CNDO/2 calculations of the relative stability of poly (l-proline I) and poly (l-proline II)

The CNDO/2 method using the tight binding approximation for polymers was applied to poly(l-proline I) and poly(l-proline II). The calculations were also carried out for poly(l-alanines) and model molecules which have the same backbone geometrics as those of poly(l-prolines). The results obtained show that both forms of poly(l-proline I) and poly(l-proline II) have nearly the same energy in agreement with experimental results. From the analysis of the total energy, it was found that the intrasegment energy of poly(l-proline II) was lower than that of poly(l-proline I) while the intersegment energy of poly(l-proline I) was lower than that of poly(l-proline II). This result can be considered to correspond well with the experimental fact that poly(l-proline II) is more stable in good or polar solvents and poly(l-proline I) in poor or non-polar solvents. The analysis of the total energy of poly(l-proline) leads us to the conclusion that the α and β carbons play an important role in determining the relative stability between poly(l-proline I) and poly(l-proline II) and the γ carbon does hvae a marked effect on the electronic structures of the polymers in question. This conclusion was also confirmed by comparison of the electronic structures of poly(l-prolines) with those of poly(l-alanines) and model compounds concerned.     

CNDO/2 calculation of the relative stability of poly(γ-hydroxy-l-proline)

The CNDO/2 method using the tight-binding approximation for polymers was applied to poly(γ-hydroxy-l-prolines) (PHP). The calculations were carried out for PHPs which have the same backbone structure as those of poly(l-proline I) (Pro-I) and poly(l-proline II)(Pro-II). The results obtained show the preferred orientation of the OH group at the γ-position, which is in agreement with the experimental results. The calculations were also carried out for the B form (PHP-B). The conformational stability between the A form (PHP-A) and PHP-B was explained by using the calculated results in connection with the previous experimental and theoretical treatments. From the analysis of the total energy, the dominant stabilizing factors for the two forms are discussed.     

Relative stability of poly(β-hydroxy-l-proline)

The semiempirical CNDO/2 SCF MO method using the tight-binding approximation for polymers has been applied to poly(β-hydroxy-l-proline), β-PHP, to compare the electronic structure of β-PHP with that of poly(γ-hydroxy-l-proline), γ-PHP, which we have described in a previous publication. The results obtained show the preferred orientation of the OH group at the β-position of the pyrrolidine ring. The different situation between β-PHP and γ-PHP is briefly discussed. Analysis of the calculated results shows that the energy difference between the two species is not sufficient to deny the existence of either form. This agrees well with the experimental results. The conformational stability between the trans and cis forms of the H:C:O:H group is explained by using the calculated results in connection with the previous experimental and theoretical treatments. From the analysis of the total energy, the dominant stabilizing factors are discussed.     

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).     

Relative stability of poly(β-hydroxy-l-proline)

The semiempirical CNDO/2 SCF MO method using the tight-binding approximation for polymers has been applied to poly(β-hydroxy-l-proline), β-PHP, to compare the electronic structure of β-PHP with that of poly(γ-hydroxy-l-proline), γ-PHP, which we have described in a previous publication. The results obtained show the preferred orientation of the OH group at the β-position of the pyrrolidine ring. The different situation between β-PHP and γ-PHP is briefly discussed. Analysis of the calculated results shows that the energy difference between the two species is not sufficient to deny the existence of either form. This agrees well with the experimental results. The conformational stability between the trans and cis forms of the H---:C---:O---:H group is explained by using the calculated results in connection with the previous experimental and theoretical treatments. From the analysis of the total energy, the dominant stabilizing factors are discussed.     

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.     

