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Hydrogen bonding stabilizes globular proteins

Abstract

It is clear that intramolecular hydrogen bonds are essential to the structure and stability of globular proteins. It is not clear, however, whether they make a net favorable contribution to this stability. Experimental and theoretical studies are at odds over this important question. Measurements of the change in conformational stability, delta (delta G), for the mutation of a hydrogen bonded residue to one incapable of hydrogen bonding suggest a stabilization of 1.0 kcal/mol per hydrogen bond. If the delta (delta G) values are corrected for differences in side-chain hydrophobicity and conformational entropy, then the estimated stabilization becomes 2.2 kcal/mol per hydrogen bond. These and other experimental studies discussed here are consistent and compelling: hydrogen bonding stabilizes globular proteins.

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Selected References

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  1. Alber T., Sun D. P., Wilson K., Wozniak J. A., Cook S. P., Matthews B. W. Contributions of hydrogen bonds of Thr 157 to the thermodynamic stability of phage T4 lysozyme. Nature. 1987 Nov 5;330(6143):41–46. doi: 10.1038/330041a0. [DOI] [PubMed] [Google Scholar]
  2. Baker E. N., Hubbard R. E. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol. 1984;44(2):97–179. doi: 10.1016/0079-6107(84)90007-5. [DOI] [PubMed] [Google Scholar]
  3. Bhat T. N., Bentley G. A., Boulot G., Greene M. I., Tello D., Dall'Acqua W., Souchon H., Schwarz F. P., Mariuzza R. A., Poljak R. J. Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc Natl Acad Sci U S A. 1994 Feb 1;91(3):1089–1093. doi: 10.1073/pnas.91.3.1089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Blaber M., Lindstrom J. D., Gassner N., Xu J., Heinz D. W., Matthews B. W. Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. Biochemistry. 1993 Oct 26;32(42):11363–11373. doi: 10.1021/bi00093a013. [DOI] [PubMed] [Google Scholar]
  5. Bruch M. D., Dhingra M. M., Gierasch L. M. Side chain-backbone hydrogen bonding contributes to helix stability in peptides derived from an alpha-helical region of carboxypeptidase A. Proteins. 1991;10(2):130–139. doi: 10.1002/prot.340100206. [DOI] [PubMed] [Google Scholar]
  6. Buckle A. M., Cramer P., Fersht A. R. Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. Biochemistry. 1996 Apr 9;35(14):4298–4305. doi: 10.1021/bi9524676. [DOI] [PubMed] [Google Scholar]
  7. Byrne M. P., Manuel R. L., Lowe L. G., Stites W. E. Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease. Biochemistry. 1995 Oct 24;34(42):13949–13960. doi: 10.1021/bi00042a029. [DOI] [PubMed] [Google Scholar]
  8. Connelly P. R., Aldape R. A., Bruzzese F. J., Chambers S. P., Fitzgibbon M. J., Fleming M. A., Itoh S., Livingston D. J., Navia M. A., Thomson J. A. Enthalpy of hydrogen bond formation in a protein-ligand binding reaction. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1964–1968. doi: 10.1073/pnas.91.5.1964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cordes M. H., Davidson A. R., Sauer R. T. Sequence space, folding and protein design. Curr Opin Struct Biol. 1996 Feb;6(1):3–10. doi: 10.1016/s0959-440x(96)80088-1. [DOI] [PubMed] [Google Scholar]
  10. Creamer T. P., Srinivasan R., Rose G. D. Modeling unfolded states of peptides and proteins. Biochemistry. 1995 Dec 19;34(50):16245–16250. doi: 10.1021/bi00050a003. [DOI] [PubMed] [Google Scholar]
