Vibrational spectroscopy of L-valyl-glycyl-glycine,a parallel-chain β-structure

Bands in the ir and Raman spectra of L -valyl-glycyl-glycine (VGG) and VGG-ND have been assigned on the basis of a normal mode analysis of the known parallel-chain β-structure of this tripeptide. Amide I, II, III, and V mode shifts are obtained by the interactions of dipole derivatives in symmetry coordinates, referred to as dipole derivative coupling. These derivatives, obtained from ab initio studies, are also used to calculate ir intensities of amide I, II, and V modes. The agreement between predicted and observed frequencies and intensities is very good, providing confidence in the application of our force fields to the calculation of the vibrational modes of the general parallel-chain β-sheet structure (following paper).     

Normal mode spectrum of the parallel-chain β-sheet

Normal mode calculations have been carried out for parallel-chain β-sheet structures. These include the parallel-chain pleated sheet of poly(L -alanine) and the parallel-chain rippled sheet of polyglycine. Dipole derivative coupling has been included for amide I and II modes, and the effects of parallel-sheet and antiparallel-sheet arrangements of varying separation have been examined for the poly(L -alanine) case. Some amide and nonamide modes are distinctly different from their antiparallel-chain counterparts, thus providing a basis for distinguishing between such structures from their ir and Raman spectra. As in our previous studies, these results emphasize the need for both kinds of spectral data in order to draw definitive conclusions about conformation.     

Infrared spectra and resonance interactions of amide-I and II vibration of alpha-helix.

Amide-I and II vibrations of α-helix have been treated on the basis of the perturbation theory in a dipole–dipole approximation. The infinite helix and its finite fragments have been considered as models. The calculated infrared spectra for the infinite helix are in good agreement with the spectra of synthetic polypeptides. In the case of finite fragments of the α-helix, the characteristic contours of the amide-I and II bands appear when the nuimber of peptide groups is about 10 and 6, respectively.     

Normal vibrations of crystalline polyglycine I

A valence force field has been refined for crystalline polyglycine I using its known antiparallel chain pleated-sheet structure and without replacing the CH₂ group by a point mass. Polyglycine I and four of its isotopic derivatives were used in the refinement. The calculated frequencies are in good agreement with the observed, except for the amide I modes. It is shown that this is a consequence of the fact that no reasonable force field predicts a large D₁₀ term of the Miyazawa perturbation treatment. The amide I splittings can, however, be satisfactorily accounted for by introducing a direct interaction force constant between adjacent C?O groups in neighboring chains. This can reasonably arise from transition dipole coupling and corresponds to the heretofore neglected D₁₁ term.     

Junctional structures in digestive epithelia of a cephalopod

Intercellular junctions have been studied in the epithelia of digestive organs of Sepia officinalis (digestive gland, digestive duct appendages and caecum) by conventional staining, lanthanum tracer and freeze-fracturing techniques. In the three organs studied the same junctional complex occurs, consisting of a belt desmosome, a septate junction and gap junctions. The septate junction is of pleated-sheet type and the gap junction has its particles on the P face of the fracture. Circular structures have been found in the digestive gland septate junctions. Neither continuous nor tight junctions have been found. These results show that Cephalopods have junctional structures very close to those of other Molluscs and of Annelids. Some small differences between the septate junctions of the three organs could be related to their different physiology.     

Infrared spectra and resonance interaction of amide-I vibration of the antiparallel-chain pleated sheet.

Theoretical treatment of resonance interaction of amide-I vibration has been done in a dipole–dipole approximation on the basis of perturbation theory. A single infinite antiparallel-chain pleated sheet as well as different kinds of its finite fragments have been considered. A good agreement has been obtained between calculated spectral parameters of amide I of the infinite sheet and observed ones in infrared and Raman spectra of synthetic polypeptides and fibrous proteins. A theoretical dependence of the resonance frequency shift of the main component and frequency splitting of two components active in the infrared spectra on the number of polypeptide chains in the finite sheet has been found.     

