Literature DB >> 19757837

Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values.

Michael W Capp1, Laurel M Pegram, Ruth M Saecker, Megan Kratz, Demian Riccardi, Timothy Wendorff, Jonathan G Cannon, M Thomas Record.   

Abstract

Noncovalent self-assembly of biopolymers is driven by molecular interactions between functional groups on complementary biopolymer surfaces, replacing interactions with water. Since individually these interactions are comparable in strength to interactions with water, they have been difficult to quantify. Solutes (osmolytes, denaturants) exert often large effects on these self-assembly interactions, determined in sign and magnitude by how well the solute competes with water to interact with the relevant biopolymer surfaces. Here, an osmometric method and a water-accessible surface area (ASA) analysis are developed to quantify and interpret the interactions of the remarkable osmolyte glycine betaine (GB) with molecular surfaces in water. We find that GB, lacking hydrogen bond donors, is unable to compete with water to interact with anionic and amide oxygens; this explains its effectiveness as an osmolyte in the Escherichia coli cytoplasm. GB competes effectively with water to interact with amide and cationic nitrogens (hydrogen bonding) and especially with aromatic hydrocarbon (cation-pi). The large stabilizing effect of GB on lac repressor-lac operator binding is predicted quantitatively from ASA information and shown to result largely from dehydration of anionic DNA phosphate oxygens in the protein-DNA interface. The incorporation of these results into theoretical and computational analyses will likely improve the ability to accurately model intra- and interprotein interactions. Additionally, these results pave the way for development of solutes as kinetic/mechanistic and thermodynamic probes of conformational changes and formation/disruption of molecular interfaces that occur in the steps of biomolecular self-assembly processes.

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Year:  2009        PMID: 19757837      PMCID: PMC2783871          DOI: 10.1021/bi901273r

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  43 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces.

Authors:  Lubos Vrbka; Jirí Vondrásek; Barbara Jagoda-Cwiklik; Robert Vácha; Pavel Jungwirth
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-10       Impact factor: 11.205

3.  Application of the transfer model to understand how naturally occurring osmolytes affect protein stability.

Authors:  Matthew Auton; D Wayne Bolen
Journal:  Methods Enzymol       Date:  2007       Impact factor: 1.600

Review 4.  Water as a biomolecule.

Authors:  Philip Ball
Journal:  Chemphyschem       Date:  2008-12-22       Impact factor: 3.102

5.  Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding.

Authors:  Jiang Hong; Mike W Capp; Ruth M Saecker; M Thomas Record
Journal:  Biochemistry       Date:  2005-12-27       Impact factor: 3.162

Review 6.  Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts.

Authors:  M T Record; W Zhang; C F Anderson
Journal:  Adv Protein Chem       Date:  1998

7.  Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding.

Authors:  J K Myers; C N Pace; J M Scholtz
Journal:  Protein Sci       Date:  1995-10       Impact factor: 6.725

8.  Hofmeister salt effects on surface tension arise from partitioning of anions and cations between bulk water and the air-water interface.

Authors:  Laurel M Pegram; M Thomas Record
Journal:  J Phys Chem B       Date:  2007-04-14       Impact factor: 2.991

9.  Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions.

Authors:  Dominic Lambert; David E Draper
Journal:  J Mol Biol       Date:  2007-05-05       Impact factor: 5.469

10.  ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble.

Authors:  Jorge Estrada; Pau Bernadó; Martin Blackledge; Javier Sancho
Journal:  BMC Bioinformatics       Date:  2009-04-08       Impact factor: 3.169

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  44 in total

1.  Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer.

Authors:  Emily J Guinn; Laurel M Pegram; Michael W Capp; Michelle N Pollock; M Thomas Record
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-19       Impact factor: 11.205

2.  Why Hofmeister effects of many salts favor protein folding but not DNA helix formation.

Authors:  Laurel M Pegram; Timothy Wendorff; Robert Erdmann; Irina Shkel; Dana Bellissimo; Daniel J Felitsky; M Thomas Record
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-12       Impact factor: 11.205

3.  The osmolyte TMAO stabilizes native RNA tertiary structures in the absence of Mg2+: evidence for a large barrier to folding from phosphate dehydration.

Authors:  Dominic Lambert; Desirae Leipply; David E Draper
Journal:  J Mol Biol       Date:  2010-09-25       Impact factor: 5.469

4.  Probing the protein-folding mechanism using denaturant and temperature effects on rate constants.

Authors:  Emily J Guinn; Wayne S Kontur; Oleg V Tsodikov; Irina Shkel; M Thomas Record
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-16       Impact factor: 11.205

5.  Its preferential interactions with biopolymers account for diverse observed effects of trehalose.

Authors:  Jiang Hong; Lila M Gierasch; Zhicheng Liu
Journal:  Biophys J       Date:  2015-07-07       Impact factor: 4.033

6.  Interactions of the DNA polymerase X from African Swine Fever Virus with the ssDNA. Properties of the total DNA-binding site and the strong DNA-binding subsite.

Authors:  Maria J Jezewska; Michal R Szymanski; Wlodzimierz Bujalowski
Journal:  Biophys Chem       Date:  2011-04-28       Impact factor: 2.352

7.  Putting the Piezolyte Hypothesis under Pressure.

Authors:  Christina M Papini; Pranav P Pandharipande; Catherine A Royer; George I Makhatadze
Journal:  Biophys J       Date:  2017-08-10       Impact factor: 4.033

8.  Molecular mechanism for the preferential exclusion of TMAO from protein surfaces.

Authors:  Deepak R Canchi; Pruthvi Jayasimha; Donald C Rau; George I Makhatadze; Angel E Garcia
Journal:  J Phys Chem B       Date:  2012-10-01       Impact factor: 2.991

9.  In Vivo Titration of Folate Pathway Enzymes.

Authors:  Deepika Nambiar; Timkhite-Kulu Berhane; Robert Shew; Bryan Schwarz; Michael R Duff; Elizabeth E Howell
Journal:  Appl Environ Microbiol       Date:  2018-09-17       Impact factor: 4.792

10.  Quantifying the temperature dependence of glycine-betaine RNA duplex destabilization.

Authors:  Jeffrey J Schwinefus; Ryan J Menssen; James M Kohler; Elliot C Schmidt; Alexandra L Thomas
Journal:  Biochemistry       Date:  2013-11-22       Impact factor: 3.162

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