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Protein Structure, Stability, and Interactions pp 195–225Cite as

Molecular Crowding and Solvation: Direct and Indirect Impact on Protein Reactions

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 490))

Abstract

The typical environment for biomolecules in vivo is highly crowded. Under such conditions chemical activities, rather than simply concentrations, govern the behavior of the molecules. In this chapter we discuss the underlying solvation principles that give rise to the chemical activities. We focus on simple experimentally accessible examples, macromolecular crowding, protein folding, and ligand binding under crowded conditions. We discuss effects of high concentrations of both macromolecules and small molecules in terms of the Kirkwood–Buff theory, which couples solution structure to thermodynamics.

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References

  1. Ostwald, W. (1893). On chemical energy. J Am Chem Soc 15, 421–430.

    Article  Google Scholar 

  2. Hochachka, P. W., Somero, G. N. (2002). Biochemical Adaptation. Mechanism and Process in Physiological Evolution. Oxford University Press, Oxford.

    Google Scholar 

  3. Tanford, C. (1969). Extension of the theory of linked functions to incorporate the effects of protein hydration. J Mol Biol 39, 539–44.

    Article  PubMed  CAS  Google Scholar 

  4. Schellman, J. A. (1994). The thermodynamics of solvent exchange. Biopolymers 34, 1015–26.

    Article  PubMed  CAS  Google Scholar 

  5. Ben-Naim, A. (1977). Inversion of Kirkwood–Buff theory of solutions – Application to water–ethanol system. J Chem Phys 67, 4884–4890.

    Article  CAS  Google Scholar 

  6. Ben-Naim, A. (1988). Theory of preferential solvation of nonelectrolytes. Cell Biophysics 12, 255–269.

    PubMed  CAS  Google Scholar 

  7. Abui, M., Smith, P. E. (2004). A combined simulation and Kirkwood–Buff approach to quantify cosolvent effects on the conformational preferences of peptides in solution. Journal of Physical Chemistry B 108, 7382–7388.

    Article  CAS  Google Scholar 

  8. Shimizu, S. (2004). Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments. Proc Nat Acad Sci USA 101, 1195–1199.

    Article  PubMed  CAS  Google Scholar 

  9. Shimizu, S., Boon, C. L. (2004). The Kirkwood–Buff theory and the effect of cosolvents on biochemical reactions. J Chem Phys 121, 9147–9155.

    Article  PubMed  CAS  Google Scholar 

  10. Shimizu, S., Smith, D. J. (2004). Preferential hydration and the exclusion of cosolvents from protein surfaces. J Chem Phys 121, 1148–54.

    Article  PubMed  CAS  Google Scholar 

  11. Smith, P. E. (2004). Local chemical potential equalization model for cosolvent effects on biomolecular equilibria. J Phys Chem B 108, 16271–16278.

    Article  CAS  Google Scholar 

  12. Smith, P. E. (2004). Cosolvent interactions with biomolecules: Relating computer simulation data to experimental thermodynamic data. J Phys Chem B 108, 18716–18724.

    Article  CAS  Google Scholar 

  13. Kirkwood, J. G., Buff, F. P. (1951). The statistical mechanical theory of solutions. I. J Chem Phys 19, 774–777.

    Article  CAS  Google Scholar 

  14. Hansen, J. P., McDonald, I. R. (1986). Theory of Simple Liquids. Academic Press, London.

    Google Scholar 

  15. Rösgen, J., Pettitt, B. M., Bolen, D. W. (2005). Protein folding, stability, and solvation structure in osmolyte solutions. Biophys J 89, 2988–97.

    Article  PubMed  Google Scholar 

  16. Rösgen, J., Pettitt, B. M., Bolen, D. W. (2004). Uncovering the basis for nonideal behavior of biological molecules. Biochemistry 43, 14472–14484.

    Article  PubMed  CAS  Google Scholar 

  17. Kokubo, H., Rösgen, J., Bolen, D. W., et al. (2007). Molecular basis of the apparent near ideality of urea solutions. Biophys J 93, 3392–3407.

