Self-Assembled Materials Based on Fully Aromatic Peptides: The Impact of Tryptophan, Tyrosine, and Dopa Residues.

Peptides are able to self-organize in structural elements including cross-ß structures. Taking advantage of this tendency, in the last decades, peptides have been scrutinized as molecular elements for the development of multivalent supramolecular architectures. In this context, different classes of peptides, also with completely aromatic sequences, were proposed. Our previous studies highlighted that the (FY)3 peptide, which alternates hydrophobic phenylalanine and more hydrophilic tyrosine residues, is able to self-assemble, thanks to the formation of both polar and apolar interfaces. It was observed that the replacement of Phe and Tyr residues with other noncoded aromatic amino acids like 2-naphthylalanine (Nal) and Dopa affects the interactions among peptides with consequences on the supramolecular organization. Herein, we have investigated the self-assembling behavior of two novel (FY)3 analogues with Trp and Dopa residues in place of the Phe and Tyr ones, respectively. Additionally, PEGylation of the N-terminus was analyzed too. The supramolecular organization, morphology, and capability to gel were evaluated using complementary techniques, including fluorescence, Fourier transform infrared spectroscopy, and scanning electron microscopy. Structural periodicities along and perpendicular to the fiber axis were detected by grazing incidence wide-angle X-ray scattering. Finally, molecular dynamics studies provided interesting insights into the atomic structure of the cross-ß that constitutes the basic motif of the assemblies formed by these novel peptide systems.

[Advances in separation and analysis of aromatic amino acids in food].

Amino acids are important building blocks of proteins in the human body, which are involved in many metabolic pathways. Patients with metabolic diseases such as phenylketonuria, tyrosinemia, and hepatic encephalopathy are genetically defective and cannot metabolize aromatic amino acids (AAA) in food; hence, a regular diet may lead to permanent physiological damage. For this reason, it is necessary to restrict the intake of AAA in their daily diet by limiting natural protein intake, while ensuring normal intake of low protein foods and supplementation with low-AAA protein equivalents. Sources of low-AAA protein equivalents currently rely on free amino acid complex mixtures and low-AAA peptides (also known as high-Fischer-ratio peptides), which have better absorption availability and palatability. AAA separation and analysis techniques are essential for the preparation and detection of low-AAA peptides. Researchers in this field have explored a variety of efficient adsorption materials to selectively remove AAA from complex protein hydrolysates and thus prepare low-AAA peptide foods, or to establish analysis strategies for AAA. Covering more than 70 publications on AAA removal and separation in the last decade from Web of Science Core Collection and China National Knowledge Infrastructure, this review analyzes the structural characteristics and physicochemical properties of AAA, and summarizes the technological progress of AAA removal based on adsorbents such as activated carbon and resin. The applications of two-dimensional nanomaterials, molecular imprinting, cyclodextrins, and metal-organic frameworks in AAA adsorption and analysis from three dimensions, i. e., sample pretreatment, chiral separation and adsorption sensing, are also reviewed. The mainstream adsorbents for AAA removal, such as activated carbon, still suffer from poor specificity and cause environmental pollution during post-use treatment. Existing AAA separating materials show impressive selective adsorption capability in food samples and chiral mixtures as well as high sensitivity in adsorption sensing. The development of an efficient detection technology for AAA may help in detecting trace AAA in food and in evaluating chiral AAA adulteration in food samples. By exploring the advantages and disadvantages of each type of technology, we provide support for the advancement of the removal and analysis techniques for AAA.

Amino acid-based hydrophobic affinity cryogel for protein purification from ora-pro-nobis (Pereskia aculeata Miller) leaves.

The surfaces of the polyacrylamide cryogels were coated with L-tryptophan (cryogel-Trp) or L-phenylalanine (cryogel-Phe) to enhance crude leaf extract-derived ora-pro-nobis (OPN) protein binding via pseudo-specific hydrophobic interactions. Cryogels functionalized with amino acids were prepared and characterized through morphological, hydrodynamic, and thermal analyses. The adsorption capacities of cryogel-Phe and cryogel-Trp were evaluated in terms of type (sodium sulfate or sodium phosphate) and concentration (0.02 or 0.10 mol∙L-1) of saline solution, pH (4.0, 5.5, or 7.0), and NaCl concentration (0.0 or 0.5 mol∙L-1). The cryogel-Phe presented a higher adsorptive capacity, achieving its maximum value (q = 92.53 mg∙g-1) when the crude OPN crude leaf extract was diluted in sodium sulfate 0.02 mol∙L-1 + NaCl 0.50 mol∙L-1, at pH = 7.0. The dilution rate significantly (p < 0.05) affected the recovered protein amount after the adsorption and elution processes, reaching 94.45% when the feedstock solution was prepared with a crude extract 5 times. The zeta potential for the eluted OPN proteins was 5.76 mV (pH = 3.23) for both dilution rates. The secondary structure composition mainly included ß-sheets (46.50%) and α-helices (13.93%). The cryogel-Phe exhibited interconnected pores ranging 20-300 µm in size, with a Young modulus of 1.51 MPa, and thermal degradation started at 230 °C. These results indicate that the cryogel-Phe exhibited satisfactory properties as promising chromatography support for use in high-throughput purification of crude leaf extract-derived OPN proteins.

