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D Stigter

Publications and source records attributed to D Stigter.

17 recordsLinked to original sources
PubMed2001

The length dependence of translational diffusion, free solution electrophoretic mobility, and electrophoretic tether force of rigid rod-like model duplex DNA.

In this work, boundary element modeling is used to study the transport of highly charged rod-like model polyions of various length under a variety of different aqueous salt conditions. Transport properties considered include free solution electrophoretic mobility, translational diffusion, and the components of the "tether force" tensor. The model parameters are chosen to coincide with transport measurements of duplex DNA carried out under six different salt/temperature conditions. The focus of the analysis is on the length dependence of the free solution electrophoretic mobility. In a solution containing 0.04 M Tris-acetate buffer at 25 degrees C, calculated mobilities using straight rod models show a stronger dependence on fragment length than that observed experimentally. By carrying out model studies on curved rod models, it is concluded that the "leveling off" of mobility with fragment length is due, in part at least, to the finite curvature of DNA. Experimental mobilities of long duplex DNA in monovalent alkali salts are reasonably well explained once account is taken of long-range bending and the simplifying assumptions of the model studies.

DNA↗
PubMed2000

A commentary on the screened-Oseen, counterion-condensation formalism of polyion electrophoresis.

The use of linear theory, in particular, counterion condensation (CC) theory, in describing electrophoresis of polyelectrolyte chains, is criticized on several grounds. First, there are problems with CC theory in describing the equilibrium distribution of ions around polyelectrolytes. Second, CC theory is used to treat ion relaxation in a linear theory with respect to the polyion charge despite the fact that ion relaxation arises as a consequence of nonlinear charge effects. This nonlinearity has been well established by several investigators over the last 70 years for spherical, cylindrical, and arbitrarily shaped model polyions. Third, current use of CC theory ignores the electrophoretic hindrance as well as the ion relaxation for condensed counterions and only includes such interactions for uncondensed counterions. Because most of the condensed counterions lie outside the shear surface of the polyion (in the example of DNA), the assumption of ion condensation is artificial and unphysical. Fourth, the singular solution, based on a screened Oseen tensor, currently used in the above mentioned theories is simply wrong and fails to account for the incompressibility of the solvent. The actual singular solution, which has long been available, is discussed. In conclusion, it is pointed out that numerical alternatives based on classic electrophoresis theory (J.T.G. Overbeek, Kolloid-Beih, 1943, 54:287-364) are now available.

Biopolymers↗
PubMed1998

An electrostatic model of B-DNA for its stability against unwinding.

In single molecule experiments Smith et al. (Science 271 (1996) 795) have unwound the B-DNA helix by stretching it in an aqueous salt solution. They found that the stretching force required for the transition decreases significantly with lowering of the salt concentration. We show that the observed salt effect is consistent with a uniformly charged cylinder model of DNA surrounded by a Poisson-Boltzmann ionic atmosphere. We also derive a simple connection between the sharpness of the center part of the transition and its cooperativity in terms of an average block size of base pairs that unwinds or rewinds.

Bacteriophage lambda↗
PubMed1998

Theory for the hydrodynamic and electrophoretic stretch of tethered B-DNA.

We have developed a theory for the extension and force of B-DNA tethered at a fixed point in a uniform hydrodynamic flow or in a uniform applied electric field. The chain tethered in an electric field is considered to be subject to free electrophoresis compensated by free sedimentation in the opposite direction. This allows the use of results of free electrophoresis for including the effects of small ions. The force on the chain is derived for a sequence of ellipsoidal segments, each twice the persistence length of the wormlike chain. Hydrodynamic interaction between these segments is based on the long-range limit of flow around the prolate ellipsoids, as derived from equivalent Stokes spheres. The chain extension is derived by applying the entropic elasticity relation of Marko and Siggia (1995 Macromolecules. 28:8759-8770) to each segment for polymer chains under constant tension. We justify this procedure by comparing with extension results based on the Boltzmann averaged orientation of straight, freely jointed segments. Predicted results agree well with recent extension-flow experiments by Perkins et al., 1995. Science. 258:83-87, and with electrophoretic stretch experiments by Smith and Bendich (1990 Biopolymers. 29:1167-1173) on fluorescently stained B-DNA. We find that the equivalence of hydrodynamic and electrophoretic stretch, proposed by Long et al. (1996 Phys. Rev. Lett. 76:3858-3861; 1996 Biopolymers 39:755-759), is valid only for very small chain deformations, but not in general.

