Influence of the solvent on the conformational-dependent properties of random coil polypeptides. II. Mean square optical anisotropies and Kerr constants

Mean square optical anisotropies and molar Kerr constants were calculated for homopolypeptides of the 20 natural amino acids and of several enzymes and proteins in the random-coil state. The effect of hydration was taken into account in constructing the molecular potential that gives the conformational energies as a function of the rotational angles phi and psi of the backbone and chi(1) of the side chain. The Rotational Isomeric State model was used in calculated energies, the Valence Optical Scheme and the matrix calculus technique of Flory being employed in the evaluation of the optical properties. The results are compared with calculations for the same substances that were performed without taking into account the solvent, as well as with other similar studies. The Kerr constant is confirmed as being one of the most sensitive properties of a given polypeptide to the residue class and to the sequence of those residues.     

The dipole moment of cytochrome c.

Vertebrate cytochromes c and the cytochromes c of insects and plants have, on average, dipole moments of 320 and 340 debye, respectively. The direction of the dipole vector with respect to the haem plane, at the solvent-accessible edge of which electron transfer presumably takes place, is conserved in these two groups--at 32 degrees +/- 7 degrees and 22 degrees +/- 10 degrees, respectively. The variation of dipole orientations and magnitudes observed in these species is compared with the results of a model in which charge distributions occur randomly. Since this model does not generate the observed charge asymmetries of the various cytochromes c, it is concluded that the dipole moment of cytochrome c is a feature that is evolutionarily conserved, apparently because it has an important influence on the interaction of this mobile electron carrier with its physiological electron donors and acceptors in the intermembrane space of mitochondria.     

Vibrational circular dichroism of polypeptides. VI. Polytyrosine alpha-helical and random-coil results

We have measured the VCD of polytyrosine in the amide I and II regions in dimethyl sulfoxide (DMSO) and in 80:20 mixtures of DMSO with trifluoroethanol, trifluoroacetic acid (TFA), and dichloroacetic acid and in 50:50 mixtures of DMSO and trimethyl phosphate (TMP). Additionally, VCD was obtained for deuterated polytyrosine in DMSO and DMSO:D₂O, DMSO:TFA(d₁), and DMSO:TMP mixtures as before. Amide A VCD was obtained in DMSO and DMSO:TMP mixtures. In the pure solvent, VCD of an opposite sign was seen as compared with that seen in the mixtures. The latter were characteristic in sign pattern and shape of right-handed α-helices for poly(L -tyrosine). The pure polytyrosine:DMSO results are similar to those of polylysine:D₂O at neutral pH and poly(β-benzyl-aspartate) in DMSO and may be characteristic of random-coil VCD.     

The determination of the thermodynamic parameters of the helix-coil transition of polypeptides by means of dipole moment measurements

The theoretical change of the mean-square dipole moment of a polypeptide during the helix-coil transition is compared with the change in helix content. It is shown that, according to the theory, the determination of the helix initiation parameter σ and the enthalpy of helix formation ΔH can be determined. Experimental data on poly-benzyl-L -gluatamate in two different solvent mixtures are given.     

Dielectric properties of hemoglobin and myoglobin. I. Influence of solvent and particle size on the dielectric dispersion

Dielectric dispersion measurements with aqueous solutions of hemoglobin and myoglobin have been performed in the frequency range from 100 kcps to 15 Mcps. The influence of preparation, particle size, and solvent conditions was studied. The results are analyzed in terms of an orientational polarization mechanism.     

The dipole moment of membrane proteins: potassium channel protein and beta-subunit.

