Interchain heterogeneity in 2-hydroxyethylglutamine-l-valine random copolymers

Solid state circular dichroism (c.d.) and infrared (i.r.) studies of water soluble and insoluble fractions of poly(hydroxyethylglutamine-valine) random copolymers, prepared from parent γ-benzyl l-glutamate valine copolymers, show that interchain conformational heterogeneity with interchain compositional heterogeneity is present when the respective N-carboxyanhydrides are copolymerized in dioxan or benzene/methylene chloride. Use of previously determined reactivity ratios for the aforementioned copolymer systems permits the determination of the variation of the average copolymer composition, $\text{f}$_G, with conversion. The experimentally determined average copolymer composition.$\text{f}$_G for the use of the respective reactivity ratios and the copolymer hydroxyethylglutamine, valine are predicted by the use of the respective reactivity ratios and the copolymer composition equation. As the valine content of the copolymer chains in the fractions increases, the expected increase in β-sheet contribution is seen. Comparison of the experimentally determined solid state c.d. spectra with Greenfield and Fasman's computer generated c.d. spectra for varying amounts of α-helix, β-sheet and random structures, shows that the water insoluble fractions with their increased valine contents have a greater contribution of β-sheet structure than the respective soluble fractions.     

Secondary structure of peptides. 4: 13C-Nmr CP/MAS investigation of solid oligo- and poly(L-alanines)

Primary and tertiary amine-initiated polymerizations of L -alanine-N-carboxyanhydride (L -Ala-NCA) were conducted at 20 or 100°C in a variety of solvents. The 75.5-MHz ¹³C-nmr CP/MAS spectra of the resulting poly(L -alanines) revealed that all samples contain both α-helix and pleated-sheet structures. Depending on the reaction conditions the α-helix content varied between ca. 1 and 99%. Reprecipitation from aprotic nonsolvents does not change the α-helix/β-sheet ratio, indicating that this ratio is thermodynamically controlled. Since relatively large amounts of oligopeptides of degree of polymerization (DP ) 4–6 can be extracted by means of acetic acid, it is concluded that (a) most poly(L -alanines) possess a bimodal molecular weight distribution, (b) the oligopeptide fraction with DP ? 11 is responsible for the β-sheet fraction of all samples, and (c) the two-stage crystal growth proposed by Komoto and Kawai is not correct. Solubilizing initiators such as poly(ethylene oxide) NH₂ prevent the precipitation of oligoalanine and, thus, the formation of a β-sheet structure. ¹³C-nmr CP/MAS measurements also show that tri- and tetra-L -alanines form insoluble β-sheet structures.     

The dependence of the conformation of a (1→3)-β-D-glucan on chain-length in alkaline solution

(1→3)-β-D-Glucans of various degrees of polymerization were prepared by degradation of a gel-forming D-glucan with formic acid. The degraded D-glucans were separated into a water-soluble fraction (soluble D-glucan) and an insoluble fraction (insoluble D-glucan). Both D-glucans were further fractionated. The optical rotation including determination of the o.r.d. curves of the fractions and of the original gel-forming D-glucans was measured at various sodium hydroxide concentrations (0–5M). The results indicate that (1→3)-β-D-glucans of $\text{DP}$n below ca. 25 (the soluble D-glucan) took a disordered form in both neutral and alkaline solutions, whereas the D-glucans of higher $\text{DP}$n (the insoluble and the original D-glucans) took an ordered structure in dilute alkaline solution (0.1M). The proportion of ordered structure in the insoluble D-glucan increases with $\text{DP}$n to attain a maximum value at a $\text{DP}$n of around 200; this may be the lower limit of $\text{DP}$n to permit gel formation in neutral media. The formation of complexes with Congo Red in alkaline solutions by the soluble and the insoluble D-glucans supports the same conclusions.     

