Analysis of chemical and physical relaxation processes of polyelectrolytes by electric field pulse methods: A comparison of critical comments with facts

Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier

Because of open problems in the relation between results obtained by relaxation experiments and molecular dynamics simulations on the B-A transition of DNA, relaxation measurements of the B-A dynamics have been extended to a wider range of conditions. Field-induced reaction effects are measured selectively by the magic angle technique using a novel cell construction preventing perturbations from cell window anisotropy. The kinetics was recorded for the case of poly[d(AT)] up to the salt concentration limit of 4.4 mM, where aggregation does not yet interfere. Now experimental data on the B-A dynamics are available for poly[d(AT)] at salt concentrations of 0.18, 0.73, 2.44 and 4.4 mM. In all cases, a spectrum of time constants is found, ranging from ~ 10 μs up to components approaching ~ 1 ms. The relatively small dependence of these data on the salt concentration indicates that electrostatic effects on the kinetics are not as strong as may be expected. The ethanol content at the transition center is a linear function of the logarithm of the salt concentration, and the slope is close to that expected from polyelectrolyte theory. The B-A transition dynamics was also measured in D₂O at a salt concentration of 2.4 mM: the center of the transition is found at 20.0 mol/l H₂O and at 20.1 mol/l D₂O with an estimated accuracy of ± 0.1 mol/l; the spectrum of time constants at the respective transition centers is very similar. The experimental results are discussed regarding the data obtained by molecular dynamics simulations.

Electric field induced changes in protein conformation

The effect of a low strength oscillating electric field on the conformation of Bovine Serum Albumin (BSA) and Lysozyme in solution has been measured. A purpose built cell has been used to measure the real time autofluorescence and Circular Dichroism of the protein solutions exposed to electric fields of differing strength and frequency. Exposure to the electric fields results in protein unfolding for both Lysozyme and BSA. The applied field strengths are extremely small compared to the protein inter-chain intra-molecular forces. We propose a model whereby the electrophoretic motion of the proteins leads to a frictional force that results in protein unfolding. For BSA and Lysozyme in the electric fields used in this study, the shear rates at the protein surface under electrophoretic motion are of order 10(3) and 10(4) s(-1) respectively. Prolonged electric field exposure results in significant frictional energy dissipation in the proteins. The energy dissipated in the proteins results in protein unfolding, which is a critical initial step for protein aggregation and potentially amyloid fibril formation.

Electric birefringence at small angles from crossed position: enhanced sensitivity and special effects

Measurements of electric birefringence with increased sensitivity are possible using lasers with high intensity and stability, provided that perturbations resulting from stray light and strain in cell windows can be reduced. A new type of cell window is designed for minimal strain and is used in a standard birefringence setup with optimized components. The new instrument is characterized by a stray-light constant of 2 × 10(-7) and a negligible residual birefringence. Thus, measurements can be extended to small angles from the crossed position providing birefringence signals of high amplitudes at favorable signal-to-noise ratios. Special effects at small angles from the crossed position like a divergent increase of relative amplitudes to extreme values, a nonlinear response, a new type of electro-optical anomaly, and a simple bypass around this anomaly are observed and shown to be consistent with the theory. The technique proves to be particularly useful for measurements at physiological salt concentrations, where signals for most systems are too small under conventional conditions.

Macrodipoles. Unusual electric properties of biological macromolecules

The wide range of different effects induced by electric fields in biological macromolecules is clearly due to the unusual quality and quantity of their electric parameters. A general concept for a quantitative description of the polarizability of macromolecules remains to be established. In the case of DNA, experimental data indicate the existence of an effective polarization length N(p); at chain lengths N < N(p) the polarizability increases with N(2), whereas saturation is approached at N > or = N(p). The polarization length decreases with increasing ionic strength in close analogy to the Debye length, but is approximately 10 times larger than the Debye length. The dynamics of DNA polarization at high field strengths has been observed in the ns time range and is consistent with biased field induced ion dissociation. In the range of chain lengths from approximately 400 to approximately 850 base pairs DNA molecules exhibit permanent dipole moments, which are in a preferentially perpendicular direction to the end-to-end-vector, leading to a positive electric dichroism. These results are consistent with a "frozen" ensemble of bent DNA configurations and provide evidence for the existence of slow, non-elastic bending transitions. The electric parameters of proteins are usually dominated by a permanent anisotropy of the charge distribution, corresponding to permanent dipole moments of the order of several hundred Debye up to about 1500 Debye. Relatively small dipole moments of protein monomers add up to millions of Debye, when these proteins are in a vectorial organization in membrane patches, as found for bacteriorhodopsin and Na (+)K (+)-ATPase . In these cases the dipole vector may support vectorial ion transport. It is remarkable that the dipole moments of proteins usually show a relatively small dependence on the salt concentration; a rational for these observations is provided by a dipole potential at the plane of shear for rotational diffusion, which is defined in close analogy to the zeta-potential for translational diffusion. Symmetry breaking leading to huge electric dipole moments may be expected for mixed lipid vesicles: according to model calculations the phase separation of lipid components with and without net charges may lead to very high dipole moments; the expectation has been verified experimentally for vesicles containing DMPA and DMPC. The state of these systems should be extremely sensitive to electric fields. In summary, there is an unusual wide variation of electric parameters associated with biological macromolecules and with biomolecular assemblies, which is the basis for the complexity of different phenomena induced by electric fields in biological systems.

