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Amino Acids: The Forum for Amino Acid, Peptide and Protein Research (v.34, #4)

Inducible heat shock protein 70 and its role in preconditioning and exercise by Leigh A. Madden; Marie E. Sandström; Ric J. Lovell; Lars McNaughton (pp. 511-516).

Heat shock proteins (Hsp) are well known to be expressed in response to a range of cellular stresses. They are known to convey protection against protein denaturation and a subsequent immediate stress. Inducible heat shock protein 70 (Hsp70) is among the most studied of these stress proteins and its role and function are discussed here in terms of thermal and in particular exercise preconditioning. Preconditioning has been shown to confer cellular protection via expression Hsp, which may be of benefit in preventing protein damage following subsequent periods of exercise. Many studies have used animal models to gather data on Hsp70 and these and the most recent human studies are discussed.

Keywords: Hsp70; Thermal preconditioning; Exercise

Transport of amino acids through the placenta and their role by M. A. Grillo; A. Lanza; S. Colombatto (pp. 517-523).

Amino acids are transported across the human placenta mediated by transporter proteins that differ in structure, mechanism and substrate specificity. Some of them are Na⁺-dependent systems, whereas others are Na⁺-independent. Among these there are transporters composed of a heavy chain, a glycoprotein, and a light chain. Moreover, they can be differently distributed in the two membranes forming the syncytiotrophoblast. The transport mechanisms involved and their regulation are only partially known. In the placenta itself, part of the amino acids is metabolized to form other compounds important for the fetus. This occurs for instance for arginine, which gives rise to polyamines and to NO. Interconversion occurs among few other amino acids Transport is altered in pregnancy complications, such as restricted fetal growth.

Keywords: Transport systems; Glycoprotein associated transporters; Indoleamino 2,3-dioxygenase; Polyamines

Taurine inhibits osteoblastic differentiation of vascular smooth muscle cells via the ERK pathway by Xiao-bo Liao; Xin-min Zhou; Jian-ming Li; Jin-fu Yang; Zhi-ping Tan; Zhuo-wei Hu; Wei Liu; Ying Lu; Ling-qing Yuan (pp. 525-530).

Vascular calcification develops within atherosclerotic lesions and results from a process similar to osteogenesis. Taurine is a free β-amino acid and plays an important physiological role in mammals. We have recently demonstrated that vascular smooth muscle cells (VSMCs) express a functional taurine transporter. To evaluate the possible role of taurine in vascular calcification, we assessed its effects on osteoblastic differentiation of VSMCs in vitro. The results showed that taurine inhibited the β-glycerophosphate-induced osteoblastic differentiation of VSMCs as evidenced by both the decreasing alkaline phosphate (ALP) activity and expression of the core binding factor α1 (Cbfα1). Taurine also activated the extracellular signal-regulated protein kinase (ERK) pathway. Inhibition of ERK pathway reversed the effect of taurine on ALP activity and Cbfα1 expression. These results suggested that taurine inhibited osteoblastic differentiation of vascular cells via the ERK pathway.

Keywords: Taurine; Vascular smooth muscular cells; Extracellular signal-regulated kinases; Osteoblast

Synthesis and characterization of novel organosoluble and optically active aromatic polyesters containing l-methionine and phthalimide pendent groups by Shadpour Mallakpour; Hojjat Seyedjamali (pp. 531-538).

5-(4-Methylthio-2-phthalimidylbutanoylamino)isophthalic acid (5) as a novel diacid monomer containing phthalimide and flexible chiral groups was prepared by dehydration of l-methionine and phthalic anhydride followed by reacting with thionyl chloride and then treating with 5-aminoisophthalic acid (5AIPA) in dry N,N-dimethylacetamide (DMAc). A series of novel polyesters (PEs) containing phthalimide group was prepared by the reaction of diacid monomer 5 with several aromatic diols via direct polyesterification with tosyl chloride/pyridine/dimethylformamide (DMF) system as condensing agent. The resulting new polymers were obtained in good yields and inherent viscosities ranging between 0.21 and 0.51 dLg⁻¹ were characterized with FT-IR, ¹H NMR, elemental and thermogravimetric analysis techniques. These polymers are readily soluble in polar organic solvents such as DMAc, DMF, dimethyl sulfoxide and protic solvents such as sulfuric acid. Specific rotation experiments demonstrate the optical activity induction due to successful insertion of l-methionine in the structure of pendent groups. Thermogravimetric analysis showed that the 10% weight loss temperature in a nitrogen atmosphere were more than 315°C, which indicates that the resulting PEs have good thermal stability.

Keywords: l-methionine; Optically active polyester; Direct polycondensation

Up-regulation of vimentin expression in low-density malignant glioma cells as immediate and late effects under irradiation and temozolomide treatment by Daniela Trog; Kristina Yeghiazaryan; Hans H. Schild; Olga Golubnitschaja (pp. 539-545).

