Far-infrared spectra of polyalanines with alpha-helical and beta-form structures

Far-infrared spectra of poly-L -alanines having the α-helical conformation and the β-form structure were measured. The spectra of glycine–L -alanine copolymer, silk fibroin, and copoly-D ,L -alanines with different D :L compositions were also measured. In addition to the bands so far reported, four bands at 190, 107, 120, and 90 cm^?1were found for the α-helix conformation and the two bands at 442 and 247 cm^?1 were found for the β form. The 442 cm^?1 band consists of the parallel 432 cm^?1 and perpendicular 445 cm^?1 bands. The 247 cm^?1 band is well defined and has strong dichroism parallel to the direction of stretching. These two bands appear also for silk fibroin and glycine–L -alanine copolymer. All the far-infrared bands of copoly-D ,L -alanines can be interpreted as α-helix bands, the three peaks at 580, 478, and 420 cm^?1 being ascribed to the D -residue incorporated into the right-handed α-helix or to the L -residue in the left-handed α-helix.     

Far-infrared spectra of sequential copolymers of amino acids with alkyl group side chains

Far-infrared spectra were measured for the sequential copolymers of amino acids with alkyl group side chains. The analysis of the spectra showed that (L -Ala-L -Ala-Gly)_n, (L -Ala-Gly)_n, (L -Ala-Gly-Gly)_n, (L -Val-L -Ala-L -Ala)_n, and (L -Val-L -Ala)_n, have the antiparallel pleated sheet structures and that the backbone conformations of (L -Val-L -Val-L -Ala)_n and (L -Val-L -Val-Gly)_n are the same as that of poly-L -valine. The far-infrared bands characteristic of the antiparallel pleated sheet structure were assigned on the basis of the result of the normal coordinate analysis of poly-L -alanine with this structure. The intersheet and interchain spacings of the sequential copolymers with the antiparallel pleated sheet structure were determined from the x-ray powder-diffraction patterns of these samples.     

Vibrational analysis of peptides,polypeptides, and proteins. XV. Crystalline polyglycine II

A force field has been refined for the 3₁-helix structure of polyglycine II, using the polyglycine I force field plus previous C^αH^α…?O force constants as a starting point. Besides force constants associated with the hydrogen bonds, which must change since the hydrogen-bond characteristics are different in the two structures, we have had to modify only 10 force constants from the polyglycine I force field to make it suitable for reproducing the polyglycine II frequencies. Most involve the NC^α bond, which is the torsion angle that changes from the I to the II structure. Calculations were done for parallel chain and antiparallel chain crystal structures of polyglycine II, the observed spectra being found to agree best with the latter structure. Since this provides strong evidence for the loss of strict threefold symmetry in the chain, our analysis strengthens the support for the existence of C^αH^α…?O hydrogen bonds in the structure of polyglycine II.     

Normal vibrations of polyglycine II

A valence force field has been refined for single-chain polyglycine II using the known structure and four isotopic derivatives. The calculated frequencies are in good agreement with the observed. The force field is compared with that derived from polyglycine I and for the nylons.     

Spectroscopic studies of random chain and -helical polypeptides in hexafluoroisopropanol

The infrared, ultraviolet, circular dichroism, and optical rotatory dispersion spectra of five synthetic polypeptides dissolved in hexafluoroisopropanol are reported. This solvent is useful because it dissolves most proteins and non-ionic polypeptides and also is transparent in spectral regions critical for polypeptide conformational diagnoses. Poly-γ-morpholinylethyl-L -glutamamide has random chain type spectra in this solvent, whereas the spectra of poly-γ-methyl-L -glutamate, poly-L -methionine, poly-ε, N -Carbo-benzoxy-L -lysine, and poly-L -homoserine indicate that these four polypeptides are α-helical. Small but significant variability between the different α-helical polypeptides is seen in their circular dichroism spectra and optical rotatory dispersions. An argument is presented that these differences may be due to slight geometry differences between different α-helices.     

Far-infrared spectra of some globular proteins

The far-infrared absorption spectrum (40–400 cm^?1) of solid pellets and films of several globular proteins (lysozyme, myoglobin, hemoglobin, serum albumin, ribonuclease, chymotrypsinogen, subtilisin) and of some representative polypeptides [nylon 66, poly (γ-benzyl L -glutamate)] have been investigated by using a Michelson interferometer. While polypeptides are known to present several peaks which can be assigned mostly to hydrogen-bond modes, all the investigated globular proteins display only one broad, intense baud in the 100–200 cm^?1 region. The origin of this band, which persists even after denaturation or partial digestion, is discussed.     

Vibrational dynamics and heat capacity in polyglycine II

The earlier works on the vibrational dynamics of polyglycine II (PG II) suffer from several infirmities, which not only suppress the dynamical nature of normal modes, but also lead to several incorrect assignments and interactive constants of the potential field. In this study, we have re-examined the phonon dispersion profiles of PG II using Higgs method for evaluation of phase-related normal modes and have attempted to remove the infirmities, as far as possible. The Wilson's GF matrix method combined with the Urey-Bradley force field has been used for normal mode analysis. This potential field leads to correct assignments of Raman, infrared and inelastic neutron scattering frequencies. Characteristic features of the dispersion curve (v versus delta/pi plot), such as repulsion and regions of high density-of-states have been interpreted. In addition, the heat capacity as a function of temperature has been obtained via density-of-states. It agrees well with the experimental data and is being reported for the first time.     