Secondary structure of peptidese: 13. 15N and 13C n.m.r. spectroscopic investigation of the helix stability of poly(l-alanine) in acidic solutions

¹⁵N-enriched poly(l-alanines) of various molecular weights were prepared from $\text{l}\text{-alanine}\text{-N-}\text{carboxyanhydride}$ (l-Ala-NCA) and their helix/coil equilibrium in trifluoroacetic acid (TFA) investigated by means of 40.5 MHz ¹⁵N nuclear magneic resonance (n.m.r.), 22.3 MHz ¹³C n.m.r. and circular dichroism (c.d.) spectra. The ¹⁵N n.m.r. spectra exhibit at least three peaks, and the dependence of their intensities on molecular weight, molecular weight distribution and temperature, as well as dynamic nuclear Overhauser effect (NOE) measurements, indicate that the high-field peak represents the helix fraction. All three spectroscopic methods agree that a helix→coil transition takes place with decreasing concentration. Furthermore, poly(l-alanines) containing d-alanine or glycine in various mole ratios were synthesizsed by copolymerizations of N-carboxyanhydrides (NCAs). The ¹⁵N n.m.r. spetra demonstrate that one d-Ala unit per 100 l-Ala units suffices to affect significantly the helix/coil equilibrium in TFA. In other words, the helix content under equilibrium conditions is highly sensitive to racemization. Furthermore, ¹³ C n.m.r. cross-polarization/magic angle spinning (CP/MAS) spectra demonstrate that the presence of d-Ala units also affects the α-helix content in the solid state.     

Silk fibroin model,poly(l-alanylglycyl-l-alanylglycyl-l-alanylglycyl-l-seryglycine)

l-Alanylglycyl-l-alanylglycyl-l-alanylglycyl-l-serylglycine and its pentachlorophenyl ester methanesulphonate have been synthesized as monomers for the preparation of silk fibroin model polypeptide. The former octapeptide was polymerized with diphenylphosphorylazide (DPPA) and triethylamine in DMSO or in HMPA—pyridine, and the latter octapeptide pentachlorophenylester was polymerized by adding triethylamine in DMSO to give poly(l-alanylglycyl-l-alanylglycyl-l-alanylglycyl-l-serylglycine). This sequential polypeptide gave a similar i.r. pattern to the crystalline part of Bombyx mori silk fibroin, which indicated antiparallel β-conformation. Dialysis of the solution of this polymer in 60%, aqueous LiBr against water gave mainly the polymer of α-form. O.r.d. measurements suggest that this polypeptide exists as a random structure in dichloroacetic acid on in 60% aqueous LiBr.     

Azobenzene-containing poly(l-glutamates). Photochromism and conformation in solution

Photochromic polypeptides having various contents of azobenzene chromophores attached to th side chains have been prepared by condensing poly(l-glutamic acid) with p-amino-azobenzene. The photochemical and thermal cis-trans isomerizations of the azo chromophores have been investigated by absorption and circular dichroism spectroscopy, and the photochromic behaviour has been related to the conformation in solution. The azopolypeptides exhibit the α-helix c.d. pattern, in trimethylphosphate. The α-helix content markedly depends on the azo content, but it is not affected by the cis or trans geometric forms of the azo side chains. Strong solvent effects by H₂O or trifluoroethanol on the extrinsic azo c.d. bands, suggest the existence, in trimethylphosphate solution, of a super-ordered secondary structure involving a regular arrangement of the side chains, on th periphery of the helical peptide backbone.     

CNDO/2 calculations of the relative stability of the goniomers in poly(dl-alanine)

Goniomers of single-stranded poly(dl-alanine) $\text{π}{}_{\mathrm{<mtext>dl</mtext>}}$ helices were treated by the semiempircal CNDO/2 MO procedure. The α_R and $\text{α}{}_{\mathrm{<mtext>dl</mtext>}}$ forms were also calculated. From the calculated total energies and partitioned energies we discuss the conformational stablity of goniomers of poly(dl-alanines). The conformational stability of the α and π forms is also compared.     

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.     

