Abstract
Changes in solvent environment greatly affect macromolecular structure and stability. To investigate the role of excluded volume in solvation, scaled-particle theory is often used to calculate delta G(tr)(ev), the excluded-volume portion of the solute transfer free energy, delta G(tr). The inputs to SPT are the solvent radii and molarities. Real molecules are not spheres. Hence, molecular radii are not uniquely defined and vary for any given species. Since delta G(tr)(ev) is extremely sensitive to solvent radii, uncertainty in these radii causes a large uncertainty in delta G(tr)(ev)-several kcal/mol for amino acid solutes transferring from water to aqueous mixtures. This uncertainty is larger than the experimental delta G(tr) values. Also, delta G(tr)(ev) can be either positive or negative. Adding neutral crowding molecules may not necessarily reduce solubility. Lastly, delta G(tr)(ev) is very sensitive to solvent density, rho. A few percent error in rho may even cause qualitative deviations in delta G(tr)(ev). For example, if rho is calculated by assuming the hard-sphere pressure to be constant, then delta G(tr)(ev) values and uncertainties are now only tenths of a kcal/mol and are positive. Because delta G(tr)(ev) values calculated by scaled-particle theory are strongly sensitive to solvent radii and densities, determining the excluded-volume contribution to transfer free energies using SPT may be problematic.
Full Text
The Full Text of this article is available as a PDF (256.7 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Ben-Naim A., Ting K. L., Jernigan R. L. Solvation thermodynamics of biopolymers. I. Separation of the volume and surface interactions with estimates for proteins. Biopolymers. 1989 Jul;28(7):1309–1325. doi: 10.1002/bip.360280711. [DOI] [PubMed] [Google Scholar]
- Berg O. G. The influence of macromolecular crowding on thermodynamic activity: solubility and dimerization constants for spherical and dumbbell-shaped molecules in a hard-sphere mixture. Biopolymers. 1990;30(11-12):1027–1037. doi: 10.1002/bip.360301104. [DOI] [PubMed] [Google Scholar]
- Connolly M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science. 1983 Aug 19;221(4612):709–713. doi: 10.1126/science.6879170. [DOI] [PubMed] [Google Scholar]
- GOLDSTEIN D. A., SOLOMON A. K. Determination of equivalent pore radius for human red cells by osmotic pressure measurement. J Gen Physiol. 1960 Sep;44:1–17. doi: 10.1085/jgp.44.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guttman H. J., Anderson C. F., Record M. T., Jr Analyses of thermodynamic data for concentrated hemoglobin solutions using scaled particle theory: implications for a simple two-state model of water in thermodynamic analyses of crowding in vitro and in vivo. Biophys J. 1995 Mar;68(3):835–846. doi: 10.1016/S0006-3495(95)80260-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
- Lee B. The physical origin of the low solubility of nonpolar solutes in water. Biopolymers. 1985 May;24(5):813–823. doi: 10.1002/bip.360240507. [DOI] [PubMed] [Google Scholar]
- Liu Y., Bolen D. W. The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes. Biochemistry. 1995 Oct 3;34(39):12884–12891. doi: 10.1021/bi00039a051. [DOI] [PubMed] [Google Scholar]
- Madan B., Lee B. Role of hydrogen bonds in hydrophobicity: the free energy of cavity formation in water models with and without the hydrogen bonds. Biophys Chem. 1994 Aug;51(2-3):279–289. doi: 10.1016/0301-4622(94)00049-2. [DOI] [PubMed] [Google Scholar]
- Minton A. P. The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences. Mol Cell Biochem. 1983;55(2):119–140. doi: 10.1007/BF00673707. [DOI] [PubMed] [Google Scholar]
- Nozaki Y., Tanford C. The solubility of amino acids and related compounds in aqueous thylene glycol solutions. J Biol Chem. 1965 Sep;240(9):3568–3575. [PubMed] [Google Scholar]
- Nozaki Y., Tanford C. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J Biol Chem. 1971 Apr 10;246(7):2211–2217. [PubMed] [Google Scholar]
- Pohorille A., Pratt L. R. Cavities in molecular liquids and the theory of hydrophobic solubilities. J Am Chem Soc. 1990;112(13):5066–5074. doi: 10.1021/ja00169a011. [DOI] [PubMed] [Google Scholar]
- SCHULTZ S. G., SOLOMON A. K. Determination of the effective hydrodynamic radii of small molecules by viscometry. J Gen Physiol. 1961 Jul;44:1189–1199. doi: 10.1085/jgp.44.6.1189. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saunders A. J., Davis-Searles P. R., Allen D. L., Pielak G. J., Erie D. A. Osmolyte-induced changes in protein conformational equilibria. Biopolymers. 2000 Apr 5;53(4):293–307. doi: 10.1002/(SICI)1097-0282(20000405)53:4<293::AID-BIP2>3.0.CO;2-T. [DOI] [PubMed] [Google Scholar]
- Shrake A., Rupley J. A. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol. 1973 Sep 15;79(2):351–371. doi: 10.1016/0022-2836(73)90011-9. [DOI] [PubMed] [Google Scholar]
- Wang A., Bolen D. W. A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea denaturation. Biochemistry. 1997 Jul 29;36(30):9101–9108. doi: 10.1021/bi970247h. [DOI] [PubMed] [Google Scholar]