  11. Dao-pin S., Anderson D. E., Baase W. A., Dahlquist F. W., Matthews B. W. Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme. Biochemistry. 1991 Dec 10;30(49):11521–11529. doi: 10.1021/bi00113a006. [DOI] [PubMed] [Google Scholar]
  12. Dill K. A. Dominant forces in protein folding. Biochemistry. 1990 Aug 7;29(31):7133–7155. doi: 10.1021/bi00483a001. [DOI] [PubMed] [Google Scholar]
  13. Doig A. J., Sternberg M. J. Side-chain conformational entropy in protein folding. Protein Sci. 1995 Nov;4(11):2247–2251. doi: 10.1002/pro.5560041101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Eriksson A. E., Baase W. A., Zhang X. J., Heinz D. W., Blaber M., Baldwin E. P., Matthews B. W. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 1992 Jan 10;255(5041):178–183. doi: 10.1126/science.1553543. [DOI] [PubMed] [Google Scholar]
  15. Ernst J. A., Clubb R. T., Zhou H. X., Gronenborn A. M., Clore G. M. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science. 1995 Mar 24;267(5205):1813–1817. doi: 10.1126/science.7892604. [DOI] [PubMed] [Google Scholar]
  16. Forood B., Feliciano E. J., Nambiar K. P. Stabilization of alpha-helical structures in short peptides via end capping. Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):838–842. doi: 10.1073/pnas.90.3.838. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Green S. M., Meeker A. K., Shortle D. Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state. Biochemistry. 1992 Jun 30;31(25):5717–5728. doi: 10.1021/bi00140a005. [DOI] [PubMed] [Google Scholar]
  18. Habermann S. M., Murphy K. P. Energetics of hydrogen bonding in proteins: a model compound study. Protein Sci. 1996 Jul;5(7):1229–1239. doi: 10.1002/pro.5560050702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hammen P. K., Scholtz J. M., Anderson J. W., Waygood E. B., Klevit R. E. Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy. Protein Sci. 1995 May;4(5):936–944. doi: 10.1002/pro.5560040513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Harpaz Y., Gerstein M., Chothia C. Volume changes on protein folding. Structure. 1994 Jul 15;2(7):641–649. doi: 10.1016/s0969-2126(00)00065-4. [DOI] [PubMed] [Google Scholar]
  21. Hellinga H. W., Wynn R., Richards F. M. The hydrophobic core of Escherichia coli thioredoxin shows a high tolerance to nonconservative single amino acid substitutions. Biochemistry. 1992 Nov 17;31(45):11203–11209. doi: 10.1021/bi00160a034. [DOI] [PubMed] [Google Scholar]
  22. Honig B., Yang A. S. Free energy balance in protein folding. Adv Protein Chem. 1995;46:27–58. doi: 10.1016/s0065-3233(08)60331-9. [DOI] [PubMed] [Google Scholar]
  23. Huyghues-Despointes B. M., Klingler T. M., Baldwin R. L. Measuring the strength of side-chain hydrogen bonds in peptide helices: the Gln.Asp (i, i + 4) interaction. Biochemistry. 1995 Oct 17;34(41):13267–13271. doi: 10.1021/bi00041a001. [DOI] [PubMed] [Google Scholar]
  24. KAUZMANN W. Some factors in the interpretation of protein denaturation. Adv Protein Chem. 1959;14:1–63. doi: 10.1016/s0065-3233(08)60608-7. [DOI] [PubMed] [Google Scholar]
  25. Kaarsholm N. C., Norris K., Jørgensen R. J., Mikkelsen J., Ludvigsen S., Olsen O. H., Sørensen A. R., Havelund S. Engineering stability of the insulin monomer fold with application to structure-activity relationships. Biochemistry. 1993 Oct 12;32(40):10773–10778. doi: 10.1021/bi00091a031. [DOI] [PubMed] [Google Scholar]
  26. Klapper M. H. On the nature of the protein interior. Biochim Biophys Acta. 1971 Mar 23;229(3):557–566. doi: 10.1016/0005-2795(71)90271-6. [DOI] [PubMed] [Google Scholar]
