Conformational study of poly(α-L-aspartic acid)

The conformation of poly(α-L -aspartic acid) was investigated on a sample in which β-bonds were not detected. CD and ir spectroscopy showed that poly(α-L -aspartic acid) passes through a conformational change induced by changes of the degree of ionization that is accompanied by precipitation; the precipitate is probably highly helical. The change was also detected by potentiometric titration.     

Solid-state conformation of copolymers of β-benzyl-L-aspartate with L-alanine,L-leucine,L-valine, γ-benzyl-L-glutamate,or ϵ-carbobenzoxy-L-lysine

The solid-state conformation of copolymers of β-benzyl-L -aspartate [L -Asp(OBzl)] with L -leucine (L -Leu), L -alanine (L -Ala), L -valine (L -Val), γ-benzyl-L -glutamate [L -Glu(OBzl)], or ?-carbobenzoxy-L -lysine (Cbz-L -Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in the region of the amide I and II bands and in the region of 700–250 cm^?1 have been determined. The results from the ir studies are in good agreement with data obtained by CD experiments. Incorporation of the amino acid residues mentioned above into poly[L -Asp(OBzl)] induces a change from the left-handed into the right-handed α-helix. This conformational change for the poly[L -Asp(OBzl)] copolymers was observed in the following composition ranges: L -Leu, 0–15 mol %; L -Ala, 0–32 mol %; L -Val, 0–8 mol %; L -Glu(OBzl), 3–10 mol %; and Cbz-L -Lys, 0–9 mol %.     

Raman spectroscopic study of poly (β-benzyl-L-aspartate) and sequential polypeptides

Poly-β-benzyl-L -aspartate (poly[Asp(OBzl)]) forms either a lefthanded α-helix, β-sheet, ω-helix, or random coil under appropriate conditions. In this paper the Raman spectra of the above poly[Asp(OBzl)] conformations are compared. The Raman active amide I line shifts from 1663 cm^?1 to 1679 cm^?1 upon thermal conversion of poly[Asp(OBzl)] from the α-helical to β-sheet conformation while an intense line appearing at 890 cm^?1 in the spectrum of the α-helix decreases in intensity. The 890 cm^?1 line also displays weak intensity when the polymer is dissolved in chloroform–dichloroacetic acid solution and therefore is converted to the random coil. This line probably arises from a skeletal vibration and is expected to be conformationally sensitive. Similar behavior in the intensity of skeletal vibrations is discussed for other polypeptides undergoing conformational transitions. The Raman spectra of two cross-β-sheet copolypeptides, poly(Ala-Gly) and poly(Ser-Gly), are examined. These sequential polypeptides are model compounds for the crystalline regions of Bombyx mori silk fibroin which forms an extensive β-sheet structure. The amide I, III, and skeletal vibrations appeared in the Raman spectra of these polypeptides at the frequencies and intensities associated with β-sheet homopolypeptides. Since the sequential copolypeptides are intermediate in complexity between the homopolypeptides and the proteins, these results indicate that Raman structure–frequency correlations obtained from homopolypeptide studies can now be applied to protein spectra with greater confidence. The perturbation scheme developed by Krimm and Abe for explaining the frequency splitting of the amide I vibrations in β-sheet polyglycine is applied to poly(L -valine), poly-(Ala-Gly), poly(Ser-Gly), and poly[Asp(OBzl)]. The value of the “unperturbed” frequency, V₀, for poly[Asp(OBzl)] was significantly greater than the corresponding values for the other polypeptides. A structural origin for this difference may be displacement of adjacent hydrogen-bonded chains relative to the standard β-sheet conformation.     

Nmr study of poly(aspartic acid). I. α- and β-Peptide bonds in poly(aspartic acid) prepared by thermal polycondensation

The structure of poly(aspartic acid) prepared by thermal polycondensation has been studied by means of nmr spectroscopy. The analysis of the ¹³C-nmr spectra of the polymer at various pH values and comparison with the spectrum of poly(α-L -aspartic acid) revealed that the polymer contained aspartic acid linked in α- and β-peptide bonds. The mole fraction of the β-peptide bonds has been found to be 0.8 ± 0.1. The significance of the results for the evolutionary theory of S. W. Fox is mentioned.     

