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Trevitt CR, Yashwanth Kumar DR, Fowler NJ, Williamson MP. Interactions between the protein barnase and co-solutes studied by NMR. Commun Chem 2024; 7:44. [PMID: 38418894 PMCID: PMC10902301 DOI: 10.1038/s42004-024-01127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.
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Affiliation(s)
- Clare R Trevitt
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
- Certara UK Ltd, Level 2-Acero, 1 Concourse Way, Sheffield, S1 3BJ, UK
| | | | - Nicholas J Fowler
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
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2
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Yao W, Wang K, Wu A, Reed WF, Gibb BC. Anion binding to ubiquitin and its relevance to the Hofmeister effects. Chem Sci 2020; 12:320-330. [PMID: 34163600 PMCID: PMC8178748 DOI: 10.1039/d0sc04245e] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/29/2020] [Indexed: 02/01/2023] Open
Abstract
Although the non-covalent interactions between proteins and salts contributing to the Hofmeister effects have been generally mapped, there are many questions regarding the specifics of these interactions. We report here studies involving the small protein ubiquitin and salts of polarizable anions. These studies reveal a complex interplay between the reverse Hofmeister effect at low pH, the salting-in Hofmeister effect at higher pH, and six anion binding sites in ubiquitin at the root of these phenomena. These sites are all located at protuberances of preorganized secondary structure, and although stronger at low pH, are still apparent when ubiquitin possesses no net charge. These results demonstrate the traceability of these Hofmeister phenomena and suggest new strategies for understanding the supramolecular properties of proteins.
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Affiliation(s)
- Wei Yao
- Department of Chemistry, Tulane University New Orleans LA 70118 USA
| | - Kaiyu Wang
- Department of Chemistry, Tulane University New Orleans LA 70118 USA
| | - Aide Wu
- Department of Physics and Engineering Physics, Tulane University New Orleans LA 70118 USA
| | - Wayne F Reed
- Department of Physics and Engineering Physics, Tulane University New Orleans LA 70118 USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University New Orleans LA 70118 USA
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Abstract
AbstractThe strong, long-range electrostatic forces described by Coulomb's law disappear for ions in water, and the behavior of these ions is instead controlled by their water affinity – a weak, short-range force which arises from their charge density. This was established experimentally in the mid-1980s by size-exclusion chromatography on carefully calibrated Sephadex®G-10 (which measures the effective volume and thus the water affinity of an ion) and by neutron diffraction with isotopic substitution (which measures the density and orientation of water molecules near the diffracting ion and thus its water affinity). These conclusions have been confirmed more recently by molecular dynamics simulations, which explicitly model each individual water molecule. This surprising change in force regime occurs because the oppositely charged ions in aqueous salt solutions exist functionally as ion pairs (separated by 0, 1 or 2 water molecules) as has now been shown by dielectric relaxation spectroscopy; this cancels out the strong long-range electrostatic forces and allows the weak, short-range water affinity effects to come to the fore. This microscopic structure of aqueous salt solutions is not captured by models utilizing a macroscopic dielectric constant. Additionally, the Law of Matching Water Affinity, first described in 1997 and 2004, establishes that contact ion pair formation is controlled by water affinity and is a major determinant of the solubility of charged species since only a net neutral species can change phases.
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Bye JW, Baxter NJ, Hounslow AM, Falconer R, Williamson MP. Molecular Mechanism for the Hofmeister Effect Derived from NMR and DSC Measurements on Barnase. ACS OMEGA 2016; 1:669-679. [PMID: 31457155 PMCID: PMC6640789 DOI: 10.1021/acsomega.6b00223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/10/2016] [Indexed: 05/27/2023]
Abstract
The effects of sodium thiocyanate, sodium chloride, and sodium sulfate on the ribonuclease barnase were studied using differential scanning calorimetry (DSC) and NMR. Both measurements reveal specific and saturable binding at low anion concentrations (up to 250 mM), which produces localized conformational and energetic effects that are unrelated to the Hofmeister series. The binding of sulfate slows intramolecular motions, as revealed by peak broadening in 13C heteronuclear single quantum coherence spectroscopy. None of the anions shows significant binding to hydrophobic groups. Above 250 mM, the DSC results are consistent with the expected Hofmeister effects in that the chaotropic anion thiocyanate destabilizes barnase. In this higher concentration range, the anions have approximately linear effects on protein NMR chemical shifts, with no evidence for direct interaction of the anions with the protein surface. We conclude that the effects of the anions on barnase are mediated by solvent interactions. The results are not consistent with the predictions of the preferential interaction, preferential hydration, and excluded volume models commonly used to describe Hofmeister effects. Instead, they suggest that the Hofmeister anion effects on both stability and solubility of barnase are due to the way in which the protein interacts with water molecules, and in particular with water dipoles, which are more ordered around sulfate anions and less ordered around thiocyanate anions.
