Solution properties of synthetic polypeptides. VI. Helix-coil transition of poly-N5-(3-hydroxypropyl)-L-glutamine

A new procedure for evaluating u and σ characterizing σ-helix-forming polypeptides in solution was derived from Nagai's theory for the helix–coil transition of such polymers. Here u is the activity for helix formation from random coil, and σ is the helix initiation parameter. The necessary data are the helical content f_N at fixed solvent and temperature as a function of N, where N is the degree of polymerization of the polypeptide sample. Such data were obtained from ORD measurements on a number of fractionated samples of poly-N⁵-(3-hydroxypropyl)-L -glutamine (PHPG) in mixtures of water and methanol covering the complete range of composition and at various termperatures (5–40°C). When analyzed in terms of the proposed procedure, they yielded values of σ which were in the range (3.2 ± 0.6) × 10^?4, substantially independent of solvent composition and temperature. These values were much larger than those obtained recently for σ of poly(β-benzyl-L -aspartate) in m-cresol and in a mixture of chloroform and DCA. The data for [η] and s₀ (limiting sedimentation coefficient) as functions of molecular weight indicated that the molecular shape of PHPG in pure methanol is essentially rodlike, whereas that in pure water is not entirely randomly coiled but rather may be regarded as an interrupted helix. These indications were consistent with the results from ORD measurements. When plotted against the corresponding values of f_N, the values of [η] and [s₀] for PHPG in mixtures of water and methanol of various compositions and temperatures formed smooth composite curves, and we attributed these phenomena to the fact that σ of PHPG was nearly constant under these solvent conditions. Here [s₀] stands for a reduced limiting sedimentation coefficient which is equal to the inverse friction factor of the solute molecule.     

Proton magnetic resonance and optical spectroscopic studies of watr-soluble polypeptides: poly-L-lysine HBr, poly(L-glutamic acid), and copoly(L-glutamic acid42, L-lysine HBr28, L-alanine)

The helix-coil transition has been studied by high-resolution NMR for three water-soluble polypeptides. Such systems are better models for protein behavior than those in TFA-CDCl₃ solvent. An upfield shift of ～7 cps is observed for the α-CH peak of poly(L -glutamic acid) and poly-L -lysine as the helix content increases over the transition. No such shift is found for copoly(L -glutamic acid⁴², L -lysine²⁸, L -alanine³⁰). The width of the α-CH peak for poly L-lysine increases rapidly as helix content rises but for poly L -glutamic acid and the copolymer, the width of this peak remains unchanged up to 60% helicity. This demonstrates a rapid rate of interconversion between helical and random conformations in partly helical polymer for the latter two polypeptides. All three polymers however, show no apparent α-CH peak at 100% helicity. Side-chain resonance lines also broaden as helix content increases and, to a greater extent, the closer the proton is to the main chain.     

Synthetic Analogues of Conantokin-G: NMDA Antagonists Acting Through a Novel Polyamine-Coupled Site

Abstract: Conantokin-G (con-G) is a 17-amino-acid polypeptide that acts as an N-methyl-d -aspartate (NMDA) antagonist. This action has been attributed to a specific but noncompetitive inhibition of the positive modulatory effects of polyamines at NMDA receptors. Con-G possesses several unusual structural features, including five γ-carboxyglutamate (Gla) residues and a high degree of helicity in aqueous media. Previous structure-activity studies indicated that one or more Gla residues are necessary for NMDA antagonist activity. Con-G analogues were synthesized with alanine (Ala), serine (Ser), and phosphoserine substituted for Gla to assess the contribution of individual Gla residues to biological activity and secondary structure. Replacement of Gla in positions 3 and 4 resulted in polypeptides with markedly reduced and no NMDA antagonist actions, respectively. In contrast, Gla residues in positions 7, 10, and 14 are not required for NMDA antagonist actions because the potencies of con-G analogues containing Ser⁷, Ser¹⁰, Ala¹⁴, and Ser¹⁴ to inhibit spermine-stimulated [³H]MK-801 binding are similar to the parent peptide. Moreover, the Ala⁷ derivative of con-G was about fourfold more potent than the parent peptide both as an inhibitor of spermine-stimulated increases in [³H]MK-801 binding (IC₅₀ of ～45 nM) and in reducing NMDA-stimulated increases in cyclic GMP levels (IC₅₀ of ～77 nM) in cerebellar granule cell cultures. Although con-G and its analogues assumed mixtures of 3₁₀ and α-helices, no clear-cut relationship was evinced between the NMDA antagonist properties of these peptides and the degree of helicity they assumed in aqueous solutions. Together with the inability of con-G to affect 5,7-dichloro[³H]kynurenic acid, [³H]CGP-39653, and [³H]ifenprodil binding, these data are consistent with the hypothesis that this polypeptide acts at a unique, polyamine-associated site on NMDA receptors.     

