Energetics of hydrogen bonding in proteins: A model compound study

Protein Science

Volumn 5, Issue 7, 1996, Pages 1229-1239

  Habermann, Susan M ^a   Murphy, Kenneth P ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

calorimetry; enthalpy; heat capacity; hydrogen bonding; hydroxyl; model compounds; solvation

Indexed keywords

AMIDE; CYCLOPEPTIDE; DIPEPTIDE; GLOBULAR PROTEIN; HYDROXYL GROUP; WATER;

ARTICLE; CALORIMETRY; CRYSTAL STRUCTURE; DISSOLUTION; ENERGY TRANSFER; ENTHALPY; ENTROPY; HYDROGEN BOND; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; SOLUBILITY;

EID: 0029941271     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050702     Document Type: Article

References (54)

1. Baker EN, Hubbard RE. 1984. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 44:97-179.
2. Baldwin RL. 1986. Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci USA 83:8069-8072.
3. Benedetti E, Corradini P, Pedone C. 1969. Crystal and molecular structure of l-cis-3,6-dimethyl-2,5-piperazinedione. Biopolymers 7:751-764.
4. Blaber M, Lindstrom JD, Gassner N, Xu J, Heinz DW, Matthews BW. 1993. 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 32:11363-11373.
5. Briggner LE, Wadsö I. 1991. Test and calibration processes for microcalorimeters, with special reference to heat conduction instruments used with aqueous systems. J Biochem Biophys Methods 22:101-118.
6. Cabani S, Gianni P, Mollica V, Lepori L. 1981. Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution. J Solution Chem 10:563-595.
7. Chan HS, Dill KA. 1994. Solvation: Effects of molecular size and shape. J Chem Phys 101:7007-7026.
8. Chothia C. 1984. Principles that determine the structure of proteins. Annu Rev Biochem 53:537-572.
9. Christensen JJ, Hansen LD, Izatt RM. 1976. Handbook of proton tonization heats and related thermodynamic quantities. New York: John Wiley and Sons.
10. Connelly PR, Aldape RA, Bruzzese FJ, Chambers SP, Fitzgibbon MJ, Fleming MA, Itoh S, Livingston DJ, Navia MA, Thomson JA, Wilson KP. 1994. Enthalpy of hydrogen bond formation in a protein-ligand binding reaction. Proc Natl Acad Sci USA 91:1964-1968.
11. Corey RB. 1938. The crystal structure of diketopiperazine. J Am Chem Soc 60:1598-1604.
12. Degeilh R, Marsh RE. 1959. A refinement of the crystal structure of diketopiperazine (2,5-piperazinedione). Acta Crystallogr 12:1007-1014.
13. DeYoung LR, Dill KA. 1990. Partitioning of nonpolar solutes into bilayers and amorphous n-alkanes. J Phys Chem 94:801-809.
14. Dill KA. 1990. The meaning of hydrophobicity. Science 250:297.
15. Fava GG, Belicchi MF, Marchelli R, Dossena A. 1981. Synthesis, crystal structure and conformation of the cyclic dipeptide cyclo(-L-Seryl-L-seryl-). Acta Crystallogr B 37:625-629.
16. Gill SJ, Dec SF, Olofsson G, Wadso I. 1985. Anomalous heat capacity of hydrophobic hydration. J Phys Chem 89:3758-3761.
17. Gill SJ, Hutson J, Clopton JR, Downing M. 1961. Solubility of diketopiperazine in aqueous solutions of urea. J Phys Chem 65:1432-1435.
18. Gill SJ, Noll L. 1972. Calorimetric study of association of diketopiperazine in water. J Phys Chem 76:3065-3068.
19. Gill SJ, Wadsö I. 1976. An equation of state describing hydrophobic interactions. Proc Natl Acad Sci USA 73:2955-2958.
20. Gömez J, Hilser VJ, Xie D, Freire E. 1995. The heat capacity of proteins. Proteins Struct Funct Genet 22:404-412.
21. Harpaz Y, Gerstein M, Chothia C. 1994. Volume changes on protein folding. Structure 2:641-649.
22. Jorgensen WL, Gao J, Ravimohan C. 1985. Monte Carlo simulations of alkanes in water: Hydration numbers and the hydrophobic effect. J Phys Chem 89:3470-3473.
23. Klotz IM. 1993. Solvent water and protein behavior: View through a retroscope. Protein Sci 2:1992-1999.
24. Klotz IM, Franzen JS. 1962. Hydrogen bonds between model peptide groups in solution. J Am Chem Soc 84:3461-3466.
25. Lee KH, Xie D, Freire E, Amzel LM. 1994. Entropy changes in biological processes: Loss of side chain configurational entropy in binding and folding. Proteins Struct Funct Genet 20:68-84.