Electron diffraction study on single crystals of l-type and dl-type lecithins

An electron diffraction study was carried out on thin single micro-crystals of l-type and dl-type dipalmitoyl lecithins grown in xylene suspensions and fine net patterns were obtained and the mechanism of the thermotropic phase transitions of them was clarified.From the apparent structure of diffraction patterns in low temperature, it is confirmed that the two dimensional lattices have p mm symmetry in l-type and in dl-type lecithins. Lattice parameters from the [001] projection are $\text{d}{}_{100}\text{= 9.9}\text{A}\text{?}$ and $\text{d}{}_{010}\text{= 8.8}\text{A}\text{?}$ in l-type, and $\text{d}{}_{100}\text{= 17.2}\text{A}\text{?}$ and $\text{d}{}_{010}\text{= 8.9}\text{A}\text{?}$ in dl-type.With anisotropic variation of dimensions along a and b axes, i.e. contraction for a and expansion for b, induced by temperature rise by electron irradiation during the observation, these diffraction patterns of the lattices of l-type and dl-type were transformed into those characterized by the six diffraction spots having nearly the same spacings. Four of them are observed on slightly outer and two are slightly inner positions as compared with their mean spacings of about (4.1 Å)^?1 in l-type and about (4.2 Å)^?1 in dl-type. The changes in the patterns observed indicate that at low temperatures the hydrocarbon chains are nearly perpendicular to the layer in dl-type lipid, and tilted with a more complicated packing in l-type ones. The dimension along a in dl-type is twice as large as that in l-type.     

Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins

The packing of α-helices and β-sheets in six $\text{α}\text{β}$ proteins (e.g. flavodoxin) has been analysed. The results provide the basis for a computer algorithm to predict the tertiary structure of an $\text{α}\text{β}$ protein from its amino acid sequence and actual assignment of secondary structure.The packing of an individual α-helix against a β-sheet generally involves two adjacent ± 4 rows of non-polar residues on the α-helix at the positions i, i + 4, i + 8, i + 1, i + 5, i + 9. The pattern of interacting β-sheet residues results from the twisted nature of the sheet surface and the attendant rotation of the side-chains. At a more detailed level, four of the α-helical residues (i + 1, i + 4, i + 5 and i + 8) form a diamond that surrounds one particular β-sheet residue, generally isoleucine, leucine or valine. In general, the α-helix sits 10 Å above the sheet and lies parallel to the strand direction.The prediction follows a combinational approach. First, a list of possible β-sheet structures (10⁶ to 10¹⁴) is constructed by the generation of all β-sheet topologies and β-strand alignments. This list is reduced by constraints on topology and the location of non-polar residues to mediate the sheet/helix packing, and then rank-ordered on the extent of hydrogen bonding. This algorithm was uniformly applied to 16 $\text{α}\text{β}$ domains in 13 proteins. For every structure, one member of the reduced list was close to the crystal structure; the root-mean-square deviation between equivalenced C^α atoms averaged 5.6 Å for 100 residues. For the $\text{α}\text{β}$ proteins with pure parallel β-sheets, the total number of structures comparable to or better than the native in terms of hydrogen bonds was between 1 and 148. For proteins with mixed β-sheets, the worst case is glyceraldehyde-3-phosphate dehydrogenase, where as many as 3800 structures would have to be sampled. The evolutionary significance of these results as well as the potential use of a combinatorial approach to the protein folding problem are discussed.     

S-Adenosylmethionine synthetase isozyme patterns from rat hepatoma induced by N-2-fluorenylacetamide

Isozyme patterns of $\text{S}$-adenosylmethionine synthetase have been measured with and without dimethylsulfoxide in hepatoma of rats induced by $\text{N}$-2-fluorenylacetamide. The isozymes of α- and β-types existing in normal rat liver gradually decreased with the progress of hepatocarcinoma, and the kidney type γ-enzyme appears along with disappearance of both α- and β-enzymes. The liver from rat fetus contains a greater part of γ-type enzyme.     

