Conformational aspects of polypeptides. XXIX. Conformational assignments for some aromatic polypeptides by far-UV Cotton effects. New results

Recent improvements in apparatus permit the examination of circular dichroism (CD) and optical rotatory dispersion (ORD) spectra to 185 mμ. In addition, new solvents which are transparent to 185 mμ have become available for synthetic polypeptides. The spectral region 185–250 mμ is extremely important for the amide (peptide) chromophore, because of the presence at these wavelengths of the n–π* and π–π* bands,¹ and of another transition, the assignment of which remains unsettled.²     

Conformational studies of proteins with aromatic side-chain effects

We present here a brief analysis of ultraviolet isotropic absorption and related circular dichroism of the n–π* and π–π* transitions for the peptide (amide) chromophore in the 185–240 mμ region. Investigations by ultraviolet absorption and circular dichroism techniques on natural amino acids with aromatic chromophores in their side chains are also reported. By taking into account both the peptide and aromatic transitions we discuss the conformational studies of proteins with aromatic side-chain effects. Our attention is largely focused on the optical rotatory dispersion and circular dichroism spectra of these proteins in the near ultraviolet region, where characteristic aromatic side-chain bands occur. The 185–240 mμ region is also discussed when evidence exists of overlapping Cotton effects of aromatic and peptide groups.     

Optical activity of single-stranded polydeoxyadenylic and polyriboadenylic acids; dependence of adenine chromophore cotton effects on polymer conformation

Circular dichroism (CD) curves are reported for poly dA, (pdA)₆, (pdA)₂, poly A, ApAp, ApA, AMP, dApA, pdApA, A-2′-O-methyl pA, and A-2′-O-methyl pAp. Analysis of these curves indicated the presence of single CD bands at 228–230 mμ and at 278–280 mμ in oligomers longer than dinucleotides. In the case of dinucleotides and mononucleotides (from the literature, in addition to those studied here), the 230 mμ CD of band appears but the 280 mμ CD band does not. We assign the 230 mμ band to a very weak π–π* transition at this wavelength. From theoretical considerations, we show that the 280 mμ band is not an exciton component of the strong π–π* transition at 260 mμ in adenine. We conclude that the 280 mμ CD band must be assigned to a distinct absorption, not previously reported, which we suggest arises from an n–π* transition. The fact that the n–π* CD band at 280 mμ is not seen in mononucleotides or dinucleotides is ascribed to solvation of the adenine ring by water, which shifts the band to shorter wavelengths. Therefore, only interior residues of oligomers have the 280 mμ band, and the optical activity of a polymer cannot be computed from that of a dinucleotide, by using a nearest-neighbor approximation. The existence of this end effect hag been tested, by taking it into account in computing the rotational strengths of the 278 mμ n–π* transition for several oligomers; it is pointed out that a more sensitive test of this end effect would require CD data for the oligo dA series of 3 to 5 residues. We speculate about the structural and optical differences between poly dA and poly A, and point out the need for a theoretical treatment of n–π* Cotton effects in polynucleotides.     

Circular dichroism calculation for random-coil polypeptide chains

A method of calculation of the circular dichroism (CD) of random-coil polypeptides has been developed by means of a Monte-Carlo approach to the treatment of statistical systems and exciton theory of optical activity of polymers. The contribution of π–π^* and n–π^* amide transitions to the CD has been taken into account. The π–π^* transition gives rise to two CD bands: a negative short-wavelength band and a weak positive long-wavelength one. The n –π^* transition gives rise to one negative CD band.     

Theoretical optical properties of poly-L-proline

A non-perturbational technique is used to calculate the circular dichroism and absorption spectra of polypeptide chains having conformations similar to that of poly-L -proline II. The method employs a Bogoliubov exciton formalism, from which the various optical terms associated with parallel and perpendicular components of the exciton band are obtained. A simple model for the peptide unit, consisting of three Gaussian absorption bands, leads to reasonable results for the polymer spectra, provided the lowest energy peptide π → π* transition is taken at 207 mμ and the value of the Ramachandran angle Ψ is taken to be 390°. The calculations suggest that the polymer circular dichroism spectrum is the resultant of strong interference among the two Gaussian exciton terms and the non-Gaussian helix term. Consequently, the CD spectrum is very sensitive to the value of Ψ. It is found that the small positive CD band in the vicinity of 230 mμ arises partly from the effect of the static (crystal) field interactions on the n → π* CD band.     