Honey as Source of Nitrogen Compounds: Aromatic Amino Acids, Free Nucleosides and Their Derivatives.

The content of selected major nitrogen compounds including nucleosides and their derivatives was evaluated in 75 samples of seven varieties of honey (heather, buckwheat, black locust, goldenrod, canola, fir, linden) by targeted ultra-high performance liquid chromatography-diode array detector - high-resolution quadrupole time-of-flight mass spectrometry (UHPLC-DAD-QqTOF-MS) and determined by UHPLC-DAD. The honey samples contained nucleosides, nucleobases and their derivatives (adenine: 8.9 to 18.4 mg/kg, xanthine: 1.2 to 3.3 mg/kg, uridine: 17.5 to 51.2 mg/kg, guanosine: 2.0 to 4.1 mg/kg; mean amounts), aromatic amino acids (tyrosine: 7.8 to 263.9 mg/kg, phenylalanine: 9.5 to 64.1 mg/kg; mean amounts). The amounts of compounds significantly differed between some honey types. For example, canola honey contained a much lower amount of uridine (17.5 ± 3.9 mg/kg) than black locust where it was most abundant (51.2 ± 7.8 mg/kg). The presence of free nucleosides and nucleobases in different honey varieties is reported first time and supports previous findings on medicinal activities of honey reported in the literature as well as traditional therapy and may contribute for their explanation. This applies, e.g., to the topical application of honey in herpes infections, as well as its beneficial activity on cognitive functions as nootropic and neuroprotective, in neuralgia and is also important for the understanding of nutritional values of honey.

Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds.

The production of aromatic amino acids using fermentation processes with recombinant microorganisms can be an advantageous approach to reach their global demands. In addition, a large array of compounds with alimentary and pharmaceutical applications can potentially be synthesized from intermediates of this metabolic pathway. However, contrary to other amino acids and primary metabolites, the artificial channelling of building blocks from central metabolism towards the aromatic amino acid pathway is complicated to achieve in an efficient manner. The length and complex regulation of this pathway have progressively called for the employment of more integral approaches, promoting the merge of complementary tools and techniques in order to surpass metabolic and regulatory bottlenecks. As a result, relevant insights on the subject have been obtained during the last years, especially with genetically modified strains of Escherichia coli. By combining metabolic engineering strategies with developments in synthetic biology, systems biology and bioprocess engineering, notable advances were achieved regarding the generation, characterization and optimization of E. coli strains for the overproduction of aromatic amino acids, some of their precursors and related compounds. In this paper we review and compare recent successful reports dealing with the modification of metabolic traits to attain these objectives.

The activity of GAT107, an allosteric activator and positive modulator of α7 nicotinic acetylcholine receptors (nAChR), is regulated by aromatic amino acids that span the subunit interface.

GAT107, the (+)-enantiomer of racemic 4-(4-bromophenyl)-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-8-sulfonamide, is a strong positive allosteric modulator (PAM) of α7 nicotinic acetylcholine receptor (nAChR) activation by orthosteric agonists with intrinsic allosteric agonist activities. The direct activation produced by GAT107 in electrophysiological studies is observed only as long as GAT107 is freely diffusible in solution, although the potentiating activity primed by GAT107 can persist for over 30 min after drug washout. Direct activation is sensitive to α7 nAChR antagonist methyllycaconitine, although the primed potentiation is not. The data are consistent with GAT107 activity arising from two different sites. We show that the coupling between PAMs and the binding of orthosteric ligands requires tryptophan 55 (Trp-55), which is located at the subunit interface on the complementary surface of the orthosteric binding site. Mutations of Trp-55 increase the direct activation produced by GAT107 and reduce or prevent the synergy between allosteric and orthosteric binding sites, so that these mutants can also be directly activated by other PAMs such as PNU-120596 and TQS, which do not activate wild-type α7 in the absence of orthosteric agonists. We identify Tyr-93 as an essential element for orthosteric activation, because Y93C mutants are insensitive to orthosteric agonists but respond to GAT107. Our data show that both orthosteric and allosteric activation of α7 nAChR require cooperative activity at the interface between the subunits in the extracellular domain. These cooperative effects rely on key aromatic residues, and although mutations of Trp-55 reduce the restraints placed on the requirement for orthosteric agonists, Tyr-93 can conduct both orthosteric activation and desensitization among the subunits.

