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D C Rau

Publications and source records attributed to D C Rau.

At least 37 records · Page 2Linked to original sources
PubMed1994

Reevaluation of chloride's regulation of hemoglobin oxygen uptake: the neglected contribution of protein hydration in allosterism.

We have measured hemoglobin oxygen uptake vs. the partial pressure of oxygen, with independently controlled activities of chloride and water. This control is effected by combining different concentrations of NaCl and sucrose in the bathing solution to achieve: (i) water activities were varied and Cl- activity was fixed, (ii) both water and Cl- activities were varied with a traditional NaCl titration, or (iii) Cl- activities were varied and water activity was fixed by adding compensating sucrose. Within this analysis, the Cl(-)-regulated loading of four oxygens can be described by the reaction Hb.Cl- + 4 O2 + 65 H2O in equilibrium with Hb.4O2.65H2O + Cl-. The dissociation of a neatly integral chloride, rather than the nonintegral 1.6 chlorides inferred earlier from simple salt titration, demonstrates the need to recognize the potentially large contribution from changes in water activity when titrating weakly binding solutes. The single-chloride result might simplify structural considerations of the action of Cl- in hemoglobin regulation.

Allosteric Regulation↗
PubMed1994

Direct measurement of forces between self-assembled proteins: temperature-dependent exponential forces between collagen triple helices.

We report direct measurements of force vs. separation between self-assembled proteins. These forces are observed between collagen triple helices in native and reconstituted fibers. They are a combination of a short-range repulsion, which varies exponentially over at least five decay lengths, and an inferred, longer-ranged attraction responsible for spontaneous assembly. From 5 degrees C to 35 degrees C the relative contribution of the attraction to the net force increases with temperature. These forces are strikingly similar to the "hydration" forces measured between several other linear macromolecules (DNA, polysaccharides) and between lipid bilayer membranes. The decay length of the repulsive force agrees well with a theoretical estimate based on axial periodicity of the triple helix, suggesting another connection between molecular architecture and protein-protein interaction.

Animals↗
PubMed1994

Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations.

Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed molecules of variable separation and mutual angle. This "toolbox" of intermolecular forces is intended for use in modelling molecular interactions, assembly, and conformation. The coefficients characterizing both the exponential hydration and the electrostatic interactions depend strongly on the univalent counterion species in solution, but are only weakly sensitive to anion type and temperature (from 5 to 50 degrees C). Interaction coefficients for the exponentially varying hydration force seen at spacings less than 10 to 15 A between surfaces are extracted directly from pressure versus interaxial distance curves. Electrostatic interactions are only observed at larger spacings and are always coupled with configurational fluctuation forces that result in observed exponential decay lengths that are twice the expected Debye-Huckel length. The extraction of electrostatic force parameters relies on a theoretical expression describing steric forces of molecules "colliding" through soft exponentially varying direct interactions.

Animals↗
PubMed1993

A structural difference between filaments of phosphorylated and dephosphorylated Acanthamoeba myosin II revealed by electric birefringence.

The actin-activated Mg(2+)-ATPase activity of filamentous Acanthamoeba myosin II is regulated by the state of phosphorylation of three sites at the C terminus of each heavy chain. This phosphorylation at the tip of the tails of monomers in a bipolar filament abolishes the activity of sites some 90 nm distant in the globular heads. Previous studies with copolymeric filaments of phosphorylated and dephosphorylated monomers strongly indicated that the activity of each monomer in a filament is dependent on the level of phosphorylation of neighboring monomers in the filament. We report here electric birefringence measurements showing that, although the overall structures of phosphorylated and dephosphorylated filaments are very similar, large, Mg2+ concentration-dependent differences in internal motion and flexibility are observed. Filaments of dephosphorylated myosin II appear to be about 50-fold stiffer than filaments of phosphorylated myosin II at 4 mM Mg2+. These results are consistent with a model in which the stiffness of the putative hinge region within the rod-like tail of each monomer is determined by the phosphorylation state of the C-terminal tails of overlapping, neighboring monomers. The flexibility of the filaments appears to be directly related to their actin-activated Mg(2+)-ATPase activity.

Acanthamoeba↗
PubMed1993

Hydration forces.

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Aluminum Silicates↗
PubMed1992

Zinc induces a bend within the transcription factor IIIA-binding region of the 5 S RNA gene.

Binding of Zn2+ to the 5 S RNA gene sequence of Xenopus borealis results in strong bending of the DNA, as inferred from transient electric birefringence data. The effect is specific for Zn2+; several other divalent ions are not able to induce a bend of a similar magnitude. Using five different fragments that span the binding sequence, we are able to estimate a bend magnitude of at least 55 degrees centered at base-pair +65 within the gene. This places the bend within the binding domain of the gene-regulatory protein transcription factor (TF) IIIA. Recent evidence has shown that the protein-DNA complex is also bent. Although our data do not allow us directly to link the two bends, our results suggest that TFIIIA could form a folded structure by stabilizing the same bent conformation that is induced by binding of Zn2+. The chemistry of Zn2+ binding to DNA, and the sequence around the bend center, suggest that the bend is most probably caused by joint co-ordination of Zn2+ to the N-7 groups of stacked purine residues.