Preventing N‐ and O‐formylation of proteins when incubated in concentrated formic acid

Concentrated formic acid is among the most effective solvents for protein solubilization. Unfortunately, this acid also presents a risk of inducing chemical modifications thereby limiting its use in proteomics. Previous reports have supported the esterification of serine and threonine residues (O‐formylation) for peptides incubated in formic acid. However as shown here, exposure of histone H4 to 80% formic (1 h, 20^oC) induces N‐formylation of two independent lysine residues. Furthermore, incubating a mixture of Escherichia coli proteins in formic acid demonstrates a clear preference toward lysine modification over reactions at serine/threonine. N‐formylation accounts for 84% of the 225 uniquely identified formylation sites. To prevent formylation, we provide a detailed investigation of reaction conditions (temperature, time, acid concentration) that define the parameters permitting the use of concentrated formic acid in a proteomics workflow for MS characterization. Proteins can be maintained in 80% formic acid for extended periods (24 h) without inducing modification, so long as the temperature is maintained at or below –20^oC.     

Experimental characterization of poly(hydroxyalkyl-L-glutamine) conformations in aqueous calcium chloride and sodium perchlorate solutions

Poly(hydroxyalkyl-L -glutamine) (alkyl = ethyl, propyl, butyl) solutions have been studied by CD as functions of temperature and activity of calcium chloride and sodium perchlorate. Helical content is altered by changes in salt activity and temperature. The helicity of poly(hydroxybutyl-L -glutamine) and poly(hydroxypropyl-L -glutamine) falls to zero in a monotonic fashion with increasing calcium chloride activity. A nonzero helicity reappears at activities in excess of 5–50 mol kg^?1. Poly(hydroxypropyl-L -glutamine) is much more sensitive to calcium chloride than is poly(hydroxybutyl-L -glutamine), and both polypeptides are more sensitive to calcium chloride than are typical proteins. Markedly different behavior is observed with sodium perchlorate. This salt acts as a helix stabilizer at low activities but becomes a destabilizer at activities higher than 0.3–1.0 mol kg^?1. In this respect the effect of sodium perchlorate on nonionic poly(hydroxyalkyl-L -glutamines) resembles that seen with cationic poly(L -lysine) and poly(L -arginine). Helix stabilization at low sodium perchlorate activity is moderate for poly(hydroxybutyl-L -glutamine) and large for poly(hydroxypropyl-L -glutamine) and poly(hydroxyethyl-L -glutamine).     

Model nucleoproteins: binding of actinomycin D to complexes of DNA with lysine-containing polypeptides

Complexes of DNA with histone H1 and random and sequential polypeptides containing 30–100% of lysine were studied using actinomycin D as a probe. The binding of actinomycin D was measured by spectrophotometric titration in 0.15M NaCl and in 0.01M Tris buffer. The excluded-site model was used for the evaluation of binding data. Polypeptides reduce the number of binding sites on DNA available for actinomycin D binding. The extent of this change depends mainly on the content and distribution of basic lysine residues. Of the hydrophobic residues constituting the peptides, only leucine strongly depresses the actinomycin D binding. The helix-forming and helix-breaking amino acid residues are without effect.     

The Light Harvesting System of the Diatom Cyclotella cryptica. Isolation and Characterization of the Main Light Harvesting Complex and Evidence for the Existence of Minor Pigment Proteins*

The main chlorophyll a/c light harvesting complex of the diatom Cyclotella cryptica was isolated by sucrose density gradient centrifugation. It consisted of two polypeptides of Mrs 18000 and 22000. Both polypeptides and fragments thereof, obtained by formic acid treatment, were blocked at their N-ter-mini. An antiserum raised against the two subunits selectively immunolabeled the thylakoid within the chloroplasts. The subunits were nuclear encoded and could be immunoprecipitated from poly (A)⁺ RNA as precursor proteins in the Mr range of 20000 to 24000. The existence of minor chlorophyll protein complexes and their possible function in light climate adaptation processes was investigated in cells adapted to low light and high light conditions. Low light grown cells contained more fucoxanthin and less β-carotene relative to chlorophyll a than high light adapted cells. The xanthophyll cycle pigments diatoxanthin and diadinoxanthin increased five-fold relative to chlorophyll a under high light conditions. Western-immunoblotting experiments with antisera raised against several chlorophyll a/b and chlorophyll a/c antenna complexes demonstrated that, beside the dominating chlorophyll a/c light harvesting complex, minor antenna complexes might exist, which, in part, seem to react to the light climate applied.     