    Google Scholar 

  18. Ben-Naim, A. (1992). Statistical Themodynamics for Chemists and Biochemists. Plenum, NewYork.

    Google Scholar 

  19. Smith, P. E. (2006). Chemical potential derivatives and preferential interaction parameters in biological systems from Kirkwood–Buff theory. Biophys J 91, 849–56.

    Article  PubMed  CAS  Google Scholar 

  20. Mello, C. C., Barrick, D. (2003). Measuring the stability of partly folded proteins using TMAO. Protein Sci 12, 1522–9.

    Article  PubMed  CAS  Google Scholar 

  21. Holthauzen, L. M., Bolen, D. W. (2007). Mixed osmolytes: The degree to which one osmolyte affects the protein stabilizing ability of another. Protein Sci 16, 293–8.

    Article  PubMed  CAS  Google Scholar 

  22. Ferreon, A. C., Bolen, D. W. (2004). Thermodynamics of denaturant-induced unfolding of a protein that exhibits variable two-state denaturation. Biochemistry 43, 13357–69.

    Article  PubMed  CAS  Google Scholar 

  23. Timasheff, S. N., Xie, G. (2003). Preferential interactions of urea with lysozyme and their linkage to protein denaturation. Biophys Chem 105, 421–48.

    Article  PubMed  CAS  Google Scholar 

  24. Courtenay, E. S., Capp, M. W., Saecker, R. M., et al. (2000). Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model. Proteins Suppl. 4, 72–85.

    Article  PubMed  Google Scholar 

  25. Makhatadze, G. I. (1999). Thermodynamics of protein interactions with urea and guanidinium hydrochloride. J Phys Chem B 103, 4781–4785.

    Article  CAS  Google Scholar 

  26. Santoro, M. M., Bolen, D. W. (1988). Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27, 8063–8.

    Article  PubMed  CAS  Google Scholar 

  27. Greene, R. F., Jr., Pace, C. N. (1974). Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, alpha-chymotrypsin, and beta-lactoglobulin. J Biol Chem 249, 5388–93.

    PubMed  CAS  Google Scholar 

  28. Felitsky, D. J., Record, M. T., Jr. (2004). Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface. Biochemistry 43, 9276–88.

    Article  PubMed  CAS  Google Scholar 

  29. Ben-Naim, A. (1978). Standard thermodynamics of transfer – Uses and misuses. J Phys Chem 82, 792–803.

    Article  CAS  Google Scholar 

  30. Harries, D., Rösgen, J. (2008). A practical guide on how osmolytes modulate macromolecular properties, in (Correia, J. J., Detrich, H. W., eds.) Methods in Cell Biology 84, 679–735. Elsevier, New York.

    Google Scholar 

  31. Rösgen, J. (2007). Molecular basis of osmolyte effects on protein and metabolites, in (Häussinger, D., Sies, H., eds.) Methods in Enzymology: Osmosensing and Osmosignalling, Vol. 428, pp. 459–486. Academic Press, New York.

    Google Scholar 

  32. Ross, P. D., Minton, A. P. (1977). Analysis of non-ideal behavior in concentrated hemoglobin solutions. J Mol Biol 112, 437–52.

    Article  PubMed  CAS  Google Scholar 

  33. Carnahan, N. F., Starling, K. E. (1969). Equation of state for nonattracting rigid spheres. J Chem Phys 51, 635–636.

    Article  CAS  Google Scholar 

  34. Ross, P. D., Minton, A. P. (1977). Hard quasispherical model for the viscosity of hemoglobin solutions. Biochem Biophys Res Commun 76, 971–6.

    Article  PubMed  CAS  Google Scholar 

  35. Minton, A. P. (1995). A molecular-model for the dependence of the osmotic-pressure of bovine serum-albumin upon concentration and pH. Biophys Chem 57, 65–70.

    Article  PubMed  CAS  Google Scholar 

  36. Cheung, J. K., Truskett, T. M. (2005). Coarse-grained strategy for modeling protein stability in concentrated solutions. Biophys J 89, 2372–84.