The mechanism of ion channel opening is one of the most fascinating problems in membrane biology. Based on phenomenological studies, early researchers suggested that the elementary process of ion channel opening may be the intramembrane charge movement or the orientation of dipolar proteins in the channel. In spite of the far reaching significance of these hypotheses, it has not been possible to formulate a comprehensive molecular theory for the mechanism of channel opening. This is because of the lack of the detailed knowledge on the structure of channel proteins. In recent years, however, the research on the structure of channel proteins made marked advances and, at present, we are beginning to have sufficient information on the structure of some of the channel proteins, e.g. potassium-channel protein and beta-subunits. With these new information, we are now ready to have another look at the old hypothesis, in particular, the dipole moment of channel proteins being the voltage sensor for the opening and closing of ion channels. In this paper, the dipole moments of potassium channel protein and beta-subunit, are calculated using X-ray diffraction data. A large dipole moment was found for beta-subunits while the dipole moment of K-channel protein was found to be considerably smaller than that of beta-subunits. These calculations were conducted as a preliminary study of the comprehensive research on the dipolar structure of channel proteins in excitable membranes, above all, sodium channel proteins.     

The electric dipole moment of rhodopsin solubilized in Triton X-100.

The electric dipole moment of solubilized rhodopsin was determined with dielectric dispersion measurements. Rhodopsin was extracted from disc membranes of cattle rod outer segments with the nonionic detergent Triton X-100. The dipole moment of rhodopsin at its isoionic point in the detergent micelle is 720 D (150 charge-A). This value is comparable to dipole moments of nonmembrane proteins, especially those which tend to aggregate or polymerize. Flash irradiation of the rhodopsin results in an increase in the dipole moment of about 25 D (5 charge-A). The light-induced increase in dipole moment appears to be composed of two parts--a faster component related to a change in the number of protons bound by rhodopsin and a slower component apparently independent of the change in proton binding.     

Influence of carbamoylation on some analytical properties of basic polypeptides

The effect of carbamoylation on the assay or identification of histones and polylysine was investigated. Incubation with sodium cyanate decreased the positive charge on these polypeptides as judged by changes in the binding of methyl orange or the electrophoretic mobility. Histones in chromatin appeared less accessible to carbamoylation than isolated histones. Carbamoylation of proteins under conditions in which there was little or no effect on the Lowry procedure could affect their assay by methods utilizing metachromasia with Coomassie Blue G. The Bradford assay has low sensitivity for Hl histone and polylysine but this can be increased by preincubation with sodium cyanate. More extensive carbamoylation of polylysine caused decreased sensitivity which was the only response seen with core nucleosomal histones and bovine serum albumin when preincubated with sodium cyanate. It was concluded that the sensitivity for Hl histone and polylysine in assays dependent on metachromasia with Coomassie Blue G may be changed by factors which decrease the positive charge on these polypeptides.     

The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment

The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and electro-optical methods. The search for the origin of these dipolemoments, however, must be based on the detailed knowledge on protein structure with atomic resolutions. At present, we have two sources of information on the structure of protein molecules: (1) x-ray databases obtained in crystalline state; (2) NMR databases obtained in solution state. While x-ray databases consist of only one model, NMR databases, because of the fluctuation of the protein folding in solution, consist of a number of models, thus enabling the computation of dipole moment repeated for all these models. The aim of this work, using these databases, is the detailed investigation on the interdependence between the structure and dipole moment of protein molecules. The dipole moment of protein molecules has roughly two components: one dipole moment is due to surface charges and the other, core dipole moment, is due to polar groups such as N--H and C==O bonds. The computation of surface charge dipole moment consists of two steps: (A) calculation of the pK shifts of charged groups for electrostatic interactions and (B) calculation of the dipole moment using the pK corrected for electrostatic shifts. The dipole moments of several proteins were computed using both NMR and x-ray databases. The dipole moments of these two sets of calculations are, with a few exceptions, in good agreement with one another and also with measured dipole moments.     

Influence of solvent composition on the mechanical properties of arterial elastin

We have investigated the effects of changes in solution composition on the mechanical properties of rings of arterial elastin. The time course of force equilibration at constant strain following a change in the composition of the bathing solution was measured. Both the force developed during slow extension and force relaxation following rapid straining were also measured in each of the test solutions. The results are difficult to summarize because all of the primitive quantities measured--sample dimension, slope of the force-extension curve, force overshoot and time of relaxation--as well as the derived quantities such as elastic modulus changed in different and apparently uncorrelated ways. Changes in pH and ionic composition of the bathing solution had small effects consistent with the low fixed charge density of elastin. Solutions of glucose, sucrose, and ethylene glycol had larger effects consistent with changes in hydrophobic interactions. The viscosity of the solution that penetrated the intrafibrillar space of the elastin appeared to be a major determinant of the dynamic response.     

