Poly(L-alanine): investigation of alpha-helix and beta-sheet forms by low-temperature specific heat measurements (1.5-20 degrees K)

For an ideal one-dimensional solid, the low-temperature specific heat, C, is proportional to temperature T¹, for an ideal two-dimensional solid C is proportional to T². We have observed such one- and two-dimensional behavior in alpha- and beta-poly(L -alanine) in the temperature range 1.5–20°K (also intermixed with a three-dimensional behavior). A specific heat anomaly has also been observed. These measurements are important in evaluating the effective elastic constants, including hydrogen bonding, of the biopolymers. They also provide essential information for vibrational theories of poly(L -alanine), which up until now have been based on high-energy data.     

Estimation of the circular dichroism exhibited by statistical coils of poly(L-alanine) and unionized poly(L-lysine) in water

The circular dichroism of Ac-(Ala)_x-OMe and H-Lys-(Lys)_x-OH with x = 1, 2, 3, and 4 has been measured in aqueous solutions. The oligomers with x = 4 show similar circular dichroism spectra in water when the lysyl amino groups are protonated, and they respond in similar fashion to heating and to sodium perchlorate. Both oligomers at 15°C exhibit a positive circular dichroism band at 217–218 nm, which is eliminated by the isothermal addition of 4 M sodium perchlorate or by heating. The positive circular dichroism of the lysine oligomer is also eliminated when the pH is elevated to deprotonate the amino groups. Positive circular dichroism is still observed for Ac-(Ala)₄-OMe at elevated pH. Circular dichroism spectra have been estimated for poly(L -alanine) and poly(L -lysine) as statistical coils under the above conditions, based on the trends established with the oligomers. Poly(L -lysine) and poly(L -alanine) are predicted to exhibit similar circular dichroism behavior in aqueous solution so long as the lysyl amino groups are protonated. The circular dichroism of the statistical coil of poly(L -lysine), but not poly(L -alanine), is predicted to change when the pH is elevated sufficiently to deprotonate the lysyl amino groups. These results suggest that the unionized lysyl side chains participate in interactions that are not available to poly(L -alanine). Hydrophobic interactions may occur between the unionized lysyl side chains. Protonation of the lysyl amino groups is proposed to disrupt these interactions, causing poly(L -alanine) and protonated poly(L -lysine) to have similar circular dichroism properties.     

Synthesis and conformational study of poly(N delta-carbobenzoxy, N delta-benzyl-L-ornithine) and poly(N delta-benzyl-L-ornithine)

Poly(N^δ-carbobenzoxy, N^δ-benzyl-L -ornithine) (PCBLO) was prepared by the standard NCA method. PCBLO was converted into poly(N^δ-benzyl-L -ornithine) (PBLO) through decarbobenzoxylation with hydrogen bromide. The monomer N^δ-benzyl-L -ornithine was synthesized by reacting L -ornithine with benzaldehyde, followed by hydrogenation. The conformation of the two polypeptides was studied by optical rotatory dispersion and circular dichroism. PCBLO forms a right-handed helix in helix-promoting solvents. In mixed solvents of chloroform and dichloroacetic acid (DCA) it undergoes a sharp helix–coil transition at 12% (v/v) DCA at 25°C, as compared with 36% for poly(N^δ-carbobenzoxy-L -ornithine) (PCLO). Like PCLO, the helix–coil transition is “inverse,” that is, high temperature favors the helical form. PBLO is soluble in water at pH below 7 and has a “coiled” conformation. In 88% (v/v) 1-propanol above pH (apparent) 9.6 it is completely helical. In 50% 1-propanol the transition pH (apparent) is about 7.4; this compares with a pH_tr of about 10 for poly-L -ornithine in the same solvent.     