    Article  PubMed  CAS  Google Scholar 

  37. Zhou, H. X., Dill, K. A. (2001). Stabilization of proteins in confined spaces. Biochemistry 40, 11289–93.

    Article  PubMed  CAS  Google Scholar 

  38. Ziv, G., Haran, G., Thirumalai, D. (2005). Ribosome exit tunnel can entropically stabilize alpha-helices. Proc Natl Acad Sci USA 102, 18956–61.

    Article  PubMed  CAS  Google Scholar 

  39. Minton, A. P. (1992). Confinement as a determinant of macromolecular structure and reactivity. Biophys J 63, 1090–100.

    Article  PubMed  CAS  Google Scholar 

  40. Wills, P. R., Georgalis, Y., Dijk, J., et al. (1995). Measurement of thermodynamic nonideality arising from volume-exclusion interactions between proteins and polymers. Biophys Chem 57, 37–46.

    Article  PubMed  CAS  Google Scholar 

  41. Cheung, M. S., Thirumalai, D. (2006). Nanopore–protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol 357, 632–43.

    Article  PubMed  CAS  Google Scholar 

  42. Minton, A. P. (1995). Confinement as a determinant of macromolecular structure and reactivity. 2. Effects of weakly attractive interactions between confined macrosolutes and confining structures. Biophys J 68, 1311–1322.

    Article  PubMed  CAS  Google Scholar 

  43. Takagi, F., Koga, N., Takada, S. (2003). How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations. Proc Natl Acad Sci USA 100, 11367–72.

    Article  PubMed  CAS  Google Scholar 

  44. Cheung, M. S., Klimov, D., Thirumalai, D. (2005). Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci USA 102, 4753–8.

    Article  PubMed  CAS  Google Scholar 

  45. Eggers, D. K., Valentine, J. S. (2001). Crowding and hydration effects on protein conformation: a study with sol-gel encapsulated proteins. J Mol Biol 314, 911–22.

    Article  PubMed  CAS  Google Scholar 

  46. Ravindra, R., Zhao, S., Gies, H., et al. (2004). Protein Encapsulation in mesoporous silicate: The effects of confinement on protein stability, hydration, and volumetric properties. J Am Chem Soc 126, 12224–12225.

    Article  PubMed  CAS  Google Scholar 

  47. Minton, A. P., Wilf, J. (1981). Effect of macromolecular crowding upon the structure and function of an enzyme: glyceraldehyde-3-phosphate dehydrogenase. Biochemistry 20, 4821–6.

    Article  PubMed  CAS  Google Scholar 

  48. McNulty, B. C., Young, G. B., Pielak, G. J. (2006). Macromolecular crowding in the Escherichia coli periplasm maintains alpha-Synuclein disorder. J Mol Biol 355, 893–7.

    Article  PubMed  CAS  Google Scholar 

  49. Ghaemmaghami, S., Oas, T. G. (2001). Quantitative protein stability measurement in vivo. Nat Struct Biol 8, 879–82.

    Article  PubMed  CAS  Google Scholar 

  50. Ignatova, Z., Gierasch, L. M. (2004). Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling. Proc Natl Acad Sci USA 101, 523–8.

    Article  PubMed  CAS  Google Scholar 

  51. Ignatova, Z., Krishnan, B., Bombardier, J. P., et al. (2007). From the test tube to the cell: Exploring the flooding and aggregation of a beta-clam protein. Biopolymers 88, 157–163.

    Article  PubMed  CAS  Google Scholar 

  52. Qu, Y., Bolen, D. W. (2002). Efficacy of macromolecular crowding in forcing proteins to fold. Biophys Chem 101–102, 155–65.

    Article  PubMed  Google Scholar 

  53. Zhou, H. X. (2004). Protein folding and binding in confined spaces and in crowded solutions. J Mol Recognit 17, 368–75.

    Article  PubMed  CAS  Google Scholar 

  54. Mezzasalma, T. M., Kranz, J. K., Chan, W., et al. (2007). Enhancing recombinant protein quality and yield by protein stability profiling. J Biomol Screen 12, 418–428.

