12.961. [DOI] [PubMed] [Google Scholar]
  23. Murphy K. P., Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem. 1992;43:313–361. doi: 10.1016/s0065-3233(08)60556-2. [DOI] [PubMed] [Google Scholar]
  24. Myers J. K., Pace C. N., Scholtz J. M. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci. 1995 Oct;4(10):2138–2148. doi: 10.1002/pro.5560041020. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Nojima H., Ikai A., Oshima T., Noda H. Reversible thermal unfolding of thermostable phosphoglycerate kinase. Thermostability associated with mean zero enthalpy change. J Mol Biol. 1977 Nov 5;116(3):429–442. doi: 10.1016/0022-2836(77)90078-x. [DOI] [PubMed] [Google Scholar]
  26. Perl D., Mueller U., Heinemann U., Schmid F. X. Two exposed amino acid residues confer thermostability on a cold shock protein. Nat Struct Biol. 2000 May;7(5):380–383. doi: 10.1038/75151. [DOI] [PubMed] [Google Scholar]
  27. Perutz M. F. Electrostatic effects in proteins. Science. 1978 Sep 29;201(4362):1187–1191. doi: 10.1126/science.694508. [DOI] [PubMed] [Google Scholar]
  28. Perutz M. F., Raidt H. Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature. 1975 May 15;255(5505):256–259. doi: 10.1038/255256a0. [DOI] [PubMed] [Google Scholar]
  29. Petrosian S. A., Makhatadze G. I. Contribution of proton linkage to the thermodynamic stability of the major cold-shock protein of Escherichia coli CspA. Protein Sci. 2000 Feb;9(2):387–394. doi: 10.1110/ps.9.2.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Petsko G. A. Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat". Methods Enzymol. 2001;334:469–478. doi: 10.1016/s0076-6879(01)34486-5. [DOI] [PubMed] [Google Scholar]
  31. Privalov P. L., Makhatadze G. I. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects. J Mol Biol. 1990 May 20;213(2):385–391. doi: 10.1016/S0022-2836(05)80198-6. [DOI] [PubMed] [Google Scholar]
  32. Robertson Andrew D., Murphy Kenneth P. Protein Structure and the Energetics of Protein Stability. Chem Rev. 1997 Aug 5;97(5):1251–1268. doi: 10.1021/cr960383c. [DOI] [PubMed] [Google Scholar]
  33. Robic Srebrenka, Berger James M., Marqusee Susan. Contributions of folding cores to the thermostabilities of two ribonucleases H. Protein Sci. 2002 Feb;11(2):381–389. doi: 10.1110/ps.38602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sanchez-Ruiz J. M., Makhatadze G. I. To charge or not to charge? Trends Biotechnol. 2001 Apr;19(4):132–135. doi: 10.1016/s0167-7799(00)01548-1. [DOI] [PubMed] [Google Scholar]
  35. Schindelin H., Marahiel M. A., Heinemann U. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature. 1993 Jul 8;364(6433):164–168. doi: 10.1038/364164a0. [DOI] [PubMed] [Google Scholar]
  36. Shiraki K., Nishikori S., Fujiwara S., Hashimoto H., Kai Y., Takagi M., Imanaka T. Comparative analyses of the conformational stability of a hyperthermophilic protein and its mesophilic counterpart. Eur J Biochem. 2001 Aug;268(15):4144–4150. doi: 10.1046/j.1432-1327.2001.02324.x. [DOI] [PubMed] [Google Scholar]
  37. Spolar R. S., Livingstone J. R., Record M. T., Jr Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry. 1992 Apr 28;31(16):3947–3955. doi: 10.1021/bi00131a009. [DOI] [PubMed] [Google Scholar]
  38. Szilágyi A., Závodszky P. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure. 2000 May 15;8(5):493–504. doi: 10.1016/s0969-2126(00)00133-7. [DOI] [PubMed] [Google Scholar]
  39. Vogt G., Argos P. Protein thermal stability: hydrogen bonds or internal packing? Fold Des. 1997;2(4):S40–S46. doi: 10.1016/s1359-0278(97)00062-x. [DOI] [PubMed] [Google Scholar]
  40. Wassenberg D., Welker C., Jaenicke R. Thermodynamics of the unfolding of the cold-shock protein from Thermotoga maritima. J Mol Biol. 1999 May 28;289(1):187–193. doi: 10.1006/jmbi.1999.2772. [DOI] [PubMed] [Google Scholar]
  41. Xiao L., Honig B. Electrostatic contributions to the stability of hyperthermophilic proteins. J Mol Biol. 1999 Jun 25;289(5):1435–1444. doi: 10.1006/jmbi.1999.2810. [DOI] [PubMed] [Google Scholar]
  42. Zhou Huan-Xiang. A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins. Proc Natl Acad Sci U S A. 2002 Mar 12;99(6):3569–3574. doi: 10.1073/pnas.052030599. [DOI] [PMC free article] [PubMed] [Google Scholar]

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