Homochiral oligopeptides via surface recognition and enantiomeric cross impediment in the polymerization of racemic phenylalanine N-carboxyanhydride crystals suspended in water

As part of our program on the search of possible prebiotic routes for the formation of oligopeptides of homochiral sequence (isotactic) from racemic precursors in aqueous environment, we report the polymerization of racemic crystals of phenylalanine N-carboxyanhydrides, enantioselectively tagged with five deuterium atoms, suspended in water containing various amine initiators. Racemic mixtures of isotactic oligopeptides, comprising up to 25 repeat units of the same handedness, as the dominant component for each length, were observed in a MALDI-TOF mass spectrometry analysis. The racemic mixtures of the peptides could be desymmetrized by initiating the polymerization reaction with water-soluble methyl esters of either enantiopure alpha-amino acids or dipeptides. A three-step mechanism is proposed to account for these results: (i) Surface recognition of the chiral initiator by the chiral sites present at specific faces of the crystal; (ii) Oligopeptide elongation at the polymer/crystal interface; and (iii) Self-assembly of the short isotactic peptides into racemic antiparallel beta-sheets as templates followed by cross-enantiomeric impediment in the growth of enantiomeric chains at the peptide beta-sheet/crystal interface.     

Chiral Amplification of Oligopeptides via Polymerization in Two-dimensional Crystallites on Water

A possible role that might have been played by ordered clusters at the air/water interface for the generation of homochiral oligopeptides under prebiotic conditions has been probed by a catalyzed polymerization of amphiphilic activated alpha-amino acids that assembled as two-dimensional (2-D) crystallites at this interface. Three type of processes are described: (i) polymerization of racemates of activated alpha-amino acids that undergo spontaneous resolution into enantiomorphous 2-D crystallites to yield racemic mixtures of oligopeptides enriched with the oligomers of homochiral sequence, (ii) enhanced formation of racemic mixtures of homochiral oligopeptides via lattice-controlled polymerization within 2-D racemic compounds and (iii) generation of homochiral oligopeptides of a single handedness from chiral non-racemic mixtures of monomers that self-assemble into two different phases, racemic crystallites composed from both enantiomers and enantiomorphous crystallites of the enantiomer in excess. The structures of the 2-D crystallites have been determined by grazing incidence X-ray diffraction and the diastereoisomeric composition of the oligopeptides by matrix-assisted laser-desorption time-of-flight mass spectrometry with enantio-labeling.     

Liposome-assisted selective polycondensation of alpha-amino acids and peptides

The main question of this paper is whether and to what extend lipid bilayers can aid in the polycondensation of amino acids and peptides. This means in particular how such bilayers can favor the selection of certain sequences out of a large number of theoretical possible ones. In a first series of experiments we started from a library of Trp-containing dipeptides of the type Trp-X where X is an amino acid residue; and we could show that, when adding this mixture to the POPC liposomes containing a hydrophobic quinoline condensing agent (EEDQ), only the hydrophobic Trp-Trp dipeptide is selected out by the liposomes and transformed into a longer oligomer. Trp-oligomers up to 29 monomers long (water insoluble) could be obtained by using the matrix support of liposomes. Mixed POPC/DDAB liposomes (positive charge) were used to produce co-oligopeptides that contain Trp and Glu residues in the same sequence. Arg/Trp and His/Trp containing sequences were obtained in presence of negatively charged liposomes (mixed POPC/DOPA-liposomes). The polycondensation of racemic NCA-amino acids has been studied to clarify if homochiral sequences are produced preferentially in presence or absence of liposomes. LC-MS and isotope labeling of the L-amino acid, participating in the polymerization reaction achieved this on the level of a direct product analysis. So the individual stereoisomer distribution up to a polymerization degree of 10 (in the case of Trp) could be determined. The data for Trp and other amino acids (Leu, Ile) and amino acid mixtures (Trp/Leu, Trp/Ile, Leu/Ile and Trp/Leu/Ile) show that homochiral sequences are produced preferentially if compared with a random (Bernoulli) distribution.     