    Article  PubMed  CAS  Google Scholar 

  55. Kueltzo, L. A., Ersoy, B., Ralston, J. P., et al. (2003). Derivative absorbance spectroscopy and protein phase diagrams as tools for comprehensive protein characterization: a bGCSF case study. J Pharm Sci 92, 1805–20.

    Article  PubMed  CAS  Google Scholar 

  56. Tsai, P. K., Volkin, D. B., Dabora, J. M., et al. (1993). Formulation design of acidic fibroblast growth factor. Pharm Res 10, 649–59.

    Article  PubMed  CAS  Google Scholar 

  57. Parsegian, V. A. (2002). Protein–water interactions. Int Rev Cytol 215, 1–31.

    Article  PubMed  CAS  Google Scholar 

  58. Parsegian, V. A., Rand, R. P., Fuller, N. L., et al. (1986). Osmotic stress for the direct measurement of intermolecular forces. Methods Enzymol 127, 400–16.

    Article  PubMed  CAS  Google Scholar 

  59. Leikin, S., Parsegian, V. A., Rau, D. C., et al. (1993). Hydration forces. Ann Rev Phys Chem 44, 369–395.

    Article  CAS  Google Scholar 

  60. Rand, R. P., Parsegian, V. A. (1992). The forces between interacting bilayer membranes and the hydration of phospholipid assemblies, in (Yeagle, P. ed.) The Structure of Biological Membranes, pp. 251–306. CRC Press, Boca Raton.

    Google Scholar 

  61. Rand, R. P., Fuller, N. L., Gruner, S. M., et al. (1990). Membrane curvature, lipid segregation, and structural transitions for phospholipids under dual-solvent stress. Biochemistry 29, 76–87.

    Article  PubMed  CAS  Google Scholar 

  62. Petrache, H. I., Tristram-Nagle, S., Harries, D., et al. (2006). Swelling of phospholipids by monovalent salt. J Lipid Res 47, 302–9.

    Article  PubMed  CAS  Google Scholar 

  63. Rostovtseva, T. K., Nestorovich, E. M., Bezrukov, S. M. (2002). Partitioning of differently sized poly(ethylene glycol)s into OmpF porin. Biophys J 82, 160–169.

    Article  PubMed  CAS  Google Scholar 

  64. Vodyanoy, I., Bezrukov, S. M., Parsegian, V. A. (1993). Probing alamethicin channels with water-soluble polymers. Size-modulated osmotic action. Biophys J 65, 2097–105.

    Article  PubMed  CAS  Google Scholar 

  65. Timasheff, S. N. (1992). Solvent effects on protein stability. Curr Opin Struct Biol 2, 34–39.

    Article  Google Scholar 

  66. Selenko, P., Serber, Z., Gadea, B., et al. (2006). Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes. Proc Natl Acad Sci USA103, 11904–9.

    Article  PubMed  CAS  Google Scholar 

  67. Weerasinghe, S., Smith, P. E. (2003). Kirkwood–Buff derived force field for mixtures of acetone and water. J Chem Phys 118, 10663–10670.

    Article  CAS  Google Scholar 

  68. Weerasinghe, S., Smith, P. E. (2003). A Kirkwood–Buff derived force field for mixtures of urea and water. J Phys Chem B 107, 3891–3898.

    Article  CAS  Google Scholar 

  69. Weerasinghe, S., Smith, P. E. (2004). A Kirkwood–Buff derived force field for the simulation of aqueous guanidinium chloride solutions. J Chem Phys 121, 2180–6.

    Article  PubMed  CAS  Google Scholar 

  70. Kang, M., Smith, P. E. (2006). A Kirkwood–Buff derived force field for amides. J Comput Chem 27, 1477–1485.

    Article  PubMed  CAS  Google Scholar 

  71. Kokubo, H., Pettitt, B. M. (2007). Preferential solvation in urea solutions at different concentrations: properties from simulation studies. J Phys Chem B 111, 5233–42.

    Article  PubMed  CAS  Google Scholar 

  72. Winzor, D. J., Wills, P. R. (1995). Thermodynamic nonideality of enzyme solutions supplemented with inert solutes – Yeast hexokinase revisited. Biophys Chem 57, 103–110.

