Amino Acid Monomers Research Articles

Synthesis and Properties of Alternating Polypeptoids and Polyampholytes as Protein-Resistant Polymers

Alternating polypeptoids are particularly appealing because alternating sequence may impart highly ordered structure and special functions, while their simple synthesis still remains a key challenge. We describe that natural amino acid monomers can be polymerized via Ugi reaction in a step-growth fashion as an AA' BB' system, which leads to alternating polypeptoids with molecular weight up to 15 kg/mol. These alternating polypeptoids are thermally responsive and exhibit cloud points ( Tcp) between 27 and 37 °C. Importantly, the marriage of high functionality of amino acids with Ugi reaction also enables the preparation of polypeptoids encoding both protected amino and carboxyl groups in the side chains with alternating arrangement. The cleavage of the protecting groups leads to alternating polyampholytes without any compositional drift. Such alternating polyampholytes not only exhibit high water solubility (>100 mg/mL) but also demonstrate the ability to resist aggregation with proteins. Moreover, the cell viability measurements reveal that these materials have minimal cytotoxicity to HeLa cells. Overall, this study offers us a simple way to prepare a variety of polypeptoids and polyampholytes as new protein-resistant materials for bioapplications.

Peptide Solubility Limits: Backbone and Side-Chain Interactions.

We calculate the solubility limit of pentapeptides in water by simulating the phase separation in an oversaturated aqueous solution. The solubility limit order followed by our model peptides (GGRGG > GGDGG > GGGGG > GGVGG > GGQGG > GGNGG > GGFGG) is found to be the same as that reported for amino acid monomers from experiment (R > D > G > V > Q > N > F). Investigation of dynamical properties of peptides shows that the higher the solubility of a peptide is, the lower the time spent by the peptide in the aggregated cluster is. We also demonstrate that fluctuations in conformation and hydration number of peptide in monomeric form are correlated with the solubility of the peptide. We considered energetic mechanisms and dynamical properties of interbackbone CO-CO and CO···HN interactions. Our results confirm that CO-CO interactions more than the interbackbone H-bonds are important in peptide self-assembly and association. Further, we find that the stability of H-bonded peptide pairs arises mainly from coexisting CO-CO and CO···HN interactions.

Studies on sugar puckering and glycosidic stabilities of 3'-amino-5'-carboxymethyl-3',5'-dideoxy nucleoside mimics.

The synthesis of nucleoside amino acid monomers and dimers has been carried out to evaluate and characterize the impact of the neutral amide backbone on key attributes like puckering of the sugar rings and glycosidic bond strengths of these analogs. The conformational analysis suggests that amide-linked nucleotides have a high predilection towards N-type conformers. The glycosidic bond strength was found to be slightly weaker compared to ribonucleosides under acidic conditions at high temperatures. The results will be helpful to explore in future the development of fully amide-linked oligonucleotides for therapeutic purposes.

Hyperbranched polypeptides synthesized from phototriggered ROP of a photocaged Nε-[1-(2-nitrophenyl)ethoxycarbonyl]-l-lysine-N-carboxyanhydride: microstructures and effects of irradiation intensity and nitrogen flow rate

A new photocaged amino acid monomer Nε-(1-(2-nitrophenyl)ethoxycarbonyl)-l-lysine-N-carboxyanhydride (NPE-Lys NCA) was designed to directly synthesize hyperbranched polypeptides by phototriggered ROP.

Geometrical effect of 3D-memory cavity on the imprinting efficiency of transition-state analogue-built artificial hydrolases

Highlighting biomimetic recognition and shape-selective binding, highly crosslinked transition-state analogue-imprinted artificial hydrolases are synthesized from amino acid monomers. Two different transition-state analogues—TSAs—are used for the preparation of the enzyme mimic polymer catalysts. The catalytic hydrolysis of amino acid p-nitroanilides is found to be dependent on the geometry of the TSA imprints on the polymer matrix. The imprinted TSA facilitates tetrahedral complementarity to the transition-state intermediate of hydrolysis. The geometry of the 3D-memory cavity fabricated by the print molecule along with the catalytic entities is accountable for the higher catalytic competence of the imprinted enzyme mimics over the non-imprinted control polymers. The super crosslinked macroporous polymer matrix, in which the catalytic functions are suitably oriented in a ‘3D pocket’ for selective binding of the substrate through H-bonding, is accountable for the high imprinting efficiency of the imprinted polymer catalysts. The imprinted mimics are found to be exhibiting cross-selectivity in their catalytic properties. Even though the mimics could not compete with native enzyme, they exhibit higher thermal stability, increased shelf-life and superior reusability.