Freezing effect on chirality generation of DL-alanine-N-carboxy-anhydride oligomerization in aqueous solution

This article is concerned with a study of the role of ice in the synthesis of oligopeptides containing L- or D-enantiomeric excess (ee) from racemic alanine. With this aim, the oligomerization of DL-alanine-N-carboxyanhydride was investigated by keeping this activated derivative in liquid (+22 degrees C) or frozen (-20 degrees C) aqueous solutions for 30 days. The aqueous solution of the peptide mixtures were gel-filtered and the aliquots of the fractions were completely hydrolyzed to alanine monomers. These monomers were then derivatized with 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide (Marfey's reagent) and analyzed by RP-HPLC to reveal the occasional enantiomeric excess of L- or D-Ala. The mass spectrometry of the gel-filtered fractions pointed to open-chain peptide mixtures together with a slight amount of cyclic ones, where the residue numbers ranged between 5-8. Our studies indicated that an enantiomeric excess of L- or D-Ala appeared in some oligopeptide fractions. Their excesses were significantly larger in the frozen than liquid solution. Speculations are made as concerns the implications of our findings in the events of prebiotic chemistry.     

Stimuli-responsive zwitterionic block copolypeptides: poly(N-isopropylacrylamide)-block-poly(lysine-co-glutamic acid)

Synthesis of novel zwitterionic block copolypeptides, poly(N-isopropylacrylamide)-block-poly(L-glutamic acid-co-L-lysine) [PNiPAM(n)(PLG(x)-co-PLLys(y))m , where n is the number-average degree of polymerization (DP(n)) of PNiPAM block, x and y are the mole fraction of glutamic acid and lysine residues, respectively, and m is the total DP(n) of the peptide block], and their stimuli-responsiveness to temperature and pH variation in aqueous solutions are described. Initiated with the amino-terminated poly(N-isopropylacrylamide) (PNiPAM(n)-NH2), ring-opening polymerization (ROP) of a mixture of gamma-benzyl-L-glutamate N-carboxyanhydride (BLG-NCA), and Boc-L-lysine N-carboxyanhydride (BLLys-NCA) afforded the block copolypeptides PNiPAM(n)(PBLG(x)-co-PBLLys(y))m, with a poly(N-isopropylacrylamide) block together with a random copolypeptide block, which was then deprotected with HBr/trifluoroacetic acid into the double hydrophilic block copolypeptides, PNiPAM(n)(PLG(x)-co-PLLys(y))m. Their block ratios and lengths, as well as the amino acid residue ratios in the random copolypeptide block are varied (n = 360, x = 0.4-0.5, y = 0.4-0.6, and m = 220-252). The secondary structures of the copolypeptides in aqueous solution at different pH conditions were examined. Phase transitions in aqueous solutions induced by both pH and temperature variation were investigated by (1)H NMR spectroscopy. The transitions induced by temperature were also explored by turbidity measurements using UV/vis spectroscopy for their lower critical aggregation temperature (LCAT) determination. Furthermore, these aggregation processes were followed by dynamic light scattering measurements.     

The radiolysis and radioracemization of poly-L-leucines.

The brief history of the discovery of radioracemization, the racemization of an optically active substance induced by ionizing radiation, is reviewed. Our early studies involving the radiolysis and radioracemization of D- and L-leucine using gamma radiation from a 111-TBq 60Co gamma-ray source are described briefly, as are later experiments involving other protein amino acids and their salts, as well as the nonprotein amino acid, isovaline. The implications of the results of such studies for the Vester-Ulbricht mechanism which proposes longitudinally polarized beta radiation as the origin of molecular chirality, for the cosmological question of the enantiomeric compositions of amino acids in the Murchison meteorite, and for the use of D/L ratios of amino acids for geochronological and geothermal estimates are reviewed briefly. These past radiolysis-radio- racemization studies have involved only monomeric amino acids. The present research, extending such investigations to two homochiral L-leucine polypeptides, (L-Leu)10 and (L-Leu)78, was undertaken to see if a polymer of an amino acid might be more stable to radiolysis and radioracemization than the corresponding monomer. It was found that these polypeptides were more stable to radiolysis than was the leucine monomer, but that the extents of radioracemization in all samples were comparable.     