Spectroscopic Studies on Nicotine and Nornicotine in the UV Region

The UV absorption and electronic circular dichroism (ECD) spectra of (R)‐ and (S)‐nicotine and (S)‐nornicotine in aqueous solution were measured to a significantly lower wavelength range than previously reported, allowing the identification of four previously unobserved electronic transitions. The ECD spectra of the two enantiomers of nicotine were equal in magnitude and opposite in sign, while the UV absorption spectra were coincidental. In line with previous observations, (S)‐nicotine exhibited a negative cotton effect centered on 263 nm with vibronic structure (π–π₁* transition) and a broad, positive ECD signal at around 240 nm associated with the n–π₁* transition. As expected this band disappeared when the pyridyl aromatic moiety was protonated. Four further electronic transitions are reported between 215 and 180 nm; it is proposed the negative maxima around 206 nm is either an n–σ* transition or a charge transfer band resulting from the movement of charge from the pyrrolidyl N lone pair to the pyridyl π* orbital. The pyridyl π–π₂* transition may be contained within the negative ECD signal envelope at around 200 nm. Another negative maximum at 188 nm is thought to be the pyridyl π–π₃* transition, while the lowest wavelength end‐absorption and positive ECD may be associated with the π–π₄* transition. The UV absorption spectra of (S)‐nornicotine was similar to that of (S)‐nicotine in the range 280–220 nm and acidification of the aqueous solution enhanced the absorption. The ECD signals of (S)‐nornicotine were considerably less intense compared to (S)‐nicotine and declined further on acidification; in the far UV region the ECD spectra diverge considerably. Chirality 25:288–293, 2013. © 2013 Wiley Periodicals, Inc.     

Optical rotatory dispersion studies of poly-O-acetyl-gamma-hydroxy-L-proline forms I and II

Poly-O-acetyl-hydroxy-L -proline, forms I and II have been studied by optical rotatory dispersion (ORD) and ultraviolet spectrophotometry in solution and in the solid state. Cotton effects of opposite sign, but not mirror images, were observed in the 250 mμ region for the two forms (Form I, peak 278 mμ; crossover, 254 mμ; trough, 244 mμ: Form II, trough 270 mμ; crossover, 248 mμ; peak, 238 mμ). Thus, the Cotton effects for a right-handed and left-handed helix have been shown to be opposite for the proline type helices I and II. The ORD of films of form I was found to have a positive Cotton effect further into the ultraviolet region with peak at 218 mμ. Absorption spectra showed a shift of 8 mμ in the absorption peak in the 200 mμ region for the two forms (form. I, 211 mμ; form II, 203 mμ). A shoulder was demonstrated in the film absorption spectra in the 250 mμ region where the Cotton effects are found. The mixing of the n, π* and π, π* states of the amide chromophore and n, π* state of the ester chromophore was suggested as being responsible for the Cotton effects in the 250 mμ region.     

Circular dichroism of collagen, gelatin, and poly(proline) II in the vacuum ultraviolet.

Circular dichroism spectra for acid-soluble calfskin collagen, gelatin, and poly(proline) II in solution have been extended into the vacuum ultraviolet region. The extended spectrum of gelatin reveals that the circular dichroism of this unordered polymer is more closely related to the spectrum of charged polypeptides than might be evident from near ultraviolet work. A short-wavelength band is found at about 172 nm, which corresponds in position, magnitude, and sign to a band recorded earlier for poly(L -glutamic acid) at pH 8.0. This band is observed in a helical structure for the first time in the vacuum ultraviolet circular dichroism and absorption spectra of poly(proline) II. Both circular dichroism and absorption spectra point to the assignement of this band as the nσ*. Neither the nσ* nor the expected positive lobe of the ππ* helix band is observed in the extended circular dichroism spectrum of collagen. We postulate that these two bands cancel here in analogy to the case of α-helical poly(L -glutamic acid).     