Characterization of novel 2-oxoglutarate dependent dioxygenases converting l-proline to cis-4-hydroxy-l-proline

Hydroxyprolines are valuable chiral building blocks for organic synthesis of pharmaceuticals. Several microorganisms producing l-proline trans-4- and cis-3-hydroxylase were discovered and these enzymes were applied to the industrial production of trans-4- and cis-3-hydroxy-l-proline, respectively. Meanwhile, other hydroxyproline isomers, cis-4- and trans-3-hydroxy-l-proline, were not easily available because the corresponding hydroxylase have not been discovered. Herein we report novel l-proline cis-4-hydroxylases converting free l-proline to cis-4-hydroxy-l-proline. Two genes encoding uncharacterized proteins from Mesorhizobium loti and Sinorhizobium meliloti were cloned and overexpressed in Escherichia coli, respectively. The functions of purified proteins were investigated in detail, and consequently we detected l-proline cis-4-hydroxylase activity in both proteins. Likewise l-proline trans-4-, cis-3-hydroxylase and prolyl hydroxylase, these enzymes belonged to a 2-oxoglutarate dependent dioxygenase family and required a non-heme ferrous ion. Although their reaction mechanisms were similar to other hydroxylases, the amino acid sequence homology was not observed (less than 40%).     

Conformational studies of sequential polypeptides containing l-β-3,4-dihydroxyphenyl-α-alanine (DOPA) and l-glutamic acid

The conformations of random and sequential copolypeptides containing l-β-3,4-dihydroxyphenyl-α-alanine (DOPA) and l-glutamic acid (Glu) as well as their protected precursors have been investigated mainly by means of circular dichroism (c.d.) spectroscopy in chloroform or trimethylphosphate as solvent. Protected and deprotected DOPA-containing polypeptides showed a positive ellipticity hand at 285 nm due to the stacked side-chains. The c.d. behaviour depended on the amino acid sequence as well as the amino acid composition. In random copolypeptides, ellipticities versus DOPA content showed a smooth variation, without any sharp changes. This supported the conclusion that poly(DOPA) is a right-handed helix. Although the ellipticities were low compared with the values of a typical α-helix, deprotected DOPA-containing sequential polypeptides are helical from the results of the induced dichroic band at 285 nm and the infrared amide I and II absorption bands. The results obtained were compared with those of sequential polypeptides containing l-tyrosine and l-Glu.     

Single crystals of a random copolypeptide composed of γ-benzyl l-glutamate and l-phenylalanine

Lamellar single crystals were formed from a random copolypeptide composed of γ-benzyl l-glutamate and l-phenylalanine at the ratio of 4 to 1. The copolypeptide takes the αhelical structure. The crystals were formed by casting dilute solutions at room temperature from a solvent consisting of a 1 to 1 mixture of chloroform and trifluoroacetic acid and were observed by electron microscopy. The average crystal thickness was 670 a in the as-polymerized sample, and 580 a in a fractionated sample. The thickness was decreased by annealing at temperatures above 110 C. A hexagonal form, a group of three orthorhombic forms (group 1), and a group of an orthorhombic form and two monoclinic forms (group II) were observed by electron diffraction. The diversity of the crystal structures is suggested to be caused by a variation in crystallization conditions during evaporation of the solvent. The hexagonal form and the structures of group I are changed into the structures of group II by annealing. The crystal structures other than the hexagonal form indicate on ordered arrangements of side chains in the crystals.     

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.     

l-Proline transport in Saccharomyces cerevisiae

Transport of l-proline into Saccharomyces cerevisiae K is mediated by two systems, one with a K_T of 31 μM and J_max of 40 nmol · s^?1 · (g dry wt.)^?1, the other with K_T > 2.5 mM and J_max of 150–165 nmol · s^?1 · (g dry wt.)^?1, The kinetic properties of the high-affinity system were studied in detail. It proved to be highly specific, the only potent competitive inhibitors being (i) l-proline and its analogs l-azetidine-2-carboxylic acid, sarcosine, d-proline and 3,4-dehydro-dl-proline, and (ii) l-alanine. The other amino acids tested behaved as noncompetitive inhibitors. The high-affinity system is active, has a sharp pH optimum at 5.8–5.9 and, in an Arrhenius plot, exhibits two inflection points at 15°C and 20–21°C. It is trans-inhibited by most amino acids (but probably only the natural substrates act in a trans-noncompetitive manner) and its activity depends to a considerable extent on growth conditions. In cells grown in a rich medium with yeast extract maximum activity is attained during the stationary phase, on a poor medium it is maximal during the early exponential phase. Some 50–60% of accumulated l-proline can leave cells in 90 min (and more if washing is done repeatedly), the efflux being insensitive to 0.5 mM 2,4-dinitrophenol and uranyl ions, to pH between 3 and 7.3, as well as to the presence of 10–100 mM unlabeled l-proline in the outside medium. Its rate and extent are increased by 1% d-glucose and by 10 μg nystatin per ml.     