Electric properties and structure of DNA-restriction fragments from measurements of the electric dichroism

The electric dichroism of 17 homogeneous DNA fragments, ranging in size from 43 to 4362 base-pairs, has been analyzed in high electric fields. The orientation of the small fragments can be described in terms of an induced dipole moment, whereas the large fragments are oriented according to a constant dipole mechanism. In the intermediate size range, DNA orients according to an induced dipole mechanism at low field strengths and according to a constant dipole mechanism at high field strengths. From these observations we propose an orientation mechanism with a saturating induced dipole. The induced dipole observed at low field strengths is saturated at a field strength Eo within a transition range Em to give a constant dipole moment at high field strengths. These parameters together with the polarizability and the limit reduced dichroism are evaluated by a least-squares analysis of the experimental data. Eo and Em are found to decrease with increasing chain length from Eo approximately 40 kV/cm (Em approximately 14 kV/cm) at 65 base-pairs to 10 kV/cm (6 kV/cm) at 194 base-pairs. The polarizability is found to increase with the square of the chain length, whereas the saturated dipole increases with chain length N at low N and goes to a limit value at high N. The temperature dependence of the orientation parameters is found to be very small. The values obtained for the limit dichroism are between -1.0 and -1.3 for chain lengths between 60 and 1000 base-pairs, whereas values around -1.4 are observed at chain lengths greater than 1000 base-pairs. These data indicate that electric fields extend the contour of DNA strands at high chain lengths from a weakly bent to a more linear form. The variations of the limit dichroism observed for short fragments suggest sequence-dependent differences in the secondary structure of the helix. The experimental results are compared with numerical calculations based on simple polyelectrolyte models. For short fragments the magnitude of several electrochemical parameters can be adequately explained by a polarization of the ion cloud around the DNA molecules. However, these polyelectrolyte models do not adequately describe the observed chain length dependence of the orientation phenomena.     

Electric birefringence of restriction enzyme fragments of DNA: optical factor and electric polarizability as a function of molecular weight

The electric birefringence of restriction enzyme fragments of DNA has been investigated as a function of DNA concentration, buffer concentration, and molecular weight, covering a molecular weight range from 80 to 4364 base pairs (bp) (6 × 10⁴–3 × 10⁶ daltons). The specific birefringence of the DNA fragments is independent of DNA concentration below 20 μg DNA/ml, but decreases with increasing buffer concentration, or conductivity, of the solvent. At sufficiently low field strengths, the Kerr law is obeyed for all fragments. The electric field at which the Kerr law ends is inversely proportional to molecular weight. In the Kerr law region the rise of the birefringence is accurately symmetrical with the decay for fragments ≤ 389 bp, indicating an induced dipole orientation mechanism. The optical factor calculated from a 1/E extrapolation of the high field birefringence data is ?0.028, independent of molecular weight; if a 1/E² extrapolation is used, the optical factor is ?0.023. The induced polarizability, calculated from the Kerr constant and the optical factor, is proportional to the square of the length of the DNA fragments, and inversely proportional to temperature. Saturation curves for DNA fragments ≤ 161 bp can be described by theoretical saturation curves for induced dipole orientation. The saturation curves of larger fragments are broadened, because of a polarization term which is approximately linear in E, possibly related to the saturation of the induced dipole in high electric fields. This “saturated induced dipole” is found to be 6400 D, independent of molecular weight. The melting temperature of a 216-bp sample is decreased 6°C in an electric field of 8 kV/cm, because the lower charge density of the coil form of DNA makes it more stable in an electric field than the helix form.     

Elastic Moduli of Helical Polypeptide Chain Structures

The elastic moduli of the α-helix, polyglycine II, and the parallel-chain and antiparallel-chain pleated sheet structures have been calculated. A Urey-Bradley type of potential was used, extended by the inclusion of hydrogen bond stretching terms where appropriate. In the one instance where a valid comparison with experimental data can be made, viz, α-keratin, the calculations indicate that the matrix component, rather than being amorphous, probably contains an ordered structure of higher modulus than the α-helix.     