Rotatory dispersion and circular dichroism of low-molecular-weight poly- -benzyl-L-glutamate

Rotatory dispersion and circular dichroism of low-molecular-weight poly-γ-benzyl-L -glutamate, which was prepared from the N-carboxyanhydride by n-hexylamine initiation at [A]/[I] 3, 4, and 8, have been measured in ethylene dichloride and dioxane at different concentrations. The rotatory properties of the polypeptides are all characterized by a trough at 233 mμ of a negative Cotton effect or by a negative circular dichroic band at 223 mμ. With increasing A/I value or concentration, dextrorotation increases and the negative dichroic band becomes deeper. Both the trough magnitude and the negative ellipticity are linearly dependent on the content of β-structure, and the rotatory parameters for the pure β-structure are estimated by extrapolation of the linear relations. Circular dichroism and infrared spectra of the polypeptides have also been measured in trifluoroethanol, and the effect of solvents on the polypeptide conformation is discussed.     

Vacuum ultraviolet absorption spectra of sublimed films of nucleic acid bases

Measurements of the optical absorption spectra of the sublimed films of adenine, guanine, cytosine, thymine, and uracil were extended down to 120 mμ at room temperature. Several remarkable absorption peaks were found to exist below 190 mμ in addition to the already known ones near 260 mμ and 200 mμ. The intensities of these peaks were comparable to or, in some cases, even larger than those near 260 mμ and 200 mμ. It was found that the relative intensities of the absorption peaks differed considerably from sample to sample for all five bases, probably due to variation in the arrangement of the bases in the sublimed films. It was found also that the absorption spectra of the sublimed films change with aging on standing in vacuo at room temperature. On comparing the spectra of several fresh samples it was found that the intensities of the transitions with wavelength longer than 160 mμ of adenine, guanine, and uracil films are inversely correlated with those of the transitions shorter than 160mμ.     

Ultraviolet dichroic ratio of DNA from T2 and T5 bacteriophages

The dichroic ratios of T5st-O and T2H bacteriophage DNA molecules were measured throughout the ultraviolet region of the spectrum. Two methods of DNA orientation were studied: (1) orientation in solution in a Shimadzu flow dichroism instrument attached to a Beckman DU spectrophotometer, and (2) alcohol precipitation of the DNA from solution and orientation in a thin film on the quartz face of a humidity chamber. Spectra in the latter case were recorded using a Gary Model 14 spectrophotomcter fitted with Glan prisms. The lower wavelength limit was 215 mμ in both systems. The DNA preparations were carefully characterized as to spectral purity, sedimentation coefficient, hyperchromicity, protein content, and DNA content. In addition, the structure of the DNA oriented in films was inferred from x-ray diffraction patterns of fibers of the precipitated DXA. The A and B configurations of DNA in films could not be distinguished by the dichroic ratio measuiements. The dichroic ratio obtained for the film-oriented DNA at high relative humidity shows the same wavelength dependence as for the flow-oriented DNA. The same wavelength dependence for DNA in the fibrous state and in solution, when considered together with the x-ray diffract ion results, indicates that DNA in solution maintains an orientation of bases which is similar to that in fibers. I¹Or both solutions and films of DNA, the dichroic ratio is constant from 290mμ to 240 mμ and increases at wavelengths below 240 mμ. The increased parallel absorption below 240 mμ is consistent with the existence of an n→π* transition. The inherent molecular dichroic ratio is found to be the same for T5st-O DNA and T2H DNA in solution, and is a maximum of 0.09 ± 0.02 at 260 mμ.     

Optical properties and viscosity of hyaluronic acid in mixed solvents: Evidence of conformational transition