Biophysical Phenomena↗
PubMed1996

Binding of ionic ligands to polyelectrolytes.

Ionic ligands can bind to polyelectrolytes such as DNA or charged polysaccharides. We develop a Poisson-Boltzmann treatment to compute binding constants as a function of ligand charge and salt concentration in the limit of low ligand concentration. For flexible chain ligands, such as oligopeptides, we treat their conformations using lattice statistics. The theory predicts the salt dependence and binding free energies, of Mg(2+) ions to polynucleotides, of hexamine cobalt(III) to calf thymus DNA, of polyamines to T7 DNA, of oligolysines to poly(U) and poly(a), and of tripeptides to heparin, a charged polysaccharide. One parameter is required to obtain absolute binding constants, the distance of closest separation of the ligand to the polyion. Some, but not all, of the binding entropies and enthalpies are also predicted accurately by the model.

Animals↗
PubMed1995

Evaluation of the counterion condensation theory of polyelectrolytes.

We compare free energies of counterion distributions in polyelectrolyte solutions predicted from the cylindrical Poisson-Boltzmann (PB) model and from the counterion condensation theories of Manning: CC1 (Manning, 1969a, b), which assumes an infinitely thin region of condensed counterions, and CC2 (Manning, 1977), which assumes a region of finite thickness. We consider rods of finite radius with the linear charge density of B-DNA in 1-1 valent and 2-2 valent salt solutions. We find that under all conditions considered here the free energy of the CC1 and the CC2 models is higher than that of the PB model. We argue that counterion condensation theory imposes nonphysical constraints and is, therefore, a poorer approximation to the underlying physics based on continuum dielectrics, point-charge small ions, Poisson electrostatics, and Boltzmann distributions. The errors in counterion condensation theory diminish with increasing distance from, or radius of, the polyion.

Biophysical Phenomena↗
PubMed1992

Phospholipid interactions in model membrane systems. I. Experiments on monolayers.

We study the lateral headgroup interactions among phosphatidylcholine (PC) molecules and among phosphatidylethanolamine (PE) molecules in monolayers and extend our previous models. In this paper, we present an extensive set of pressure-area isotherms and surface potential experiments on monolayers of phospholipids ranging from 14 to 22 carbons in length at the n-heptane/water interface, over a wide range of temperature, salt concentration, and pH on the acid side. The pressure data presented here are a considerable extension of previous data (1) to higher surface densities, comprehensively checked for monolayer loss, and include new data on PE molecules. We explore surface densities ranging from extremely low to intermediate, near to the main phase transition, in which range the surface pressures and potentials are found to be independent of the chain length. Thus, these data bear directly on the headgroup interactions. These interactions are observed to be independent of ionic strength. PC and PE molecules differ strongly in two respects: (a) the lateral repulsion among PC molecules is much stronger than for PE, and (b) the lateral repulsion among PC molecules increases strongly with temperature whereas PE interactions are almost independent of temperature. Similarly, the surface potential for PC is found to increase with temperature whereas for PE it does not. In this and the following paper we show that these data from dilute to semidilute monolayers are consistent with a theoretical model that predicts that, independent of coverage, for PC the P-N+ dipole is oriented slightly into the oil phase because of the hydrophobicity of the methyl groups, increasingly so with temperature, whereas for PE the P-N+ dipole is directed into the water phase.

Electrochemistry↗
PubMed1992

Phospholipid interactions in model membrane systems. II. Theory.

We describe statistical thermodynamic theory for the lateral interactions among phospholipid head groups in monolayers and bilayers. Extensive monolayer experiments show that at low surface densities, PC head groups have strong lateral repulsions which increase considerably with temperature, whereas PE interactions are much weaker and have no significant temperature dependence (see the preceding paper). In previous work, we showed that the second virial coefficients for these interactions can be explained by: (a) steric repulsions among the head groups, and (b) a tilting of the P-N+ dipole of PC so that the N+ end enters the oil phase, to an extent that increases with temperature. It was also predicted that PE interactions should be weaker and less temperature dependent because the N+ terminal of the PE head-group is hydrophilic, hence, it is tilted into the water phase, so dipolar contributions among PE's are negligible due to the high dielectric constant of water. In the present work, we broaden the theory to treat phospholipid interactions up to higher lateral surface densities. We generalize the Hill interfacial virial expansion to account for dipoles and to include the third virial term. We show that to account for the large third virial coefficients for both PC and PE requires that the short range lateral attractions among the head groups also be taken into account. In addition, the third virial coefficient includes fluctuating head group dipoles, computed by Monte Carlo integration assuming pairwise additivity of the instantaneous pair potentials. We find that because the dipole fluctuations are correlated, the average triplet interactions do not equal the sum of the average dipole pair potentials. This is important for predicting, the magnitude and the independence of temperature of the third virial coefficients for PC. The consistency of the theory with data of both the second and the third virial coefficients extends the applicability of the head-group model to semiconcentrated monolayers, in agreement with the surface potential data in the foregoing paper.