A small DNA restriction fragment with an apparent permanent dipole moment

The electric birefringence of two DNA restriction fragments, each containing 147 base-pairs, has been investigated. The decay of the birefringence was the same for the two fragments, with a relaxation time corresponding to the reorientation of fully extended, rod-like molecules. However, the birefringence saturation behavior of the two fragments was markedly different: one fragment oriented by the expected induced-dipole mechanism, while orientation of the other fragment followed the theoretical curve for permanent dipole orientation. This difference in behavior must be due to differences in the base-pair sequences of the two fragments.     

Vibrational analysis of crystalline tri-L-alanine

We have found that tri-L-alanine (Ala3) can crystallize in a parallel-chain beta structure in addition to the previously known antiparallel-chain beta structure. Although the chain conformations in each structure are essentially similar, the ir and Raman spectra are distinctively different. We have calculated the normal modes of each structure, and can account in significant detail for these differences. This demonstrates the essential validity of our empirically refined force fields, as well as showing that deeper insights into polypeptide and protein structure can be achieved through the rigorous analyses of normal mode calculations.     

Linear contour length dependence of electrical polarizability of nucleosomal DNA fragments: implications for the flexibility of DNA

The transient electric birefringence of monodisperse oligonucleosomal DNA ranging from 145 to 990 base pairs has been studied. The orientation of fragments can be described in terms of an induced dipole moment with a small contribution of a permanent dipole. The electrical polarizability delta alpha was found to increase linearly with the DNA contour length. This unexpected dependence might result from a bent structure of DNA already considerable for very short segments. The observed delta alpha values agree with a segmental orientation of rigid subunits of length 13-18 nm as estimated in the elastic model of DNA with a kink angle of about 41 degrees.     

Infrared and Raman study in the solid state of fully protected,monodispersed homooligopeptides of L-valine,L-isoleucine,and L-phenylalanine

An ir-absorption and Raman-scattering study, in the solid state, has been carried out on monodispersed, N- and C-protected homooligopeptides (number of residues, n, from 2 to 7) of L -valine, L -isoleucine, and L -phenylalanine. The amide I, II, III, V, and vNH regions have been examined. Some deuterated (ND) samples have been examined to complete the assignments. L -Phenylalanine dipeptide displays spectral characteristics compatible with the parallel β-structure; L -isoleucine and L -valine dipeptides are probably in a distorted structure. A mixture of parallel and antiparallel extended chains cannot be excluded for the peptides with n = 3. In the amide I region the spectra of peptides with n ≥ 4 show the existence of the β-conformation. The problem of chain orientation within the pleated-sheet structure is discussed on the basis of a recent theoretical treatment of vibrational interactions of the amide I mode.     

The structure of rubredoxin at 1.2 A resolution

Structural details of the model of Clostridium pasteurianum rubredoxin are presented, based on the refined model at 1.2 Å resolution. The molecule contains no extensive regions of pleated-sheet or helical structure. Regular secondary structure consists primarily of residues 3 to 7, 11 to 13 and 48 to 52 in a small region of pleated-sheet; and residues 14 to 18, 19 to 23, 29 to 33 and 45 to 49 in 3₁₀ helical corners. Interbond angles in the helical corners average as much as 10 ° greater than normally accepted values and a number of the peptide groups deviate significantly from planarity.Rubredoxin has a pronounced asymmetry in the distribution of charged groups on its surface. This would lead to highly favored molecular orientations when the protein interacts with other charged molecules.Bond lengths in the iron-sulfur complex range from 2.24 å to 2.33 Å, and bond angles range from 104 ° to 114 °.     

Permeability barrier in the mantle epithelium lining the testis in the apple-snail Pomacea canaliculata (Gastropoda: Ampullariidae)

Intercellular junctions are studied in the epithelium lining the testis of the freshwater snail Pomacea canaliculata by conventional staining and lanthanum tracer techniques. The junctional complex consists of belt desmosomes and septate junctions. Septate junctions are of the pleated-sheet type and they are constantly associated with mitochondria. Gap and tight junctions appear to be absent. These septate junctions seem to be the structural correlate of an epithelial permeability barrier that separate the testis from the extrapallial space where the shell elements are deposited. These junctions may contribute to a functional barrier in the male gonad of Pomacea canaliculata. The results indicate that freshwater prosobranchs have junctional structures very close to those found in other molluscs.     