Dynamic viscoelastic properties of glycinin and β-conglycinin gels from soybeans

The effects of heating temperature on gel properties and conformational changes were investigated in glycinin and β-conglycinin gels using Theological and Fourier transform ir (FTIR) methods. Solutions of 15 wt % glycinin or β-conglycinin in 35 mM phosphate buffer at pH 7.6 were heated at various temperatures for 30 min and rheological properties were measured at 20°C. The storage modulus G′ as a function of frequency changed from a monotonical decrease with decreasing frequency to a plateau in the range from 0.0018 to 40 Hz by heating at temperatures higher than 80°C for glycinin and 65°C for β-conglycinin. A band at 1618 cm^?1 (associated with the β-sheet structure) on ir spectra increased with the formation of heat-induced gels. The value of the storage modulus G′ correlated well with the increase in absorbance at 1618 cm^?1. These results suggest that the formation of a β-sheet structure may be closely related to the value of the storage modulus G′ for heat-induced gels in soybean proteins and that heat-induced gels of glycinin and β-conglycinin are formed by cross-links with intermolecular β-sheet structures. © 1994 John Wiley & Sons, Inc.     

Interaction of poly(α-L-glutamic acid) and sodium poly(α-L-glutamate) with solvent components in water–2-chloroethanol mixtures

The preferential interaction of sodium poly(α-L -glutamate) and poly(α-L -glutamic acid) with the solvent components in water/2-chloroethanol mixtures has been determined using density-increment measurements. The degree of preferential interaction was deduced from the density increments at constant molality of 2-chloroethanol and at constant chemical potential of 2-chloroethanol. Sodium poly(α-L -glutamate) and poly(α-L -glutamic acid) are both preferentially hydrated in the whole range of solvent composition. A dehydration process occurs during the 2-chloroethanol-induced coil-to-helix transition of sodium poly(α-L -glutamate). This dehydration process was attributed to the release of some moles of water from the neighborhood of the peptide bond during the nucleation of the helix. After the conformational transition, sodium poly(α-L -glutamate) is solvated by one 2-chloroethanol molecule. The location of water and 2-chloroethanol molecules in the different parts of the residue (more polar and less polar portions) is also discussed.     

Absolute configuration determination and conformational analysis of (−)‐(3S,6S)‐3α,6β‐diacetoxytropane using vibrational circular dichroism and DFT techniques

The absolute configuration of semisynthetic (?)‐3α,6β‐acetoxytropane 1 , prepared from (?)‐6β‐hydroxyhyoscyamine 2 , has been determined using vibrational circular dichroism (VCD) spectroscopy. The vibrational spectra (IR and VCD) were calculated using DFT at the B3LYP/DGDZVP level of theory for the eight more stable conformers which account for 99.97% of the total relative abundance in the first 10 kcal/mol range. The calculated VCD spectra of all considered conformations showed two distinctive spectral ranges, one between 1300 and 1200 cm^?1, and the other one in the 1150–950 cm^?1 region. When compared with the experimental VCD spectrum, the first spectral region confirmed the calculated conformational preferences, whereas the second region showed little change with conformation, thus allowing the determination of the absolute configuration of 1 as (3S,6S)‐3α,6β‐diacetoxytropane. Also, the bands in the second region showed similarities between 1 and 2 in both the experimental and calculated VCD spectra, suggesting that these bands are mainly related to the absolute configuration of the rigid tropane ring system, since they show conformational independency, no variations with the nature of the substituent, and are composed by closely related vibrational modes. Chirality, 2010. © 2009 Wiley‐Liss, Inc.     

Preferred conformation of peptides from Cα,α-symmetrically disubstituted glycines: Aromatic residues

The conformational preference of C^α,α-diphenylglycinc (Døg) and C^α,α-dibenzylglycine (Dbz) residues was assessed in selected derivatives and small peptides by conformational energy computations, ir absorption, ¹H-nmr, and x-ray diffraction. Conformational energy computations on the two monopeptides strongly support the view that these C^α,α-symmetrically disubstituted glycines are conformationally restricted and that their minimum energy conformation falls in the fully extended (C₅) region. The results of the theoretical analyses appear to be in agreement with the solution and crystal-state structural propensities of three derivatives and seven di-and tripeptides.     