Lipid Bilayers↗
PubMed1991

Protein stability: electrostatics and compact denatured states.

Globular proteins can be denatured by changing pH and ionic strength. Much recent evidence has led to the surprising conclusion that there are two acid-denatured states: one highly unfolded and the other more compact, sometimes called the "molten globule." Here we describe a molecular theory for electrostatic stability of globular proteins based on the properties of the constituent amino acids: oil/water partition coefficients, pK values of the titratable groups, and their temperature dependences. Predicted denaturation temperatures vs. pH are in good agreement with experiments of other workers on myoglobin. The theory also predicts two populations of denatured species, one open and the other more compact, with densities in the range found experimentally for molten globular states. In addition, it predicts a phase diagram (stability vs. pH, ionic strength) in good agreement with experiments of Goto and Fink [Goto, Y. & Fink, A. L. (1989) Biochemistry 28, 945-952; and Goto, Y. & Fink, A. L. (1990) J. Mol. Biol. 214, 803-805]. The well-known salt destabilization of myoglobin has been generally considered evidence for ion pairing, but the present theory, based on smeared charge repulsion, explains the salt destabilization at low pH without ion pairing. In addition, for myoglobin the theory predicts salt stabilization at high pH, as observed for beta-lactamase by Goto and Fink.

Drug Stability↗
PubMed1991

Shielding effects of small ions in gel electrophoresis of DNA.

Results of free electrophoresis and free sedimentation of charged rods are introduced to allow for electrical double-layer effects in the gel electrophoresis of DNA, modeled as a random flight sequence of rodlike Kuhn chain elements. The kinetics of DNA is shown to depend strongly on the orientation of the chain elements with respect to the external field and with respect to the direction of their velocity. The new theory gives approximate agreement between the DNA charge derived from electrophoresis of free and tethered DNA (close to 1.0e per DNA phosphate in both cases), compared with the earlier discrepancy of a factor 10 or 20 for the theory without shielding by salt. As part of a realistic force field for macromolecular dynamics simulation, the small ion effects are included in an expression for the gel forces restraining the DNA in gel electrophoresis from moving as in free electrophoresis.

DNA↗
PubMed1991

The three states of globular proteins: acid denaturation.

We describe statistical mechanical theory that aims to predict protein stabilities as a function of temperature, pH, and salt concentration, from the physical properties of the constituent amino acids: (1) the number of nonpolar groups, (2) the chain length, (3) the temperature-dependent free energy of transfer, (4) the pKa's (including those in the native state) and their temperature dependencies. We calculate here the phase diagrams for apomyoglobin and hypothetical variant proteins. The theory captures essential features of protein stability including myoglobin's Tm vs pH as measured by P. L. Privalov [(1979) Advances in Protein Chemistry, Vol. 33, pp. 167-241] and its ionic strength vs pH phase diagram as measured by Y. Goto and A. L. Fink [(1990) Journal of Molecular Biology, Vol. 214, pp. 803-805]. The main predictions here are the following: (1) There are three stable states, corresponding to native (N), compact denatured (C), and highly unfolded (U), with transitions between them. (2) In agreement with experiments, the compact denatured state is predicted to have enthalpy closer to U than N because even though there is considerable hydrophobic "clustering" in C, this nevertheless represents a major loss of hydrophobic contacts relative to configurations (N) that have a hydrophobic "core." (3) C becomes more prominent in the phase diagram with increasing nonpolar content or decreasing chain length, perhaps thus accounting for (a) why lysozyme and alpha-lactalbumin differ in their denatured states, and (b) why shortened Staph nuclease molecules are compact. (4) Of major importance for protein calorimetry is Privalov's observation that the enthalpy of folding, delta H (T, pH) is independent of pH. The theory accounts for this through the prediction that the main electrostatic contribution to stability is not enthalpic; the main contribution is the entropy, mainly due to the different distributions of protons and small ions in the native and denatured states.

