Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.

We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids-Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid-on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations.

Quinoline appended pillar[5]arene (QPA) as Fe3+ sensor and complex of Fe3+ (FeQPA) as a selective sensor for F-, arginine and lysine in the aqueous medium.

A quinoline functionalized pillar[5]arene, QPA has been prepared and its interaction with biologically relevant ions and molecules in aqueous solution has been demonstrated. The sensor molecule, QPA has shown selectivity towards Fe3+ among eleven metal ions studied. The Fe3+ complex of QPA (FeQPA) selectively interacts with F- among halides by ∼4 fold fluorescence enhancement. Further, FeQPA has shown selectivity towards arginine and lysine among twenty naturally occurring amino acids. The binding of QPA with Fe3+ has been confirmed by MALDI-TOF and 1H NMR titrations.

High-sensitive liquid chromatography-tandem mass spectrometry-based chiral metabolic profiling focusing on amino acids and related metabolites.

Metabolomics has been an evolving science with a wide range of applications in various fields. However, previous studies have rarely focused on metabolite chirality. In this study, to achieve metabolic profiling of chiral amino acids and related metabolites, we developed a high-throughput method using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The combination of two types of chiral columns (with binaphthyl-based crown ether and cinchona alkaloid-derived zwitterionic stationary phases) enabled the analysis of 115 chiral and non-chiral metabolites. By finely optimizing MS/MS parameters, the method allowed the highly sensitive (0.001-50 nmol/mL) and wide dynamic range detection of targeted analytes in a standard solution without derivatization. We applied the method to food samples (cheese), and successfully quantified trace levels of metabolites such as d-amino acids in samples. Additionally, we performed principal component analysis on the metabolome data and obtained unique profiles that reflected metabolite chirality. These results demonstrated the applicability and feasibility of the LC-MS/MS method as an effective tool for wide-targeted chiral metabolome analysis.

A molecular rotor based ratiometric sensor for basic amino acids.

The inevitable importance of basic amino acids, arginine and lysine, in human health and metabolism demands construction of efficient sensor systems for them. However, there are only limited reports on the 'ratiometric' detection of basic amino acids which is further restricted by the use of chemically complex sensor molecules, which impedes their prospect for practical applications. Herein, we report a ratiometric sensor system build on simple mechanism of disassociation of novel emissive Thioflavin-T H-aggregates from heparin surface, when subjected to interaction with basic amino acids. The strong and selective electrostatic and hydrogen bonding interaction of basic amino acids with heparin leads to large alteration in photophysical attributes of heparin bound Thioflavin-T, which forms a highly sensitive sensor platform for detection of basic amino acids in aqueous solution. These selective interactions between basic amino acids and heparin allow our sensor system to discriminate arginine and lysine from other amino acids. This unique mechanism of dissociation of Thioflavin-T aggregates from heparin surface provides ratiometric response on both fluorimetric and colorimetric outputs for detection of arginine and lysine, and thus it holds a significant advantage over other developed sensor systems which are restricted to single wavelength detection. Apart from the sensitivity and selectivity, our system also provides the advantage of simplicity, dual mode of sensing, and more importantly, it employs an inexpensive commercially available probe molecule, which is a significant advantage over other developed sensor systems that uses tedious synthesis protocol for the employed probe in the detection scheme, an impediment for practical applications. Additionally, our sensor system also shows response in complex biological media of serum samples.

Cluster shading modifies amino acids in grape (Vitis vinifera L.) berries in a genotype- and tissue-dependent manner.

Amino acid composition of the grape berry at harvest is important for wine making. The present study investigates the complex interplay between tissue, cultivar and light conditions that determine berry amino acid content. Twenty amino acids were assessed in the berry skin and pulp of two grape cultivars (Gamay Noir and Gamay Fréaux), grown under either light exposure or cluster shading conditions. In all samples, cluster shading significantly reduced most amino acids, except gamma-aminobutyric acid (GABA) and phenylalanine. However, the magnitude of the decrease was stronger in the skin (67.0% decrease) than in the pulp (30.4%) and stronger in cv. Gamay Noir (69.7%) than in Gamay Fréaux (30.7%). Cluster shading also significantly modified amino acid composition by decreasing the proline content while increasing the GABA content. These results are of oenological interest for shaping the amino acid composition of the must and improving wine quality.

Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization.

BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND356-58, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3.

"Turn-on" fluorescent sensor array for basic amino acids in water.

Amino acids and their derivatives are recognized and analyzed in water using a turn-on fluorescent cucurbituril based sensor array. Multivariate analysis (LDA and HCA) clearly shows that the sensor array can discriminate amino acids from the corresponding amines which are produced by the action of amino acid decarboxylases.

