Effect of hydrophobic side chains on the pressure-induced changes in the NMR spectra of water-soluble biopolymers

Measurements have been made of the high-resolution nmr spectra of the polyamino acids poly[N⁵-(2-hydroxyethyl)-L -glutamine] and poly[N⁵-(4-hydroxybutyl)-L -glutamine] in mixed deuterium oxide and water solvent at varying pressures from 1.03 to 3163.7 kg/cm². The results are compared with previously reported results for the polymer poly[N⁵-(3-hydroxypropyl)-L -glutamine] under similar conditions. The significance of the behaviour of the polymers is considered in terms of the effect of the presence of hydrophobic residues in their side chains.     

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 far-infrared properties of polyamino acids

The far-infrared absorption between 3 and 650 cm^?1 of several amino acids and polyamino acids is measured under a variety of conditions. The far-infrared spectra of amino acids and short-chain oligomers are extremely temperature dependent with the appearance of numerous narrow absorption lines at 4.2 K. These absorption lines broaden or disappear at 300 K or for absorption measurements on samples in solution. For longer polymers, relatively broad nearly temperature-independent absorption lines are observed with little difference between the spectra of polymers in solution or in the solid state. These results are explained in terms of the crystalline order of the samples.     

Facile Synthesis of N α -Protected Amino/Peptide Hydroxamic Acids Mediated by COMU

One-pot preparation of N ^α -protected amino/peptide hydroxamic acids from corresponding carboxylic acids is described using uronium-type coupling reagent COMU. The present protocol is simple and mild conditions are used. Thus the resulting hydroxamic acids are obtained in good yields without racemization.     

Synthesis and properties of optically active nanostructured polymers bearing amino acid moieties by direct polycondensation of 4,4′-thiobis(2-tert-butyl-5-methylphenol) with chiral diacids

Four derivatives of N-trimellitylimido-l-amino acid (4a–4d) were prepared by the reaction of trimellitic anhydride (1) with the l-amino acids (2a–2d) in acetic acid as diacid monomers and were used with the aim to obtain a new family of amino acid based poly(ester-imide)s (PEI)s. The polymerization was performed by direct polycondensation of chiral diacids (4a–4d) with 4,4′-thiobis(2-tert-butyl-5-methylphenol) (5) in the presence of tosyl chloride (TsCl), pyridine and N,N-dimethyl formamide (DMF). Step-growth polymerization was carried out by varying the time of heating and the molar ratio of TsCl/diacid and the optimum conditions were achieved. The synthesized polymers were characterized by means of specific rotation experiments, FT-IR, ¹H-NMR, X-ray diffraction techniques and elemental analysis. The surface morphology of the obtained polymers was studied by field emission scanning electron microscopy. The result showed nanostructure morphology of the resulting polymers. The obtained PEIs were soluble in polar aprotic solvents such as DMF, N,N-dimethyl acetamide, dimethyl sulfoxide, N-methyl-2-pyrrolidone and protic solvents such as sulfuric acid. Thermal stability and the weight-loss behavior of the PEIs were studied by thermal gravimetric analysis (TGA) techniques. TGA showed that the 10% weight loss temperature in a nitrogen atmosphere was more than 402°C, therefore they had useful levels of thermal stability associated with excellent solubility.     

Inclusion of nonproteinous amino acids in thermally prepared models for prebiotic protein

Sixteen nonproteinous amino acids (those not coded for in contemporary protein biosynthesis) were incorporated during the thermal formation of polyamino acids under postulated prebiotic conditions, although not all into a single polyamino acid. The copresence of proteinous or even α-amino acids was not required. (Norleucine color equivalents and elution times on a Beckman model 120C amino acid analyzer were determined for these nonproteinous amino acids). The results suggest that prebiotically available nonproteinous amino acids would have been constituents of prebiotic protein if the latter were formed thermally. Some differences in properties of the polyamino acids could be attributed to particular nonproteinous amino acid residues; however, the tested properties did not suggest a means for evolutionary selection against nonproteinous amino acids as a group. Selection against this class of amino acids in toto was likely a later, biotic, event.     