Binding of the GTPase Sar1 to a Lipid Membrane Monolayer: Insertion and Orientation Studied by Infrared Reflection⁻Absorption Spectroscopy.

Membrane-interacting proteins are polyphilic polymers that engage in dynamic protein–protein and protein–lipid interactions while undergoing changes in conformation, orientation and binding interfaces. Predicting the sites of interactions between such polypeptides and phospholipid membranes is still a challenge. One example is the small eukaryotic GTPase Sar1, which functions in phospholipid bilayer remodeling and vesicle formation as part of the multimeric coat protein complex (COPII). The membrane interaction of Sar1 is strongly dependent on its N-terminal 23 amino acids. By monolayer adsorption experiments and infrared reflection-absorption spectroscopy (IRRAS), we elucidate the role of lipids in inducing the amphipathicity of this N-terminal stretch, which inserts into the monolayer as an amphipathic helix (AH). The AH inserting angle is determined and is consistent with the philicities and spatial distribution of the amino acid monomers. Using an advanced method of IRRAS data evaluation, the orientation of Sar1 with respect to the lipid layer prior to the recruitment of further COPII proteins is determined. The result indicates that only a slight reorientation of the membrane-bound Sar1 is needed to allow coat assembly. The time-course of the IRRAS analysis corroborates a role of slow GTP hydrolysis in Sar1 desorption from the membrane.

Pre-exfoliated nanoclay through two consecutive reaction systems: Silane functionalization followed by grafting of amino acid monomers

This work presents a novel way to produce a thermally stable nanoclay with an increased interlayer space, which are the essential requirements in fabricating clay-polymer nanocomposites. Sodium montmorillonite (Na-Mt) was functionalized through two separate, consecutive reaction systems. Functionalization with an aminosilane was first performed, in order to produce reactive groups at the silicate nanolayers. In the second step, amino acid monomers were employed for a further reaction with silane-modified nanoclay. X-ray diffraction results demonstrated an increased d001-value (24Å) using 10mmol γ-aminobutyric acid. The 001 reflection peak disappeared when 5mmol ω-aminoundecanoic acid/g Mt was used as the second type of amino acid. Transmission electron microscopy images of modified Mt with 10mmol ω-aminoundecanoic acid exhibited a well separated or exfoliated structure of nanolayers. Thermogravimetric measurements indicated a trend of increasing thermal stability of the modified nanoclays (350°C to 400°C) with increasing amounts of initial ω-aminoundecanoic acid. Based on these results, optimizing the modifiers and synthesis conditions can control the properties of modified nanoclay. Tensile modulus and strain at break of HDPE/2 mass% modified Mt showed 10% and 14% enhancements, respectively, due to the increased d001-value of the nanofiller, which results in greater filler-polymer interaction.

Wet and Functional Adhesives from One‐Step Aqueous Self‐Assembly of Natural Amino Acids and Polyoxometalates

AbstractSessile organisms have undergone long‐term evolution to develop the unique ability by positioning themselves on wet solid surface through secreting adhesive proteins. The present study reveals that natural amino acid monomers can also exhibit similar adhesion capacity. This kind of biomimetic adhesives were created by the one‐step aqueous assembly of basic amino acids with assistance of anionic polyoxometalates. The polyoxometalates not only serve as multivalent scaffold to initiate the supramolecular cross‐linking of amino acid molecules, but also function as a redox component, bestowing the wet adhesives with electrochromic features.

Wet and Functional Adhesives from One-Step Aqueous Self-Assembly of Natural Amino Acids and Polyoxometalates.

Sessile organisms have undergone long-term evolution to develop the unique ability by positioning themselves on wet solid surface through secreting adhesive proteins. The present study reveals that natural amino acid monomers can also exhibit similar adhesion capacity. This kind of biomimetic adhesives were created by the one-step aqueous assembly of basic amino acids with assistance of anionic polyoxometalates. The polyoxometalates not only serve as multivalent scaffold to initiate the supramolecular cross-linking of amino acid molecules, but also function as a redox component, bestowing the wet adhesives with electrochromic features.