Amino acid composition and antioxidant activities of hydrolysates and peptide fractions from porcine collagen.

The amino acid composition and antioxidant activities of different hydrolysates from porcine collagen were analyzed. The gelatin was hydrolyzed for antioxidative peptides with various proteases, namely papain, protease from bovine pancreas, protease from Streptomyces, and cocktail mixture of protease from bovine pancreas and protease from Streptomyces. The hydrolysates were assessed using methods of DPPH radical-scavenging ability, metal-chelating ability and lipid peroxidation inhibition activity. It was found that the collagen hydrolysates by different protease treatments had different amino acid compositions and antioxidant properties. However, the contents of Hyp and Pro were improved and the content of Gly was decreased in each collagen hydrolysate compared with collagen. The hydrolysate prepared with the cocktail mixture of proteases, which exhibited the highest antioxidant activity, was separated into 6 fractions by gel filtration chromatography. Fraction 2 was further separated by ion exchange chromatography. Fraction 2b with abundant basic amino acids and Fraction 2d which was slightly acidic fractions had higher radical-scavenging and metal-chelating activities, and both Fraction 2b and 2d contained more hydrophobic amino acids. The results confirmed that the antioxidative peptides were rich in Hyp, Pro and Gly, which accounted for half of amino acid composition. This article added further support to the preparation of natural antioxidative peptides from porcine skin collagen.

Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment.

Metal and metal oxide chelating-based phosphopeptide enrichment technologies provide powerful tools for the in-depth profiling of phosphoproteomes. One weakness inherent to current enrichment strategies is poor binding of phosphopeptides containing multiple basic residues. The problem is exacerbated when strong cation exchange (SCX) is used for pre-fractionation, as under low pH SCX conditions phosphorylated peptides with multiple basic residues elute with the bulk of the tryptic digest and therefore require more stringent enrichment. Here, we report a systematic evaluation of the characteristics of a novel phosphopeptide enrichment approach based on a combination of low pH SCX and Ti(4+)-immobilized metal ion affinity chromatography (IMAC) comparing it one-to-one with the well established low pH SCX-TiO(2) enrichment method. We also examined the effect of 1,1,1,3,3,3-hexafluoroisopropanol (HFP), trifluoroacetic acid (TFA), or 2,5-dihydroxybenzoic acid (DHB) in the loading buffer, as it has been hypothesized that high levels of TFA and the perfluorinated solvent HFP improve the enrichment of phosphopeptides containing multiple basic residues. We found that Ti(4+)-IMAC in combination with TFA in the loading buffer, outperformed all other methods tested, enabling the identification of around 5000 unique phosphopeptides containing multiple basic residues from 400 µg of a HeLa cell lysate digest. In comparison, ∼ 2000 unique phosphopeptides could be identified by Ti(4+)-IMAC with HFP and close to 3000 by TiO(2). We confirmed, by motif analysis, the basic phosphopeptides enrich the number of putative basophilic kinases substrates. In addition, we performed an experiment using the SCX/Ti(4+)-IMAC methodology alongside the use of collision-induced dissociation (CID), higher energy collision induced dissociation (HCD) and electron transfer dissociation with supplementary activation (ETD) on considerably more complex sample, consisting of a total of 400 µg of triple dimethyl labeled MCF-7 digest. This analysis led to the identification of over 9,000 unique phosphorylation sites. The use of three peptide activation methods confirmed that ETD is best capable of sequencing multiply charged peptides. Collectively, our data show that the combination of SCX and Ti(4+)-IMAC is particularly advantageous for phosphopeptides with multiple basic residues.

[Study on basic amino acid contents in Dendrobium officinale].

OBJECTIVE: To investigate the contents of 16 basic amino acid and find out the variation of them in Dendrobium officinale with different germplasms and physiological ages, and then provide scientific basis for the quality evaluation and the breeding of D. officinale. METHOD: Thirty-three samples with 1-3 ages were collected from cultivated fields of Zhejiang. The samples were acid hydrolyzed, and then 16 basic amino acid contents of samples were determined by amino acid analyzer. RESULT: The average contents of 7 necessary amino acid were in 0.28 - 2.96 mg x g(-1), the average contents of other 9 basic amino acid were in 0.53 - 4.20 mg x g(-1). The contents of many amino acids were impacted by germplasms significantly, and contents of several amino acids were impacted by physiological ages significantly. CONCLUSION: There were rich basic amino acids in D. officinale. The breeding of D. officinale can increase the contents of essential amino acids and other basic amino acids. The relations among physiological age and amino acid contents were as follows: three years > two years > one year. The contents of Asp and Tyr have significantly negative correlation with magnesium, the content of Pro has significantly positive correlation with copper.