Synthesis and conformational properties of polypeptides containing long aliphatic side chains. Poly(Nepsilon-stearyl-L-lysine) and poly(Nepsilon-pelargonyl-L-lysine).

Poly(N^ε-stearyl-L -lysine) and poly(N^ε-pelargonyl-L -lysine) were synthesized both by polymerization of N^ε-pelargonyl and N^ε-stearyl-L -lysine NCA and by acylation of poly(L-lysine) with pelargonyl and stearyl chloride. This second route has proven to be very useful, since completely acylated polymers are obtained in almost quantitative yield, whereas the usual scheme of preparation of ε protected poly(L-lysine) cannot easily be applied due to solubility problems. Poly(N^εpelargonyl and stearyl-L -lysine) are soluble in alcohols containing linear aliphatic chains such as n-butanol and n-octanol and in mixtures of these alcohols with hydrocarbons such as n-hexane and n-heptane. Both polymers show an α-helical conformation in the above solvents, which can be disrupted upon addition of sulfuric acid. Also in the solid state, poly(N^ε-stearyl-L -lysine) and poly(N^ε-pelargonyl-L -lysine) show X-ray diffraction patterns typical of order structure.     

Effect of side-chain hydrophobic bonding on the stability of homopolyamino acid alpha-helices: conformational studies of poly-l-leucine in water

The conformational properties of block copolymers of poly-L -leucine in water have been examined. The degree of polymerization of the poly-L -leucine block was 11 and 21, respectively, for samples prepared by the Merrifield procedure, and 56 for a sample prepared by the polymerization of leucine N-carboxyanhydride. The optical rotatory dispersion parameter b₀ was used to obtain the helix content θ_h at various temperatures. Application of the Lifson-Roig theory gave the following parameters for the transition of a residue from a coil to a helical state: v = 0.05–0.011, ΔH = +100 cal/mole, ΔS = +0.70–1.00 e. u. These parameters, as well as those for other polyamino acids, are accounted for by hydrophobic bonds involving the nonpolar side chains in the helical and randomly coiled forms. From the data for poly-L -alanine and theoretical values of the thermodynamic parameters for hydrophobic bond formation, the parameters for formation of a polyglycine helix are computed. By separating the contributions of the backbone, it is possible to obtain a set of thermodynamic parameters for the side-chain contributions of a number of polyamino acids. Increased size of the nonpolar side chain (with a larger contribution from hydrophobic bonding) makes a larger contribution to the stability of the α-helix which is reflected, among other ways, in a higher helix content at given temperature.     

New polymer syntheses. IV. Polypeptides of lysine and ornithine with pending pyrimidine bases

Starting with β-methoxy methacryloylisocyanate, β-methoxy methacrylisothiocyanate, and β-isocyanatopropionyl chloride, on the one hand, and N^α-Z-lysine or N^α-Z-ornithine, on the other hand, N^α-Z-amino acids with pyrimidine bases in the side chain were synthesized. These Z-protected nucleoamino acids were converted to the corresponding N-carboxyanhydrides (NCAs) via the silylester method. In the case of 2-thiothymine derivatives, the reaction intermediate of the NCA synthesis caused benzylation of the thioxo- group, so that a new class of 2-mercaptopyrimidine derivatives was isolated unexpectedly. The poly(nucleoamino acids) obtained by polymerization of the nucleoamino acid NCAs were characterized by elemental analyses, optical rotations ¹H-nmr and ¹³C-nmr spectra. Vapor pressure osmometry revealed that the DP s were in the range of 20–30. Their spectra suggest a helical secondary structure. While all homopolypeptides are insoluble in water, copolypeptides containing L -lysine N^ε-hydrobromide possess good solubility in water.     