The dynamics of the B-A transition of natural DNA double helices

The dynamics of the B-A transition of DNA double helices with different GC contents and various chain lengths has been characterized by an electric field pulse technique. The field-induced B-A reaction is separated from orientation effects using the magic angle technique. Amplitudes reflecting the B-A reaction are observed selectively in the limited range of ethanol contents, where CD spectra demonstrate the B-A transition. The maximum amplitude appears at 1-2% higher ethanol content than the center of the B-A transition observed by CD because electric field pulses induce a relatively large perturbation from the A- toward the B-form. The relaxation curves measured after pulse termination reflect a spectrum of up to three relaxation processes. For DNA's with approximately 50% GC, the main part of the amplitude ( approximately 75%) is associated with time constants of approximately 2 micros, and another major component appears with time constants of 50-100 micros. These relaxation effects have been observed for DNA samples with 859, 2629, 7160, and 48501 bp. The time constant associated with the main amplitude increases with decreasing GC content from approximately 2 micros at 50% GC to approximately 3 mus at 41% GC and approximately 10 micros at 0% GC at the center of the B-A transition. Model calculations on the kinetics of cooperative linear Ising lattices predict the appearance of a distinct maximum of the mean relaxation time at the center of the transition. The absence of such maximum in our experimental data indicates a low cooperativity of the B-A transition with a nucleation parameter of approximately 0.1. The rate of the B-A transition is lower by approximately 3 orders of magnitude than that predicted by molecular dynamics simulations.

Strong bending of purple membranes in the M-state

Structure changes of purple membranes during the photocycle were analysed in solution by measurements of the electric dichroism. The D96N-mutant was used to characterize the M-state at neutral pH. The transition from the resting state to 61% photo-stationary M-state is associated with a strong reduction of the dichroism decay time constant by a factor of approximately 2. Because the change of the time constant is independent of the bacteriorhodopsin concentration, the effect is not attributed to light-induced dissociation but to light-induced bending of purple membranes. After termination of light-activation the dichroism decay of the resting state is restored with a time constant close to that of the M-state decay, which is more than two orders of magnitude slower than proton transfer to the bulk. Thus, bending is not due to asymmetric protonation but to the structure of the M-state. A very similar reduction of decay time constants at a corresponding degree of light-activation was found for wild-type bacteriorhodopsin at pH-values 7.8-9.3, where the lifetime of the M-state is extended. Light-induced bending is also reflected in changes of the stationary dichroism, whereas the overall permanent dipole moment remains almost constant, suggesting compensation of changes in molecular and global contributions. Bead model simulations indicate that disks of approximately 1 microm diameter are bent at a degree of photo-activation of 61% to a radius of approximately 0.25 microm, assuming a cylindrical bending modus. The large light-induced bending effect is consistent with light-induced opening of the protein on the cytoplasmic side of the membrane detected by electron crystallography, which is amplified due to coupling of monomers in the membrane. Bending may function as a mechanical signal.

Global structure and flexibility of hairpin ribozymes with extended terminal helices

Global structure and flexibility of three different hairpin ribozyme constructs have been analyzed by measuring their electric dichroism decay in various buffers at temperatures between 2 and 30 degrees C. The hairpin ribozyme is characterized by two independently folding domains A and B that are connected through a hinge and have to interact to enable catalysis. The analyzed constructs feature extended terminal helices 1 and 4 with 27 and 25 bp, respectively, to increase the sensitivity of the molecular rotational diffusion time constants with respect to the interdomain bending angle. Constructs HP1 and HP2 cannot cleave because of a G+1A change at the 3'-side of the cleavage site; in HP1 the helices 2 and 3 that flank the hinge form a continuous double helical segment; in HP2 and HP3, a six nucleotide bulge confers flexibility to the expected bending site; HP3 is a cleavable form of HP2 with a G+1-base. For comparison, a standard RNA double helix with 72 bp was included in our analysis. The dichroism decay curves of the hairpin constructs after pulses of low electric field strengths can be fitted to single exponentials taus, whereas the curves after pulses of high field strengths require two exponentials. In all cases, time constants increase with RNA concentration, indicating intermolecular interactions. Extrapolation of the tausvalues measured in standard buffer (50 mM Tris (pH 7.5) and 12 mM MgCl2) to zero RNA concentration provide values of 112, 93, and 73 ns for HP1, HP2 and HP3, respectively, at 30 degrees C, indicating increasingly compact structures. The 72 bp RNA reference under corresponding conditions did not show a dependence of its decay time constant on the RNA concentration nor on the field strength; its time constant is 175 ns (standard buffer, 30 degrees C). The observation of two relaxation processes for the hairpin constructs at high field strengths indicates stretching to a more elongated state; the fast process with a time constant of the order of 50 ns is assigned to reversion of stretching, the slow process to overall rotation. The overall rotational time of the stretched state at 20 degrees C is close to that for a completely stretched rigid state; at 30 degrees C the experimental values are around 70 % of that expected for a completely stretched rigid state, indicating flexibility and/or residual bending. Bead models were constructed to simulate dichroism decay curves. The time constants observed for the 72 bp RNA are as expected for a rigid rod with a rise of 2.8 A per base-pair. Based on this rise per base-pair for models of a V and a Y-shape, we estimate average bending angles of 80(+/-20) degrees and 105 (+/-25) degrees, respectively, for the catalytically active hairpin ribozyme HP3. The energy required for stretching is of the order of the thermal energy.