Differential transport properties of D-leucine and L-leucine in the archaeon, Halobacterium salinarum

The transport of D-leucine was compared with that of L-leucine in Halobacterium salinarum. When a high-outside/low-inside Na+ gradient was imposed, D-leucine as well as L-leucine accumulated in envelope vesicles, supporting the hypothesis that D-leucine is transported via a symport system along with Na+. Kinetic analyses, including inhibition experiments, indicated that both enantiomers are transported via a common carrier. However, a Hill plot indicated a single binding site for Na+ during L-leucine transport, but dual binding sites for Na+ during D-leucine transport. Furthermore, D-leucine transport was dependent on electrical membrane potential, suggesting that a transporter bound with D-leucine is positively charged. L-leucine transport was slightly, if at all, dependent on membrane potential, suggesting that a transporter bound with L-leucine is electrically neutral. These results indicate that the leucine carrier in Halobacterium salinarum translocates two moles of Na+ per mole of D-leucine, and one mole of Na+ per mole of L-leucine.     

Experiments on the origins of optical activity

Two recent reports claim that (1) aqueous L-aspartic acid polymerizes faster than D-Asplin the presence of kaolin at 90°, and (2) L-phenylalanine is adsorbed by kaolin more extensively than D-Phe at pH 6 (the reverse being true at pH 2). The novelty of these observations and their potential significance for the origin of optical activity has prompted us to duplicate these experiments using more sensitive methods. L- and D, L-Asp in 0.01M solution were incubated with kaolin at 90° for 8 days. Careful examination of the aqueous residues from such experiments failed to demonstrate any preferential polymerization of L-Asp over D-Asp, or indeed any significant gross polymerization of Asp at all. In other experiments 0.001M solutions of D, L-Phe at pH 6 and pH 2 were stirred with large excesses of kaolin for 24 hr, and the aqueous extracts from these mixtures were examined for gross adsorption using the amino acid analyzer. No significant gross adsorption was noted. We then looked for asymmetric adsorption in the aqueous residues using optical ratatory dispersion, gas chromatography and thin layer chromatography. By none of these analytical criteria could we find any evidence whatsoever for the preferential adsorption of D- versus L-Phe from either pH 6 or pH 2 solutions. Finally, in experiments bearing on the origin of optical activity by parity violation during β-decay, we have irradiated solid samples of D-, L- and D, L-leucine in a 61700 Ci Sr-90 source at Oak Ridge National Lab. for 1.34 yr (total dose: 4.2×10⁸ rad). Gas chromatographic examination of the (appropriately derivitized) recovered samples showed that the L-Leu was 16.7% decomposed, the D-Leu 11.4% and the D,L-Leu 13.8% decomposed. The recovered D,L-Leu sample had a gas-chromatographically determined enantiomeric composition of 50.8% D-leu and 49.2% L-Leu. These data, though very close to expermental error, may indicate a slight preferential radiolysis of L-Leu compared to D-Leu by the Bremsstrahlung from Sr-90 β-decay. These high intensity irradiation experiments are being continued on a prolonged basis in order to reach more definitive conclusions.     

Enantiomeric Crystallization from DL-Aspartic and DL-Glutamic Acids: Implications for Biomolecular Chirality in the Origin of Life

Amino acids in living systems consist almost exclusively of the L-enantiomer. How and when this homochiral characteristic of life came to be has been a matter of intense investigation for many years. Among the hypotheses proposed to explain theappearance of chiral homogeneity, the spontaneous resolution of conglomerates seems one of the most plausible. Racemic solids may crystallize from solution either as racemic compounds(both enantiomeric molecules in the same crystal), or lesscommonly as conglomerates (each enantiomer molecule separate indifferent enantiomeric crystals). Only conglomerates can developa spontaneous resolution (one of the enantiomeric molecule crystallizes preferentially, the other one remains in solution).Most of natural amino acids are racemic compounds at moderatetemperatures. How can we expect a hypothetical spontaneous resolution of these amino acids if they are not conglomerates?In this paper we show how DL-aspartic and DL-glutamic amino acids(racemic compounds), crystallize at ambient conditions as trueconglomerates. The experimental conditions here described,that allows this `anomalous' behaviour, could be also found innatural sedimentary environments. We suggest that these experimental procedures and its natural equivalents, have apotential interest for the investigation of the spontaneous resolution of racemic compounds comprising molecules associatedwith the origin of life.     

