The B Form to Z Form Transition of Poly(dG-m5dC) Is Sensitive to Neutral Solutes Through an Osmotic Stress

Preisler, Richard S.; Chen, Holly H.; Colombo, Marcio F.; Choe, Yoon; Short, Billy Joe; Rau, Donald C.

doi:10.1021/bi00044a017

Cited by 48 publications

(51 citation statements)

References 32 publications

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“…By using two different model approaches, the Wyman linkage equation or the Gibbs Duhem equation, we found that 65-72 1 water molecules are linked to the binding of four oxygen molecules to human Hb under the experimental conditions used. Furthermore, this hydration change was found to be in agreement with the difference between the solvent-accessible surface areas of deoxy-and oxy-Hb computed from x-ray structures by Clothia et al (5,6).The experimental approach and analyses originally used by us to assess and quantify the role of water on the allosteric control of Hb have been tested in several other biochemical systems (7)(8)(9)(10)(11)(12)(13)(14). A standard linear dependence of equilibrium and kinetic free energy parameters on water activity rather than solute activity has been lately reported.…”

supporting

confidence: 74%

The Water Effect on Allosteric Regulation of Hemoglobin Probed in Water/Glucose and Water/Glycine Solutions

Colombo

Bonilla-Rodriguez

1996

Journal of Biological Chemistry

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We present data which indicate that glycine and glucose influence HbA oxygen affinity to the same extent, despite the fact that glycine increases and glucose decreases the bulk dielectric constant of the solution. Furthermore, we derive an equation linking changes in oxygen affinity to changes in differential solute and water binding to test critically the possibility of neutral solute heterotropic binding. Applied to the data, these analyses support our original interpretation that neutral solutes act indirectly on the regulation of allosteric behavior of hemoglobin by varying the chemical potential of water in solution. This leads to a displacement of the equilibrium between Hb conformational states in proportion to their differential hydration.It is well established that differential water binding occurs between distinct conformations of a protein. Hence, whether or not differential water binding contributes to the energetic of protein reactions, as some ions and metabolites do, is a key question to fully comprehend the mechanism of biological control. The role of water on allosteric regulation had been previously investigated, using Hb oxygenation as a model, by the so-called osmotic stress method (1, 2). The concept of this method is to use solutes, which are potentially excluded from the protein surface, to set the bulk water activity a w (3). Haire and Hedlund (4), using ethylene glycol, observed that at a low concentration range ethylene glycol decreases Hb oxygen affinity while at a higher concentration causes the opposite effect. They interpreted these results as reflecting preferential binding of ethylene glycol to Hb at the low solute concentration range, whereas, at high ethylene glycol concentration range, the increased O 2 binding affinity of Hb was attributed to an effect of water activity on the R to T allosteric equilibrium (4). In our former studies of the effect of water activity on Hb O 2 binding properties, we have used chemically different solutes like sucrose, stachyose, and polyethylene glycols to distinguish solute from water binding to Hb (1). Besides finding evidences for an indirect effect of solutes through water on the deoxy-to oxy-Hb conformational equilibrium, we have also determined quantitatively this solvation effect on Hb allosteric transition in terms of the differential number of water molecules bound between the two extreme conformations of Hb. By using two different model approaches, the Wyman linkage equation or the Gibbs Duhem equation, we found that 65-72 1 water molecules are linked to the binding of four oxygen molecules to human Hb under the experimental conditions used. Furthermore, this hydration change was found to be in agreement with the difference between the solvent-accessible surface areas of deoxy-and oxy-Hb computed from x-ray structures by Clothia et al. (5,6).The experimental approach and analyses originally used by us to assess and quantify the role of water on the allosteric control of Hb have been tested in several other biochemical systems (7)(8)(9)...

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supporting

confidence: 74%

The Water Effect on Allosteric Regulation of Hemoglobin Probed in Water/Glucose and Water/Glycine Solutions

Colombo

Bonilla-Rodriguez

1996

Journal of Biological Chemistry

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“…The negative sign means that the nonspecific complex sequesters more water than the specific one. (18). The apparent Anw for sucrose, for example, is about 3-4 times larger than for glycerol.…”

Section: [4]mentioning

confidence: 94%

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

Sidorova

Rau

1996

Proc. Natl. Acad. Sci. U.S.A.