Animals↗
PubMed1992

Protein solvation in allosteric regulation: a water effect on hemoglobin.

The oxygen affinity of hemoglobin varies linearly with the chemical potential of water in the bathing medium, as seen from the osmotic effect of several neutral solutes, namely sucrose, stachyose, and two polyethyleneglycols (molecular weights of 150 and 400). The data, analyzed either by Wyman linkage equations or by Gibbs-Duhem relations, show that approximately 60 extra water molecules bind to hemoglobin during the transition from the fully deoxygenated tense (T) state to the fully oxygenated relaxed (R) state. This number, independent of the nature of the solute, agrees with the difference in water-accessible surface areas previously computed for the two conformations. The work of solvation in allosteric regulation can no longer go unrecognized.

Allosteric Regulation↗
PubMed1992

Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces.

Rather than acting by modifying van der Waals or electrostatic double layer interactions or by directly bridging neighboring molecules, polyvalent ligands bound to DNA double helices appear to act by reconfiguring the water between macromolecular surfaces to create attractive long range hydration forces. We have reached this conclusion by directly measuring the repulsive forces between parallel B-form DNA double helices pushed together from the separations at which they have self organized into hexagonal arrays of parallel rods. For all of the wide variety of "condensing agents" from divalent Mn to polymeric protamines, the resulting intermolecular force varies exponentially with a decay rate of 1.4-1.5 A, exactly one-half that seen previously for hydration repulsion. Such behavior qualitatively contradicts the predictions of all electrostatic double layer and van der Waals force potentials previously suggested. It fits remarkably well with the idea, developed and tested here, that multivalent counterion adsorption reorganizes the water at discrete sites complementary to unadsorbed sites on the apposing surface. The measured strength and range of these attractive forces together with their apparent specificity suggest the presence of a previously unexpected force in molecular organization.

Animals↗
PubMed1992

Direct measurement of temperature-dependent solvation forces between DNA double helices.

The assembly of double stranded DNA helices with divalent manganese ion is favored by increasing temperature. Direct force measurements, obtained from the osmotic stress technique coupled with x-ray diffraction, show that the force characteristics of spontaneously precipitated Mn(2+)-DNA closely resemble those observed previously by us for other counterion condensed DNA assemblies. At temperatures below the critical one for spontaneous assembly, we have quantitated the changes in entropy and manganese ion binding associated with the transition from repulsive to attractive interactions between helices mediated by osmotic stress. The release of structured water surrounding the DNA helix to the bulk solution is the most probable source of increased entropy after assembly. Increasing the water entropy of the bulk solution by changing the manganese salt anion from CI- to ClO4- predictably and quantitatively increases the transition entropy. This is further evidence for the dominating role of water in the close interaction of polar surfaces.

Animals↗
PubMed1991

The flexibility of A-form DNA.

We have determined the rise per base pair and persistence length of A-form DNA in trifluoroethanol solutions for fragments 350-900 base pairs in length that best describe rotational diffusion coefficients determined by transient electric birefringence. The 2.6 A spacing between base pairs found in crystal and fiber A-form structures is preserved in solution. The persistence length is about 1500 A, or about three times longer than for B-form DNA. There is no apparent electrostatic contribution to the persistence length in the salt concentration range 0.2-2.0 mM Na cacodylate. This suggests an even closer association between DNA and its neutralizing counterions than predicted by condensation theory, perhaps due to a sheath of trifluoroethanol excluded water surrounding the A-form helix.

Birefringence↗
PubMed1990

Direct measurement of forces between linear polysaccharides xanthan and schizophyllan.

Direct osmotic stress measurements have been made of forces between helices of xanthan, an industrially important charged polysaccharide. Exponentially decaying hydration forces, much like those already measured between lipid bilayer membranes or DNA double helices, dominate the interactions at close separation. Interactions between uncharged schizophyllans also show the same kind of hydration force seen between xanthans. In addition to the practical possibilities for modifying solution and suspension properties through recognition and control of molecular forces, there is now finally the opportunity for theorists to relate macroscopic properties of a polymer solution to the microscopic properties that underlie them.

Carbohydrate Sequence↗
PubMed1988

Variation in hydration forces between neutral phospholipid bilayers: evidence for hydration attraction.