26. Makhatadze GI, Privalov PL. 1990. Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect. J Mot Biol 213:375-384.
27. Makhatadze GI, Privalov PL. 1993. Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration. J Mol Biol 232:639-659.
28. Murphy KP. 1994. Hydration and convergence temperatures: On the use and interpretation of correlation plots. Biophys Chem 51:311-326.
29. Murphy KP, Freire E. 1992. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem 43:313-361.
30. Murphy KP, Gill SJ. 1989a. Calorimetric measurement of the enthalpy of dissolution of diketopiperazine in water as a function of temperature. Thermochim Acta 139:279-290.
31. Murphy KP, Gill SJ. 1989b. Thermodynamics of dissolution of cyclic dipeptide solids containing hydrophobic side groups. J Chem Thermo 21:903-913.
32. Murphy KP, Gill SJ. 1990. Group additivity thermodynamics for dissolution of solid cyclic dipeptides into water. Thermochim Acta 172:11-20.
33. Murphy KP, Gill SJ. 1991. Solid model compounds and the thermodynamics of protein unfolding. J Mol Biol 222:699-709.
34. Murphy KP, Privalov PL, Gill SJ. 1990. Common features of protein unfolding and dissolution of hydrophobic compounds. Science 247:559-561.
35. Némethy G, Scheraga HA. 1962. The structure of water and hydrophobic bonding in proteins. III. The thermodynamic properties of hydrophobic bonds in proteins. J Phys Chem 66:1773-1789.
36. Nichols N, Sköld R, Spink C, Wadsö I. 1976. Additivity relations for the heat capacities of non-electrolytes in aqueous solution. J Chem Thermo 8:1081-1093.
37. Nilar SH, Pluta TS. 1995. Hydrogen-bonding capabilities based on polarizability studies of model peptide systems. J Am Chem Soc 117:12603-12607.
38. 1. Biochemistry 31:11196-11202.
39. Privalov PL, Makhatadze GI. 1990. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. J Mol Biol 213:385-391.
40. Privalov PL, Makhatadze GI. 1992. Contribution of hydration and non-covalent interactions to the heat capacity effect on protein unfolding. J Mol Biol 224:715-723.
41. Rashin AA, Bukatin MA. 1994. Magnitude of hydration entropies of non-polar and polar molecules. J Phys Chem 98:386-389.
42. Richards FM. 1977. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng 6:151-176.
43. Schellman JA. 1955. Thermodynamics of urea solutions and the heat of formation of the peptide hydrogen bond. C R Trav Lab Carlsberg Ser Chim 29:223-229.
44. Scholtz JM, Marqusee S, Baldwin RL, York EJ, Stewart JM, Santoro M, Bolen DW. 1991. Calorimetric determination of the enthalpy change for the α-helix to coil transition of an alanine peptide in water. Proc Natl Acad Sci USA 88:2854-2858.
45. Sharp KA, Nicholls A, Fine RF, Honig B. 1991. Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models. Biochemistry 30:9686-9697.
46. Shirley BA, Stanssens P, Hahn U, Pace CN. 1992. Contribution of hydrogen bonding to the conformational stability of ribonuclease T1. Biochemistry 31:725-732.
47. Sletten E 1970. Conformation of cyclic dipeptides. The crystal and molecular structures of cyclo-D-alanyl-L-alanyl and cyclo-L-alanyl-L-alanyl (3,6-dimethylpiperazine-2,5-dione). J Am Chem Soc 92:172-177.
48. Spolar RS, Livingstone JR, Record MT Jr. 1992. 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 31:3947-3955.
49. Susi H, Timasheff SN, Ard JS. 1964. Near infrared investigation of interamide hydrogen bonding in aqueous solution. J Biol Chem 239:3051-3054.
50. 2O and cyclo(glycyl-L-seryl). Acta Crystallogr C 52:383-387.
51. van de Kleut GJ, Sijpkes AH, Gill SC. 1994. The solubilities of five cyclic dipeptides in water at the temperature 298.15 K. J Chem Thermo 26:1115-1120.
52. Yang AS, Sharp KA, Honig B. 1992. Analysis of the heat capacity dependence of protein folding. J Mol Biol 227:889-900.
53. Zamyatnin AA. 1984. Amino acid, peptide, and protein volume in solution. Annu Rev Biophys Bioeng 13:145-165.
54. Zhang XJ, Baase WA, Matthews BW. 1991. Toward a simplification of the protein folding problem: A stabilizing polyalanine α-helix engineered in T4 lysozyme. Biochemistry 30:2012-2017.