Profilin oligomerization and its effect on poly (l-proline) binding and phosphorylation

Profilin is a cytoskeletal protein that interacts specifically with actin, phosphoinositides and poly (l-proline). Experimental results and in silico studies revealed that profilin exists as dimer and tetramer. Profilin oligomers possess weak affinity to poly (l-proline) due to unavailability of binding sites in dimers and tetramers. Phosphorylation studies indicate that profilin dimers are not phosphorylated while teramers are preferentially phosphorylated over monomers. In silico studies revealed that PKC phosphorylation site, S137 is buried in dimer while it is accessible in tetramer.     

Synthesis and conformational analysis of cyclo-TRI[l-valyl-d-hexahydromandelyl]

The synthesis of the cyclo-hexadepsipeptide [l-valyl-d-hexahydromandelyl]₃ is described. Examination of this macrocyclic compound by 220-MHz nuclear magnetic resonance spectroscopy shows that symmetrical conformations are stabilized in strongly polar solvents (trifluoroacetic acid, acetonitrile), whereas asymmetric conformations are preferred in nonpolar or slightly polar media such as carbon tetrachloride, chloroform, cyclohexane, and benzene.From analysis of the temperature dependence of the chemical shift and of the coupling constants, together with conformational energy calculations, a model is proposed for the preferred conformation of this molecule in nonpolar solvents.     

Phenylalanine ammonia-lyase: Mirror-image packing of d- and l-phenylalanine and d- and l-transition state analogs into the active site

The binding of substrate and product analogs to phenylalanine ammonia-lyase (EC 4.3.1.5) from maize has been studied by a protection method. The ligand dissociation constants, K_L, were estimated from the variation with [L] of the pseudo-first-order rate constants for enzyme inactivation by nitromethane. The phenylalanine analogs d- and l-2-aminooxy-3-phenylpropionic acid showed K_L, values over 20,000-fold lower than the K_m for l-phenylalanine. From these and other K_L values it is deduced that when the enzyme binds l-phenylalanine the structural free energy stored in the protein is higher than when it binds the superinhibitors. Models for binding d- and l-phenylalanine and the superinhibitors are described. The enantiomeric pairs are considered to have similar K_L values because they pack into the active site in a mirror-image relationship. If the elimination reaction approximates to the least-motion course deduced on stereoelectronic grounds, the mirror-image packing of the superinhibitors into the active site mimics the conformation inferred for a transition state in the elimination. It appears, therefore, that structural changes take place in the enzyme as the transition state conformation is approached causing stored free energy to be released. This lowers the activation free energy for the elimination reaction and accounts for the strong binding by the above analogs.     

Coordination ability of the thyrotropin releasing factor, l-pyroglutamyl-l-histidyl-l-prolinamide(TRF).III. Cu(II) and Ni(II) complexes with TRF and its di- and tripeptide analogues

The results are reported of a spectroscopic and potentiometric study of the copper(II) and nickel(II) complexes of the thyrotropin releasing factor (L-pyroglutamyl-L-histidyl-L-prolinamide, TRF) and some of its di- and tripeptide analogues Spectroscopic techniques used include absorption, circular dichroism and electron paramagnetic resonance spectroscopy TRF and pyroglutamyl-histidine behave similarly. At low pH the metal ions coordinate to the imidazole nitrogen and then cause the ionization of the amide protons of both the peptide linkage and the pyroglutamic acid with equal ease. Hence the concentration of MH_?1 L species is always very low. The C-terminal proline amide residue plays an insignificant role in the complex formation Replacement of pyroglutamic acid with picolinic acid in the hormone molecule causes a major change in the structures of its complexes. The dipeptide analogue, Pic-His. forms dimeric species with Cu(II) that are not found in Cu(II) Pyr-His orCu(II) TRF solutions The introduction of tyrosine residue in the TRF sequence in place of histidine can, in some cases, lead to the direct involvement of proline amide in the binding of metal ions, e.g. , Ni(II) Pyr-Tyr-Pro-NH₂     