Biochemical constraints in a protobiotic earth devoid of basic amino acids: the "BAA(-) world".

It has been hypothesized in this journal and elsewhere, based on surveys of published data from prebiotic synthesis experiments and carbonaceous meteorite analyses, that basic amino acids such as lysine and arginine were not abundant on prebiotic Earth. If the basic amino acids were incorporated only rarely into the first peptides formed in that environment, it is important to understand what protobiotic chemistry is possible in their absence. As an initial test of the hypothesis that basic amino acid negative [BAA(-)] proteins could have performed at least a subset of protobiotic chemistry, the current work reports on a survey of 13 archaeal and 13 bacterial genomes that has identified 61 modern gene sequences coding for known or putative proteins not containing arginine or lysine. Eleven of the sequences found code for proteins whose functions are well known and important in the biochemistry of modern microbial life: lysine biosynthesis protein LysW, arginine cluster proteins, copper ion binding proteins, bacterial flagellar proteins, and PE or PPE family proteins. These data indicate that the lack of basic amino acids does not prevent peptides or proteins from serving useful structural and biochemical functions. However, as would be predicted from fundamental physicochemical principles, we see no fossil evidence of prebiotic BAA(-) peptide sequences capable of interacting directly with nucleic acids.

Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II.

The extended Fes-CIP4 homology (EFC)/FCH-BAR (F-BAR) domain tubulates membranes. Overexpression of the pacsin2 EFC/F-BAR domain resulted in tubular localization inside cells and deformed liposomes into tubules in vitro. We found that overexpression of the pacsin2 EFC/F-BAR domain induced cellular microspikes, with the pacsin2 EFC/F-BAR domain concentrated at the neck. The hydrophobic loops and the basic amino-acid residues on the concave surface of the pacsin2 EFC/F-BAR domain are essential for both the microspike formation and tubulation. Since the curvature of the neck of the microspike and that of the tubulation share similar geometry, the pacsin2 EFC/F-BAR domain is considered to facilitate both microspike formation and tubulation.

Development of an in-capillary derivatization method by CE for the determination of chiral amino acids in dietary supplements and wines.

A fast in-capillary derivatization method by CE with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate was developed for the first time for the determination of amino acid enantiomers (arginine, lysine, and ornithine) in dietary supplements and wines. Because of the initial current problems due to the formation of precipitates into the capillary during the derivatization reaction, a washing step with an organic solvent as DMSO between injections was necessary. Different approaches were also investigated to enhance the sensitivity of detection. A derivatization procedure, where plugs of ACN, derivatizing agent (10 mM 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate), and sample in borate (1:1 v/v) were injected in tandem (2, 3, and 6 s, respectively, at 50 mbar), was selected because it enabled to obtain the most sensitive and reproducible results. Appropriate analytical characteristics (linearity, LOD and LOQ, precision, absence of matrix interferences, and accuracy) were obtained for this method. Finally, the optimized method was successfully applied to the determination of the enantiomers of arginine, lysine, and ornithine in food samples of different complexities (dietary supplements and wines).

Reactivity of basic amino acid pairs in prohormone processing: model of pro-ocytocin/neurophysin processing domain.

Statistical analysis of several potential dibasic cleavage sites reveals differences in the distribution of basic doublets when the in vivo cleaved sites were compared to those which are not cleaved. Analysis of the substrate specificity of protease Kex2 towards the pro-ocytocin/neurophysin processing domain (pro-OT/Np(7-15) with altered basic pairs shows a cleavage efficiency order in accord with the statistical data. Structural analysis of these substrates indicates that each basic pair is associated with a local and specific conformational change. Thus, the in vivo cleavage hierarchy of dibasic sites is encoded by both the nature of basic pairs and the plasticity of proteolytic processing domains.

The second AT-hook of the architectural transcription factor HMGA2 is determinant for nuclear localization and function.

High Mobility Group A (HMGA) is a family of architectural nuclear factors which play an important role in neoplastic transformation. HMGA proteins are multifunctional factors that associate both with DNA and nuclear proteins that have been involved in several nuclear processes including transcription. HMGA localization is exclusively nuclear but, to date, the mechanism of nuclear import for these proteins remains unknown. Here, we report the identification and characterization of a nuclear localization signal (NLS) for HMGA2, a member of the HMGA family. The NLS overlaps with the second of the three AT-hooks, the DNA-binding domains characteristic for this group of proteins. The functionality of this NLS was demonstrated by its ability to target a heterologous beta-galactosidase/green fluorescent protein fusion protein to the nucleus. Mutations to alanine of basic residues within the second AT-hook resulted in inhibition of HMGA2 nuclear localization and impairment of its function in activating the cyclin A promoter. In addition, HMGA2 was shown to directly interact with the nuclear import receptor importin-alpha2 via the second AT-hook. HMGA proteins are overexpressed and rearranged in a variety of tumors; our findings can thus help elucidating their role in neoplastic transformation.