Circular dichroism, optical rotatory dispersion, and viscosity of hyaluronic acid at various solvents compositions, concentrations, and pH values have been studied. The data show a large change in the molecular properties in organic/water solvents such as ethanol, p-dioxane, or acetonitrile/water at pH ? pK_a. At this pH range of aqueous solution, hyaluronic acid shows a CD minimum near 210 nm whereas in the presence of organic solvent it exhibits a strong negative dichroism (below 200 nm) and a positive band near 226 nm. It undergoes a sharp, cooperative transition with respect to pH and solvent. The observed CD features are assigned to the π-π* and n-π* transitions of the amide and carboxyl chromophores. The ORD results show a gradual blue shift of trough at 220 nm with increasing magnitude of rotation when the organic solvents and hydrogen ion concentrations are increased. A one-term Drude's equation was used to analyze the ORD data, and the result show a variation of dispersion parameters with different solvents in accordance with the observed CD changes. The intrinsic viscosity of hyaluronic acid in mixed solvent at pH 2.6 is lower than that of aqueous solution. All the observed property changes of hyaluronic acid are reversed on addition of foramide in mixed solvents indicating that the hydrogen bonds are involved in this transition. The observed spectroscopic and hydrodynamic features are attributed to a conformational change of hyaluronic acid in a mixed solvent involving intramolecular hydrogen bonding between the acetamido and carboxyl groups. The possible conformational state of hyaluronic acid in solution under various conditions is discussed in terms of the reported helical structure of hyaluronic acid from x-ray diffraction studies.     

Circular dichroism measurements of benzyl L-aspartate–nitrobenzyl L-aspartate copolymers and their use in detecting and characterizing preferred polymer conformations

We have examined the nature of the circular dichroism band at 330 mμ for a series of copolymers of β-p-nitrobenzyl L -aspartate with β-benzyl L -aspartate. The circular dichroism band arises from an electronic transition in the nitroaromatic group. In order to interpret the effect quantitatively, we employed a simplified statistical treatment and curve fitting for six copolymers. Both approaches gave consistent results, which indicates that the dichroism comes from pairwise interactions between two nitrobenzyl groups. We constructed a molecular model that meets the constraints and requirements of the analyses developed in this paper. In this model, it is proposed that the main chain forms a right-handed α-helix and that nitrobenzyl groups separated by four residues interact with each other.     

Steric structure of L-proline oligopeptides. II. Far-ultraviolet absorption spectra and optical rotations of L-proline oligopeptides

The results of the measurement of the far-ultraviolet absorption spectra of L -proline oligomers in water and acetonitrile are summarized as follows. The monomer has an absorption maximum at 182.5 mμ in acetonitrile. The absorption maximum of the dimer is found at 185 mμ and a shoulder appears around 200 mμ, that is, splitting of the absorption spectrum is observed in the dimer. As the degree of polymerization increases, the position of the shoulder shifts toward the wavelength of the absorption maximum of poly-L -proline II, with an accompanying increase in intensity. We may describe the absorption peak around 203 mμ of poly-L -proline II as identical with the shoulder with an increased intensity. By measurements of optical rotatory dispersion and circular dichroic spectra, it was also confirmed that the appearance of the helical conformation commences at the tetramer. When the number of residues is five or greater, the conformation of the helical structure of poly-L -proline II seems to be completed.     

Optical rotary dispersion of mucopolysaccharides. 3. Ultraviolet circular dichroism and conformational specificity in amide groups

The circular dichroism of glycosaminoglycans and ganglioside in distilled water are described, showing two bands in the region of amide and carboxyl transitions. The first, negative hand is common to all polymers and the amino sugar derivatives. The characteristics of the second band depend upon polymer structure. Those containing 4–1-linked amino sugars show a second, positive, resolved band about 190 mμ, while those with 3–1-linked amino sugars show a second, negative band less resolved from the first usually ≤185mμ, but clearly centered at 188mμ for dermatan sulfate. Ultraviolet optical absorption from 300 to ～183 mμ showed inflection regions around 190 mμ for most compounds.     

Circular dichroism of some mononucleosides.

The circular dichroism (CD) and absorption spectra of uridine, thymidine, purine ribonucleoside, and the four adenine derivatives 2′-deoxyadenosine, adenosine, adenosine-3′,5′-cyclic phosphate, and arabinosyl adenine were measured in water at pH 7 and pH 2. The absorption and CD spectra of the pyrimidines were simultaneously fitted to four Gaussian bands, and the dipole and rotational strengths of the electronic transitions determined. Adenine-derivative CD spectra were determined by computer averaging six runs. The spectra showed CD bands at 268, 226, 209, and 195 nm. The band at 226 nm probably is an n–π* transition; the band at 209 nm cannot be detected without a computer. The CD and absorption spectra of purine ribonucleoside indicate three transitions in the 230–310-nm region.     

Random copolymers of alpha-benzyl-L-aspartate with ortho- and para-nitrobenzyl-L-aspartates. Intrinsic and extrinsic dichroic bands and the left-to-right-handed alpha-helical transition.

