Literature DB >> 12023211

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

Karen E S Tang1, Victor A Bloomfield.   

Abstract

Biological macromolecules are often studied in mixed solvents. To understand cosolvent-macromolecule interactions, the preferential interaction coefficient, Gamma(3), may help determine surface solvent compositions. Gamma(3) measures the amounts of water, B(1), and cosolvent, B(3), within the "local domain," the (possibly far-reaching) region surrounding the macromolecule where the solvent is non-bulk-like. The local domain's boundary is, however, vague and it is unclear which molecules are counted in B(i). It is useful to explore a simple model system to make B(i) more concrete and to understand which aspects of the surface solvent distribution, rho(x), are sampled by Gamma(3). We performed computer simulations on a two-dimensional (2D) system consisting of a hard-wall solute (the macromolecule) in a mixed solvent (hard disks of different radii). We simultaneously calculated Gamma(3) and rho(x). We found that 1) in practice, the local domain's boundary is demarked by the outer limit of the first cosolvent (not water) layer; B(i) mainly counts the solvent near the macromolecule; 2) assuming B(1) to count only the waters within the first water layer is a poor approximation; 3) when determining B(1) and B(3), water and cosolvent molecules must be counted from the same region of space. We speculate that these 2D results may serve as a first-order approximation for the dominant contributions to Gamma(3) even in three dimensions, so long as the cosolvent is not strongly excluded from the macromolecular surface and there is no significant long-ranged solvent structure.

Entities:  

Mesh:

Substances:

Year:  2002        PMID: 12023211      PMCID: PMC1302076          DOI: 10.1016/S0006-3495(02)75629-4

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


  44 in total

1.  Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives.

Authors:  V A Parsegian; R P Rand; D C Rau
Journal:  Proc Natl Acad Sci U S A       Date:  2000-04-11       Impact factor: 11.205

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

Authors:  K E Tang; V A Bloomfield
Journal:  Biophys J       Date:  2000-11       Impact factor: 4.033

3.  Protein hydration in aqueous solution.

Authors:  G Otting; E Liepinsh; K Wüthrich
Journal:  Science       Date:  1991-11-15       Impact factor: 47.728

Review 4.  Hydration of proteins and polypeptides.

Authors:  I D Kuntz; W Kauzmann
Journal:  Adv Protein Chem       Date:  1974

5.  Partial specific volumes and interactions with solvent components of proteins in guanidine hydrochloride.

Authors:  J C Lee; S N Timasheff
Journal:  Biochemistry       Date:  1974-01-15       Impact factor: 3.162

6.  Preferential and absolute interactions of solvent components with proteins in mixed solvent systems.

Authors:  H Inoue; S N Timasheff
Journal:  Biopolymers       Date:  1972       Impact factor: 2.505

7.  Hydration of macromolecules. IV. Polypeptide conformation in frozen solutions.

Authors:  I D Kuntz
Journal:  J Am Chem Soc       Date:  1971-01-27       Impact factor: 15.419

8.  Protein hydration. I. Binding sites.

Authors:  H B Bull; K Breese
Journal:  Arch Biochem Biophys       Date:  1968-11       Impact factor: 4.013

9.  Solvation study of the non-specific lipid transfer protein from wheat by intermolecular NOEs with water and small organic molecules.

Authors:  E Liepinsh; P Sodano; S Tassin; D Marion; F Vovelle; G Otting
Journal:  J Biomol NMR       Date:  1999-11       Impact factor: 2.835

10.  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.

Authors:  E S Courtenay; M W Capp; R M Saecker; M T Record
Journal:  Proteins       Date:  2000
View more
  7 in total

1.  Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments.

Authors:  Seishi Shimizu
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-19       Impact factor: 11.205

2.  Chemical potential derivatives and preferential interaction parameters in biological systems from Kirkwood-Buff theory.

Authors:  Paul E Smith
Journal:  Biophys J       Date:  2006-05-05       Impact factor: 4.033

Review 3.  Recent applications of Kirkwood-Buff theory to biological systems.

Authors:  Veronica Pierce; Myungshim Kang; Mahalaxmi Aburi; Samantha Weerasinghe; Paul E Smith
Journal:  Cell Biochem Biophys       Date:  2007-11-28       Impact factor: 2.194

4.  SANS/SAXS study of the BSA solvation properties in aqueous urea solutions via a global fit approach.

Authors:  Raffaele Sinibaldi; Maria Grazia Ortore; Francesco Spinozzi; Sérgio de Souza Funari; José Teixeira; Paolo Mariani
Journal:  Eur Biophys J       Date:  2008-03-26       Impact factor: 1.733

5.  Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation.

Authors:  R B Pandey; D J Jacobs; B L Farmer
Journal:  J Chem Phys       Date:  2017-05-21       Impact factor: 3.488

Review 6.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

7.  Comparison of the effect of water release on the interaction of the Saccharomyces cerevisiae TATA binding protein (TBP) with "TATA Box" sequences composed of adenosine or inosine.

Authors:  Sergei Khrapunov; Michael Brenowitz
Journal:  Biophys J       Date:  2004-01       Impact factor: 4.033

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.