Literature DB >> 23795491

Introductory lecture: interpreting and predicting Hofmeister salt ion and solute effects on biopolymer and model processes using the solute partitioning model.

M Thomas Record1, Emily Guinn, Laurel Pegram, Michael Capp.   

Abstract

Understanding how Hofmeister salt ions and other solutes interact with proteins, nucleic acids, other bion class="Chemical">polymers and water and thereby affect protein and nucleic acid processes as well as model processes (e.g. solubility of model compounds) in aqueous solution is a longstanding goal of biophysical research. Empirical Hofmeister salt and solute "m-values" (derivatives of the observed standard free energy change for a model or biopolymer process with respect to solute or salt concentration m3) are equal to differences in chemical potential derivatives: m-value = delta(dmu2/dm3) = delta mu23, which quantify the preferential interactions of the solute or salt with the surface of the biopolymer or model system (component 2) exposed or buried in the process. Using the solute partitioning model (SPM), we dissect mu23 values for interactions of a solute or Hofmeister salt with a set of model compounds displaying the key functional groups of biopolymers to obtain interaction potentials (called alpha-values) that quantify the interaction of the solute or salt per unit area of each functional group or type of surface. Interpreted using the SPM, these alpha-values provide quantitative information about both the hydration of functional groups and the competitive interaction of water and the solute or salt with functional groups. The analysis corroborates and quantifies previous proposals that the Hofmeister anion and cation series for biopolymer processes are determined by ion-specific, mostly unfavorable interactions with hydrocarbon surfaces; the balance between these unfavorable nonpolar interactions and often-favorable interactions of ions with polar functional groups determine the series null points. The placement of urea and glycine betaine (GB) at opposite ends of the corresponding series of nonelectrolytes results from the favorable interactions of urea, and unfavorable interactions of GB, with many (but not all) biopolymer functional groups. Interaction potentials and local-bulk partition coefficients quantifying the distribution of solutes (e.g. urea, glycine betaine) and Hofmeister salt ions in the vicinity of each functional group make good chemical sense when interpreted in terms of competitive noncovalent interactions. These interaction potentials allow solute and Hofmeister (noncoulombic) salt effects on protein and nucleic acid processes to be interpreted or predicted, and allow the use of solutes and salts as probes of

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Year:  2013        PMID: 23795491      PMCID: PMC3694758          DOI: 10.1039/c2fd20128c

Source DB:  PubMed          Journal:  Faraday Discuss        ISSN: 1359-6640            Impact factor:   4.008


  66 in total

1.  Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.

Authors:  Charalampos G Kalodimos; Alexandre M J J Bonvin; Roberto K Salinas; Rainer Wechselberger; Rolf Boelens; Robert Kaptein
Journal:  EMBO J       Date:  2002-06-17       Impact factor: 11.598

2.  Negligible effect of ions on the hydrogen-bond structure in liquid water.

Authors:  Anne Willem Omta; Michel F Kropman; Sander Woutersen; Huib J Bakker
Journal:  Science       Date:  2003-07-18       Impact factor: 47.728

3.  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

4.  Anatomy of energetic changes accompanying urea-induced protein denaturation.

Authors:  Matthew Auton; Luis Marcelo F Holthauzen; D Wayne Bolen
Journal:  Proc Natl Acad Sci U S A       Date:  2007-09-18       Impact factor: 11.205

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

6.  The inverse and direct Hofmeister series for lysozyme.

Authors:  Yanjie Zhang; Paul S Cremer
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-21       Impact factor: 11.205

7.  Can simulations quantitatively predict peptide transfer free energies to urea solutions? Thermodynamic concepts and force field limitations.

Authors:  Dominik Horinek; Roland R Netz
Journal:  J Phys Chem A       Date:  2011-03-01       Impact factor: 2.781

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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  32 in total

1.  Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.

Authors:  Alex S Holehouse; Kanchan Garai; Nicholas Lyle; Andreas Vitalis; Rohit V Pappu
Journal:  J Am Chem Soc       Date:  2015-02-23       Impact factor: 15.419

2.  Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation.

Authors:  Emily F Ruff; Wayne S Kontur; M Thomas Record
Journal:  Methods Mol Biol       Date:  2015

3.  Charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms.

Authors:  Daria V Fedyukina; Theodore S Jennaro; Silvia Cavagnero
Journal:  J Biol Chem       Date:  2014-01-07       Impact factor: 5.157

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.  Analysis of strains lacking known osmolyte accumulation mechanisms reveals contributions of osmolytes and transporters to protection against abiotic stress.

Authors:  Lindsay Murdock; Tangi Burke; Chelsea Coumoundouros; Doreen E Culham; Charles E Deutch; James Ellinger; Craig H Kerr; Samantha M Plater; Eric To; Geordie Wright; Janet M Wood
Journal:  Appl Environ Microbiol       Date:  2014-06-20       Impact factor: 4.792

7.  Controlling chitosan-based encapsulation for protein and vaccine delivery.

Authors:  Bhanu Prasanth Koppolu; Sean G Smith; Sruthi Ravindranathan; Srinivas Jayanthi; Thallapuranam K Suresh Kumar; David A Zaharoff
Journal:  Biomaterials       Date:  2014-02-21       Impact factor: 12.479

8.  Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.

Authors:  Gustavo Fuertes; Niccolò Banterle; Kiersten M Ruff; Aritra Chowdhury; Davide Mercadante; Christine Koehler; Michael Kachala; Gemma Estrada Girona; Sigrid Milles; Ankur Mishra; Patrick R Onck; Frauke Gräter; Santiago Esteban-Martín; Rohit V Pappu; Dmitri I Svergun; Edward A Lemke
Journal:  Proc Natl Acad Sci U S A       Date:  2017-07-17       Impact factor: 11.205

9.  Quantitative Interpretation of Solvent Paramagnetic Relaxation for Probing Protein-Cosolute Interactions.

Authors:  Yusuke Okuno; Attila Szabo; G Marius Clore
Journal:  J Am Chem Soc       Date:  2020-04-24       Impact factor: 15.419

10.  Effects of End Group Termination on Salting-Out Constants for Triglycine.

Authors:  Jana Hladílková; Jan Heyda; Kelvin B Rembert; Halil I Okur; Yadagiri Kurra; Wenshe R Liu; Christian Hilty; Paul S Cremer; Pavel Jungwirth
Journal:  J Phys Chem Lett       Date:  2013-12-05       Impact factor: 6.475

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