Solid Tryptophan as a Pseudoracemate: Physicochemical and Crystallographic Characterization

The crystalline nature of solid tryptophan has been characterized by X‐ray single crystal and powder diffraction analyses, differential scanning calorimetry, as well as measurement of solid–liquid equilibrium in water/isopropanol solution. Both the thermodynamic and crystallographic investigations have demonstrated unambiguously that solid tryptophan crystallizes in the form of a pseudoracemate (i.e., solid solution) with maximum melting over the entire enantiomeric composition range. Comparative single‐crystal X‐ray studies show that the crystal structures of racemic and enantiomeric tryptophan give very similar solid‐state packing geometries dictated by hydrogen bonding interactions. Our results indicate that the insignificant difference between homochiral and heterochiral interactions accounts for the formation of a pseudoracemate for this system. Chirality 27:88–94, 2015. © 2014 Wiley Periodicals, Inc.     

Search for functional domain boundaries and localization of functional sites based on oligopeptide vocabularies]

A new method based on the analysis of oligopeptide composition of the amino acid sequences from different protein families is presented. We assume, that any protein family can be characterized by the set of oligopeptides (oligopeptides vocabulary). We demonstrate, that oligopeptides vocabulary comparison can distinguish different families from each other and from random sequences. It should be noted, that this comparison can be successfully performed on the set of only 25 dipeptides and without preliminary alignment. We demonstrate, that characteristic peptides are localized in the regions of functional significance, as shown on the example of GTP-binding domain of translation elongation factors. We suggest how to use this method to localize the boundaries of functional domains in amino sequences. On the example of few functional domains we demonstrate, that the average error of prediction does not exceed 3-4 amino acid residue.     

A comparison of three models for the diffusion of oxygen in electrolyte solutions

Diffusion of oxygen through aqueous solutions is of great importance in biological systems. In this work, three models for the diffusion of oxygen through aqueous salt solutions are compared. One model uses mole fraction as the driving force (Fick's Law) and another uses chemical potential. The third model uses the gradient in oxygen activity as the driving force. This new model was chosen because of the availability of oxygen electrodes which directly measure oxygen activity in aqueous solution. These models have been used to reevaluate the technique of measuring O(2) diffusivities. We show that Pick's Law diffusion coefficients do not vary strongly with salt concentration as was erroneously reported in the literature. In addition, we compare the predicted O(2) fluxes of the three models over a wide range in O(2) concentrations. For oxygen concentrations of biological interest, the three models give identical predictions of the flux.     

A novel and efficient enzymatic method for the production of peptides from unprotected starting materials

We report herein the development of a novel and efficient enzymatic method for the production of oligopeptides. This newly discovered method is a simple, cost-effective process, using unprotected amino acids as substrates in an aqueous solution and producing peptides in high yield. The target of our initial screen was l-alanyl-L-glutamine, a dipeptide of significant industrial interest by virtue of its widespread use in infusion therapy. By means of the screening of microorganisms that can catalyze the peptide-forming reaction producing l-alanyl-L-glutamine from L-alanine methylester (acyl donor) and L-glutamine (nucleophile), we discovered that Empedobacter brevis ATCC 14234 produced l-alanyl-L-glutamine most efficiently. The newly found enzyme purified from E. brevis ATCC 14234 facilitates significantly high production yields of l-alanyl-L-glutamine from L-alanine methylester and L-glutamine in an aqueous solution--more than 80% yield based on L-alanine methylester. In addition, this enzyme has wide substrate specificity--both for acyl donors and nucleophiles--and can catalyze peptide-forming reactions not only to produce various dipeptides from the corresponding amino acid esters and amino acids but also to produce various oligopeptides from the corresponding amino acid esters and peptides.     

