Literature DB >> 9241426

Solvation: how to obtain microscopic energies from partitioning and solvation experiments.

H S Chan1, K A Dill.   

Abstract

Oil-water partitioning, solubilities, and vapor pressure experiments on small-molecule compounds are often used as models to obtain energies for biomolecular modeling. For example, measured partition coefficients, K, are often inserted into the formula -RT in K to obtain quantities thought to represent microscopic contact interaction free energies. We review evidence here that this procedure does not always give microscopically meaningful free energies. Some partitioning processes, particularly involving polymeric solvents such as octanol or hexadecane, are governed not only by translational entropies and contact interactions, but also by free energies resulting from changes in the conformations of the polymer chains upon solute insertion. The Flory-Huggins theory is more suitable for these situations than is the classical approach. We discuss the physical bases for both approaches.

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Year:  1997        PMID: 9241426     DOI: 10.1146/annurev.biophys.26.1.425

Source DB:  PubMed          Journal:  Annu Rev Biophys Biomol Struct        ISSN: 1056-8700


  15 in total

1.  An amino acid code for protein folding.

Authors:  J Rumbley; L Hoang; L Mayne; S W Englander
Journal:  Proc Natl Acad Sci U S A       Date:  2001-01-02       Impact factor: 11.205

2.  Folding protein models with a simple hydrophobic energy function: the fundamental importance of monomer inside/outside segregation.

Authors:  A F Pereira De Araújo
Journal:  Proc Natl Acad Sci U S A       Date:  1999-10-26       Impact factor: 11.205

3.  Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

Authors:  J Mendes; A M Baptista; M A Carrondo; C M Soares
Journal:  J Comput Aided Mol Des       Date:  2001-08       Impact factor: 3.686

4.  Computer simulations of membrane protein folding: structure and dynamics.

Authors:  C-M Chen; C-C Chen
Journal:  Biophys J       Date:  2003-03       Impact factor: 4.033

5.  A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA).

Authors:  Patrick J Fleming; Nicholas C Fitzkee; Mihaly Mezei; Rajgopal Srinivasan; George D Rose
Journal:  Protein Sci       Date:  2004-12-02       Impact factor: 6.725

6.  Redesign of a protein-peptide interaction: characterization and applications.

Authors:  Meredith E Jackrel; Roberto Valverde; Lynne Regan
Journal:  Protein Sci       Date:  2009-04       Impact factor: 6.725

7.  Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core.

Authors:  Zachary P Gates; Michael C Baxa; Wookyung Yu; Joshua A Riback; Hui Li; Benoît Roux; Stephen B H Kent; Tobin R Sosnick
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-13       Impact factor: 11.205

8.  Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins.

Authors:  Suman Das; Yi-Hsuan Lin; Robert M Vernon; Julie D Forman-Kay; Hue Sun Chan
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-02       Impact factor: 11.205

9.  Contribution of hydrophobic interactions to protein stability.

Authors:  C Nick Pace; Hailong Fu; Katrina Lee Fryar; John Landua; Saul R Trevino; Bret A Shirley; Marsha McNutt Hendricks; Satoshi Iimura; Ketan Gajiwala; J Martin Scholtz; Gerald R Grimsley
Journal:  J Mol Biol       Date:  2011-03-04       Impact factor: 5.469

10.  Mechanisms of antimicrobial, cytolytic, and cell-penetrating peptides: from kinetics to thermodynamics.

Authors:  Paulo F Almeida; Antje Pokorny
Journal:  Biochemistry       Date:  2009-09-01       Impact factor: 3.162

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