Secondary structure of peptides. 18. 15N-nmr and 13C-nmr CP/MAS investigation of the primary and secondary structure of (Ala/Val) copolypeptides

Various copolypeptides were prepared by benzylamine or tertiary amine-initiated copolymerizations of alanine–N-carboxyanhydride (Ala-NCA) and valine–N-carboxyanhydride (Val-NCA). The number-average molecular weights of these copolypeptides were detemined by ¹H-nmr spectroscopic end-group analyses and viscosity measurements. The sequences were characterized by ¹⁵N-nmr spectra in solution, and the average lengths of the homogeneous blocks were determined from the signal intensities. The 50.3-and 75.4-MHz ¹³C-nmr CP/MAS spectra of the solid copolypeptides are not sensitive to sequence effects, but allow qualitative and quantitative analyses of the secondary structures. In contrast to other methods, the ¹³C-nmr spectra allow determination of the extent to which individual amino acids are incorporated into β-sheet or α-helix phases. Depending on primary structure and molecular weight, the secondary structure of (Ala/Val) copolypeptides may vary significantly. Both monomer units may be predominantly helical or predominantly β-sheet structure, or the Val units may prefer the β-sheet structure with most Ala-units forming β-helices. However, these secondary structures are more or less thermodynamically unstable and revert to the stable conformations on reprecipitation from trifluoroacetic acid/water.     

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.     

Morphology and structure of γ-benzyl-l-glutamate copolymerized with l-phenylalanine, l-valine and l-alanine

Observation of random copolypeptides of γ-benzyl-l-glutamate with l-phenylalanine, l-valine and l-alanine was carried out in an electron microscope with samples cast from dilute solution. The relationship between the morphology and the molecular conformation in solution was studied with mixed solvents composed of chloroform and trifluoroacetic acid; these show a preference for α-helix and random coil, respectively. From the solutions in which molecules take α-helical conformation, fibrous films of nematic structure were formed. From random coil solutions discrete precipitates with folded molecules such as lamellar single crystals, piles of lamellae and structureless particles were formed. A copolypeptide containing l-valine in sufficiently large quantity to form β-structure also showed a variation in morphology with solvent, from films to discrete precipitates. It is suggested that the change in stiffness of the molecules contributes to the morphological variation.     

Conformational studies on synthetic polypeptides: poly (d-phenylglycine) and poly(d-cyclohexylglycine)

Poly(d-phenylglycine) and poly(d-cyclohexylglycine) containing phenyl and cyclohexyl rings bound to the α-carbon of the polypeptide chain, have been synthesized. Circular dichroism measurements show that both polymers undergo a conformational transition from the random-coil form to an ordered form, upon addition of water, ethanol or trifluoroethanol to sulphuric acid solutions. Solid state measurements indicate that the ordered structures of poly(d-phenylglycine) and poly(d-cyclohexylglycine) are of the β-type. While for the former the antiparallel arrangement is predominant, for the latter there seems to be a greater tendency towards the parallel form. The ordered form of poly(d-cyclohexylglycine) is slightly more stable than the corresponding form of poly(d-phenylglycine) in all the above solvent systems. This can be interpreted in terms of stronger non covalent bond formation in the former polypeptide. Our results have been compared with literature on poly(l-phenylalanine) and poly(l-cyclohexylalanine).     

Phlorizin as a probe of the small-intestinal Na+,d-glucose cotransporter. A model

(1)‘Uptake’ of phlorizin by intestinal brush border membrane vesicles is stimulated, much as that of d-glucose, by the simultaneous presence of Na_out⁺ and $\text{Δψ?0}$. However, phlorizin contrary to d-glucose, fulfills all criteria of a non-translocated ligand (i.e., of a fully competitive inhibitor) of the Na⁺,d-glucose cotransporter. (2) The stoicheiometry of Na⁺/phlorizin binding is 1, as shown by a Hill coefficient of approx. 1 in the Na_out⁺-dependence of phlorizin binding. (3) The preferred order of binding at $\text{Δψ?0}$ is Na⁺ first, phlorizin second (4) The velocity of association of phlorizin to the cotransporter, but not the velocity of its dissociation therefrom, responds to Δψ. These observations while agreeing with the effect of $\text{Δψ?0}$ on the $\text{K}{}_{\mathrm{<mtext>d</mtext>}}$ of phlorizin binding in the steady-state time range, also confirm that the mobile part of the cotransporter bears a negative charge of 1. (5) A model is proposed describing the Na⁺,Δψ-dependent interaction of phlorizin with the cotransporter and agreeing with a more general model of Na⁺,d-glucose cotransport. (6) The $\text{k}{}_{\mathrm{<mtext>on</mtext>}}$, $\text{k}{}_{\mathrm{<mtext>off</mtext>}}$ and $\text{K}{}_{\mathrm{<mtext>d</mtext>}}$ constants of phlorizin interaction with the Na⁺,d-glucose cotransporter are smaller in the kidney than in the small-intestinal brush border membrane, which results in a number of quantitative differences in the overall behaviour of the two systems.     