Rheological properties and conformational states of β-conglycinin gels at acidic pH

The heat-induced gelation of β-conglycinin was investigated by dynamic viscoelastic measurements as a function of pH. At pH values below 5.5–6.0, the storage modulus G′ rapidly increased with decreasing pH. The conformational states of both sols and gels of β-conglycinin were investigated by Fourier transform ir (FTIR) and by differential scanning calorimetry (DSC). The degree of protonation of the carboxyl groups of β-conglycinin, when examined by FTIR indicated that, as would be expected, the degree of protonation increased with decreasing pH below pH 6.0. DSC measurements suggest that β-conglycinin tends toward thermal denaturation with decreasing pH (below pH 6.0). Second-derivative FTIR spectra for β-conglycinin gels show that a band at 1620 cm^?1 (associated with exposed β-strands) develops with decreasing pH. The results suggest that β-conglycinin undergoes denaturation with increasing protonation of its carboxyl groups, resulting in an increase in the amount of exposed β-strands. The exposed β-strands then intermolecularly bond to form gel networks. This process is promoted with decreasing pH, and as a result, rigid gels form at acidic pH values. © 1994 John Wiley & Sons, Inc.     

Far-infrared spectra of poly(-α-amino acids) with basic alkyl group side chains

Far-infrared spectra in the region from 700 to 60 cm^?1 have been measured for the α-helix structures of poly(L -α-amino-n-butyric acid), poly-L -norvaline, poly-L -norleucine, and poly-L -leucine and for the β-form structures of poly(L -α-amino-n-butyric acid), poly-L -valine, poly(DL -amino-n-butyric acid), poly-DL -norvaline, and poly-DL -norleucine. The changes of the spectra on N-deuteration have been measured in the region between 700 and 400 cm^?1. It is concluded that, the α-helix has characteristic bauds near 690, 650, 610, 380, 150, and 100 cm^?1, and that the β-form has characteristic bands near 700, 240, and 120 cm^?1. The main-chain vibrations in the region from 600 to 200 cm^?1 are strongly coupled with the side-chain deformation vibrations.     

Conformation of poly(γ‐glutamic acid) in aqueous solution

Local conformation and overall conformation of poly(γ‐DL‐glutamic acid) (PγDLGA) and poly(γ‐L‐glutamic acid) (PγLGA) in aqueous solution was studied as a function of degree of ionization ε by ¹H‐NMR, circular dichroism, and potentiometric titration. It was clarified that their local conformation is represented by random coil over an entire ε range and their overall conformation is represented by expanded random‐coil in a range of ε > ε^*, where ε^* is about 0.3, 0.35, 0.45, and 0.5 for added‐salt concentration of 0.02M, 0.05M, 0.1M, and 0.2M, respectively. In a range of ε < ε^*, however, ε dependence of their overall conformation is significantly differentiated from each other. PγDLGA tends to aggregate intramolecularly and/or intermolecularly with decreasing ε, but PγLGA still behaves as expanded random‐coil. It is speculated that spatial arrangement of adjacent carboxyl groups along the backbone chain essentially affects the overall conformation of PγGA in acidic media. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 191–198, 2016.     

Characterization of β-bend ribbon spiral forming peptides using electronic and vibrational CD

Terminally blocked (L-Pro-Aib)_n and Aib-(L-Pro-Aib)_n sequential oligopeptides are known to form right-handed β-bend ribbon spirals under a variety of experimental conditions. Here we describe the results of a complete CD and ir characterization of this subtype of 3₁₀-helical structure. The electronic CD spectra were obtained in solvents of different polarity in the 260-180 nm region. The vibrational CD and Fourier transform ir (FTIR) spectra were measured in deuterochloroform solution in the amide I and amide II (1750-1500 cm^?1) regions. The critical chain length for full development of the β-bend ribbon spiral structure is found to be five to six residues. Spectral effects related to concentration-induced stabilization of the structures of the longer peptides were seen in the resolution-enhanced FTIR spectra. Comparison to previous studies of (Aib)_n and (Pro)_n oligomers indicate that the low frequency of the amide I mode is due to the interaction of secondary and tertiary amide bonds and not to a strong difference in conformation from a regular 3₁₀-helix. © 1995 John Wiley & Sons, Inc.     