13C-nmr chemical shift and conformation of L-alanine residues incorporated into poly(β-benzyl L-aspartate) in the solid state

¹³C-nmr spectra of poly(β-benzyl L-aspartate) containing ¹³C-enriched [3-¹³C]L -alanine residues in the solid state were recorded by the cross polarization–magic angle spinning method, in order to elucidate the conformation-dependent ¹³C chemical shifts of L -alanine residues taking various conformations such as the antiparallel β-sheet, the right-handed α-helix, the left-handed α-helix, and the left-handed ω-helix forms obtained by appropriate treatment. The latter two conformations for L -alanine residues are achieved when L -alanine residues are incorporated into poly(β-benzyl L -aspartate). We found that the alanine C_β carbon show significant ¹³C chemical shift displacement depending on conformational change, and gave the ¹³C chemical shift values at about 17 ppm for the left-handed ω-helix, 14 ppm for the left-handed α-helix, 15.5 ppm for the right-handed α-helix, and 21.0 ppm for the antiparallel β-sheet relative to tetramethylsilane.     

Low-frequency dynamics of solid poly(L-alanine) from Raman spectroscopy

Raman modes from amorphous α-helical poly(L -alanine) in the low-frequency region < 150 cm^?1 have been observed and assignments and values compared with mode-analysis calculations. The temperature dependence of the complete Raman spectrum of α-poly(L -Ala) is also reported.     

Polypeptides. 53. Water-soluble copolypeptides of L-glutamic acid, L-lysine, and L-alanine

The synthesis and some of the physical-chemical properties of tricopolymers of L -glutamic acid, L -lysine, and L -alanine are reported here. The molar ratios of the glutamyl: lysyl: alanyl residues were 1:1:X or 3:2:X, where the alanyl content X was increased in regular steps. The α-helix content calculated from the optical rotatory dispersion of the polypeptides is compared with a predicted helix content estimated from the composition of the polymers and the known behavior of the homopolypeptides at pH 3, 8, and 12. At pH 3 copolypeptides containing 20 mole-% or more alanine exhibit a helix content equal to the sum of their alanyl and glutamyl residue contents. At pH 8 the helix content equals the alanyl content when the latter was 40 mole-% or higher; at lower alanyl contents the electrostatic interaction between charged glutamyl and lysyl residues makes some contribution. At pH 12 the amount of helix observed is proportional to the mole ratio of alanine residues present in the polymer. The helix content of a tricopolymer containing 1:1:3 mole ratios of glutamyl: lysyl: alanyl residues was determined in solutions of lithium bromide and in urea solutions. Both reagents led to a decrease in helix content at pH 3 and 8 to a minimum of approximately 20% helix in 8M urea or 5.5M LiBr. The helix–random chain transition curves at pH 3 and 8 are parallel when the urea concentration is varied, but differ in shape when the lithium bromide concentration is varied at pH 3 and 8. The mode of action of these two “denaturing” reagents may thus be different. Heating the same tricopolypeptide at pH 3 or 8 from 5 to 80°C. also led to a helix–random chain transition centered at approximately 45°C.     

Laser-Raman spectroscopy of biomolecules. XI. Conformational study of poly(L-valine) and copolymers of L-valine and L-alanine

Raman spectroscopic studies have been carried out on polymers of L -valine ranging in degree of polymerization (DP) from 2 to 930. The spectrum of the hexapeptide (DP = 6) is closely similar over the entire range 40–1750 cm^?1 to those of polymers with much higher DP, and the structure is clearly shown to be that of the antiparallel pleated sheet (β-structure) by the amide I and III frequencies. The formation of a little α-helical structure occurs in polymers with DP above 500, although the amount does not appear to be a linear function of DP. The α-helical structure is unstable and readily destroyed in samples cast from trifluoroacetic acid solution. It is stabilized by the incorporation of L -alanine, a strong helix-former; polymers of the latter may in turn be forced into a α-structure in copolymers sufficiently rich in L -valine.     

Susceptibility behaviour and specific heat anomaly in single crystals of alanine and valine

Magnetization of single crystals ofD-,L-alanine andD-valine were measured as a function of temperature using the SQUID magnetometer. An obvious lambda transition at 270 ± 1 K was shown in the specific heat measurement of alanine and valine enantiomers by differential scanning calorimetry (DSC). Magnetic transition temperature seems coincident with that of lambda transition. Temperature dependence of the X-ray powder diffraction forD-valine showed no crystal lattice change under the temperature cooling down from 293 K to 123 K. We propose that the difference of theX T curve between theD-alanine andL-alanine is attributable to the variation of intramolecular geometry of chirality density in the presence of an external magnetic field. The chirality characteristics of alanine and valine enantiomers by the specific heat and susceptibility behaviour are discussed.     