  27. Lazaridis T., Archontis G., Karplus M. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Adv Protein Chem. 1995;47:231–306. doi: 10.1016/s0065-3233(08)60547-1. [DOI] [PubMed] [Google Scholar]
  28. Lee K. H., Xie D., Freire E., Amzel L. M. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins. 1994 Sep;20(1):68–84. doi: 10.1002/prot.340200108. [DOI] [PubMed] [Google Scholar]
  29. Lesser G. J., Rose G. D. Hydrophobicity of amino acid subgroups in proteins. Proteins. 1990;8(1):6–13. doi: 10.1002/prot.340080104. [DOI] [PubMed] [Google Scholar]
  30. Levitt M., Park B. H. Water: now you see it, now you don't. Structure. 1993 Dec 15;1(4):223–226. doi: 10.1016/0969-2126(93)90011-5. [DOI] [PubMed] [Google Scholar]
  31. Lin T. Y., Timasheff S. N. Why do some organisms use a urea-methylamine mixture as osmolyte? Thermodynamic compensation of urea and trimethylamine N-oxide interactions with protein. Biochemistry. 1994 Oct 25;33(42):12695–12701. doi: 10.1021/bi00208a021. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. Malin R., Zielenkiewicz P., Saenger W. Structurally conserved water molecules in ribonuclease T1. J Biol Chem. 1991 Mar 15;266(8):4848–4852. [PubMed] [Google Scholar]
  34. Marqusee S., Sauer R. T. Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor. Protein Sci. 1994 Dec;3(12):2217–2225. doi: 10.1002/pro.5560031207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Matthews B. W., Morton A. G., Dahlquist F. W. Use of NMR to detect water within nonpolar protein cavities. Science. 1995 Dec 15;270(5243):1847–1849. doi: 10.1126/science.270.5243.1847. [DOI] [PubMed] [Google Scholar]
  36. Matthews B. W. Studies on protein stability with T4 lysozyme. Adv Protein Chem. 1995;46:249–278. doi: 10.1016/s0065-3233(08)60337-x. [DOI] [PubMed] [Google Scholar]
  37. McDonald I. K., Thornton J. M. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 1994 May 20;238(5):777–793. doi: 10.1006/jmbi.1994.1334. [DOI] [PubMed] [Google Scholar]
  38. Milla M. E., Brown B. M., Sauer R. T. Protein stability effects of a complete set of alanine substitutions in Arc repressor. Nat Struct Biol. 1994 Aug;1(8):518–523. doi: 10.1038/nsb0894-518. [DOI] [PubMed] [Google Scholar]
  39. Muñoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides. J Mol Biol. 1995 Jan 20;245(3):275–296. doi: 10.1006/jmbi.1994.0023. [DOI] [PubMed] [Google Scholar]
  40. Pace C. N. Contribution of the hydrophobic effect to globular protein stability. J Mol Biol. 1992 Jul 5;226(1):29–35. doi: 10.1016/0022-2836(92)90121-y. [DOI] [PubMed] [Google Scholar]
  41. Pace C. N. Evaluating contribution of hydrogen bonding and hydrophobic bonding to protein folding. Methods Enzymol. 1995;259:538–554. doi: 10.1016/0076-6879(95)59060-9. [DOI] [PubMed] [Google Scholar]
  42. Pace C. N., Shirley B. A., McNutt M., Gajiwala K. Forces contributing to the conformational stability of proteins. FASEB J. 1996 Jan;10(1):75–83. doi: 10.1096/fasebj.10.1.8566551. [DOI] [PubMed] [Google Scholar]
  43. Petukhov M., Yumoto N., Murase S., Onmura R., Yoshikawa S. Factors that affect the stabilization of alpha-helices in short peptides by a capping box. Biochemistry. 1996 Jan 16;35(2):387–397. doi: 10.1021/bi9513766. [DOI] [PubMed] [Google Scholar]
  44. Richards F. M. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng. 1977;6:151–176. doi: 10.1146/annurev.bb.06.060177.001055. [DOI] [PubMed] [Google Scholar]
  45. Rose G. D., Wolfenden R. Hydrogen bonding, hydrophobicity, packing, and protein folding. Annu Rev Biophys Biomol Struct. 1993;22:381–415. doi: 10.1146/annurev.bb.22.060193.002121. [DOI] [PubMed] [Google Scholar]