Solvolysis of charged active esters of carboxylic acids with cyclo (l- or d-Glu-l-His)

Cyclic dipeptide cyclo(l- or d-Glu-l-His) carrying an anionic site and a nucleophilic site has been synthesized and used as a catalyst for the solvolysis of cationic esters in aqueous alcohols. In the solvolysis of 3-acyloxy-N-trimethylanilinium iodide (S⁺_n, n = 2 and 10) and Cl^?H₃N⁺(CH₂)₁₁COOPh(NO₂), no efficient nucleophilic catalysis was observed. On the other hand, in the solvolysis of Gly-OPh(NO₂)·HCl, Val-OPh(NO₂)·HCl and Leu-OPh(NO₂)·HCl a very efficient general base-type catalysis by cyclo(l-Glu-l-His) was observed. In particular, with the latter two substrates the catalysis by cyclo(l-Glul-His) was more efficient than that by imidazole, although the catalysis was not enantiomer-selective. The diastereomeric cyclic dipeptide cyclo(d-Glu-l-His) was almost inactive under the same conditions. Confomation of cyclo(l- or d-Glu-l-His) in aqueous solution was investigated and the structure/catalysis relationship is discussed.     

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.     

Differential fixation of poly(L-arginine) and poly(L-lysine) by tannic acid and its application to the fixation of collagen in electron microscopy

A differential fixation of poly(L-arginine) and poly(L-lysine) has been demonstrated by means of cellulose acetate electrophoresis and colorimetric titration. Electrophoresis showed that at pH 3.0 and concentrations between 0.025% and 2% the reagent interacts with poly(L-arginine) but not with poly(L-lysine). at pH 7.5, however, poly(L-lysine) also reacts, although at a higher concentration of tannic acid than was required to fix poly(L-arginine) at this pH. Colorimetric titration revealed that for poly(L-arginine) the reaction with tannic acid commences at pH 3.0 and is complete at pH 4.1 whereas for poly(L-lysine) the reaction commences at pH 3.5 and is complete at pH 4.9. It is suggested that the reaction is predominantly electrostatic. The results are discussed in relation to the use of tannic acid as a protein fixative in electron microscopy.     

Simultaneous determination of d- and l-thyroxine in human serum by liquid chromatography with electrochemical detection

A method for the determination of d- and l-thyroxine in human serum is described. The method involves extraction of thyroxine from serum and the separation of thyroxine enantiomers on a reversed-phase, high-performance liquid chromatographic column by use of a chiral eluent containing l-proline and cupric sulfate. Satisfactory resolution of the enantiomers of thyroxine, triiodothyronine, and reverse triiodothyronine can be achieved in 12 min and, employing amperometric detection to monitor the separation, the detection limit for serum thyroxine is in the range of 1–3 ng per injected sample.     

l-DOPA (l-3,4-dihydroxyphenylalanine) uptake by human red blood cells

The uptake of l-DOPA (l-3,4-dihydroxyphenylalanine) was studied in normal human red blood cells in vitro using l-[3-¹⁴C]DOPA. Uptake was slow, tending towards a distribution ratio close to unity with a half-time to equilibrium of one hour. Uptake was not Na⁺-dependent. Concentration dependence studies showed both saturable and non-saturable components of uptake, and inhibition studies using l-leucine and l-tryptophan suggest that the L and T systems of red cell amino acid uptake are involved. A powerful inhibitor of both systems, 3,4-dihydroxy-2-methylpropriophenone (U-0521), is described. It is concluded that uptake is by carrier-mediated facilitated diffusion via the L and T systems for which l-DOPA has low affinity.