Ab initio-based vibrational analysis of α-poly(L-alanine)

Polarized ir and Raman spectra have been obtained on oriented films of α-helical poly(L -alanine) (α-PLA) and its N-deuterated derivative. These improved spectra permit a more complete assignment of observed bands to A-, E₁-, and E₂-species modes. A new empirical force field has been refined, based on ab initio force fields of N-methylacetamide and L -alanyl-L -alanine, which reproduces observed frequencies above 200 cm⁻¹ to less than 5 cm⁻¹. A new transition dipole coupling treatment avoids the weak coupling and perturbation approximations, and can now account for the newly observed and reassigned amide I (E₂) mode. As a result of this improved force field, several other observed bands have also been reassigned. © 1998 John Wiley & Sons, Inc. Biopoly 46: 283–317, 1998     

Ir spectra and conformational behavior of N-acetyl-(glycine,L-alanine,L-leucine)-N′-methylamides in chloroform

NH stretching bands of N-acetyl-(glycine, L -alanine, L -leucine)-N′-methylamides in dilute chloroform solution have shown that these dipeptides are present as a mixture of intramolecularly hydrogen-bonded five-membered ring species and nonhydrogen bonded species. Integrated absorption intensity measurements revealed that the concentration of the intramolecularly hydrogen bonded species decreased from 62% in glycine to 35% in the L -leucine derivatives.     

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.     

Relaxation processes on a picosecond time scale in hemoglobin and poly(L-alanine) observed by millimeter-wave spectroscopy

Broadband measurements of the millimeter-wave and far-ir absorption (10–10⁴ GHz) of lyophilized hemoglobin are reported. Additionally, the absorption of poly(L -alanine) and crystalline L -alanine at 70 GHz was measured for comparison. All measurements were extended over the temperature range from liquid helium to room temperature. For the millimeter range, this was attained by using the novel oversized-cavity technique. It was found that the millimeter-wave absorption of the materials increased nearly exponentially with temperature and increased as ν^1.2–ν² with frequency. The far-ir absorption of hemoglobin showed broadbands with almost no temperature dependence. The frequency and temperature dependence of the millimeter-wave absorption is quantitatively described as due to three distinct relaxation processes on a picosecond time scale occurring in asymmetric double-well potentials. These processes are most probably assigned to the NH ?OC hydrogen bonds of the peptide backbone.     

Fluctuations and mechanical strength of α-helices of polyglycine and poly(L-alanine)

By using the static correlations of fluctuations in the dihedral angles of the α-helices of polyglycine and poly(L -alanine) calculated previously, geometrical fluctuations of a section (consisting of up to 18 peptide units) of the α-helices of infinite length are calculated. These fluctuations are found to differ in some respects (e.g., the dependence of amplitudes on the length of section) from those of a circular rod made of homogeneous continuous material. However, the moduli of the mechanical strengths (tensile Young's modulus, bending Young's modulus, and the shear modulus) of a circular rod are calculated, whose geometrical fluctuations are approximately equal to the fluctuations of a section consisting of 18 peptide units. They are of the order of 10¹¹ dyn/cm². The tensile rigidity, flexural rigidity, and torsional rigidity are calculated to be 1.20 × 10^?3 dyn, 2.46 × 10^?19 dyn·cm² and 1.79 × 10^?19 dyn·cm² for polyglycine, and 1.96 × 10^?3 dyn, 4.05 × 10^?19 dyn·cm² and 3.28 × 10^?19 dyn·cm² for poly(L -alanine), respectively.     

Poly(L-alanine): specific heat measurements at low temperatures (1.8-20 degrees K) and one-dimensionality

Low-temperature specific heat measurements have been made on random poly(L -alanine) (Pilot). The effective one-dimensional (intra-molecular polymeric) Debye temperature is 323°K, and the corresponding three-dimensional temperature is 54°K. An anomaly, similar to that seen in polyethylene and other high polymers, is observed. The method will be a useful tool for the study of low-frequency vibrations in polypeptides.     