New structures and composition of cell wall teichoic acids from Nocardiopsis synnemataformans,Nocardiopsis halotolerans,Nocardiopsis composta and Nocardiopsis metallicus: a chemotaxonomic value

The structures of the cell wall teichoic acids (TA) from some species of the genus Nocardiopsis were established by chemical and NMR spectroscopic methods. The cell walls of Nocardiopsis synnemataformans VKM Ac-2518^T and Nocardiopsis halotolerans VKM Ac-2519^T both contain two TA with unique structures—poly(polyol phosphate-glycosylpolyol phosphate)—belonging to the type IV TA. In both organisms, the minor TA have identical structures: poly(glycerol phosphate-N-acetyl-β-galactosaminylglycerol phosphate) with the phosphodiester bond between C-3 of glycerol and C-4 of the amino sugar. This structure is found for the first time. The major TA of N. halotolerans has a hitherto unknown structure: poly(glycerol phosphate-N-acetyl-β-galactosaminylglycerol phosphate), the N-acetyl-β-galactosamine being acetalated with pyruvic acid at positions 4 and 6. The major TA of N. synnemataformans is a poly(glycerol phosphate-N-acetyl-β-galactosaminylglycerol phosphate) with the phosphodiester bond between C-3 of glycerol and C-3 of the amino sugar. The cell walls of Nocardiopsis composta VKM Ac-2520 and N. composta VKM Ac-2521^T contain only one TA, namely 1,3-poly(glycerol phosphate) partially substituted with N-acetyl-α-glucosamine. The cell wall of Nocardiopsis metallicus VKM Ac-2522^T contains two TA. The major TA is 1,5-poly(ribitol phosphate), each ribitol unit carrying a pyruvate ketal group at positions 2 and 4. The structure of the minor TA is the same as that of N. composta. The results presented correlate well with the phylogenetic grouping of strains and confirm the species and strain specific features of cell wall TA in members of the genus Nocardiopsis.     

Activity of foot-and-mouth disease virus RNA-dependent RNA polymerase in vitro: inhibition by polyamines and poly(amino acid)s

Replication of foot-and-mouth disease virus RNA in vitro is inhibited by high concentrations of the following polyamines in decreasing order of effectiveness: putrescine, spermine, and cadaverine. The basic poly(amino acids), polylysine, polyornithine, and polyarginine, as well as the basic protein salmine, are several orders of magnitude more inhibitory than polyamines. The interaction between polyornithine and foot-and-mouth disease virus RNA and its inhibition of replicase activity are related to the ability of basic polypeptides to bind to the RNA template. The neutral polymer, polysarcosine, and the polyanions, polyglutamic acid and heparin sulfate, do not inhibit replication; however, both polyanions relieve the inhibition by polyamines and polyamino acids. The mode of inhibition by polyamines and poly(amino acids) and the antagonism by heparin is discussed.     

Amino acid sequencing by gas chromatography-mass spectrometry using perfluoro-dideuteroalkylated peptide derivatives: B. Interpretation of the mass spectra

The mass spectra of the O-trimethylsilylated trifluoro-dideuteroethyl polyamino alcohols, produced by LiAlD₄-reduction and O-trimethylsilylation of N-trifluororacetyl oligopeptide methyl esters, are evaluated. Characteristic mass spectra of derivatives are shown which are derived from peptides containing all protein amino acids including Arg, His, Trp, Gln, Asn and carboxyl terminal amides as well as modified Cys-residues. The mass spectra of these derivatives can be easily interpreted in terms of the amino acid sequence of the original peptides since they contain abundant and intensity-balanced sequence-determining ions.     

Solid-phase peptide synthesis using Nα-trityl-amino acids

Summary The preparation of N^α-trityl-amino acids is described. Several derivatives of trifunctional amino acids carrying acid-and base-labile side-chain protecting groups and the trityl group at the N^α position are prepared for first time. The incorporation of N^α-trityl-amino acids into peptide sequences using solid-phase protocols was achieved. The use of the trityl group for the protection of the α-amino group in conjunction with base-labile side-chain protecting groups constitutes a new method for the assembly of peptides in mild conditions.     