Fragmentation of singly protonated peptides via a combination of infrared and collisional activation.

The coupling of matrix-assisted laser desorption/ionization (MALDI) to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) provides an exceptionally capable platform for peptide analysis, but an important limitation of this approach is the difficulty in obtaining informative tandem mass spectra (MS/MS) of singly protonated peptides. This difficulty is especially pronounced with peptide ions containing basic amino acid residues (for example, tryptic peptides). While such ions can be fragmented in some instrument configurations, most FTICR instruments have comparatively little facility for high-energy fragmentation. Here, a novel MS/MS approach implemented with MALDI-FTICR-MS and specifically intended for enhanced fragmentation of singly protonated peptides is described. The method involves infrared irradiation in concert with the simultaneous application of sustained off-resonance irradiation collision-induced dissociation (SORI-CID). This form of MS/MS, described as a combination of infrared and collisional activation (CIRCA), is shown to provide a greater capacity for dissociation of singly charged model peptide ions as compared to infrared multiphoton dissociation (IRMPD) or SORI-CID alone. Overall, the CIRCA approach is demonstrated to be a feasible technique for accessing useful fragmentation pathways of singly charged peptides, including those harboring basic amino acid residues--a crucial feature in the context of proteomics.

Ion-ion and ion-molecule reactions at the surface of proteins produced by nanospray. Information on the number of acidic residues and control of the number of ionized acidic and basic residues.

Mass Spectra of charge states of folded proteins were obtained with nanospray and aqueous solution containing 20 microM the protein (ubiquitin, cytochrome c, lysozyme) and one of the NaA salts NaCl, NaI, NaAc (acetate) (1-10 mM). At very low collision activated decomposition (CAD), the mass spectra of a protein with charge z exhibited a replacement of zH+ with zNa+ and also multiple adducts of NaA. Higher CAD converts the NaA adduct peaks to Na minus H peaks. These must be due to loss of HA where the H was provided by the protein. The degree of HA loss with increasing CAD followed the order I < Cl < Ac. Significantly, the intensity of the ions with n (Na minus H) adducts showed a downward break past an n(MAX) which is equal to the number of acidic residues of the protein plus the charge of the protein. All the observations could be rationalized within the framework of the electrospray mechanism and the charge residue model, which predict that due to extensive evaporation of solvent, the solutes will reach very high concentrations in the final charged droplets. At such high concentrations, positive ions such as Na+, NH4+ form ion pairs with ionized acidic residues and the negative A- form ion pairs with ionized basic residues of the protein. Adducts of Na+, and NaA to backbone amide groups occur also. This reaction mechanism fits all the experimental observations and provides predictions that the number of acidic and basic groups at the surface of the gaseous protein that remain ionized can be controlled by the absence or presence of additives to the solution.

Dual subcellular distribution of cytochrome b5 in plant, cauliflower, cells.

Subfractionation studies showed that cytochrome b(5) (cyt b5), which has been considered to be a typical ER protein, was localized in both the endoplasmic reticulum membrane (ER) and the outer membrane of mitochondria in cauliflower (Brassica olracea) cells and was a component of antimycin A-insensitive NADH-cytochrome c reductase system in both membranes. When cDNA for cauliflower cyt b5 was introduced into mammalian (COS-7) and yeast cells as well as into onion cells, the expressed cytochrome was localized both in the ER and mitochondria in those cells. On the other hand, rat and yeast cyt b5s were specifically localized in the ER membranes even in the onion cells. Mutation experiments showed that cauliflower cyt b5 carries information that targets it to the ER and mitochondria within the carboxy-terminal 10 amino acids, as in the case of rat and yeast cyt b5s, and that replacement of basic amino acids in this region of cauliflower cyt b5 with neutral or acidic ones resulted in its distribution only in the ER. Together with the established findings of the importance of basic amino acids in mitochondrial targeting signals, these results suggest that charged amino acids in the carboxy-terminal portion of cyt b5 determine its location in the cell, and that the same mechanism of signal recognition and of protein transport to organelles works in mammalian, plant, and yeast cells.