Copolymers of benzylaspartate with the corresponding para-nitro and ortho-nitro derivatives are known to undergo, at increasing nitro content, a transition from a left-handed α-helical conformation to a right-handed α-helical conformation. The circular dichroism associated with the n, π* transition of the amide group, as well as the extrinsic bands associated with the nitrobenzyl chromophore, have been studied for these copolymers as a function of the nitro content. The circular dichroism associated with the 330-nm extrinsic band is shown to present an abrupt change, which parallels the change in the 222-nm band characteristic of the left- to right-handed helix transition. The intensity of the 222-nm CD band seems unaffected by the interaction with the side-band chromophore. The circular dichroism associated with the 330-nm band is much stronger in the right-handed conformation and is unaffected by increasing interactions between side chains. Interpretation in the light of the possible mechanism for optical activity of helical molecules seems to indicate that the 330-nm extrinsic effect is essentially due to the Condon, Altar, and Eyring (CAE) mechanism and μ-m perturbation (in Schellmann terminology) on the side-chain chromophore n, π* transition.     

Far ultraviolet optical rotatory properties of poly-L-tryptophan. I

A block copolymer [γ-Et-DL -Glu]_m [L -Trp]_n was prepared using N-carboxy anhydrides (NCA) of L -tryptohan and γ-ethyl DL -glutamate. The block copolymer, dissolved in trifluoroethanol (TFE)–dichloroacetic acid (DCA) mixtures, exhibited a sharp change in the specific rotation at 546 mμ when the solvent composition reached 70–75% DCA content. Optical rotatory dispersion (ORD) and circular dichroism (CD) measurement were carried out in TFE solution in the spectral range 180–350 mμ. Indole side-chain chromophores were found to be optically active in the polymer. On the other hand, these groups exhibit very small optical activity in the model compound C₆H₃? CH₂? O? CO? (L -Trp)₂? O? CH₃. Indole groups therefore appear to be in a dissymmetric environment only in the polymer. From these data it was concluded that poly-L -Trp is in some type of helical conformation in TFE. Strong overlapping of CD bands from side-chain chromophores and peptides chromophores in the wavelength range 185–240 mμ does not allow definite conclusions to be drawn about the type of helical conformation which exists in poly-L -Trp in TFE solution.     

Circular dichroism of the alkyl amino acids in the vacuum ultraviolet

The circular dichroism and absorption for five alkyl amino acids as zwitterions has now been measured to 160 nm. Two bands are found, the nπ* at long wavelengths and ππ* at short wavelengths. In an effort to extract conformal information from the circular dichroism measurmenths, the circular dichroism spectra for these molecules is calculated using an independent systems apporach. It is found that the signs calculated using these methods are quite reliable, but that reliable magnitudes must await more accurate data to use in the calculations. Comparing the signs for both the measured and calculated circular dichriosm it if possible to determine the region inhabited by the carboxylate anion chromophore of these amino acid zwitterions. The greatest failure of the calculations is that thay are unable to explain the sigmoidal shape of the nπ* transition in proline. The problems facing workers trying to make calculations to relate circular dichroism measurements to conformation are discussed.     

Dichroism of TMV in pulsed electric fields

The linear dichroism induced in a solution of electrically anisotropic molecules by a pulsed electric field has been studied. Equations have been obtained which express the dichroism as a function of dipole moment, excess polarizability, field strength, and the angle α between the dipole moment and the transition moment for the absorption band. These expressions have been related to the experimentally observed difference signal in such a way that when the dichroism is measured as a function of field strength the permanent moment, excess polarizability and angle a can be determined. Experiments have been carried out on tobacco mosaic virus (TMV), which is similar in its properties to the theoretical model. The polarizability anisotropy and rotary diffusion constant for the monomer and dimer of TMV have been obtained from these experiments. In addition to the molecular parameters mentioned above, the saturated electric dichroism of the virus was measured as a function of wave length and the presence of an n–π* transition in the tryptophan spectrum was indicated. Further experiments measuring dichroism as a function of pH demonstrated the general denaturation of the virus at high pH (10–11) but also the existence of a stable fraction which is not fragmented even at the high pH involved.