A novel enzymatic dehalogenation of (R)-3-chloro-1,2-propanediol inAlcaligenes sp. DS-S-7G

The mechanism of the novel enzymatic dehalogenating action of (R)-3-chloro-1,2-propanediol [monochlorohydrin (MCH)] was investigated. The (R)-MCH-dechlorinating enzyme system ofAlcaligenes sp. DS-S-7G, which stereoselectively assimilated (R)-MCH from the racemate, was composed of two components (Enzyme 1 and Enzyme 2). Enzyme 1 was a flavoprotein with a relative molecular mass (M _r) of 70,000 and was composed of two kinds of polypeptides (58,000 and 16,000). The enzyme exhibited activity for converting (R)-MCH to hydroxyacetone with the liberation of chloride ions under aerobic conditions. On the other hand, Enzyme 2 with anM _r of 86,000, which was also composed of two kinds of polypeptides (33,000 and 53,000), showed no dechlorinating activity for (R)-MCH. However, in the presence of NAD⁺, when Enzyme 1 was conjugated with Enzyme 2 in the (R)-MCH-dechlorinating reaction, the co-operative dechlorinating activity was four to five times higher than that by Enzyme 1 alone. (R)-MCH was finally degraded to acetic acid and formic acid by the joint action of the two enzymes. These facts indicate that (R)-MCH is oxidatively dechlorinated by the two enzymes in the presence of NAD⁺ inAlcaligenes sp. DS-S-7G.     

Investigation of the origin of 0-methyl groups in griseofulvin using some14C-labelled substrates

I-^l4C-pyruvie acid, 3-¹⁴C-l-serine,¹⁴C-formic acid and¹⁴CO₂ were tested as possible sources of 0-methyl groups of griseofulvin produced byPenicillium griseofulvum. Entire radioactivity from pyruvic acid,l-serine and formic acid was found in the methoxyls of griseofulvin. By determining the activity of individual methoxyls its distribution was established, this being homogeneous only after formic acid.     

Catabolic pathways of glucose in Bacillus circulans var. alkalophilus

Enzymes and the metabolic pathways of glucose catabolism of Bacillus circulans var. alkalophilus were studied. The metabolism of the microbe was mixed acid fermentative yielding mainly acetic and formic acids as end products from glucose. It was estimated that B. circulans var. alkalophilus partitions 90%–93% of the carbon from glucose into the Embden-Meyerhof-Parnas (EMP) pathway and 7%–10% into the hexose monophosphate (HMP) and Entner-Doudoroff (ED) pathways. Rather low activities of glucose dehydrogenase and gluconokinase appeared in the early logarithmic and late stationary phases, whereas NADH oxidase was markedly high. This result can be explained by a demand to reduce NADH to NAD⁺ for the EMP pathway; when acetic and formic acids are produced, no NADH is regenerated to NAD⁺, which is required in the early steps of EMP and HMP pathways. A small percentage (1.6%–2.4%) of the total CO₂ was formed from (6-C) of glucose, which means that the tricarboxylic acid cycle was functional but its contribution was insignificant. Large differences do not seem to exist between alkaliphilic and neutrophilic bacilli in the use of glucose pathways. Received: January 29, 1999 / Accepted: July 30, 1999     

The loss of carbon-20 in C19-gibberellin biosynthesis in a cell-free system from Pisum sativum L.

The fate of the carbon-20 atom in gibberellin (GA) biosynthesis was studied in a cell-free system from Pisum sativum. This carbon atom is lost at the aldehyde stage of oxidation when C₂₀-GAs are converted to C₁₉-GAs. Gibberellin A₁₂ labeled with ¹⁴C at C-20 was prepared from [3-¹⁴C]mevalonic acid with a cell-free system from Cucurbita maxima and incubated with the pea system. Analysis of the gas and aqueous phases showed that ¹⁴CO₂ was formed at the same rate and in nearly equivalent amounts as ¹⁴C-labeled C₁₉-GAs whereas [¹⁴C]formic acid and [¹⁴C]formaldehyde were not detectable. The possibility that C-20 had been lost as formic acid which had then been converted to CO₂ was investigated by control incubations with [¹⁴C]formic acid. The rate of release of ¹⁴CO₂ from [¹⁴C]formic acid was only one fiftieth of the rate of ¹⁴CO₂ release from [¹⁴C]GA₁₂ as the substrate. We conclude that in the formation of C₁₉-GAs from C₂₀-GAs, the C-20 is removed directly as CO₂.Abbreviations GA_n Gibberellin A_n     