Characterization of β-turns in cyclic hexapeptides in solution by fourier transform IR spectroscopy

The β-turn represents a structural element frequently encountered in globular proteins. However, in spite of various theoretical and experimental studies the ir signature bands of pure β-turns are still not established beyond doubt. Although considerable information exists now on the ir spectra of β-helical and β-sheet structures, the lack of knowledge concerning turn structures in general, and that of β-turns in particular, presents a major uncertainty in the estimation of global protein secondary structures from ir spectroscopic data. To obtain more specific information about the characteristic amide bands in β-turns, we report herein an ir spectroscopic analysis of a series of five cyclic pseudo-hexapeptides known to form β-turns from previous CD and nmr studies [A. Perczel, M. Hollósi, B. M. Foxman, and G. D. Fasman (1991) Journal of the American Chemical Society, Volume 113, pp. 9772-9784 ]. We show here that in these cyclic peptides the amide groups involved in β-turns that comprise a ten-membered hydrogen-bonded ring (and represent the first H-bond pair in a β-sheet), give rise to characteristic amide I bands in the range 1638–1646 cm^?1, with the exact position depending on the solvent and the nature of the side-chain substituents. © 1993 John Wiley & Sons, Inc.     

A potentiometric and CD investigation on the conformational properties of poly (L-p-aminophenylalanine) in aqueous solution

The conformational properties of poly(L -p-aminophenylalanine) have been investigated by potentiometric and circular dichroism (CD) techniques. It has been found that the polymer in the charge-free state can assume two ordered conformations, depending upon temperature conditions. At room temperature the polymer assumes the right-handed helical form by described Goodman and Peggion.¹ At temperatures higher than 40°C a new ordered conformation has been found, whose slow rate of formation and ir absorption properties are typical of the β-structure. The thermodynamic parameters relative to the coil-β transition, determined by potentiometric titration techniques, revealed that the thermodynamic stability of the β-structure is mainly due to enthalpic factors. The formation of this structure is unfavored on a kinetic basis.     

Conformational studies of sequential polypeptides containing lysine and tyrosine

The conformation of three sequential copolypeptides, poly(L -tyrosyl-L -lysine), poly(L -tyrosyl-L -lysyl-L -lysine), and poly[L -tyrosyl-(L -lysyl)₂-L -lysine] have been studied by a variety of techniques, including CD, ir spectroscopy, analytical ultracentrifugation, and x-ray diffraction. Depending upon the pH and sovent composition, poly(L -tyrosyl-L lysyl-L -lysine) and poly [L -tyrosyl-(L lysyl)₂-L -lysine] can adopt either the α-helical or random-coil conformation, while poly(L -tyrosyl-L -lysine) forms either inter- or intramolecular β-structures.     

CD and Fourier transform ir spectroscopic studies of peptides. II. Detection of β-turns in linear peptides

Comparative CD and Fourier transform ir (FTIR) spectroscopic data on N-Boc protected linear peptides with or without the (Pro-Gly) β-turn motif (e.g., Boc-Tyr-Pro-Gly-Phe-Leu-OH and Boc-Tyr-Gly-Pro-Phe-Leu-OH) are reported herein. The CD spectra, reflecting both backbone and aromatic contributions, were not found to be characteristic of the presence of β-turns. In the amide I region of the FTIR spectra, analyzed by self-deconvolution and curve-fitting methods, the β-turn band shewed up between 1639 and 1633 cm^?1 in trifluoroethanol (TFE) but only for models containing the (Pro-Gly) core. This band war-also present in the spectra in chloroform but absent in dimethylsulfoxide. These findings, in agreement with recent ir data on cyclic models and 3₁₀-helical polypeptides and protein in D₂O [see S. J. Prestrelski, D. M. Byler, and M. P. Thompson (1991), International Journal of Peptide and Protein Research, Vol. 37, pp. 508–512; H. H. Mantsch, A. Perczel. M. Hollósi, and G. D. Fasman (1992), FASEB Journal, Vol. 6, p. A341; H. H. Mantsch. A. Perczel, M. Hollósi, and G. Fasman (1992), Biopolymers. Vol. 33, pp. 201–207; S. M. Miick, G. V. Martinez, W. R. Fiori, A. P. Tedd, and G. L. Millhauser (1992). Nature, Vol. 359, pp. 653–655], suggest that the amide I band, with a major contribution from the acceptor C ? O of the 1 ← 4 intramolecular H bond of β-turns, appears near or below 1640 cm^?1, rather than above 1660 cm^?1. In TFE, bands between 1670 and 1660 cm^?1 are mainly due to “free” carbonyls, that is, C ? O's of amides that are solvated but not involved in the characteristic H bonds of periodic secondary structures or β-turns. © 1994 John Wiley & Sons, Inc.     