Fluorometric analysis of N alpha-methylamino acids using fluorescamine

The fluorometric amino acid analyzer based on fluorescamine has been utilized for quantitative determination of N^α-methylamino acids. N-Chlorosuccinimide (1 × 10^?3m in 0.05 m HCl) was continuously introduced into the column eluate to convert N^α-methylamino acids to fluorescamine-sensitive methylamine. As little as 100 pmoles of l-N-methylalanine was detectable with a linear fluorescence response up to 10.0 nmoles. Distinction of primary and secondary amino acids was achieved by carrying out duplicate analyses with and without the introduction of the N-chlorosuccinimide solution.     

Methacrylate polymerization by AzoRNA: potential usefulness for chromosomal localization of genes

An azo pyrimidine nucleotide has been prepared and enzymatically attached to oligo(A) primers. The nucleotide's azo pyrimidine group has previously been shown to initiate polymerization of methacrylate esters designed to bind marker groups for visualization by microscopy. When attached to RNA molecules complementary to a chromosomal DNA segment, these nucleotides may allow localization of the DNA segment following in situ hybridization of the probe, methacrylate polymerization, and marker attachment. Since mRNA molecules of potential interest as probes bear a 3′-poly(A) tail, the modified nucleotides were added to oligo(A) primers as models. First, N⁴-ureidocytosine nucleotides were enzymatically added to ApApA, (Ap)₉A, or [5′-³²P]-(pA)₁₀, using the modified cytidine 5′-diphosphate and “primer-dependent” polynucleotide phosphorylase (M. luteus). In the case of the ApApA-primed reaction, the N⁴-ureidocytosine nucleotides in the product polynucleotide were converted into azo nucleotides by oxidation with N-bromosuccinimide. The other two primers were employed to study the time course of polynucleotide formation and to verify that primer was indeed being utilized by the enzyme. The suitability of the modified nucleotide for in situ hybridization studies was examined. Poly(N⁴-ureidocytidylic acid) was prepared from poly(C) and semicarbazide by the bisulfite-catalyzed transamination reaction. It was found that 95% of the N⁴-ureidocytosine nucleotides in this polynucleotide survive the elevated temperatures typically required for DNA:DNA denaturation and RNA:DNA annealing. When poly(N⁴-ureidocytidylic acid) was mixed with poly(I) in buffered aqueous salt solutions, no evidence for hybridization was found, so binding of the probe RNA to the denatured chromosomal DNA molecule via the modified nucleotides is not expected. Upon oxidation of poly(N⁴-ureidocytidylic acid) with N-bromosuccinimide, the azo nucleotides were formed, as judged by the appearance of a characteristic peak at approximately 350 nm in the uv-absorption spectrum of the yellow-orange product, azoRNA. The azo nucleotides in azoRNA exhibited the expected acid lability, which is known to be accompanied by 1-glyceryl methacrylate polymerization in the case of the simple azo pyrimidine. Because 1-glyceryl metharcylate bears substituent glycol groups for attaching heavy atoms or fluorescent markers, it is possible that probe RNA molecules bearing azo nucleotides may be useful for localizing low-multiplicity genes along eukaryotic chromosomes.     

Fluorescent 2-aza-epsilon-adenosine derivatives of polyadenylic acid, polyuridylic acid, and polyinosinic acid.