109

118

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The free energy difference between complexes of the restriction nuclease EcoRI with nonspecific DNA and with the enzyme's recognition sequence is linearly dependent on the water chemical potential of the solution, set using several very different solutes, ranging from glycine and glycerol to triethylene glycol and sucrose. This osmotic dependence indicates that the nonspecific complex sequesters some 110 waters more than the specific complex with the recognition sequence. The insensitivity of the difference in number of waters released to the solute identity further indicates that this water is sequestered in a space that is sterically inaccessible to solutes, most likely at the protein-DNA interface of the nonspecific complex. Calculations based on the structure of the specific complex suggest that the apposing DNA and protein surfaces in the nonspecific complex retain approximately a full hydration layer of water.The correct functioning of transcription factors and other regulatory proteins that recognize specific DNA sequences requires not only binding with high affinity to the proper sequence but also the ability to distinguish effectively the recognition sequence from all others, including ones that differ by only 1 or 2 bp. A key problem in biophysics is understanding how such binding strength and specificity are so tightly linked in recognition reactions. As yet, there is no simple way to connect structure, derived from x-ray crystallography or NMR, with thermodynamics and with the physics of molecular interactions between individual groups on apposing surfaces. Direct measurements of forces between macromolecules in condensed arrays (reviewed in ref. 1) have been interpreted as showing the dominance of water structuring on interaction energies at close surface separation (<10-15 A). These measurements suggest that differences in binding free energies for the association of proteins to different DNA sequences in dilute solution should correlate with differences in the number of water molecules retained in the complexes. Crystal structures of many specific DNA-protein complexes show that direct DNA-protein contacts mostly replace DNA-water and protein-water interactions with little or no water left at the interface (2, 3). Comparison of the crystal structure of the estrogen receptor-like DNA binding domain with a noncognate DNA sequence that has a binding constant about an order of magnitude smaller than the recognition sequence shows several additional waters incorporated at the interface between protein and DNA that are not seen in the specific complex (4). Just as differences in proton or salt binding accompanying macromolecular reactions can be thermodynamically probed by the sensitivity of the reaction to pH or salt activity, respectively, differences in the number of water molecules retained by different complexes can be determined from the dependence of binding equilibrium constants on the bulk water activity, controlled by the concentration of added solutes (5).A paradigm for specific recog...

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“…The macromolecular reactions we have studied that clearly involve a change in exposed surface area, as, for example, the BZ transition of poly(dG-m 5 dC) (16) and the binding of free E. coli gal repressor to its operator sequence (17), showed that the exclusion of each individual solute could be well described by a constant number of included waters, ⌬N ew ab , (over the range of solute concentrations used), but this difference in the excess number of waters between two states is very sensitive to both the size and chemical nature of the solute probing the reaction.…”

Section: Preferential Hydrationmentioning

confidence: 99%

Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives

Parsegian

Rand

Rau

2000

Proc. Natl. Acad. Sci. U.S.A.

472

606

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There has been much confusion recently about the relative merits of different approaches, osmotic stress, preferential interaction, and crowding, to describe the indirect effect of solutes on macromolecular conformations and reactions. To strengthen all interpretations of measurements and to forestall further unnecessary conceptual or linguistic confusion, we show here how the different perspectives all can be reconciled. Our approach is through the Gibbs-Duhem relation, the universal constraint on the number of ways it is possible to change the temperature, pressure, and chemical potentials of the several components in any thermodynamically defined system. From this general Gibbs-Duhem equation, it is possible to see the equivalence of the different perspectives and even to show the precise identity of the more specialized equations that the different approaches use.

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The B Form to Z Form Transition of Poly(dG-m5dC) Is Sensitive to Neutral Solutes Through an Osmotic Stress

Cited by 48 publications

References 32 publications

The Water Effect on Allosteric Regulation of Hemoglobin Probed in Water/Glucose and Water/Glycine Solutions

The Water Effect on Allosteric Regulation of Hemoglobin Probed in Water/Glucose and Water/Glycine Solutions

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

Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives

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