    Article  PubMed  CAS  Google Scholar 

  73. Jacobsen, M. P., Wills, P. R., Winzor, D. J. (1996). Thermodynamic analysis of the effects of small inert cosolutes in the ultracentrifugation of noninteracting proteins. Biochemistry 35, 13173–9.

    Article  PubMed  CAS  Google Scholar 

  74. Poon, J., Bailey, M., Winzor, D. J., et al. (1997). Effects of molecular crowding on the interaction between DNA and the Escherichia coli regulatory protein TyrR. Biophys J 73, 3257–64.

    CAS  Google Scholar 

  75. Lonhienne, T. G., Winzor, D. J. (2001). Interpretation of the reversible inhibition of adenosine deaminase by small cosolutes in terms of molecular crowding. Biochemistry 40, 9618–22.

    Article  PubMed  CAS  Google Scholar 

  76. Schachman, H. K., Luffer, M. A. (1949). The hydration, size and shape of tobacco mosaic virus. J Am Chem Soc 71, 536–541.

    Article  PubMed  CAS  Google Scholar 

  77. Morar, A. S., Wang, X., Pielak, G. J. (2001). Effects of crowding by mono-, di-, and tetrasaccharides on cytochrome c-cytochrome c peroxidase binding: comparing experiment to theory. Biochemistry 40, 281–5.

    Article  PubMed  CAS  Google Scholar 

  78. Weatherly, G. T., Pielak, G. J. (2001). Second virial coefficients as a measure of protein–osmolyte interactions. Protein Sci 10, 12–6.

    Article  PubMed  CAS  Google Scholar 

  79. Patel, C. N., Noble, S. M., Weatherly, G. T., et al. (2002). Effects of molecular crowding by saccharides on alpha-chymotrypsin dimerization. Protein Sci 11, 997–1003.

    Article  PubMed  CAS  Google Scholar 

  80. Arakawa, T., Timasheff, S. N. (1982). Stabilization of protein structure by sugars. Biochemistry 21, 6536–6544.

    Article  PubMed  CAS  Google Scholar 

  81. Matteoli, E. (1997). A study on Kirkwood–Buff integrals and preferential solvation in mixtures with small deviations from ideality and/or with size mismatch of components. Importance of a proper reference system. J Phys Chem B 101, 9800–9810.

    Article  CAS  Google Scholar 

  82. Shulgin, I. L., Ruckenstein, E. (2006). The Kirkwood–Buff theory of solutions and the local composition of liquid mixtures. J Phys Chem B 110, 12707–13.

    Article  PubMed  CAS  Google Scholar 

  83. Schellman, J. A. (2003). Protein stability in mixed solvents: a balance of contact interaction and excluded volume. Biophys J 85, 108–25.

    Article  PubMed  CAS  Google Scholar 

  84. Ben-Naim, A. (2007). A critique of some recent suggestions to correct the Kirkwood–Buff integrals. J Phys Chem B 111, 2896–2902.

    Article  PubMed  CAS  Google Scholar 

  85. Timasheff, S. N. (1992). Water as ligand – Preferential binding and exclusion of denaturants in protein unfolding. Biochemistry 31, 9857–9864.

    Article  PubMed  CAS  Google Scholar 

  86. Auton, M., Bolen, D. W. (2005). Predicting the energetics of osmolyte-induced protein folding/unfolding. Proc Natl Acad Sci USA 102, 15065–15068.

    Article  PubMed  CAS  Google Scholar 

  87. Nozaki, Y., Tanford, C. (1963). The solubility of amino acids and related compounds in aqueous urea solutions. J Biol Chem 238, 4074–4081.

    PubMed  CAS  Google Scholar 

  88. Reisler, E., Haik, Y., Eisenberg, H. (1977). Bovine serum albumin and aqueous guanidine hydrochloride solutions. Preferential and absolute interactions and comparison with other systems. Biochemistry 16, 197–203.

    Article  PubMed  CAS  Google Scholar 

  89. Rösgen, J., Pettitt, B. M., Bolen, D. W. (2007). An analysis of the molecular origin of osmolyte-dependent protein stability. Protein Sci 16, 733–743.