Permanent dipole moment of tRNA''s and variation of their structure in solution.

The structure of six different tRNA molecules has been analyzed in solution by electrooptical measurements and by bead model simulations. The electric dichroism measured as a function of the field strength shows that tRNA's are associated with substantial permanent dipole moments, which are in the range of 1 x 10(-27) cm(identical to 300 D; before correction for the internal directing field). Rotational diffusion time constants of tRNA molecules in their native state at 2 degrees C show a considerable variation. A particularly large value found for tRNA(Tyr) (50 ns) can be explained by its nine additional nucleotide residues. However, remarkable variations remain for tRNA molecules with the standard number of 76 nucleotide residues (tRNA(Phe) [yeast] 41.6 ns, tRNA(Val) [Escherichia coli] 44.9 ns, tRNA(Glu) [E. coli] 46.8 ns; tRNA(Phe) [E. coli] 48.3 ns). These variations indicate modulations of the tertiary structure, which may be due to a change of the L-hinge angle. Bead models are used to simulate both electric and hydrodynamic parameters of tRNA molecules according to the crystal structure of tRNA(Phe) (yeast). The asymmetric distribution of phosphate charges with respect to the center of diffusion leads, under the assumption of a constant charge reduction to 15% by ion condensation, to a theoretical dipole moment of 7.2 x 10(-28) cm, which is in reasonable agreement with the measurements. The dichroism decay curve calculated for tRNA(Phe) (yeast) is also consistent with the measurements and thus the structure in solution and in the crystal must be very similar in this case. However, our measurements also indicate that the structure of some other tRNA's in solution is different, even in cases with the same number of nucleotide residues.     

Resolution of end-to-end distance distributions of flexible molecules using quenching-induced variations of the Forster distance for fluorescence energy transfer.

We describe a new method to recover the distribution of donor-to-acceptor (D-A) distances in flexible molecules using steady-state measurements of the efficiency of fluorescence energy transfer. The method depends upon changes in the Forster distance (Ro) induced by collisional quenching of the donor emission. The Ro-dependent transfer efficiencies are analyzed using nonlinear least squares to recover the mean D-A distance and the width of the distribution. The method was developed and tested using three synthetic D-A pairs, in which the chromophores were separated by alkyl chains of varying lengths. As an example application we also recovered the distribution of distances from the single tryptophan residue in troponin I (trp 158) to acceptor-labeled cysteine 133. The half-width of the distribution increases from 12 A in the native state to 53 A when unfolded by guanidine hydrochloride. For both TnI and the three model compounds the distance distributions recovered from the steady-state transfer efficiencies were in excellent agreement with the distributions recovered using the more sophisticated frequency-domain method (Lakowicz, J.R., M.L. Johnson, W. Wiczk, A. Bhat, and R.F. Steiner. 1987. Chem. Phys. Lett. 138:587-593). The method was found to be reliable and should be generally useful for studies of conformational distributions of macromolecules.     

Studies on the polypeptides of poxvirus. I. Comparison of structural polypeptides in vaccina, cowpox and Shope fibroma viruses.

Radioactively labeled vaccinia, cowpox and Shope fibroma virions free from any detectable contamination with host cell protein, were dissociated into their constituent polypeptides, and these were then analyzed by SDS-polyacrylamide gel electrophoresis and autoradiography. The profiles of constituent polypeptide bands of four strains of vaccinia virus (IHD-W, IHD-J, Lister and DIs) were almost the same, except that a polypeptide of about 41,000 daltons was not detectable in the autoradiogram of strain IHD-W which has no hemagglutinin. The profile of polypeptide bands of cowpox virions was also almost the same as that of vaccinia virions, except for several polypeptides of about 40,000 to 50,000 daltons, but the profile of Shope fibroma virions differed considerably from that of vaccinia or cowpox virions.