Sodium counterion activity of poly(S-carboxymethyl-L-cysteine) and the beta–random-coil transition

Sodium ion activity was measured using a Na-glass electrode in a solution of poly(S-carboxymethyl-L -cysteine) with no added salt at various degrees of neutralization and various concentrations for samples of different molecular weights. The conformational change from random coil to the β-structure was detected from the activity coefficient of counterions, as well as from CD. At a constant degree of neutralization, the activity coefficient is insensitive to a concentration change not only in the random-coil state, but also in the range of conformational change if the concentration is below about 3 × 10^?2 monomolal. At high concentrations of about 5 × 10^?2 monomolal, however, the activity coefficient becomes low, probably due to the occurrence of the stacking of the pleated sheets.     

Theoretical π-π* absorption and circular dichroic spectra of polypeptide β-structures

Absorption and circular dichroic (CD) spectra of the π-π* transition near 200 nm are calculated for poly(Gly), poly(Ala), poly(Abu), and poly(Val) in the β_P (paralle) and β_A (antiparallel) pleated-sheet structures using the dipole interaction model and including interactions among all atoms; optical parameters were obtained from previous studies of related molecules. Most of the calculations are for structures with one or three chains of six residues each. The oscillator strength and splitting of the π-π* modes are found to be affected only to a small extent by variations in side-chain structure and conformation, whereas the CD spectrum is very sensitive to these variations. Poly(Gly) and poly(Ala) β-structures in uniform, planar lattices do not show sufficient rotational strength to account for observed CD spectra. Poly(Abu) and poly(Val) β-structures in uniform, planar lattices show rotational strengths comparable to experiment when χ¹ is near ?60° for β_A-structures or in a broad range near 140° for β_P-structures. Poly(Ala) in uniformly twisted β_A- and β_P-structures or in irregular β_A-structures corresponding to regions of the crystal structure of concanavalin A also show enhanced rotational strengths in the principal π-π* CD band. Absorption and CD spectra calculated for poly(Abu) in uniform β_A- and β_P-structures are compared with experimental data on poly(Lys) in the β-form, assuming side-chain conformations in Abu that maximize the intensity of the principal CD band. The calculations for the β_A-form show the better agreement with experiment for both types of spectra.     

Conformation of poly-L-tyrosine in aqueous solution

The conformational transition of poly-L -tyrosine in 0.1M KCl was investigated by ORD and infrared spectroscopy, potentiometric titration, and sedimentation velocity experiments. It is shown that the fully ordered conformer is obtained by slow titration of the random coil with 0.1N HCl at 25°C. The charge-induced transition, at variance with other poly-α-amino acids, is completed in a narrow range of α. An aggregation process was detected both by potentiometric titration and sedimentation velocity. The polyamino acid aggregates around α = 0.7 at 25°C when the conformational transition is almost complete. Infrared spectra, in the region of the amide I band (1650 cm^?1) showed that the transition is a random coil → antiparallel β one. Evidence exists that the form is of the intramolecular type. The foregoing interpretations of ORD and CD spectra in terms of the α-helix conformation are discussed.     

Conformation dependence of the CαDα stretch mode in peptides. II. Explicitly hydrated alanine peptide structures

Our previous studies of the potential utility of the C^αD^α stretch frequency, ν(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923–10924; 2007, 111, 5300–5303) dealt with the spectroscopic characteristics of isolated alanine peptides with α_R, β, and polyproline II structures. We have now extended these ab initio calculations to include various explicit‐water environments interacting with such conformers. We find that the structure‐discriminating feature of this technique is in fact enhanced as a result of the conformation‐specific interactions of the bonding waters, in part due to our finding (Mirkin and Krimm, J Phys Chem B 2008, 112, 15268) that C^α? D^α…O(water) hydrogen bonds can be present in addition to those expected between water and the CO and NH of the peptide groups. In fact, ν(CD) is hardly affected by the latter bonding but can be shifted by up to 70 cm^?1 by the former hydrogen bonds. We also discuss the factors that will have to be considered in developing the molecular dynamics (MD) treatment needed to satisfactorily take account of the influence of outer water layers on the structure of the first‐layer water molecules that hydrogen bond to the peptide backbone. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 791–800, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com