Literature DB >> 14732698

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

Seishi Shimizu1.   

Abstract

How do we estimate, from thermodynamic measurements, the number of water molecules adsorbed or released from biomolecules as a result of a biochemical process such as binding and allosteric effects? Volumetric and osmotic stress analyses are established methods for estimating water numbers; however, these techniques often yield conflicting results. In contrast, Kirkwood-Buff theory offers a novel way to calculate excess hydration number from volumetric data, provides a quantitative condition to gauge the accuracy of osmotic stress analysis, and clarifies the relationship between osmotic and volumetric analyses. I have applied Kirkwood-Buff theory to calculate water numbers for two processes: (i) the allosteric transition of hemoglobin and (ii) the binding of camphor to cytochrome P450. I show that osmotic stress analysis may overestimate hydration number changes for these processes.

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Year:  2004        PMID: 14732698      PMCID: PMC337029          DOI: 10.1073/pnas.0305836101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  33 in total

1.  What is the true structure of liganded haemoglobin?

Authors:  J R Tame
Journal:  Trends Biochem Sci       Date:  1999-10       Impact factor: 13.807

2.  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

Review 3.  The effects of osmotic and hydrostatic pressures on macromolecular systems.

Authors:  Jack A Kornblatt; M Judith Kornblatt
Journal:  Biochim Biophys Acta       Date:  2002-03-25

Review 4.  Interpreting the effects of small uncharged solutes on protein-folding equilibria.

Authors:  P R Davis-Searles; A J Saunders; D A Erie; D J Winzor; G J Pielak
Journal:  Annu Rev Biophys Biomol Struct       Date:  2001

5.  Probing protein hydration and conformational states in solution.

Authors:  C Reid; R P Rand
Journal:  Biophys J       Date:  1997-03       Impact factor: 4.033

6.  Measuring hydration changes of proteins in solution: applications of osmotic stress and structure-based calculations.

Authors:  V J LiCata; N M Allewell
Journal:  Methods Enzymol       Date:  1998       Impact factor: 1.600

7.  In disperse solution, "osmotic stress" is a restricted case of preferential interactions.

Authors:  S N Timasheff
Journal:  Proc Natl Acad Sci U S A       Date:  1998-06-23       Impact factor: 11.205

8.  The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data.

Authors:  T V Chalikian; M Totrov; R Abagyan; K J Breslauer
Journal:  J Mol Biol       Date:  1996-07-26       Impact factor: 5.469

9.  Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences.

Authors:  N Y Sidorova; D C Rau
Journal:  Proc Natl Acad Sci U S A       Date:  1996-10-29       Impact factor: 11.205

10.  Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro.

Authors:  E S Courtenay; M W Capp; C F Anderson; M T Record
Journal:  Biochemistry       Date:  2000-04-18       Impact factor: 3.162

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  37 in total

1.  Kirkwood-Buff integrals for ideal solutions.

Authors:  Elizabeth A Ploetz; Nikolaos Bentenitis; Paul E Smith
Journal:  J Chem Phys       Date:  2010-04-28       Impact factor: 3.488

2.  Local Fluctuations in Solution: Theory and Applications.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  Adv Chem Phys       Date:  2013       Impact factor: 1.000

3.  Hydration changes accompanying the binding of minor groove ligands with DNA.

Authors:  Natalya N Degtyareva; Bret D Wallace; Andrea R Bryant; Kristine M Loo; Jeffrey T Petty
Journal:  Biophys J       Date:  2006-11-17       Impact factor: 4.033

4.  Sodium perchlorate effects on the helical stability of a mainly alanine peptide.

Authors:  Eliana K Asciutto; Ignacio J General; Kan Xiong; Kang Xiong; Sanford A Asher; Jeffry D Madura
Journal:  Biophys J       Date:  2010-01-20       Impact factor: 4.033

5.  Surface changes of the mechanosensitive channel MscS upon its activation, inactivation, and closing.

Authors:  Wojciech Grajkowski; Andrzej Kubalski; Piotr Koprowski
Journal:  Biophys J       Date:  2005-01-21       Impact factor: 4.033

6.  Predicting the energetics of osmolyte-induced protein folding/unfolding.

Authors:  Matthew Auton; D Wayne Bolen
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-07       Impact factor: 11.205

7.  A protein molecule in a mixed solvent: the preferential binding parameter via the Kirkwood-Buff theory.

Authors:  Ivan L Shulgin; Eli Ruckenstein
Journal:  Biophys J       Date:  2005-11-04       Impact factor: 4.033

8.  Hydration changes in the association of Hoechst 33258 with DNA.

Authors:  John R Kiser; Richard W Monk; Rondey L Smalls; Jeffrey T Petty
Journal:  Biochemistry       Date:  2005-12-27       Impact factor: 3.162

9.  A contribution to the theory of preferential interaction coefficients.

Authors:  J Michael Schurr; David P Rangel; Sergio R Aragon
Journal:  Biophys J       Date:  2005-07-29       Impact factor: 4.033

10.  Theory and Simulation of Multicomponent Osmotic Systems.

Authors:  Sadish Karunaweera; Moon Bae Gee; Samantha Weerasinghe; Paul E Smith
Journal:  J Chem Theory Comput       Date:  2012-10-09       Impact factor: 6.006

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