Low temperature infrared spectra of polyglycines and C--H...O==C hydrogen bonding in polyglycine II

Infrared spectra of polyglycines I and II obtained at ?170°C. have been compared with those obtained at room temperature. The changes in frequency of some of the C—H stretching bands are consistent with the earlier suggestion that C—H …? O?C hydrogen bonds are present in the structure of polyglycine II.     

Conformational properties of a polyglycine chain with secondary and tertiary structures of lysozyme

Unperturbed dimension mean value of r2(0), dipole moment mean value of mu2, mean squared optical anisotropy mean value of gamma 2 and molar Kerr mean value of mK constant of a polyglycine chain with the secondary and tertiary structures of lysozyme have been calculated and the results compared with polyglycine chains with the same number of repeat units but different conformations including alpha-helix, beta-sheet or random coil. Thus, the influence of secondary and tertiary structures can be investigated. The results obtained show that for mean value of r2 and mean value of gamma 2 this influence is at least of the same order of magnitude as that of the primary structure, and is much greater for mean value of mu 2 and mean value of mK.     

Optical properties of the polyglycine II helix

The circular dichroism spectrum obtained from a dilute aqueous solution of poly (ala-gly-gly) resembles that described for charged polypeptides such as the salt form of poly glutamic acid. A similar spectrum is found for films cast from aqueous solution where x-ray studies reported elsewhere have indicated a poly-glycinc II conformation. Evidence is presented for a heat induced poly-glycine II to unordered state transition similar to that described for collagen. The interpretation of this, the first observation of the optical properties of a poly-amino acid in the poly glycine II conformation, is further rationalized on the basis of spectra obtained from a number of polypeptides whose conformation approaches that of a 3₁ helix.     

Changes in the c.d. spectra of calf thymus DNA induced by sequential polypeptides in trifluoroethanol solutions. Part II

Interactions between calf thymus DNA and ( -Arg-X-Gly)_n sequential polypeptides (where

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) in trifluoroethanol: water (40:60) solutions in the salt range of 0.12—0.5 NaCl, were studied using c.d. spectroscopy. It was found that DNA tertiary structure (ψ form) is modulated by the nature of the polypeptides (variation of X residue). The effect of the secondary structure of polypeptides on the formation of ψ-DNA was also analysed. Unordered polypeptides destabilized ψ aggregates, while helical polypeptides favoured DNA tertiary structure. A loss of tertiary structure was observed in the presence of the ( -Arg- -Val-Gly)_n, which can be attributed to the ability of valine to suppress ψ-type DNA.     

Synthesis of sequential polypeptides containing lysine and tyrosine

Sequential polypeptides with the repeating units L -tyrosyl-L -lysyl, L -tyrosyl-(L -lysyl)₂, and L -tyrosyl-(L -lysyl)₃ have been synthesized by solution polymerization of the N-hydroxy-succinimide esters of the corresponding di-, tri-, and tetrapeptides. The monomers for the polytripeptide and polytetrapeptide were prepared by fragment condensation, using the mixed carbonic anhydride coupoling method. Moderately high molecular weight polypeptides were obtained.     

Solid-state conformation of some basic sequential polypeptides

We have studied the structure of solid films obtained by x-ray diffraction, from several basic polypeptides with a defined sequence. The alterating polypeptides poly(Ala-Lys), poly(Leu-Lys), poly(Val-Lys), and poly(Arg-Leu) all show a cross-β-structure in which layers of hydrophilic side chains alternate with layers containing hydrophobic side chains. The other polypeptides studied are not in the β-conformation and appear to be in the α-helical conformation. The helices obtained from poly(Lys-Ala-Ala) and poly(Lys-Ala-Ala-Lys) appear to be packed in an unusual fashion, which favors interaction between alanine side chains. Such behavior is not found in poly(Lys-Leu-Ala).     

Far-infrared spectra of copoly(- -amino acids)

Far-infrared spectra in the region from 700 to 200 cm^?1 were measured for the copolymers of L -alanine and glycine, those of L -alanine and L -valine, those of L -alanine and L -leucine, and those of L -alanine and L -phenylalanine. The observed spectra were interpreted on the basis of the analysis of the far-infrared spectra of the corresponding homopolymers, and the correlation between the conformations of the copolymers and the kinds of the component amino acids was discussed.     

Block sequential polypeptides of L-alanine and glycine with D, L-glutamic acid

Sequential polypeptides of L -alanine(A) and glycine(G), which were incorporated between two blocks of poly(D ,L -glutamic acid) (DL), were synthesized by applying Merri-field's solid-phase method. On the basis of optical rotatory dispersion criteria, DL(A)₃₈-DL was found to assume the α-helix in the whole range of the water-methanol system; whereas other block sequential polypeptides were found to assume the random-coiled conformation in water and partly the α-helix at the high methanol content. The stability of the α-helix decreased in the order: DL(A)₃₈DL, DL(A₂G)₁₀DL, DL(A₂G)₆DL, and DL(A₃G)₇DL. This phenomenon may be explained in terms of the dependence of hydrophobic bonding between the C₃H group of the ith L -alanine regularly arranged on the surface of the α-helix and the C₂H group of the (i + 3)th residue on whether the residue is alanine or glycine. The role which the methanol plays in stabilizing the α-helix is also discussed.