A model for the enantiomeric enrichment of polypeptides on the primitive Earth

A mixture of D- and L-leucine N-Carboxyanhydride (NCA) having an enantiomeric composition of 65.6% L- and 34.4% D-isomer (i.e. 31.2% enantiomeric excess (e.e.)) was polymerized to the extent of 52% with sodium methoxide initiator to yield a polyleucine product the enantiomeric composition of which was 72.7% L- and 27.3% D-leucine (45.4% e.e.). This polymer was in turn partially hydrolyzed by acid, whereupon the unhydrolyzed polyleucine residue was found to have an enantiomeric composition of 77.5% L- and 22.5% D-leucine (55.0% e.e.). Thus the e.e. increase in the partial polymerization step (14.2%) and the partial hydrolysis step (9.6%) combined to total 23.8% for the overall polymerization-hydrolysis sequence. On the basis of these model experiments it is proposed that repetitive partial polymerization hydrolysis reactions, driven by environmental dry-wet cycles, might have been operative on the primitive Earth to engender the abiotic evolution of optically enriched polypeptides.Presented at the Fifth College Park Colloquium on Chemical Evolution, University of Maryland, College Park, MD, October 31, 1980. A less detailed version of the cyclic mechanism of Figure 1 was originally proposed at International Symposia on The Origins of Optical Activity in Nature, Chemical Institutes of Canada, University of British Columbia, Vancouver, B.C. June 5, 1979, and on Generation and Amplification of Chirality in Chemical Systems, University of Bremen, Bremen, F.R.G., July 17, 1980.     

Using micellar mole fractions to assess membrane protein stability in mixed micelles

The increased focus on the structural and physical properties of membrane proteins has made it critical to develop methods that provide a reliable estimate of membrane protein stability. A simple approach is to monitor the protein's conformational changes in mixed detergent systems, typically consisting of an anionic (denaturing) and non-ionic (non-denaturing) component. Linear correlations between, e.g., the melting temperature and the bulk mole fraction of the anionic component have been observed. However, a potential complication is that the bulk mole fraction is not identical to the mole fraction in the mixed micelle, which is the local environment experienced by the membrane protein. Here, we present an extensive analysis of the thermal stability of the membrane-integrated domain of the outer membrane protein AIDA in the presence of different mixed micelles. In the micelle system SDS-octyl-polyoxyethylene, the melting temperature in the absence of SDS extrapolates to 113 degrees C using bulk mole fractions. However, for mixed micelles involving short-chain detergents or phospholipids, the melting temperature calculated using bulk mole fractions reaches values up to several hundred degrees higher than 113 degrees C and can only be obtained by extrapolation over a narrow mole fraction interval. Furthermore, there is a non-linear relationship between the melting temperature and bulk mole fractions for mixed micelle systems involving cationic detergents (also denaturing). We show that if we instead use the micellar mole fraction as a parameter for denaturing detergent strength, we obtain linear correlations which extrapolate to more or less the same value of the melting temperature. There remains some scatter in the extrapolated values of the melting temperature in different binary systems, which suggest that additional micellar interactions may play a role. Nevertheless, in general terms, the mixed micellar composition is a good parameter to describe the membrane protein's microenvironment. Note, however, that for the mixed micelle system involving SDS and dodecyl maltoside, which has been used by several research groups to determine membrane protein stability, the estimate provided by bulk mole fraction leads to similar values as that of micellar mole fractions.     

Using micellar mole fractions to assess membrane protein stability in mixed micelles

The increased focus on the structural and physical properties of membrane proteins has made it critical to develop methods that provide a reliable estimate of membrane protein stability. A simple approach is to monitor the protein's conformational changes in mixed detergent systems, typically consisting of an anionic (denaturing) and non-ionic (non-denaturing) component. Linear correlations between, e.g., the melting temperature and the bulk mole fraction of the anionic component have been observed. However, a potential complication is that the bulk mole fraction is not identical to the mole fraction in the mixed micelle, which is the local environment experienced by the membrane protein. Here, we present an extensive analysis of the thermal stability of the membrane-integrated domain of the outer membrane protein AIDA in the presence of different mixed micelles. In the micelle system SDS-octyl-polyoxyethylene, the melting temperature in the absence of SDS extrapolates to 113 °C using bulk mole fractions. However, for mixed micelles involving short-chain detergents or phospholipids, the melting temperature calculated using bulk mole fractions reaches values up to several hundred degrees higher than 113 °C and can only be obtained by extrapolation over a narrow mole fraction interval. Furthermore, there is a non-linear relationship between the melting temperature and bulk mole fractions for mixed micelle systems involving cationic detergents (also denaturing). We show that if we instead use the micellar mole fraction as a parameter for denaturing detergent strength, we obtain linear correlations which extrapolate to more or less the same value of the melting temperature. There remains some scatter in the extrapolated values of the melting temperature in different binary systems, which suggest that additional micellar interactions may play a role. Nevertheless, in general terms, the mixed micellar composition is a good parameter to describe the membrane protein's microenvironment. Note, however, that for the mixed micelle system involving SDS and dodecyl maltoside, which has been used by several research groups to determine membrane protein stability, the estimate provided by bulk mole fraction leads to similar values as that of micellar mole fractions.     