    Article  PubMed  CAS  Google Scholar 

  90. Lide, D. R. (2004). CRC Handbook of Chemistry and Physics. CRC Press, Boca Raton, FL.

    Google Scholar 

  91. Rösgen, J., Pettitt, B. M., Perkyns, J., et al. (2004). Statistical thermodynamic approach to the chemical activities in two-component solutions. J Phys Chem B 108, 2048–2055.

    Article  CAS  Google Scholar 

  92. Matteoli, E., Lepori, L. (1984). Solute–solute interactions in water. 2. An analysis through the Kirkwood–Buff integrals for 14 organic solutes. J Chem Phys 80, 2856–2863.

    Article  CAS  Google Scholar 

  93. Timasheff, S. N. (1998). Control of protein stability and reactions by weakly interacting cosolvents: the simplicity of the complicated. Adv Protein Chem 51, 355–432.

    Article  PubMed  CAS  Google Scholar 

  94. Ebel, C., Eisenberg, H., Ghirlando, R. (2000). Probing protein–sugar interactions. Biophys J 78, 385–93.

    Article  PubMed  CAS  Google Scholar 

  95. Hade, E. P. K., Tanford, C. (1967). Isopiestic compositions as a measure of preferential interactions of macromolecules in two-component solvents. Application to proteins in concentrated aqueous cesium chloride and guanidine hydrochloride. J Am Chem Soc 89, 5034–5040.

    Article  PubMed  CAS  Google Scholar 

  96. Zhang, W., Capp, M. W., Bond, J. P., et al. (1996). Thermodynamic characterization of interactions of native bovine serum albumin with highly excluded (glycine betaine) and moderately accumulated (urea) solutes by a novel application of vapor pressure osmometry. Biochemistry 35, 10506–16.

    Article  PubMed  CAS  Google Scholar 

  97. Anderson, C. F., Courtenay, E. S., Record, M. T. (2002). Thermodynamic expressions relating different types of preferential interaction coefficients in solutions containing two solute components. J Phys Chem B 106, 418–433.

    Article  CAS  Google Scholar 

  98. Schurr, J. M., Rangel, D. P., Aragon, S. R. (2005). A contribution to the theory of preferential interaction coefficients. Biophys J 89, 2258–76.

    Article  PubMed  CAS  Google Scholar 

  99. Shulgin, I. L., Ruckenstein, E. (2005). A protein molecule in an aqueous mixed solvent: fluctuation theory outlook. J Chem Phys 123, 054909.

    Article  PubMed  CAS  Google Scholar 

  100. Tanford, C. (1968). Protein denaturation. Adv Protein Chem 23, 121–282.

    Article  PubMed  CAS  Google Scholar 

  101. Timasheff, S. N. (2002). Thermodynamic binding and site occupancy in the light of the Schellman exchange concept. Biophys Chem 101, 99–111.

    Article  PubMed  Google Scholar 

  102. Sidorova, N. Y., Rau, D. C. (1996). Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences. Proc Natl Acad Sci USA 93, 12272–7.

    Article  PubMed  CAS  Google Scholar 

  103. Parsegian, V. A., Rand, R. P., Rau, D. C. (2000). Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives. Proc Natl Acad Sci USA 97, 3987–92.

    Article  PubMed  CAS  Google Scholar 

  104. Sidorova, N. Y., Rau, D. C. (2004). Differences between EcoRI nonspecific and “star” sequence complexes revealed by osmotic stress. Biophys J 87, 2564–76.

    Article  PubMed  CAS  Google Scholar 

  105. Rau, D. C. (2006). Sequestered water and binding energy are coupled in complexes of lambda Cro repressor with non-consensus binding sequences. J Mol Biol 361, 352–61.

    Article  PubMed  CAS  Google Scholar 

  106. Shimizu, S. (2004). Estimation of excess solvation numbers of water and cosolvents from preferential interaction and volumetric experiments. J Chem Phys 120, 4989–4990.