A treasure reservoir of genetic resource of tea plant (Camellia sinensis) in Dayao Mountain

Components of 29 wild type tea single plants collected from Dayao Mountain, in Guangxi province, South China, were investigated. They included tea polyphenols, free amino acids, catechin, amino acid and alkaloid monomers etc. Genetic diversity and clustering analyses were conducted based on the main biochemical components. Meanwhile, genetic relationships among 6 wild type tea plants representing 3 tea populations of Daoyao Mountain with 15 tea varieties grown in Yunnan, Guangdong, Hunan, Fujian provinces were analyzed by random amplified polymorphic DNA. The results showed that wild type tea plants from Dayao Mountain were of rich genetic diversity. Furthermore, some tea germplasms with high quality, including high contents of amino acids, high epigallocatechin gallate, and high caffeine have been discovered. These wild type tea germplasms are of high values for further development values due to their geographical uniqueness.

A Generalized Michaelis-Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon.

The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a 'biologically motivated' generalization of the Michaelis-Menten formula for the average rate of enzymatic reactions. This generalized Michaelis-Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.

Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM.

A new QTAIM interpretation of the Ramachandran plot is formulated from the most and least facile eigenvectors of the second-derivative matrix of the electron density with a set of 29 magainin-2 peptide conformers. The presence of QTAIM eigenvectors associated with the most and least preferred directions of electronic charge density explained the role of hydrogen bonding, HH contacts and the glycine amino acid monomer in peptide folding. The highest degree of occupation of the QTAIM interpreted Ramachandran plot was found for the glycine amino acid monomer compared with the remaining backbone peptide bonds. The mobility of the QTAIM eigenvectors of the glycine amino acid monomer was higher than for the other amino acids and was comparable to that of the hydrogen bonding, explaining the flexibility of the magainin-2 backbone. We experimented with a variety of hybrid QTAIM-Ramachandran plots to highlight and explain why the glycine amino acid monomer largely occupies the 'forbidden' region on the Ramachandran plot. In addition, the new hybrid QTAIM-Ramachandran plots contained recognizable regions that can be associated with concepts familiar from the conventional Ramachandran plot whilst retaining the character of the QTAIM most and least preferred regions.

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures.

In this study, the solution structures of the homooligomers of a conformationally constrained bicyclic proline-type β-amino acid were studied by means of molecular dynamics (MD) calculations in explicit methanol and water using the umbrella sampling method. The ratio of trans-amide and cis-amide was estimated by NMR and the rotational barrier of the amide of acetylated bicyclic amino acid monomer was estimated by two-dimensional (2D) exchange spectroscopy (EXSY) or line-shape analysis. A bias potential was introduced with respect to the amide torsion angle ω to enhance conformational exchange including isomerization of amide bonds by lowering the rotation energy barrier. After determination of reweighting parameters to best reproduce the experimental results of the monomer amide, the free energy profile around the amide torsion angle ω was obtained from the MD trajectory by reweighting of the biased probability density. The MD simulation results support the existence of invertomers of nitrogen-pyramidalized amide. Furthermore, extended structures with a high fraction of trans-amide conformation appear to be increasingly stabilized as the oligomer is elongated, both in methanol and in water. Our conformational analysis of natural and non-natural tertiary-amide-based peptide oligomers indicates that these oligomers preferentially adopt a limited number of conformations.

Amidase activity of phosphonate TSA-built polymer catalysts derived from organic monomers in the amidolysis of amino acid p-nitroanilides

Highly crosslinked transition state analogue imprinted macromatric polymer catalysts having imidazole, carboxyl and hydroxyl functional groups in the catalytic sites were synthesized as chymotrypsin mimics using achiral organic monomers 4-vinylimidazole, methacrylic acid, allyl alcohol and phenyl-1-(N-benzyloxycarbonylamino)-2-(phenyl)ethyl phosphonate (transition state analogue of ester and amide hydrolytic reactions) as the template. The catalytic properties of the enzyme mimics were investigated in the amidolytic reactions of l-amino acid p-nitroanilides and correlated to the amidase activities of the catalysts derived from chiral methacryloyl-l-amino acid monomers methacryloyl-l-histidine, methacryloyl-l-aspartic acid and methacryloyl-l-serine. A two-fold enhancement in rate acceleration, substrate specificity, substrate shape-selectivity and stereoselectivity was observed for polymers made up of flexible amino acid monomers compared to the copolymers of organic monomers. The pre-polymerization complex of TSA with methacryloyl-l-amino acid monomers fabricates specific 3D-memory cavity preferentially of l-enantiomer of the TSA in the polymer matrix while the achiral organic monomers designs both L- and D- cavities The effect of crosslink density on the catalytic efficiencies of the polymer catalysts was also investigated. Replacement of allyl alcohol by vinylpyridine afforded catalyst with better enzymatic activity.