Metazoan innovation: from aromatic amino acids to extracellular signaling.

Tyrosine depletion in metazoan proteins was recently explained to be due to the appearance of tyrosine kinases in Metazoa. Here, we present a complementary explanation for the depletion of tyrosine, stating the importance of tyrosine in signaling not only as a phosphorylation target but also as a precursor for catecholamines and hormones. Molecules (dopamine, norepinephrine, and epinephrine, and to a lesser extent serotonin and melatonin) critical to metazoan multicellular signaling are also greatly dependent on a supply of tyrosine. These signaling molecules are synthesized in two highly linked pathways specific to metazoans. In addition, the shikimate pathway that non-metazoans use to synthesize the aromatic amino acids is not present in metazoans. These important pathway changes have occurred between Metazoa and other eukaryotes, causing significant changes to tyrosine metabolism and rendering tyrosine crucial for extracellular signaling. In addition, the evolutionary and functional linkage between these two pathways and the resulting implications for neuropathology are discussed.

Metabolic profiling for studying chemotype variations in Withania somnifera (L.) Dunal fruits using GC-MS and NMR spectroscopy.

Withania somnifera (L.) Dunal (Solanaceae), commonly known as Ashwagandha, is one of the most valued Indian medicinal plant with several pharmaceutical and nutraceutical applications. Metabolic profiling was performed by GC-MS and NMR spectroscopy on the fruits obtained from four chemotypes of W. somnifera. A combination of (1)H NMR spectroscopy and GC-MS identified 82 chemically diverse metabolites consisting of organic acids, fatty acids, aliphatic and aromatic amino acids, polyols, sugars, sterols, tocopherols, phenolic acids and withanamides in the fruits of W. somnifera. The range of metabolites identified by GC-MS and NMR of W. somnifera fruits showed various known and unknown metabolites. The primary and secondary metabolites observed in this study represent MVA, DOXP, shikimic acid and phenylpropanoid biosynthetic metabolic pathways. Squalene and tocopherol have been rated as the most potent naturally occurring compounds with antioxidant properties. These compounds have been identified by us for the first time in the fruits of W. somnifera. Multivariate principal component analysis (PCA) on GC-MS and NMR data revealed clear distinctions in the primary and secondary metabolites among the chemotypes. The variation in the metabolite concentration among different chemotypes of the fruits of W. somnifera suggest that specific chemovars can be used to obtain substantial amounts of bioactive ingredients for use as potential pharmacological and nutraceuticals agents.

Experimental and theoretical charge density distribution in two ternary cobalt(III) complexes of aromatic amino acids.

The experimental charge density distributions in two optically active isomers of a Co complex have been determined. The complexes are Delta-alpha-[Co(R,R-picchxn)(R-trp)](ClO4)2.H2O) (1) and Lambda-beta1-[Co(R,R-picchxn)(R-trp)](CF3SO3)2) (2), where picchxn is N,N'-bis(2-picolyl-1,2-diaminocyclohexane) and R-trp is the R-tryptophane anion. The molecular geometries of 1 and 2 are distinguished by the presence in complex 1 of intramolecular pi...pi stacking interactions and the presence in complex 2 of intramolecular hydrogen bonding. This pair of isomers therefore serves as an excellent model for studying noncovalent interactions and their effects on structure and electron density and the transferability of electron density properties between closely related molecules. For complex 2, a combination of X-ray and neutron diffraction data created the basis for a X-N charge density refinement. A topological analysis of the resulting density distribution using the atoms in molecules methodology is presented along with d-orbital populations, showing that the metal-ligand bonds are relatively unaltered by the geometry changes between 1 and 2. The experimental density has been supplemented by quantum chemical calculations on the cobalt complex cations: close agreement between theory and experiment is found in all cases. The energetics of the weak interactions are analyzed using both theory and experiment showing excellent quantitative agreement. In particular it is found that both methods correctly predict the stability of 2 over 1. The transferability between isomers of the charge density and derived parameters is investigated and found to be invalid for these structurally related systems.

Cloning and sequence analysis of 2 different acetylcholinesterase genes in Rhopalosiphum padi and Sitobion avenae.