Inhibitory Effect of 8-(N,N-Diethylamino)octyl-3, 4, 5-Trimethoxybenzoate Hydrochloride (TMB-8) on Germination of Bacillus cereus T Spores

Effect of 8-(N,N-diethylamino)octyl-3, 4, 5 - trimethoxybenzoate hydrochloride (TMB-8), a calcium antagonist, on germination of Bacillus cereus T spores induced by L -alanine and inosine was investigated. TMB-8 had no effect on the germination of heat-activated spores, whereas it inhibited that of nonactivated spores. The TMB-8 inhibitory effect was antagonized competitively by inosine, but not by L -alanine. Addition of Ca²⁺ reversed the inhibitory effect of TMB-8 in a dose-related fashion. Based on the results, a role of inosine and a site(s) for inhibitory action of TMB-8 in the process leading to the germination of nonactivated spores were discussed.     

Heat capacities of solid poly(amino acids). I. Polyglycine,poly(L-alanine), and poly(L-valine)

Heat capacities of polyglycine, poly(L -alanine), and poly(L -valine) were analyzed using approximate group vibrations and fitting of the skeletal vibrations to a two-parameter (Θ₁, Θ₃) Tarasov function. New experimental data were measured by differential scanning calorimetry in the temperature range of 230–390 K. Good agreement between our experimental data and the calculated data was observed for all three poly(amino acids). Previous investigations showed agreement between calculation and reported experimental data for only limited low temperature ranges. At higher temperatures, discrepancies of up to 55% existed between experiment and calculation. The cause of this discrepancy must be assumed to be experimental error. Recommended experimental data are revised on the basis of this investigation. Computed heat capacities are available for the three biopolymers in the solid state from 0 to 1000 K.     

Different physiological functions of free D- and L-alanine in three body parts of the intertidal sipunculid Phascolosoma arcuatum

Free D- and L-alanine contents were comparable in the body wall and introvert cum retractor muscles of Phascolosoma arcuatum. In contrast, the content of free D-alanine in the internal organs was twice that of free L-alanine. Since alanine aminotrans-ferase from P. arcuatum was L-alanine specific, D-alanine appeared to be synthesized from L-alanine through the action of alanine racemase. Alanine racemase activity was higher in the D-alanine-forming direction in the three body parts of P. arcuatum. In addition, the ratio of DL/LD racemase activity in the internal organs was the lowest among the body parts studied. These results indicate that free D-alanine might be of lesser importance than the free D-isomer to the internal organs as compared to the body wall and introvert cum retractor muscles. Indeed, L-alanine inhibited pyruvate kinase from the body wall and introvert cum retractor muscles but had no effect on the pyruvate kinase from the internal organs. Furthermore, the activity of alanopine dehydrogenase present in the internal organs was significantly lower than those of the body wall and introvert cum retractor muscles. L-Alanine was an essential substrate for alanopine formation in the body wall and introvert cum retractor muscles during hypoxia since alanopine dehydrogenases from these body parts were L-alanine specific. When P. arcuatum was confronted with hypo-osmotic stress, the free D-alanine/total free alanine ratio in the internal organs increased approximately from 0.6 to 0.8 as the total free alanine content decreased. In comparison, those ratios in the body wall and introvert cum retractor muscles remained relatively constant. It was concluded that D- and D-alanine had different physiological functions in the three body parts of P. arcuatum.Abbreviations ADP adenosine-5-diphosphate - ADH alanopine dehydrogenase - ALT alanine aminotransferase - AOD amino acid oxidase - BW body wall - EDTA ethylenediaminetetra-acetic acid - EGT A ethylene glyco-bis (-aminoethyl ether) - N,N,N,N tetra-acetic acid - ICRM introvert cum retractor muscles - IO internal organs - I ₅₀ inhibitor concentration producing 50% inhibition of enzyme activity - -KG -ketoglutarate - LDH lactate dehydrogenase - NAD nicotinamide adenine dinucleotide - NADH nicotinamide adenine dinucleotide (reduced form) - PEP phosphoenolpy-ruvate - PEPCK phosphoenolpyruvate carboxykinase - PK pyruvate kinase - PMSF phenylmethylsulphonyl fluoride - SE standard error - SW sea water - TCA trichloroacetic acid     