Effects of current regimes and oxygenation on particulate matter preservation on the Namibian shelf: Insights from amino acid biogeochemistry

Many reconstructions of past biogeochemical states rely on proxies such as δ15N that in turn are affected by the preservation state of organic matter. N-turnover processes in the upwelling system on the Namibian shelf are difficult to reconstruct because lateral particle advection and differential degradation under oxic to anoxic conditions complicate particle tracing in suspended matter and surface sediments as well as the interpretation of sedimentary δ15N records. We analysed the amino acid composition of suspended matter, sinking particles, phytoplankton biomass and surface sediments in order to investigate the degradation pathway of organic matter from the sea surface to the surface sediment. A principal component analysis carried out with the amino acid data set results in a triangular-shaped model. Two branches evolve from phytoplankton biomass on the apex: The suspended matter branch is characterized by relatively enhanced contents of Glu, Ser and Leu, whereas the non-protein amino acids and Lys mark the sinking particle and sediment branch. The results suggest that both pools have taken different diagenetic pathways and that there is only limited exchange between them. The preservation state of organic matter in surface sediments within the oxygen minimum zone is generally better than on the oxic outer shelf, where organic matter preservation depends on water depth.A vertical increase in δ15N ratios from phytoplankton biomass to the surface sediment by ~2.5‰ is attributed to early diagenetic degradation in the water column and at the water/sediment interface. The δ15N ratios of sediments are mainly controlled by the N-isotope signature of nitrate on the outer shelf and upper continental slope. Nutrient-enriched deep water ascends at the shelf breaks due to the influence of internal waves and tides or curl-driven shelf break upwelling. The δ15N of upwelling nitrate at the shelf breaks is ~3‰ lower than that of nitrate from the inner shelf. This difference in nitrate sources is expressed in a band of decreasing δ15N ratios of surface sediments at the shelf breaks. The hydrodynamic upwelling regime at the shelf breaks flushes significant amounts of suspended matter from the mesopelagic ocean across the shelf break as indicated by amino acid monomer patterns of suspended matter.

Effect of Aspartic Acid and Glycine on Calcite Growth

Organic molecules control calcite growth and crystal morphology, influence biomineralization processes, and offer clues for optimizing antiscalants for industry. Here we quantified the effect of amino acid monomers, aspartic acid (Asp1), and glycine (Gly1), and their polymers (Aspn, Asp5, and Gly5), on calcite growth rate, in a constant composition setup. Asp1 and its polymers inhibit growth, with rate decreasing as amino acid chain length increases. For 2 mM Asp1, fractional inhibition (FI, where 1 represents complete inhibition) was 0.54; for 0.0012 mM Aspn, FI = 0.94. Gly1 and Gly5 only marginally affect growth (−0.1 < FI < 0.1); indeed, they slightly promote growth at most tested concentrations. Fitting of adsorption isotherms (Langmuir, Langmuir–Freundlich, Flory–Huggins) confirmed that Asp polymers adsorb strongly, explaining their strong control on calcite growth, but Gly1 and Asp1 adsorb less due to competition with carbonate ions. ΔGads (Aspn) = −39 kJ/mol; ΔGads (Asp5) = −50 kJ/mol; ΔGads (Asp1)...