Electrooptic study of the deionized form of bacteriorhodopsin

Electric field induced light scattering by suspensions of cation-depleted purple membranes, obtained by deionization of purple membrane (PM) suspensions on a cation exchange column or by electrodialysis at a pH around 6, shows a strong drop (more than 5 times) in the value of the permanent dipole moment relative to that of PM fragments. The membrane dipole moments were measured both at low dc and ac electric fields as well as by using electric field pulses with reversing polarity. Some slight changes in the dispersion of the electric polarizability were also observed.Microelectrophoretic measurements showed that the electric charge of the membrane fragments is increased by 30% after deionization. The importance of these data for the understanding of the blue membrane properties and subsequently for the mechanism of proton pumping are discussed.     

Theoretical investigation of semiconductive properties in proteins. I. Electrical conductivity, charge carrier mobilities, and free paths in beta-polyglycine

Theoretical values are reported for the specific conductivity, charge carrier mobilities, and delocalized free paths in β-polyglycine using the parallel-chain pleated sheet conformation and the all-valence electron energy band structure obtained previously. The mobilities are found to be much larger along the polypeptide backbones than in the direction of the hydrogen bonds. This indicates a mechanism of conduction in which the former path is favored for electronic delocalization. The preexponential factor of the specific conductivity obtained theoretically agrees well with experimental results.     

Laser Raman spectroscopic studies of the thermal unfolding of ribonuclease A.

The reversible thermal denaturation of bovine pancreatic ribonuclease A at pH 5 in 0.1 M NaCl over the range 32-70 degrees C as studied by Raman spectroscopy proceeds in a gradual manner consistent with a stepwise unfolding process rather than as a transition between two states. Conversion of residues from helical or pleated-sheet geometry to some intermediate geometry, as followed by means of the amide I and III lines, reveals that substantial amounts of the helical and pleated-sheet conformations remain at 70 degrees C. Changes in the strength of hydrogen bonding by the tyrosyl residues are indicated by the intensity ratio of the doublet at 830-850 cm(-1) and changes in the geometry of the disulfide bridges by the frequency and half-width of the Raman line near 510 cm(-1) due to the S-S vibration. Vibrations of C-S bonds in the methionines and cystines are used to monitor conformational changes in these residues. While there are small quantitative differences in temperature dependence among these probes, all agree in placing the malting temperature at or near 62 degrees C. The Raman data are quantitatively consistent with the six-stage scheme of unfolding of A.W. Burgess and H.A. Scheraga [(1975), J. Theor, Biol. 53, 403], except that no change in the environment of the tyrosines is seen until 45 degrees C.     

紫膜碎片的电二色性研究

悬浮在水中的嗜盐菌紫膜碎片,在外电场作用下产主定向排列.在20℃时,568nm的电二色性研究表明:外加电场为2kV/m时取向程度可达60%以上;大于5.5kV/m时,取向作用趋于饱和状态;饱和时简约电二色性为-0.437左右,视黄醛生色团的跃迁矩方向与电偶极矩方向形成60.9°夹角;紫膜的永久偶极短为9.2×10~(-24)C、M,剩余电极化率为3.0×10~(-27)m~2;紫膜的旋转扩散常数为0.53秒~(-1).曲线拟合分析表明,感应偶极对紫膜碎片的定向的贡献应予考虑.本文对紫膜碎片的定向机理进行了讨论.     

Poly(ε-L-lysine): Synthesis and conformation

The synthesis of poly(ε-L -lysine) is described. This is a poly(ε-amino acid) in which the ε-amino group of lysine is condensed with the α-carboxyl group to produce a chain backbone that is a variant of the usual one seen in proteins and the side chain is the α-amino group. Conformational studies of poly(ε-L -lysine) and its t-butyloxycarbonyl derivative suggest the likelihood of a chain order that is formally similar to the antiparallel pleated-sheet conformation of proteins.