A new fluorescent analog of adenosine, 1,N⁶-etheno-2-aza-adenosine, has been incorporated into polynucleotides by polynucleotide phosphorylase polymerization of 1,N⁶-etheno-2-aza-adenosine-5′-diphosphate and adenosine-5′-diphosphate, uridine-5′-diphosphate, or inosine-5′-diphosphate. These new oligonucletides possess high fluorescence when excited at 358 nm and emit at 495 nm. The ratio of the fluorescent and nonfluorescent portions of the copolymer can be controlled by the initial composition of the 2-aza-ε-adenosine-diphosphate and the corresponding nucleoside diphosphate. Fluorescent copolymers with a ratio varying from 1.6 to 35 have thus been synthesized. The physicochemical study of copolymers containing less than 10% of the 1,N⁶-etheno-2-aza-adenosine moiety showed that they are similar to poly(A), poly(U), or poly(I). Therefore, fluorescence and polarization study of the 1,N⁶-etheno-2-aza-adenosine residues that have been incorporated into the copolymer provides a sensitive indicator for the structure of the copolymer. Potentially these new copolymers may provide unique roles in probing the structure of poly(C) and poly(A) in cellular mRNA.     

The influence of dietary calcium and phosphorus on intestinal calcium transport in rats given vitamin D metabolites.

A new method for the simple analysis of methylated amino acids based on autoradiography is introduced. With this technique a survey of protein methylation in a prokaryote, Escherichia coli, and a eukaryote, fibroblasts in culture, was carried out in an attempt to identify, quantitate, and determine the subcellular localization of all the methylated amino acids found in the proteins of these organisms.In mammalian cells using an established mouse fibroblast line (3T3), we have found that nuclei-free and mitochondria-free cytoplasm contain readily detectable amounts of four identifiable methylated amino acids: N^?,N^?-dimethyllysine, N^?,N^?,N^?-trimethyllysine, N^G,N^G-dimethylarginine (or N^G-methylarginine), and N^G,N′^G-dimethylarginine. The crude nuclear pellet also contains these methylated amino acids, but in addition contains N^?-methyllysine and a new as yet unidentified methylated compound. Histones purified from these nuclei contain essentially the same array of methylated compounds.The ribosomal subunits of the mammalian cells contained only small amounts of the methylated amino acids; the 40S subunit contained a substantial amount of just one, N^G,N^G-dimethylarginine (or N^G-methylarginine), and smaller amounts of N^G,N′^G-dimethylarginine, and an as yet unidentified methylated compound. The 60S subunit contained even smaller amounts of methylated amino acids, 50% of which was N^?,N^?,N^?-trimethyllysine and smaller amounts of N^?-methyllysine, N^?,N^?-dimethyllysine, and N^G,N^G-dimethylarginine. These subunits also contained an as yet unidentified methylated compoundThese results were in marked contrast to those that we obtained with the prokaryote, Escherichia coli. Only the proteins of the 50S ribosomal subunit of the bacteria contained methylated amino acids. Of those present 50% was N^?,N^?,N^?-trimethyllysine, with the remainder distributed about equally between N^?-methyllysine and three unknowns, one of which is apparently the same as that found in the 60S subunit of the mouse fibroblasts. All of the N^?-methyllysine was apparently in the small acidic proteins, L7 and L12.     

Racemization study on different N-acetylamino acids by a recombinant N-succinylamino acid racemase from Geobacillus kaustophilus CECT4264

N-Succinylamino acid racemase (NSAAR) with N-acylamino acid racemase (NAAAR) activity together with a d- or l-aminoacylase allows the total transformation of N-acetylamino acid racemic mixtures into optically pure d- or l-amino acids, respectively. In this work we have cloned and expressed the N-succinylamino acid racemase gene from the thermophilic Bacillus-related species Geobacillus kaustophilus CECT4264 in Escherichia coli BL21 (DE3). G. kaustophilus NSAAR (GkNSAAR) was purified in a one-step procedure by immobilized cobalt affinity chromatography and showed an apparent molecular mass of 43 kDa in SDS-gel electrophoresis. Size exclusion chromatography analysis determined a molecular mass of about 150 kDa, suggesting that the native enzyme is a homotetramer. Optimum reaction conditions for the purified enzyme were 55 °C and pH 8.0, using N-acetyl-d-methionine as substrate. GkNSAAR showed a gradual loss of activity at preincubation temperatures over 60 °C, suggesting that it is thermostable. As activity was greatly enhanced by Co²⁺, Mn²⁺ and Ni²⁺ but inhibited by metal-chelating agents, it is considered a metalloenzyme. The Co²⁺-dependent activity profile of the enzyme was studied with no detectable inhibition at higher metal ion concentrations. GkNSAAR showed activity towards both aliphatic and aromatic N-acetylamino acids such as N-acetyl-methionine and N-acetyl-phenylalanine, respectively, with k_cat/K_m values ranging from 1 × 10³ to 9 × 10³ s^?1 M^?1. Kinetic parameters were better for N-acetyl-d-amino acids than for N-acetyl-l-specific ones.     