  46. Roseman M. A. Hydrophobicity of the peptide C=O...H-N hydrogen-bonded group. J Mol Biol. 1988 Jun 5;201(3):621–623. doi: 10.1016/0022-2836(88)90642-0. [DOI] [PubMed] [Google Scholar]
  47. Scholtz J. M., Marqusee S., Baldwin R. L., York E. J., Stewart J. M., Santoro M., Bolen D. W. Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Proc Natl Acad Sci U S A. 1991 Apr 1;88(7):2854–2858. doi: 10.1073/pnas.88.7.2854. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Scholtz J. M., Qian H., Robbins V. H., Baldwin R. L. The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. Biochemistry. 1993 Sep 21;32(37):9668–9676. doi: 10.1021/bi00088a019. [DOI] [PubMed] [Google Scholar]
  49. Serrano L., Kellis J. T., Jr, Cann P., Matouschek A., Fersht A. R. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J Mol Biol. 1992 Apr 5;224(3):783–804. doi: 10.1016/0022-2836(92)90562-x. [DOI] [PubMed] [Google Scholar]
  50. Shirley B. A., Stanssens P., Hahn U., Pace C. N. Contribution of hydrogen bonding to the conformational stability of ribonuclease T1. Biochemistry. 1992 Jan 28;31(3):725–732. doi: 10.1021/bi00118a013. [DOI] [PubMed] [Google Scholar]
  51. Shortle D. The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J. 1996 Jan;10(1):27–34. doi: 10.1096/fasebj.10.1.8566543. [DOI] [PubMed] [Google Scholar]
  52. Stickle D. F., Presta L. G., Dill K. A., Rose G. D. Hydrogen bonding in globular proteins. J Mol Biol. 1992 Aug 20;226(4):1143–1159. doi: 10.1016/0022-2836(92)91058-w. [DOI] [PubMed] [Google Scholar]
  53. Tobias D. J., Sneddon S. F., Brooks C. L., 3rd Stability of a model beta-sheet in water. J Mol Biol. 1992 Oct 20;227(4):1244–1252. doi: 10.1016/0022-2836(92)90534-q. [DOI] [PubMed] [Google Scholar]
  54. Williams M. A., Goodfellow J. M., Thornton J. M. Buried waters and internal cavities in monomeric proteins. Protein Sci. 1994 Aug;3(8):1224–1235. doi: 10.1002/pro.5560030808. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Wimley W. C., Creamer T. P., White S. H. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry. 1996 Apr 23;35(16):5109–5124. doi: 10.1021/bi9600153. [DOI] [PubMed] [Google Scholar]
  56. Yamada H., Kanaya E., Ueno Y., Ikehara M., Nakamura H., Kikuchi M. Contribution of a hydrogen bond to the thermal stability of the mutant human lysozyme C77/95S. Biol Pharm Bull. 1994 May;17(5):612–616. doi: 10.1248/bpb.17.612. [DOI] [PubMed] [Google Scholar]
  57. Yang A. S., Honig B. Free energy determinants of secondary structure formation: I. alpha-Helices. J Mol Biol. 1995 Sep 22;252(3):351–365. doi: 10.1006/jmbi.1995.0502. [DOI] [PubMed] [Google Scholar]
  58. Yu M. H., Weissman J. S., Kim P. S. Contribution of individual side-chains to the stability of BPTI examined by alanine-scanning mutagenesis. J Mol Biol. 1995 Jun 2;249(2):388–397. doi: 10.1006/jmbi.1995.0304. [DOI] [PubMed] [Google Scholar]
  59. Zhang L., Hermans J. Hydrophilicity of cavities in proteins. Proteins. 1996 Apr;24(4):433–438. doi: 10.1002/(SICI)1097-0134(199604)24:4<433::AID-PROT3>3.0.CO;2-F. [DOI] [PubMed] [Google Scholar]
  60. Zhang X. J., Matthews B. W. Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme. Protein Sci. 1994 Jul;3(7):1031–1039. doi: 10.1002/pro.5560030705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Zhukovsky E. A., Mulkerrin M. G., Presta L. G. Contribution to global protein stabilization of the N-capping box in human growth hormone. Biochemistry. 1994 Aug 23;33(33):9856–9864. doi: 10.1021/bi00199a006. [DOI] [PubMed] [Google Scholar]