Biosynthesis of formic acid by the poison glands of formicine ants

The biosynthesis of formic acid in the poison glands of formicine ants is closely related to the C-1 metabolism of the glandular cells. Experiments utilizing radiolabeled amino acids revealed that serine is a major precursor, contributing both its α and β carbons to formic acids. 5,10[¹⁴C]methylene H₄folate and 5,10[¹⁴C]methenyl H₄folate also serve as precursors of formic acid in the poison gland, suggesting that they are intermediates in the pathway. Furthermore, these H₄folate derivatives were isolated from poison glands following incubation with [3-¹⁴C]serine and proved radioactive. The glandular cells are also exceptionally rich in the enzymes responsible for these reactions, supporting the proposed pathway.Although this pathway has been established in various organism, the uniqueness of the poison gland system is that it accumulates formic acid to large extent, yet avoids its cytotoxicity. This is made possible by a combination of the biochemical characteristics of the pathway and the special morphological features of the poison gland.     

Temperature-dependent optical rotatory dispersion properties of helical muscle proteins and homopolymers

Thermally induced helix–coil transitions of myosin rod, light meromyosin, and tropomyosin were studied by optical rotatory dispersion (ORD). Fractional helicity was calculated from both the Moffitt-Yang parameter, b₀, and the corrected mean residue rotation [m′] at 231.4 nm. Between 3 and 30°C, [m′] increases linearly with a slope of 59/°C, whereas b₀ is virtually constant, indicating apparently different thermal melting behavior. Poly(L -lysine) and poly(L -glutamic acid) in their helical forms and myoglobin also show a nearly linear temperature dependence of [m′]_231.4. Muscle proteins in 6M guanidine hydrochloride and the random-coil forms of the homopolymers exhibit temperature-dependent values of [m′]_231.4 and b₀. We conclude from these observations that ORD properties of both α-helices and random-coil polypeptides have significant intrinsic temperature dependencies. A new method of estimating fractional helicity as a function of temperature is proposed.     

Behavior of amphipathic helices on analysis via matrix methods, with application to glucagon, secretin, and vasoactive intestinal peptide

A configuration partition function, which incorporates concepts embodied in the amphipathic helix hypothesis, has been formulated for a polypeptide in the presence of zwitterionic phospholipid. An enhanced probability is assigned to helix formation in any region of the polypeptide chain where side chains bearing charges of opposite sign will be situated on the same side of the α-helix but displaced from one another by one turn. This situation will arise when residues i ? 4 (or i ? 3) and i bear charges of opposite sign and residue i ? 4 (or i ? 3) through i are in a helical state. Illustrative calculations are performed for polypeptide chains in which the generalized nonionic amino acid residue serving as host has Zimm-Bragg parameters of σ = 10^?4, s = 1. These calculations define conditions under which two interacting charged pairs can cooperate in a synergistic helix augmentation even when the two pairs are separated by significantly more than four generalized nonionic amino acid residues. Furthermore, the two interacting charged pairs, as well as the intervening amino acid residues, may become helical as one unit. Significant augmentation in helicity is observed with plausible values for the enhanced probablity assigned to helix formation for an interacting pair. This model predicts correctly that glucagon and secretin, but not vasoactive intestinal peptide, undergo a coil-to-helix trnsition in the presence of zwitterionic phospholipid. This prediction is made with plausible values for the parameter used to express the helicity enhancement. The experimental observation with zwitterionic phospholipids is the direct opposite of that seen for these three peptides in the presence of anionic lipids and detergents. In anionic lipids the amount of induced helicity is in the following order: glucagon < secretin < vasoactive intestinal peptide. Results obtained with these three peptides demonstrate that the nature of the head group of the lipid is important for lipid–protein interaction and that the resulting conformational changes can be rationalized by matrix methods.     