Sodium binding to d-glucuronate residues: Crystal structure of sodium d-glucuronate monohydrate

Three-dimensional X-ray diffraction data were used to determine the crystal structure of sodium β-d-glucuronate monohydrate, a model system for investigating the factors involved in the binding of sodium ions to d-glucuronate residues of glycosaminoglycans. Crystals of the salt are monoclinic, space group P2₁, with a = 9.206(3) Å, b = 7.007(2) Å, c = 7.378(3) Å, β = 96.84(3)°, and Z = 2. Intensity data for 858 reflections were measured with an automated diffractometer. A trial structure, obtained by direct methods, was refined by least squares to R = 0.035. An outstanding feature of the crystal packing is the interaction of d-glucuronate anions with sodium ions. The sodium ion is coordinated to three symmetry-related $\text{d}$-glucuronate anions and to one water molecule. The d-glucuronate anion binds sodium cations through the three following sites: one that involves a carboxyl oxygen atom combined with ring oxygen O-5; one that includes a single carboxyl oxygen atom, and one composed of the O-3–O-4 pair of hydroxyl groups.     

l-Glutamate effects on electrical potentials of synaptic plasma membrane vesicles

The electrogenic nature of the l-glutamate-stimulated Na⁺ flux was examined by measuring the distribution of the lipophilic anion [³⁵S]thiocyanate (SCN^?) into synaptic membrane vesicles that were incubated in a NaCl medium. Concentrations of l-glutamate from 10^?7 to 10^?4 M added to the incubation medium caused an enhanced intravesicular accumulation of SCN^?. Based on the SCN^? distribution in synaptic membrane vesicles it was calculated that 10 μM l-glutamate induced an average change in the membrane potential of + 13 mV. l-Glutamate enhanced both the Na⁺ and K⁺ conductance of these membranes as determined by increases in SCN^? influx. Other neuroexcitatory amino acids and amino acid analogs (d-glutamate, l-aspartate, l-cysteine sulfinate, kainate, ibotenate, quisqualate, $\text{N-}\text{methyl}\text{-}\text{d}\text{-}\text{aspartate}$, and dl-homocysteate) also increased SCN^? accumulation in synaptic membrane vesicles. These observations are indicative of the activation by l-glutamate and some of its analogs of excitatory amino acid receptor ion channel complexes in synaptic membranes.     

Variant specific surface antigens from Trypanosoma equiperdum: Chemical and physical studies

Nine variant specific surface antigens were purified from clones of $\text{Trypanosoma equiperdum}$ and characterized by amino acid analysis, isoelectric focusing and circular dichroism. The molecules showed extensive differences in their isoelectric points, and by comparison with the corresponding amino acid compositions, this variation seemed to be due to different amide contents. Circular dichroism data allowed one to divide the molecules into 4 groups according to their respective percentages inα-helical and β-sheet structure.     

Regulation of argF mRNA synthesis,performed in vitro

The specific synthesis of $\text{arg}$F mRNA directed by the $\text{arg}$F gene carried on the specialized transducing bacteriophage $\text{λh80C}{}_1\text{857darg}$F, performed $\text{in vitro}$, is described with the use of an S180 extract from a strain carrying $\text{arg}$R^?. Synthesis of $\text{arg}$F mRNA is biphasic at approximately 7 minutes. The regulation of $\text{arg}$F mRNA synthesis by the specific arginine holorepressor present in an S180 extract prepared from a strain carrying the $\text{arg}$R⁺ allele is described.