Two genes encoding different acetylcholinesterases (AChE) were successfully cloned from 2 species of aphid, Rhopalosiphum padi (L.) and Sitobion avenae (F.). They were named Rp.AChE1 (GenBank accession No. AY707318), Rp.AChE2 (AY667435), Sa.AChE1 (AY707319), and Sa.AChE2 (AY819704), and were 2133, 2363, 2131, and 2362 bp in length and encoded 664, 676, 664, and 676 amino acids, respectively. All of them shared the characteristics of the AChE family: catalytic tiads, 3 intra-chain disulfide bridges, an acyl pocket, and the conservative aromatic residues for the active site of the gorge. Sequence analysis revealed that Rp.AChE1 and Sa.AChE1 showed higher identity to the reported orthologous genes of Drosophila AChE, and Rp.AChE2 and Sa.AChE2 to paralogous genes. However, in each of the aphids, the 2 genes from the same species shared only 29% identity between one another. It was therefore concluded that each of the aphids has 2 different AChE genes, which are either orthologous or paralogous to Drosophila AChE. The high conservation of AChE1 and AChE2 indicated that 2 acetylcholinesterases exist popularly and that both might function in aphids.

Construction and characterization of Pichia pastoris strains for labeling aromatic amino acids in recombinant proteins.

Strains of the methylotrophic yeast Pichia pastoris auxotrophic for the aromatic amino acids (tyrosine, phenylalanine, and tryptophan) have been constructed by targeted gene disruption for protein labeling applications. Three strains, with defects in ARO1 (coding for a homolog of the arom pentafunctional enzyme), ARO7 (coding for chorismate mutase), and TYR1 (coding for prephenate dehydrogenase), have been engineered in a P. pastoris ura3Delta1 parent strain using standard methods. The nutritional requirements of these auxotrophic strains have been characterized and their utility as expression hosts for labeling recombinant proteins has been demonstrated. All three strains show a surprising sensitivity to rich culture medium and must be grown in supplemented minimal medium. The tyr1::URA3 strain in particular is strongly inhibited by tryptophan, and to a lesser extent by phenylalanine, leucine, and isoleucine. Highly efficient incorporation of exogenously supplied amino acids by these three auxotroph strains has been demonstrated using recombinant galactose oxidase. Stereochemically pure l-amino acids and racemic d,l-mixtures serve nearly equally well to support protein expression and labeling. These strains allow efficient labeling of aromatic amino acids in recombinant proteins, supporting NMR structural biology and a wide range of other biophysical studies.

Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.

The NMR high-resolution structure of calmodulin complexed with a fragment of the olfactory cyclic-nucleotide gated channel is described. This structure shows features that are unique for this complex, including an active role of the linker connecting the N- and C-lobes of calmodulin upon binding of the peptide. Such linker is not only involved in the formation of an hydrophobic pocket to accommodate a bulky peptide residue, but it also provides a positively charged region complementary to a negative charge of the target. This complex of calmodulin with a target not belonging to the kinase family was used to test the residual dipolar coupling (RDC) approach for the determination of calmodulin binding modes to peptides. Although the complex here characterized belongs to the (1--14) family, high Q values were obtained with all the 1:1 complexes for which crystalline structures are available. Reduction of the RDC data set used for the correlation analysis to structured regions of the complex allowed a clear identification of the binding mode. Excluded regions comprise calcium binding loops and loops connecting the EF-hand motifs.

Brain amino acid abnormalities in liver disease--a postmortem study.

In a postmortem exploratory study, we examined whether specific amino acid abnormalities associated with liver diseases in vivo may also be detected in human brain samples obtained at clinical autopsies. The branched-chain amino acids (BCAA: valine, leucine, isoleucine) were decreased in the group of patients with liver diseases compared with the control group, whereas the aromatic amino acids (AAA: phenylalanine, tyrosine) were increased. However, the ranges overlapped significantly and were not statistically different. The molar ratio BCAA/AAA was determined to be 1.92 in the collection of patients with liver diseases compared with 2.27 in the control group. In patients with liver disease, ornithine concentrations in the brain appeared significantly decreased whereas glutamine was significantly increased. No significant difference was found in the brain concentrations of proline. Amino acid analysis may contribute to the understanding of pathophysiological mechanisms of liver disease, which are discussed, and may supplement the postmortem diagnosis.

Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains.

Epidermal growth factor (EGF) regulates cell proliferation and differentiation by binding to the EGF receptor (EGFR) extracellular region, comprising domains I-IV, with the resultant dimerization of the receptor tyrosine kinase. In this study, the crystal structure of a 2:2 complex of human EGF and the EGFR extracellular region has been determined at 3.3 A resolution. EGFR domains I-III are arranged in a C shape, and EGF is docked between domains I and III. The 1:1 EGF*EGFR complex dimerizes through a direct receptor*receptor interaction, in which a protruding beta-hairpin arm of each domain II holds the body of the other. The unique "receptor-mediated dimerization" was verified by EGFR mutagenesis.