Secondary structure of peptides: 8. 13C n.m.r. CP/MAS investigation of solid poly(l-leucines) and poly(d-norvalines) prepared from N-carboxyanhydrides

¹³C n.m.r. CP/MAS spectra (50.3 and 75.4 MHz) of solid poly(l-lleucines) and poly(d-norvalines) measured with suitable acquisition parameters allow quantification of the composition of the secondary structure. The optimum acquisition parameters were found by systematic variation of the contact time by means of samples containing 5?0% α-helix structure. The polypeptides were prepared by primary or tertiary amine-initiated polymerizations of the corresponding amino acid NCAs and the average degrees of polymerization ($\text{DP}$) were determined by ¹H n.m.r. endgroup analysis. The mole fraction of α-helices increases with increasing $\text{DP}$; it depends on the nature of the solvent and to a lesser degree on the polymerization temperature. When prepared under identical conditions, poly(d-norvaline) samples contain more β-sheet structure than poly(l-leucine. Reprecipitation increases the α-helix content, demonstrating that a part of the original β-sheet structure is thermodynamically unstable. The presence of oligomers of $\text{DP}$ ?10 is mainly responsible for the thermodynamically stable part of the β-sheet structure. The chain growth mechanism is discussed.     

New Aspects of the Spontaneous Polymerization of Actin in the Presence of Salts

The mechanism of salt-induced actin polymerization involves the energetically unfavorable nucleation step, followed by filament elongation by the addition of monomers. The use of a bifunctional cross-linker, N,N′-(1,4-phenylene)dimaleimide, revealed rapid formation of the so-called lower dimers (LD) in which actin monomers are arranged in an antiparallel fashion. The filament elongation phase is characterized by a gradual LD decay and an increase in the yield of “upper dimers” (UD) characteristic of F-actin. Here we have used 90° light scattering, electron microscopy, and N,N′-(1,4-phenylene)dimaleimide cross-linking to reinvestigate relationships between changes in filament morphology, LD decay, and increase in the yield of UD during filament growth in a wide range of conditions influencing the rate of the nucleation reaction. The results show irregularity and instability of filaments at early stages of polymerization under all conditions used, and suggest that an earlier documented coassembling of LD with monomeric actin contributes to the initial disordering of the filaments rather than to the nucleation of polymerization. The effects of the type of G-actin-bound divalent cation (Ca²⁺/Mg²⁺), nucleotide (ATP/ADP), and polymerizing salt on the relation between changes in filament morphology and progress in G-actin-to-F-actin transformation show that ligand-dependent alterations in G-actin conformation determine not only the nucleation rate but also the kinetics of ordering of the filament structure in the elongation phase. The time courses of changes in the yield of UD suggest that filament maturation involves cooperative propagation of “proper” interprotomer contacts. Acceleration of this process by the initially bound MgATP supports the view that the filament-destabilizing conformational changes triggered by ATP hydrolysis and P_i liberation during polymerization are constrained by the intermolecular contacts established between MgATP monomers prior to ATP hydrolysis. An important role of contacts involving the DNase-I-binding loop and the C-terminus of actin is proposed.