Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

Mt, Record; Cf, Anderson; Tm, Lohman

doi:10.1017/s003358350000202x

Cited by 1,654 publications

(1,139 citation statements)

References 138 publications

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“…1A the peaks of the folded protein are indicated by arrows, the corresponding peaks of the unfolded protein lie within the circle. To increase the amount of folded conformation, sodium trifluoracetate, sodium sulphate, sodium chloride or glucose, which are all known to stabilize folded proteins [2,18,19], were added to the protein solution in 7 M urea. The NMR spectrum (Fig.…”

Section: Resultsmentioning

confidence: 99%

Salt‐stabilized globular protein structure in 7 M aqueous urea solution

Dötsch¹,

Wider²,

Siegal³

et al. 1995

FEBS Letters

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A 7 M aqueous urea solution of the 63-residue Nterminal domain of the 434-repressor at pH 7.5 and 18°C contains a mixture of about 10% native, folded protein and 90% unfolded protein. Interconversion between the two conformations is slow on the NMR chemical shift time scale, so that observation of separate resonances can be used to monitor the equilibrium between folded and unfolded protein when changing the solution conditions. In this paper we describe the influence of various salts or non-ionic compounds on this conformational equilibrium. Solution conditions are described which contain a homogenous preparation of the folded protein in the presence of 6 to 7 M urea, providing a basis for an NMR structure determination in concentrated urea and for studies of the solvation of the folded protein in mixed water/urea/salt environments. basic pancreatic trypsin inhibitor were measured under conditions where this protein is fully folded in the presence of urea, and specific interactions of urea molecules with the protein were detected for 'pockets and grooves on the protein surface' [11]. Similar experiments with unfolded 434-repressor(1-63) in 7 M urea indicated preferential urea solvation of methyl-bearing aliphatic side chains [12]. To pursue these studies on a more systematic level it will be desirable to study urea-protein interactions with folded and unfolded conformations of the same protein. The present work identifies solution conditions where folded and unfolded 434-repressor(1-63) can be studied at the same temperature in the presence of high, 'denaturing' urea concentrations.

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Section: Resultsmentioning

confidence: 99%

Salt‐stabilized globular protein structure in 7 M aqueous urea solution

Dötsch¹,

Wider²,

Siegal³

et al. 1995

FEBS Letters

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“…ΔG t is the nonpolyelectrolyte contribution, which arises from all other molecular interaction factors such as hydrophobic contacts, van der Waals forces, H-bonding, etc. The polyelectrolyte term may be calculated using the relationship [52]: (2) where Z is the charge on the ligand (for DB75, Z is equal to 2 for the two amidines charged, Figure 1), and ϕ is the proportion of total counterions associated with each DNA phosphate (about 0.88 for B-DNA duplex). (M + ) is salt concentration.…”

Section: Discussionmentioning

confidence: 99%

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Liu

Kumar

Boykin

et al. 2007

Biophysical Chemistry

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With the goal of developing a better understanding of the antiparasitic biological action of DB75, we have evaluated its interaction with duplex alternating and nonalternating sequence AT polymers and oligomers. These DNAs provide an important pair of sequences in a detailed thermodynamic analysis of variations in interaction of DB75 with AT sites. The results for DB75 binding to the alternating and nonalternating AT sequences are quite different at the fundamental thermodynamic level. Although the Gibbs energies are similar, the enthalpies for DB75 binding with poly(dA)·poly (dT) and poly(dA-dT)·poly(dA-dT) are +3.1 and −4.5 kcal/mole, respectively, while the binding entropies are 41.7 and 15.2 cal/mol·K, respectively. The underlying thermodynamics of binding to AT sites in the minor groove plays a key role in the recognition process. It was also observed that DB75 binding with poly(dA)·poly(dT) can induce T·A·T triplet formation and the compound binds strongly to the dT·dA·dT triplex.

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“…Ions can bind to charged residues in a pH-dependent manner at low ionic strength thus screening the charge. The binding is nonlinear with salt concentration (Steinhardt & Beychok, 1964;von Hippel & Schleich, 1969;Record et al, 1978). Assuming that there are n identical binding sites for a ligand L on the tetramer at a given pH and any ions bound to the monomer are not dissociated on tetramer formation, we can define a perturbed equilibrium:…”

Section: Effect Of Ionic Strengthmentioning

confidence: 99%

Thermodynamics of melittin tetramerization determined by circular dichroism and implications for protein folding

Wilcox

Eisenberg

1992

Protein Science

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The tetramerization of melittin, a 26-amino acid peptide from Apis mellifera bee venom, has been studied as a model for protein folding. Melittin converts from a monomeric random coil to an a-helical tetramer as the pH is raised from 4.0 to 9.5, as ionic strength is increased, as temperature is raised or lowered from about 37 "C, or as phosphate is added. The thermodynamics of this tetramerization (termed "folding") are explored using circular dichroism. The melittin tetramer has two pK, values of 7.5 and 8. [7][8][9][10][11][12][13][14][15][16][17][18] agree with experimental titration data. Greater electrostatic repulsion of these protonated groups destabilizes the tetramer by 3.6 kcal/mol at pH 4.0 compared to pH 9.5. Increasing the concentration of NaCl in the solution from 0 to 0.5 M stabilizes the tetramer by 5-6 kcal/mol at pH 4.0. The effect of NaCl is modeled with a ligand-binding approach. The melittin tetramer is found to have a temperature of maximum stability ranging from 35.5 to 43 "C depending on the pH, unfolding above and below that temperature. AC; for folding ranges from -0.085 to -0.102 cal g" K-', comparable to that of other small globular proteins (Privalov, P.L., 1979, Adv. Protein Chem. 33, 167-241). A H o and ASo are found to decrease with temperature, presumably due to the hydrophobic effect (Kauzmann, w., 1959, Adv. Protein Chem.14, 1-63). Phosphate is found to perturb the equilibrium substantially with a maximal effect at 150 mM, stabilizing the tetramer at pH 7.4 and 25 "C by 4.6 kcal/mol. The enthalpy change due to addition of phosphate (-7.5 kcal/mol at 25 "C) can be accounted for by simple dielectric screening. Both circular dichroism and crystallographic results suggest that phosphate may bind Lys 23 at the ends of the elongated tetramer. These detailed measurements give insight into the relative importance of various forces for the stability of melittin in the folded form and may provide an experimental standard for future tests of computational energetics on this simple protein system. Abbreviations: CD, circular dichroism; far UV, 260-185 nm; near UV, 330-245 nm; AzgO, light absorption at 280 nm; AC:, the standard change in heat capacity from the unfolded to the folded form; At = AL -AR, where AL and AR are the absorbance of left and right circularly polarized light, respectively; AcZU, Ac at 222 nm; AtZB2, At at 282 nm; Th, a temperature at which AHo(T) = 0; T,, a temperature at gates to form an a-helical tetramer. The amount of tetwhich ASo( T ) = 0; TES, N-tris(hydroxyrnethyl)methyl-2-aminoethane sulfonic acid. Keywords

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Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

Cited by 1,654 publications

References 138 publications

Salt‐stabilized globular protein structure in 7 M aqueous urea solution

Salt‐stabilized globular protein structure in 7 M aqueous urea solution

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Thermodynamics of melittin tetramerization determined by circular dichroism and implications for protein folding

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