A high-resolution 13C-nmr study of collagenlike polypeptides and collagen fibrils in solid state studied by the cross-polarization–magic angle-spinning method. Manifestation of conformation-dependent 13C chemical shifts and application to conformational characterization

We have recorded high-resolution ¹³C-nmr spectra of collagen fibrils in the solid state by the cross-polarization–magic-angle-spinning(CP–MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference ¹³C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 3₁-helical polypeptides [(Gly)_nII, (Pro)_nII, (Hyp)_n, and (Ala? Gly? Gly)_nII], and the triple-helical polypeptides [(Pro? Gly? Pro)_n and (Pro? Ala? Gly)_n]. Examination of the ¹³C chemical shifts of these polypeptides, together with our previous data, showed that the ¹³C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the ¹³C chemical shifts of Ala residues of the 3₁-helical (Ala? Gly? Gly)_n and triple-helical (Pro? Ala? Gly)_n are significantly displaced, compared with those of the α-helix, β-sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen-like polypeptides. Further, the ¹³C chemical shifts of Gly and Pro residues in the triple-helical polypeptides are substantially displaced from those found in (Gly)_nII and (Pro)_nII of the 3₁-helix, reflecting further conformational change from the 3₁-helix to the supercoiled triple helix. In particular, the ¹³C chemical shifts of Gly C ? O carbons of the triple-helical polypeptides are substantially displaced upfield (4.1–5.1 ppm), with respect to those of the 3₁-helical polypeptides. These displacements are interpreted by that Gly C ? O of the former is not involved in NH …? O ? C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds. On the basis of these ¹³C chemical shifts, as reference data for the collagenlike structure, we were able to assign the ¹³C-nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.     

A specific microbial sensor for formic acid

Summary A microbial sensor consisting of immobilized Clostridium butyricum, two gas permeable Teflon membranes and fuel cell type electrode was suitable for the determination of formic acid. When the sensor was inserted into the sample solution containing formic acid, the current increases to a steady state with a response time of 20 min. The relationship between the steady state current and the formic acid concentration is linear up to 1 000 mg l^–1. The currents are reproducible with an average relative error of 5%. Selectivity of the sensor is satisfactory. Results obtained with this sensor and by gas chromatography were in good agreement (regression coefficient; 0.98) when the cultivation medium of Aeromonas formicans was employed. Immobilized Clostridium butyricum is stable for more than 20 days.     

Polymer concentration effects on helix–coil transition widths

A theoretical study of effects of excluded volume intermolecular interactions on the sharpness of helix–coil transitions in solutions of polyamino acids or simple proteins indicates that the transition width may vary appreciably as a function of polymer concentration. The analysis is based on a second virial approximation for the excess free energy of mixing of a solution of polymers of varying degrees of helicity. The virial coefficients involved are roughly estimated on the basis of gross polymer geometry. For large N (degree of polymerization) the transition is found, typically to sharpen with increasing concentration, becoming second order and then first order at sufficiently high concentrations. The critical polymer concentration is found to be roughly of the order N^?1.2 ??₀^?1 for an “all or none” model and of order σ^1/2 N^?0.2 ??₀^?1 for a model with continuously variable degree of helicity (??₀ is the volume of a single helical molecule and σ^1/2 the normalized statistical weight of a helix–coil interface). In the second case for N ～ 10³ and σ ～ 10^?2–10^?4, the predicted critical concentration is in the range 10^?1–10^?3 g/cm.³ Comparison is made with experiments on solutions of poly(γ-benzyl-L glutamate).     

The identification of polypeptides synthesised during the acquisition of teichoic acid synthetic activity in Bacillus licheniformis

An attempt has been made to identify proteins synthesised during induction of teichoic acid synthesis in Bacillus licheniformis ATCC 9945. The proteins are recognised as those produced on the change from teichuronic acid to teichoic acid synthesis that occurs after the transfer of the bacteria from phosphate-limited to phosphate-rich conditions. B. licheniformis was grown in phosphate-limiting conditions in the presence of threonine to stimulate threonine uptake. The bacteria were then transferred to phosphate-rich conditions and were pulsed-labelled with [¹⁴C]threonine during the change to teichoic acid synthesis. All of the proteins were extracted from the cells with sodium dodecyl sulphate and were examined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Radioactive polypeptides were identified by fluorography of the polyacrylamide gels. The radioactive polypeptides that were formed on change from teichuronic acid to teichoic acid synthesis were compared with the polypeptides present in a membrane sub-fraction that had high teichoic acid-synthesising activity. The labelling of nine polypeptides with [¹⁴C]threonine was dependent on new RNA synthesis. Of these nine polypeptides, five were also present in the membrane sub-fraction with the highest teichoic acid-synthesising activity.