Literature DB >> 17693466

Molecular basis of the apparent near ideality of urea solutions.

Hironori Kokubo1, Jörg Rösgen, D Wayne Bolen, B Montgomery Pettitt.   

Abstract

Activity coefficients of urea solutions are calculated to explore the mechanism of its solution properties, which form the basis for its well-known use as a strong protein denaturant. We perform free energy simulations of urea solutions in different urea concentrations using two urea models (OPLS and KBFF models) to calculate and decompose the activity coefficients. For the case of urea, we clarify the concept of the ideal solution in different concentration scales and standard states and its effect on our subsequent analysis. The analytical form of activity coefficients depends on the concentration units and standard states. For both models studied, urea displays a weak concentration dependence for excess chemical potential. However, for the OPLS force-field model, this results from contributions that are independent of concentration to the van der Waals and electrostatic components whereas for the KBFF model those components are nontrivial but oppose each other. The strong ideality of urea solutions in some concentration scales (incidentally implying a lack of water perturbation) is discussed in terms of recent data and ideas on the mechanism of urea denaturation of proteins.

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Year:  2007        PMID: 17693466      PMCID: PMC2072084          DOI: 10.1529/biophysj.107.114181

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


  10 in total

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2.  Molecular theory of hydrophobic effects: "She is too mean to have her name repeated.".

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Journal:  Annu Rev Phys Chem       Date:  2002       Impact factor: 12.703

3.  Fifty years of solvent denaturation.

Authors:  John A Schellman
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Review 4.  Uncovering the basis for nonideal behavior of biological molecules.

Authors:  Jörg Rösgen; Bernard Montgomery Pettitt; David Wayne Bolen
Journal:  Biochemistry       Date:  2004-11-16       Impact factor: 3.162

5.  Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.

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Journal:  J Chem Phys       Date:  2005-04-08       Impact factor: 3.488

6.  Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

Authors:  Michael R Shirts; Vijay S Pande
Journal:  J Chem Phys       Date:  2005-04-01       Impact factor: 3.488

7.  Protein folding, stability, and solvation structure in osmolyte solutions.

Authors:  Jörg Rösgen; B Montgomery Pettitt; David Wayne Bolen
Journal:  Biophys J       Date:  2005-08-19       Impact factor: 4.033

8.  Preferential solvation in urea solutions at different concentrations: properties from simulation studies.

Authors:  Hironori Kokubo; B Montgomery Pettitt
Journal:  J Phys Chem B       Date:  2007-04-21       Impact factor: 2.991

9.  Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, alpha-chymotrypsin, and beta-lactoglobulin.

Authors:  R F Greene; C N Pace
Journal:  J Biol Chem       Date:  1974-09-10       Impact factor: 5.157

10.  The molecular basis for the chemical denaturation of proteins by urea.

Authors:  Brian J Bennion; Valerie Daggett
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-17       Impact factor: 11.205

  10 in total
  18 in total

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Journal:  J Chem Phys       Date:  2010-04-28       Impact factor: 3.488

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3.  Comment on "Can existing models quantitatively describe the mixing behavior of acetone with water" [J. Chem. Phys. 130, 124516 (2009)].

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4.  Local Fluctuations in Solution: Theory and Applications.

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Journal:  Adv Chem Phys       Date:  2013       Impact factor: 1.000

5.  Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Authors:  Bin Lin; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-08-28       Impact factor: 3.488

6.  Distinctive solvation patterns make renal osmolytes diverse.

Authors:  Ruby Jackson-Atogi; Prem Kumar Sinha; Jörg Rösgen
Journal:  Biophys J       Date:  2013-11-05       Impact factor: 4.033

7.  Analyzing the components of the free-energy landscape in a calcium selective ion channel by Widom's particle insertion method.

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Journal:  J Chem Phys       Date:  2011-02-07       Impact factor: 3.488

8.  Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field.

Authors:  Yun Luo; Wei Jiang; Haibo Yu; Alexander D MacKerell; Benoit Roux
Journal:  Faraday Discuss       Date:  2013       Impact factor: 4.008

9.  Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

Authors:  In Suk Joung; Thomas E Cheatham
Journal:  J Phys Chem B       Date:  2009-10-08       Impact factor: 2.991

10.  Osmolyte solutions and protein folding.

Authors:  Char Y Hu; B Montgomery Pettitt; Joerg Roesgen
Journal:  F1000 Biol Rep       Date:  2009-05-28
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