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Affiliation(s)
- Jordan W. Bye
- Department
of Chemical and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, U.K.
| | - Nicola J. Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
| | - Robert
J. Falconer
- Department
of Chemical and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, U.K.
| | - Mike P. Williamson
- Department of Molecular Biology and Biotechnology, Krebs Institute
for Biomolecular Research, University of
Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K.
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5
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San-José N, Gómez-Valdemoro A, Calderón V, de la Peña JL, Serna F, García FC, García JM. Polyamide model compound containing the urea group as selective colorimetric sensing probe towards aromatic diamines. Supramol Chem 2009. [DOI: 10.1080/10610270701882193] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Noelia San-José
- a Departamento de Química , Facultad de Ciencias, Universidad de Burgos , Burgos, Spain
| | - Ana Gómez-Valdemoro
- a Departamento de Química , Facultad de Ciencias, Universidad de Burgos , Burgos, Spain
| | - Verónica Calderón
- a Departamento de Química , Facultad de Ciencias, Universidad de Burgos , Burgos, Spain
| | - José Luis de la Peña
- a Departamento de Química , Facultad de Ciencias, Universidad de Burgos , Burgos, Spain
| | - Felipe Serna
- a Departamento de Química , Facultad de Ciencias, Universidad de Burgos , Burgos, Spain
| | - Félix Clemente García
- a Departamento de Química , Facultad de Ciencias, Universidad de Burgos , Burgos, Spain
| | - José Miguel García
- a Departamento de Química , Facultad de Ciencias, Universidad de Burgos , Burgos, Spain
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Lund M, Vrbka L, Jungwirth P. Specific Ion Binding to Nonpolar Surface Patches of Proteins. J Am Chem Soc 2008; 130:11582-3. [DOI: 10.1021/ja803274p] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mikael Lund
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic and Center for Biomolecules and
Complex Molecular Systems, Flemingovo nam. 2, CZ-16610 Prague 6, Czech
Republic and Institute of Physical and Theoretical Chemistry, University
of Regensburg, 93040 Regensburg, Germany
| | - Luboš Vrbka
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic and Center for Biomolecules and
Complex Molecular Systems, Flemingovo nam. 2, CZ-16610 Prague 6, Czech
Republic and Institute of Physical and Theoretical Chemistry, University
of Regensburg, 93040 Regensburg, Germany
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic and Center for Biomolecules and
Complex Molecular Systems, Flemingovo nam. 2, CZ-16610 Prague 6, Czech
Republic and Institute of Physical and Theoretical Chemistry, University
of Regensburg, 93040 Regensburg, Germany
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Collins KD. Ion hydration: Implications for cellular function, polyelectrolytes, and protein crystallization. Biophys Chem 2005; 119:271-81. [PMID: 16213082 DOI: 10.1016/j.bpc.2005.08.010] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 08/30/2005] [Accepted: 08/31/2005] [Indexed: 11/25/2022]
Abstract
Only oppositely charged ions with matching absolute free energies of hydration spontaneously form inner sphere ion pairs in free solution [K.D.Collins, Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process, Methods 34 (2004) 300-311.]. We approximate this with a Law of Matching Water Affinities which is used to examine the issues of (1) how ions are selected to be compatible with the high solubility requirements of cytosolic components; (2) how cytosolic components tend to interact weakly, so that association or dissociation can be driven by environmental signals; (3) how polyelectrolytes (nucleic acids) differ from isolated charges (in proteins); (4) how ions, osmolytes and polymers are used to crystallize proteins; and (5) how the "chelate effect" is used by macromolecules to bind ions at specific sites even when there is a mismatch in water affinity between the ion and the macromolecular ligands.
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Affiliation(s)
- Kim D Collins
- Department of Biochemistry and Molecular Biology, University of Maryland Medical School, 108 N. Greene Street, Baltimore, MD 21201-1503, USA.
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Denisov VP, Halle B. Hydrogen exchange rates in proteins from water (1)H transverse magnetic relaxation. J Am Chem Soc 2002; 124:10264-5. [PMID: 12197713 DOI: 10.1021/ja027101c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Access to the fast exchange kinetics of labile protein hydrogens in solution is provided by exchange broadening of the water 1H NMR line. We analyzed the chemical shift modulation contribution of labile hydrogens in bovine pancreatic trypsin inhibitor (BPTI) to the transverse 1H spin relaxation rate, R2, of the bulk solvent. Both the experimental pH dependence and the CPMG dispersion of R2 could be quantitatively accounted for on the basis of known chemical shifts, exchange rates, and ionization constants for BPTI. This analysis provided, for the first time, the hydrogen exchange rate constants for Lys and Arg side chains in a protein and pointed to an internal catalysis of the N-terminal amino protons in BPTI by a salt bridge. The method can be used for mapping the hydrogen exchange rates in protein solutions and biomaterials, which may be important for the control of relaxation-weighted contrast in biological MRI.
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Affiliation(s)
- Vladimir P Denisov
- Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden
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