In Silico Approach to Finding New Active Compounds from Histone Deacetylase (HDAC) Family

Histone Deacetylase (HDAC) enzymes in the human body play an important role in the transcriptional regulation of gene expression. In the last decade, HDAC inhibitors and activators have been explored and have become known as therapeutic agents for many diseases such as osteodystrophy, neurogenerative disorders, cardiomyopathy, cancer, and diabetes. In recent years, the development of HDAC inhibitors or activators to obtain new potent lead compounds has been conducted using in vitro, in vivo, and in silico methods. Some HDAC family inhibitors and activators have been discovered. But some compounds have limitations such as not selectively binding to one of the HDAC variants. At present, through bioinformation, HDAC family sequences have been revealed, and some in silico methods such as molecular modelling (homology modelling and pharmacophore modelling), virtual screening, and molecular dynamics are widely used to find and develop new potent and selective compounds. The main utilization of molecular modelling in this work is intended to complete the HDAC structure that partially lacks data regarding its amino acid monomer. Virtual screening methods are helpful in finding the best binding affinity of the test compounds. By molecular dynamic simulation, the temperature, time, and pressure can be adjusted to analyze the hydrogen bond. Combining these in silico approaches will be a more effective and efficient solution in finding new lead compounds for HDAC drug discovery research in the future.

Design and Preparation of Nano-Lignin Peroxidase (NanoLiP) by Protein Block Copolymerization Approach.

This study describes the preparation of nanoprotein particles having lignin peroxidase (LiP) using a photosensitive microemulsion polymerization technique. The protein-based nano block polymer was synthesized by cross-linking of ligninase enzyme with ruthenium-based aminoacid monomers. This type polymerization process brought stability in different reaction conditions, reusability and functionality to the protein-based nano block polymer system when compared the traditional methods. After characterization of the prepared LiP copolymer nanoparticles, enzymatic activity studies of the nanoenzymes were carried out using tetramethylbenzidine (TMB) as the substrate. The parameters such as pH, temperature and initial enzyme concentration that affect the activity, were investigated by using prepared nanoLip particles and compared to free LiP. The reusability of the nano-LiP particles was also investigated and the obtained results showed that the nano-LiP particles exhibited admirable potential as a reusable catalyst.

Papain-Catalyzed Synthesis of Polyglutamate Containing a Nylon Monomer Unit.

Peptides have the potential to serve as an alternative for petroleum-based polymers to support a sustainable society. However, they lack thermoplasticity, owing to their strong intermolecular interactions. In contrast, nylon is famous for its thermoplasticity and chemical resistance. Here, we synthesized peptides containing a nylon unit to modify their thermal properties by using papain-catalyzed chemoenzymatic polymerization. We used l-glutamic acid alkyl ester as the amino acid monomer and nylon 1, 3, 4, and 6 alkyl esters as the nylon unit. Papain catalyzed the copolymerization of glutamic acid with nylon 3, 4, and 6 alkyl esters, whereas the nylon 1 unit could not be copolymerized. Other proteases used in this study, namely, bromelain, proteinase K, and Candida antarctica lipase (CALB), were not able to copolymerize with any nylon units. The broad substrate specificity of papain enabled the copolymerization of l-glutamic acid with a nylon unit. The peptides with nylon units demonstrated different thermal profiles from that of oligo(l-glutamic acid). Therefore, the resultant peptides with various nylon units are expected to form fewer intermolecular hydrogen bonds, thus altering their thermal properties. This finding is expected to broaden the applications of peptide materials and chemoenzymatic polymerization.

Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code.

We have previously proposed that tRNAGly was the first tRNA and glycine was the first amino acid incorporated into the genetic code. The next two amino acids incorporated would have been the other two small hydrophilic amino acids serine and aspartic acid, which occurred through the duplication of the tRNAGly sequence, followed by mutation of its anticodon by single C to U transition mutations, possibly through spontaneous deamination. Interestingly, however, tRNASer has a different structure than most other tRNAs, possessing a long variable arm; because of this tRNASer is classified as a class II tRNA. Also, serine codons are found not only in the bottom right-hand corner of the genetic code table next to those for glycine and aspartic acid, but also in the top row of the table, next to those for two of the most hydrophobic amino acids, leucine and phenylalanine. In the following, I propose that the class II tRNA structure of tRNASer and the arrangement of serine codons in the genetic code provide clues to the early evolution of tRNA and the genetic code. In addition, I address Di Giulio’s recent criticism of our proposal that tRNAGly was the first tRNA, and discuss how early peptides produced from a restricted amino acid alphabet of glycine, serine and aspartic acid might have possessed proteolytic activity, which is possibly important for the early recycling of amino acid monomers.