It is now generally recognized that hydration forces dominate close interactions of lipid hydrophilic surfaces. The commonality of their characteristics has been reasonably established. However, differences in measured net repulsion, particularly evident when phosphatidylethanolamine (PE) and phosphatidylcholine (PC) bilayers are compared, suggest there exists a variety of behavior wider than expected from earlier models of hydration and fluctuation repulsion balanced by van der Waals attraction. To find a basis for this diverse behavior, we have looked more closely at measured structural parameters, degrees of hydration, and interbilayer repulsive forces for the lamellar phases of the following lipids: 1-palmitoyl-2-oleoyl-PE (POPE), egg PE, transphosphatidylated egg PE (egg PE-T), mono- and dimethylated egg PE-T (MMPE and DMPE), 1-stearoyl-2-oleoyl-PC (SOPC), and mixtures of POPE and SOPC. POPE and SOPC bilayers differ not only in their maximum degrees of hydration but also in the empirical hydration force coefficients and decay lengths that characterize their interaction. When mixed with POPE, SOPC effects sudden and disproportionate increases in hydration. POPE, egg PE, and egg PE-T differ in their degree of hydration, molecular area, and hydration repulsion. A single methylation of egg PE-T almost completely converts its hydration and bilayer repulsive properties to those of egg PC; little progression of hydration is seen with successive methylations. In order to reconcile these observations with the conventional scheme of balancing interbilayer hydration and fluctuation-enhanced repulsion with van der Waals attraction, it is necessary to relinquish the fundamental idea that the decay of hydration forces is a constant determined by the properties of the aqueous medium. Alternatively, one can retain that fundamental idea if one recognizes the possibility that polar group hydration has an attractive component to it. In the latter view, that attractive component originates from interbilayer hydrogen-bonded water bridges between apposing bilayer surfaces, arising from correlation of zwitterionic or other complementary polar groups or from factors that affect polar group solubility. The same Marcelja and Radic formalism that accounts so well for the repulsive component also leads to an estimate of the attractive one. We suggest that the full range of degrees of hydration and of interbilayer spacings observed for different neutral bilayers results in part from variable contributions of the attractive and repulsive hydration components.(ABSTRACT TRUNCATED AT 400 WORDS)

Hydrogen Bonding↗
PubMed1987

Structure of the DNA gyrase-DNA complex as revealed by transient electric dichroism.

We have analyzed the structure of complexes between DNA gyrase and four defined DNA fragments by electric dichroism. Both the extrapolated dichroism and relaxation time of these complexes suggest that a single turn of DNA is wrapped around the enzyme with the entry and exit points located close together. The average angle between the DNA tails emerging from the particle is about 120 degrees. This structure is consistent with that seen by electron microscopy. Addition of ATP or the non-hydrolyzable ATP analog 5'-adenylyl-beta, gamma-imidodiphosphate results in a structural change of the complex, consistent with the DNA tails now being wrapped around the protein. The significance of these observations with respect to the mechanism of DNA supercoiling by DNA gyrase is discussed.

Autoradiography↗
PubMed1985

The flexibility of alternating dA-dT sequences.

The flexibility of alternating poly (dA-dT) has been investigated by the technique of transient electric dichroism. Rotational relaxation times, which are very sensitive to changes in the end-to-end length of flexible polymers, are determined from the field free dichroism decay curves of four, well defined fragments of poly (dA-dT) ranging in size from 136 to 270 base pairs. Persistence lengths, calculated from the results of Hagerman and Zimm (Biopolymers (1981) 29, 1481-1502), are in the range 200-250 A. This makes alternating dA-dT sequences about twice as flexible as naturally occurring, "random" sequence DNA. Considering a bend around a nucleosome, for example, this difference in persistence length translates to an energy difference between poly (dA-dT) and random sequence DNA of 0.17 kT/base pair or 1 kcal per 10 base pair stretch. This energy difference is sufficiently large to suggest that dA-dT sequences could serve as markers in DNA packaging, for example, at sites where DNA must tightly bend to accommodate structures.

Base Sequence↗
PubMed1984

Critical amount of oligovalent ion binding required for the B-Z transition of poly (dG-m5dC).

By working at very low Na+ concentrations (1mM and less), the number of bound Mg(2+), cobalt hexamine (3+), and spermine (4+) necessary to induce the B-Z transition of poly (dG-m5dC) has been directly measured. The results show that if as little as 1 cobalt hexamine(3+) or spermine(4+) is bound per 40-50 nucleotides the transition will occur. A greater fraction of bound Mg(2+) is required, 1 bound Mg(2+)/10 nucleotides. The dependence of the transition midpoint concentrations of oligovalent ions on Na+ concentrations suggests that specific ion binding energies, not included in counterion condensation theory, are responsible for the transition.

Cations↗
PubMed1984

Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices.

We have measured the repulsive force between B-form double helices in parallel packed arrays of polymer-condensed DNA in the presence of 0.005-1.0 M ionic solutions. Molecular repulsion is consistently exponential with a 2.5-3.5 A decay distance, when the separation between DNA surfaces is 5-15 A. Only weakly dependent on ionic strength and independent of molecular size, this intermolecular repulsion does not obey the predictions of electrostatic double-layer theory. Rather, it strongly resembles the "hydration force" first recognized and quantified between phospholipid bilayers. Only beyond 15 A separation between molecules is there evidence of electrostatic double-layer forces. The quantitative failure of electrostatic double-layer theory seen here must gravely affect accepted analyses of other polyelectrolyte systems. Because the packing of condensed DNA resembles the spacings of DNA in many bacteriophages, our results permit estimation of the "DNA pressure" in phage heads.

Anions↗