Diversity of spore germination in response to inosine and L-alanine and its interaction with NaCl and pH in the Bacillus cereus group

Aims: Our aim was to assess the diversity of the nutrient germination response of Bacillus cereus spores. Methods and Results: B. cereus spore germination was monitored by decrease in optical density using a Bioscreen C analyser in response to the major germinant substances inosine and l -alanine. Spores of a set of 12 strains taken to illustrate the diversity of the B. cereus group showed ranging germination capacities. Two strains never germinated in the presence of l -alanine, at any of the germinant concentrations tested. Both the extent and rate of spore germination were affected by low pH and high NaCl concentration, but differently according to the strain. Conclusions: A broad diversity was observed in nutrient-triggered spore germination among the members of the B. cereus group. Spore germination of some strains occurred at low concentrations of inosine or l -alanine, suggesting high receptor sensitivity to germinants. The activity of these receptors was also affected by pH or high NaCl concentration. Significance and Impact of the Study: The greater ability of some strains to germinate in response to l -alanine and inosine is one criterion among others for B. cereus strain selection in food processing or storage studies, before confirmation in complex food or laboratory media. The diversity in response to germinants found among the B. cereus strains suggests a differential expression and (or) absence of some germination genes involved in the response, mainly to l -alanine.     

Calorimetric measurement of enthalpy change in the isothermal helix-coil transition of poly(L-ornithine) in aqueous solution.

The enthalpy change associated with the isothermal pH-induced uncharged coil-to-helix transition ΔH_h° in poly(L -ornithine) in 0.1 N KCl has been determnined calorimetrically to be ?1530 ± 210 and ?1270 ± 530 cal/mol at 10° and 25°C, respectively. Titration data provided information about the state of charge of the polymer in the calorimetric experiments, and optical rotatory dispersion data about its conformation. In order to compute ΔH_h°, the observed calorimetric heat was corrected for the heat of breaking the sample cell, the heat of dilution of HCl, the heat of neutralization of the OH^? ion, and the heat of ionization of the δ-amino group in the random coil. The latter was obtained from similar calorimetric measurements on poly(D ,L -ornithine). Since it was discovered that poly(L -ornithine) undergoes chain cleavage at high pH, the calorimetric measurements were carried out under conditions where no degradation occurred. From the thermally induced uncharged helix–coil transition curve for poly(L -ornithine) at pH 11.68 in 0.1 N KCl in the 0°–40°C region, the transition temperature T_tr and the quantity (?θ_h/?T)_Ttr have been obtained. From these values, together with the measured values of ΔH_h°, the changes in the standard free energy ΔG_h° and entropy ΔG_h°, associated with the uncharged coil-to-helix transition at 10°C have been calculated to be ?33 cal/mol and ?5.3 cal/mol deg, respectively. The value of the Zimm–Bragg helix–coil stability constant σ has been calculated to be 1.4 × 10^?2 and the value of s calculated to be 1.06 at 10°C, and between 0.60 and 0.92 at 25°C.     

Conformational aspects of polypeptides. XVIII. Conformational studies of oligopeptides derived from L-alanine

The conformations of oligopeptides derived from L -alanine and co-oligomers of L -alanine with γ-methyl-L -glutamate were studied in several solvents via optical rotation and far-ultraviolet spectroscopy. Calculated values for optical rotation based on model compounds were compared with experimental values for the oligomers. In trifluoroacetic and dichloroacetic acids, the oligomers and co-oligomers exhibit rotations in close agreement with predicted values based on model compounds. Thus, in these solvents only nonhelical conformations exist. In trifluoroethanol, the experimental points of molar rotation for the pentamer and larger oligomers no longer follow the predicted values. In addition, the benzyloxycarbonyl and acetyl cononamers show b₀ values of about ?150, which demonstrates the presence of stable helical forms for these peptides. We also examined the molar extinction coefficients of oligopeptides in the 190 mμ region and determined the values for nonhelical peptide groups. The molar extinction coefficients per amide bond for the benzyloxycarbonyl and acetyl cononamers show extensive hypo-chromism, once again indicating the presence of stable helices for these compounds in trifluoroethanol.