Apoproteins↗
PubMed1990

Charge effects on folded and unfolded proteins.

We develop a theory for the effects of charge on the stabilization of globular proteins. The folding process is modeled as occurring through a fictitious intermediate state along a two-part thermodynamic pathway in which the molecule (i) increases its density and then (ii) rearranges its ionic groups to the protein surface. The equilibrium for the binding of protons in salt solutions is assumed to be driven by the electrical potential due to the charge distribution, in addition to the intrinsic binding affinity and bulk proton concentration. The potential is calculated for inside and outside a porous sphere model of the protein using the Poisson-Boltzmann relation, wherein the interior dielectric constant is taken to be a linear function of the chain density. The model predicts the slope of the titration curves for native myoglobin in agreement with experiments by Breslow and Gurd (1962). From the similar experiments on the unfolded state, and from the experiments of Privalov et al. (1986) on the intrinsic viscosity of the unfolded molecules, the theory shows that the unfolded state has a much higher density than a chain in a theta solvent and that the density increases with ionic strength. In addition, from the free energy of proton binding to the protein, we also calculate the electrostatic contributions to protein stability, a major contribution deriving from changes in ionization. We consider the example of the stability of myoglobin as a function of pH, ionic strength, and ionic groups buried in the native protein structure. We show that although maximum stability of most proteins should occur at their isoelectric point, the burial of nontitratable groups should lead to maximum stabilities at pH values other than the isoelectric point.

Animals↗
PubMed1988

Lateral interactions among phosphatidylcholine and phosphatidylethanolamine head groups in phospholipid monolayers and bilayers.

We develop theory for the lateral interactions among the zwitterionic head groups of phospholipids in monolayers and bilayers, particularly phosphatidylcholine (PC) and phosphatidylethanolamine (PE). With the P- end of the head group anchored at the water/hydrocarbon interface, a balance of two effects dictates the angle that the P--N+ dipole makes with respect to the plane of the bilayer: N+ is driven toward water due to the (Born) electrostatic free energy, but the hydrophobic effect drives the methyl and methylene groups around the N+ charge toward the hydrocarbon. The only adjustable parameter of the model is the average fluctuation of the oil/water interface or, alternatively, the dielectric constant of the hydrocarbon phase. The model predicts that at 5 degrees C the head group dipole should lie largely in the bilayer plane, in accord with X-ray, neutron diffraction, and NMR studies. The theory makes the novel prediction that the N+ end of the dipole becomes increasingly submerged in hydrocarbon with increasing temperature, leading to strongly enhanced lateral repulsion between PC head groups. This prediction is in good agreement with second and third viral coefficients of monolayer lateral pressures, and with the temperature dependence of the former. The theoretical model is consistent with head group fluctuations measured by neutron diffraction of PC and PE bilayers. Because PE has a smaller hydrophobic cluster near N+, its lateral repulsion should be much smaller and less temperature dependent than for PC, also in agreement with equation-of-state measurements. This suggests why at high density PE monolayers have higher melting temperatures than PC monolayers and more propensity for reversed curvature.

Lipid Bilayers↗
PubMed1987

Donnan membrane equilibrium, sedimentation equilibrium, and coil expansion of DNA in salt solutions.

This is a review of applications of the McMillan-Mayer-Hill virial theory and the ionic double-layer theory to dilute colloidal solutions, in particular, solutions of DNA. Interactions of highly charged colloidal rods are developed in terms of the second virial coefficients between two rods, and between one rod and one small co-ion. The relevant cluster integrals are evaluated with interaction potentials based on the Poisson-Boltzmann equation. The treatment is extended to the intrachain repulsion responsible for the statistical swelling of coiled DNA (excluded volume effect). The theory is compared with three sets of experimental data: The salt distribution in Donnan membrane equilibria of DNA-salt solutions, sedimentation equilibria of short DNA fragments at different ionic strengths, and the intrinsic viscosity of T7 DNA in NaCl solutions. In all cases the theory agrees well with the experiments. The agreement is not convincing for the sedimentation equilibrium at low ionic strength, because here the experimental DNA concentration is too high for the truncated dilute solution expansion of the DNA-salt repulsion.

Biophysical Phenomena↗