Oligonucleotides as probes for studying polymerization reactions in dilute aqueous solution

We have prepared a [³²P]-labeled oligonucleotide probe carrying a free primary amine at its 3′terminus. This probe is used to initiate polymerization of aziridine (ethyleneimine) in aqueous solution. The nature of the oligomeric products and the kinetics of their formation are then monitored by gel electrophoresis. Our results are generally consistent with those obtained using conventional techniques. We have also investigated the effect of polyanionic templates on the rate of oligomerization of aziridine. We find that water-soluble polyanions generally accelerate the polymerization. The sodium salt of polymethacrylic acid is the most effective of the templates that we studied. The methods introduced in this paper should be applicable to a variety of polymerization reactions in aqueous solution. They should greatly simplify the screening of potentially prebiotic polymerization reactions. Correspondence to: L.E. Orgel on sabbatical leave     

Predominant torsional forms adopted by oligopeptide conformers in solution: parameters for molecular recognition.

In this paper, we describe the predominant conformational forms adopted by tripeptides and higher oligopeptides in aqueous solution. About 50 tripeptides and almost 20 higher oligopeptides (4-6 residues) were subjected to conformational analysis using SYBYL Random Search. As with dipeptides (Grail BM, Payne JW. J. Peptide Sci. 2000; 6: 186-199), both tripeptides and higher oligopeptides were found to occupy relatively few combinations of psi-phi space that were distinct from those associated with predominant protein secondary structures (e.g. helices and beta-sheets). Again, the preferred psi (psi) values for the first residue (i - 1) were in sectors encompassed by the ranges from +150 degrees to +/-180 degrees, +60 degrees to +90 degrees and -60 degrees to -90 degrees, which were combined with preferred phi (phi) values for the second residue (i) in sectors with ranges from -150 degrees to +/-180 degrees, -60 degrees to -90 degrees and +30 degrees to +60 degrees. It was notable that tripeptides and, to a greater extent, higher oligopeptides adopted an initial psi (psi) (Tor2) from +150 degrees to +/-180 degrees. For tripeptides, their N-C distances (distance between N-terminal nitrogen and C-terminal carbon atoms) distribute about 6.5 A to give shorter, 'folded' conformers that are similar in length to dipeptides, and longer, 'extended' conformers that are distinct. Furthermore, for higher oligopeptides, their N-C distances did not increment in relation to their increasing number of residues and short, 'folded' conformers were still present. These findings have a bearing upon the recognition of these molecules as substrates for widely distributed peptidases and peptide transporters.     

Direct, controlled synthesis of the nonimmunogenic, hydrophilic polymer, poly(N-(2-hydroxypropyl)methacrylamide) via RAFT in aqueous media

Poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) is a nonimmunogenic, neutral-hydrophilic polymer currently employed in the delivery of anticancer drugs. Herein, we report conditions that facilitate the direct, controlled RAFT polymerization of HPMA in aqueous media. We demonstrate that the use of 4-cyanopentanoic acid dithiobenzoate and 4,4'-azobis(4-cyanopentanoic acid) as the chain transfer agent (CTA) and initiating species, respectively, in the presence of an acetic acid buffer solution at 70 degrees C is a suitable condition leading to controlled polymerization. The "living" nature of these polymerizations is demonstrated via chain-extension of an HPMA macroCTA to yield the corresponding poly(HPMA-b-HPMA) "homopolymer".