    Article  PubMed  CAS  Google Scholar 

  107. Ferreon, A. C., Ferreon, J. C., Bolen, D. W., et al. (2007). Protein phase diagrams II: Nonideal behavior of biochemical reactions in the presence of osmolytes. Biophys J 92, 245–56.

    Article  PubMed  CAS  Google Scholar 

  108. Rand, R. P., Fuller, N. L., Butko, P., et al. (1993). Measured change in protein solvation with substrate binding and turnover. Biochemistry 32, 5925–9.

    Article  PubMed  CAS  Google Scholar 

  109. Vossen, K. M., Wolz, R., Daugherty, M. A., et al. (1997). Role of macromolecular hydration in the binding of the Escherichia coli cyclic AMP receptor to DNA. Biochemistry 36, 11640–7.

    Article  PubMed  CAS  Google Scholar 

  110. Kiser, J. R., Monk, R. W., Smalls, R. L., et al. (2005). Hydration changes in the association of Hoechst 33258 with DNA. Biochemistry 44, 16988–97.

    Article  PubMed  CAS  Google Scholar 

  111. Chebotareva, N. A., Kurganov, B. I., Harding, S. E., et al. (2005). Effect of osmolytes on the interaction of flavin adenine dinucleotide with muscle glycogen phosphorylase b. Biophys Chem 113, 61–6.

    Article  PubMed  CAS  Google Scholar 

  112. Harries, D., Rau, D. C., Parsegian, V. A. (2005). Solutes probe hydration in specific association of cyclodextrin and adamantane. J Am Chem Soc 127, 2184–2190.

    Article  PubMed  CAS  Google Scholar 

  113. Timasheff, S. N. (1998). In disperse solution, “osmotic stress” is a restricted case of preferential interactions. Proc Nat Acad Sci USA 95, 7363–7367.

    Article  PubMed  CAS  Google Scholar 

  114. Sinha, R., Kundu, K. K. (1998). Transfer Gibbs energies of ATP in aqueous mixtures of non-ionic glycerol and urea and ionic NaNO3. Indian J Chem Sect A 37, 789–794.

    Google Scholar 

  115. Shearwin, K. E., Winzor, D. J. (1990). Allowance for thermodynamic nonideality and Donnan effects in binding studies. Activity coefficients of charged ligands in the presence of albumin. Biophys Chem 36, 235–43.

    Article  PubMed  CAS  Google Scholar 

  116. Hong, J., Capp, M. W., Anderson, C. F., et al. (2004). Preferential interactions of glycine betaine and of urea with DNA: Implications for DNA hydration and for effects of these solutes on DNA stability. Biochemistry 43, 14744–58.

    Article  PubMed  CAS  Google Scholar 

  117. Warner, F. W. (1983). Foundations of Differentiable Manifolds and Lie Groups. Springer, New York.

    Google Scholar 

  118. Chalikian, T. V. (2003). Volumetric properties of proteins. Annu Rev Biophys Biomol Struct 32, 207–235.

    Article  PubMed  CAS  Google Scholar 

  119. Durchschlag, H. (1986). Specific volumes of biological macromolecules and some other molecules of biological interest, in (Hinz, H.-J., ed.)Thermodynamic Data for Biochemistry and Biotechnology, pp. 45–128. Springer, Berlin.

    Google Scholar 

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Acknowledgements

Thanks to Wayne Bolen, Austin Elam, and John Shriver for critically reading the manuscript. This work was supported by NIH (R01GM049760), and a training fellowship from the W.M. Keck Foundation to the Gulf Coast Consortia through the Keck Center of Computational and Structural Biology.

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  1. Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA

    Jörg Rösgen

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    Rösgen, J. (2009). Molecular Crowding and Solvation: Direct and Indirect Impact on Protein Reactions. In: Shriver, J. (eds) Protein Structure, Stability, and Interactions. Methods in Molecular Biology, vol 490. Humana Press. https://doi.org/10.1007/978-1-59745-367-7_9

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    • Publisher Name: Humana Press

    • Print ISBN: 978-1-58829-954-3

    • Online ISBN: 978-1-59745-367-7

    • eBook Packages: Springer Protocols

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