Literature DB >> 11053104

Excluded volume in solvation: sensitivity of scaled-particle theory to solvent size and density.

K E Tang1, V A Bloomfield.   

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.

Entities:  

Mesh:

Substances:

Year:  2000        PMID: 11053104      PMCID: PMC1301112          DOI: 10.1016/S0006-3495(00)76470-8

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  17 in total

1.  Osmolyte-induced changes in protein conformational equilibria.

Authors:  A J Saunders; P R Davis-Searles; D L Allen; G J Pielak; D A Erie
Journal:  Biopolymers       Date:  2000-04-05       Impact factor: 2.505

2.  Cavities in molecular liquids and the theory of hydrophobic solubilities.

Authors:  A Pohorille; L R Pratt
Journal:  J Am Chem Soc       Date:  1990       Impact factor: 15.419

3.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin.

Authors:  A Shrake; J A Rupley
Journal:  J Mol Biol       Date:  1973-09-15       Impact factor: 5.469

4.  The solubility of amino acids and related compounds in aqueous thylene glycol solutions.

Authors:  Y Nozaki; C Tanford
Journal:  J Biol Chem       Date:  1965-09       Impact factor: 5.157

5.  The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale.

Authors:  Y Nozaki; C Tanford
Journal:  J Biol Chem       Date:  1971-04-10       Impact factor: 5.157

6.  The interpretation of protein structures: estimation of static accessibility.

Authors:  B Lee; F M Richards
Journal:  J Mol Biol       Date:  1971-02-14       Impact factor: 5.469

7.  Role of hydrogen bonds in hydrophobicity: the free energy of cavity formation in water models with and without the hydrogen bonds.

Authors:  B Madan; B Lee
Journal:  Biophys Chem       Date:  1994-08       Impact factor: 2.352

8.  A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea denaturation.

Authors:  A Wang; D W Bolen
Journal:  Biochemistry       Date:  1997-07-29       Impact factor: 3.162

9.  The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes.

Authors:  Y Liu; D W Bolen
Journal:  Biochemistry       Date:  1995-10-03       Impact factor: 3.162

10.  Determination of the effective hydrodynamic radii of small molecules by viscometry.

Authors:  S G SCHULTZ; A K SOLOMON
Journal:  J Gen Physiol       Date:  1961-07       Impact factor: 4.086

View more
  11 in total

1.  Assessing accumulated solvent near a macromolecular solute by preferential interaction coefficients.

Authors:  Karen E S Tang; Victor A Bloomfield
Journal:  Biophys J       Date:  2002-06       Impact factor: 4.033

2.  The Influence of Crowding Conditions on the Thermodynamic Feasibility of Metabolic Pathways.

Authors:  Liliana Angeles-Martinez; Constantinos Theodoropoulos
Journal:  Biophys J       Date:  2015-12-01       Impact factor: 4.033

3.  Protein shape modulates crowding effects.

Authors:  Alex J Guseman; Gerardo M Perez Goncalves; Shannon L Speer; Gregory B Young; Gary J Pielak
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-09       Impact factor: 11.205

4.  The role of macromolecular crowding in the evolution of lens crystallins with high molecular refractive index.

Authors:  Huaying Zhao; M Teresa Magone; Peter Schuck
Journal:  Phys Biol       Date:  2011-05-12       Impact factor: 2.583

5.  Effects of molecular crowding by saccharides on alpha-chymotrypsin dimerization.

Authors:  Chetan N Patel; Schroeder M Noble; Gresham T Weatherly; Ashutosh Tripathy; Donald J Winzor; Gary J Pielak
Journal:  Protein Sci       Date:  2002-05       Impact factor: 6.725

Review 6.  Implicit Solvation Methods for Catalysis at Electrified Interfaces.

Authors:  Stefan Ringe; Nicolas G Hörmann; Harald Oberhofer; Karsten Reuter
Journal:  Chem Rev       Date:  2021-12-20       Impact factor: 72.087

7.  Evaluating the Effects of Hinge Flexibility on the Solution Structure of Antibodies at Concentrated Conditions.

Authors:  Marco A Blanco; Harold W Hatch; Joseph E Curtis; Vincent K Shen
Journal:  J Pharm Sci       Date:  2018-12-26       Impact factor: 3.534

8.  Bulk Droplet Vitrification: An Approach to Improve Large-Scale Hepatocyte Cryopreservation Outcome.

Authors:  Reinier J de Vries; Peony D Banik; Sonal Nagpal; Lindong Weng; Sinan Ozer; Thomas M van Gulik; Mehmet Toner; Shannon N Tessier; Korkut Uygun
Journal:  Langmuir       Date:  2019-01-09       Impact factor: 3.882

9.  On the Effect of Sodium Chloride and Sodium Sulfate on Cold Denaturation.

Authors:  Andrea Pica; Giuseppe Graziano
Journal:  PLoS One       Date:  2015-07-21       Impact factor: 3.240

10.  A Lattice-Boltzmann scheme for the simulation of diffusion in intracellular crowded systems.

Authors:  Liliana Angeles-Martinez; Constantinos Theodoropoulos
Journal:  BMC Bioinformatics       Date:  2015-11-03       Impact factor: 3.169

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.