Hydrogen bonding increases packing density in the protein interior

Proteins: Structure, Function and Genetics

Volumn 63, Issue 2, 2006, Pages 278-282

  Schell, David ^a,b   Tsai, Jerry ^a   Scholtz, J Martin ^a,b   Pace, C Nick ^a,b  

^a TEXAS A AND M UNIVERSITY   (United States)

^b TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

Author keywords

Hydrogen bonds; Protein folding; Protein stability; Van der Waals interactions

Indexed keywords

PROTEIN;

ARTICLE; CELL DENSITY; HUMAN; HYDROGEN BOND; MOLECULAR INTERACTION; PACKING DENSITY; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; PROTEINS;

EID: 33645315212     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20826     Document Type: Article

References (44)

1. Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959;14:1-63.
2. Dill KA. Dominant forces in protein folding. Biochemistry 1990;29:7133-7155.
3. Pace CN. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry 2001;40:310-313.
4. Pace CN, Trevino S, Prabhakaran E, Scholtz JM. Protein structure, stability and solubility in water and other solvents. Philos Trans R Soc Lond B Biol Sci 2004;359:1225-1234; discussion 1234-1225.
5. Eriksson AE, Baase WA, Zhang XJ, Heinz DW, Blaber M, Baldwin EP, Matthews BW. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 1992;255:178-183.
6. Chen J, Stites WE. Packing is a key selection factor in the evolution of protein hydrophobic cores. Biochemistry 2001;40:15280-15289.
7. Ponder JW, Case DA. Force fields for protein simulations. Adv Protein Chem 2003;66:27-85.
8. Klapper MH. On the nature of the protein interior. Biochim Biophys Acta 1971;229:557-566.
9. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
10. Chothia C. Structural invariants in protein folding. Nature 1975;254:304-308.
11. Richards FM. The interpretation of protein structures: total volume, group volume distributions and packing density. J Mol Biol 1974;82:1-14.
12. Harpaz Y, Gerstein M, Chothia C. Volume changes on protein-folding. Structure 1994;2:641-649.
13. Kuntz ID. Tertiary structure in carboxypeptidase. J Am Chem Soc 1972;94:8568-8572.
14. Kuntz ID, Crippen GM. Protein densities. Int J Pept Protein Res 1979;13:223-228.
15. Kurochkina N, Privalov G. Heterogeneity of packing: structural approach. Protein Sci 1998;7:897-905.
16. Hubbard SJ, Gross KH, Argos P. Intramolecular cavities in globular proteins. Protein Eng 1994;7:613-626.
17. Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 1996;264:121-136.
18. Tsai CJ, Maizel JV Jr, Nussinov R. The hydrophobic effect: a new insight from cold denaturation and a two-state water structure. Crit Rev Biochem Mol Biol 2002;37:55-69.
19. Tsai J, Taylor R, Chothia C, Gerstein M. The packing density in proteins: standard radii and volumes. J Mol Biol 1999;290:253-266.
20. Matthews BW. Studies on protein stability with T4 lysozyme. Adv Protein Chem 1995;46:249-278.
21. Sneddon SF, Tobias DJ. The role of packing interactions in stabilizing folded proteins. Biochemistry 1992;31:2842-2846.
22. Sugita Y, Kitao A, Go N. Computational analysis of thermal stability: effect of Ile → Val mutations in human lysozyme. Fold Des 1998;3:173-181.
23. Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96-Ala mutation in barnase. Proc Natl Acad Sci USA 1991;88:10880-10884.
24. Kono H, Saito M, Sarai A. Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations. Proteins 2000;38:197-209.
25. 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.
26. Honig B. Protein folding: from the levinthal paradox to structure prediction. J Mol Biol 1999;293:283-293.
27. Honig B, Yang AS. Free energy balance in protein folding. Adv Protein Chem 1995;46:27-58.
28. Chen YW, Fersht AR, Henrick K. Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants. J Mol Biol 1993;234:1158-1170.
29. Yamagata Y, Kubota M, Sumikawa Y, Funahashi J, Takano K, Fujii S, Yutani K. Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six tyrosine → phenylalanine mutants. Biochemistry 1998;37:9355-9362.
30. Takano K, Yamagata Y, Kubota M, Funahashi J, Fujii S, Yutani K. Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser → Ala mutants. Biochemistry 1999;38:6623-6629.
31. Albeck S, Unger R, Schreiber G. Evaluation of direct and cooperative contributions towards the strength of buried hydrogen bonds and salt bridges. J Mol Biol 2000;298:503-520.
32. Hamill SJ, Cota E, Chothia C, Clarke J. Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac. J Mol Biol 2000;295:641-649.
33. Takano K, Scholtz JM, Sacchettini JC, Pace CN. The contribution of polar group burial to protein stability is strongly context-dependent. J Biol Chem 2003;278:31790-31795.
34. Voronoi GF. Nouveles applications des paramétres continus à la théorie des formes quadratiques. J Reine Angew Math 1908;134:198-287.
35. Tsai J, Gerstein M. Calculations of protein volumes: sensitivity analysis and parameter database. Bioinformatics 2002;18:985-995.
36. Baker EN, Hubbard RE. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 1984;44:97-179.
37. Stickle DF, Presta LG, Dill KA, Rose GD. Hydrogen bonding in globular proteins. J Mol Biol 1992;226:1143-1159.
38. Fleming PJ, Rose GD. Do all backbone polar groups in proteins form hydrogen bonds? Protein Sci 2005;14:1911-1917.
39. Lesser GJ, Rose GD. Hydrophobicity of amino acid subgroups in proteins. Proteins 1990;8:6-13.
40. Gerstein M, Tsai J, Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J Mol Biol 1995;249:955-966.
41. Gerstein M. A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites. Acta Crystallogr A 1992;48:271-276.
42. Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
43. Connolly ML. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983;221:709-713.
44. McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994;238:777-793.