Nervous system tumors are one of the leading causes of cancer related death. Specific mechanisms facilitating the invasive behavior of gliomas remain obscure. Advanced simulation models of the in vivo response to therapy conditions should potentially improve malignant glioma treatment. Expressional profiling of vimentin––one of reliable pro-invasive tumor makers––in those simulation models was the goal of this study, in order to estimate a pro-invasive response of surviving malignant glioma cells under clinically relevant therapeutic conditions. Human U87-MG malignant glioma cells were used. These cells are characterized by the wild p53-phenotype, which is relevant for the majority of primary malignant glioblastomas. Experimental design foresaw the cells to undergo either irradiation or chemo-treatment with temozolomide alone, or combined treatment. Expression profiling of vimentin was performed by quantitative “Real-Time”-PCR under all treatment conditions simulating diverse tumor regions. Here we demonstrated that vimentin expression patterns in human malignant glioma cells strongly depend on cellular density, algorithms of drug delivery and chemo/radio treatment. Substantial differences were recognized between immediate and late therapy effects. Significant increase in vimentin expression levels was detected particularly in low-density cell cultures under durable treatment with constant concentration levels of temezolomide. Simulation of variable intratumoral regional conditions (central intratumoral regions vs. disseminated malignant cells in peripheral regions) demonstrated differential response of vimentin expression in malignant glioma cell cultures treated under clinically relevant conditions. Slight ebbing of expression levels as late effects of the treatment in confluent cultures may correspond to necrotic processes clinically observed in central intratumoral regions. Contrary, in disseminated malignant cells of peripheral regions therapy resulted in vimentin-inducing effects. This is in agreement with the clinical observations of an increased aggressiveness and malignancy grade of post-operatively chemo/radio-treated malignant gliomas.

Keywords: Human malignant gliomas; Simulation of clinical glioma treatment; Temozolomide therapy; Pro-invasive molecular marker; Vimentin expression patterns

The effects of 10 weeks of resistance training combined with β-alanine supplementation on whole body strength, force production, muscular endurance and body composition by Iain P. Kendrick; Roger C. Harris; Hyo Jeong Kim; Chang Keun Kim; Viet H. Dang; Thanh Q. Lam; Toai T. Bui; Marcus Smith; John A. Wise (pp. 547-554).

Carnosine (Carn) occurs in high concentrations in skeletal muscle is a potent physico-chemical buffer of H⁺ over the physiological range. Recent research has demonstrated that 6.4 g.day⁻¹ of β-alanine (β-ala) can significantly increase skeletal muscle Carn concentrations (M-[Carn]) whilst the resultant change in buffering capacity has been shown to be paralleled by significant improvements in anaerobic and aerobic measures of exercise performance. Muscle carnosine increase has also been linked to increased work done during resistance training. Prior research has suggested that strength training may also increase M-[Carn] although this is disputed by other studies. The aim of this investigation is to assess the effect of 10 weeks resistance training on M-[Carn], and, secondly, to investigate if increased M-[Carn] brought about through β-ala supplementation had a positive effect on training responses. Twenty-six Vietnamese sports science students completed the study. The subjects completed a 10-week resistance-training program whilst consuming 6.4 g.day⁻¹ of β-ala (β-ALG) or a matched dose of a placebo (PLG). Subjects were assessed prior to and after training for whole body strength, isokinetic force production, muscular endurance, body composition. β-Alanine supplemented subjects increased M-[Carn] by 12.81 ± 7.97 mmol.kg⁻¹ dry muscle whilst there was no change in PLG subjects. There was no significant effect of β-ala supplementation on any of the exercise parameters measured, mass or % body fat. In conclusion, 10 weeks of resistance training alone did not change M-[Carn].

Keywords: Carnsoine; Hydrogen ions; Physico-bufferring

Biological activity of antitumoural MGBG: the structural variable by M. P. M. Marques; F. P. S. C. Gil; R. Calheiros; V. Battaglia; A. M. Brunati; E. Agostinelli; A. Toninello (pp. 555-564).

The present study aims at determining the structure-activity relationships (SAR’s) ruling the biological function of MGBG (methylglyoxal bis(guanylhydrazone)), a competitive inhibitor of S-adenosyl-l-methionine decarboxylase displaying anticancer activity, involved in the biosynthesis of the naturally occurring polyamines spermidine and spermine. In order to properly understand its biochemical activity, MGBG’s structural preferences at physiological conditions were ascertained, by quantum mechanical (DFT) calculations.

Keywords: MGBG; SAMDC; Structure-activity relationships; DFT calculations; Physiological structures; Mitochondrial permeability transition (MPT)

Using the concept of Chou’s pseudo amino acid composition to predict protein subcellular localization: an approach by incorporating evolutionary information and von Neumann entropies by Shao-Wu Zhang; Yun-Long Zhang; Hui-Fang Yang; Chun-Hui Zhao; Quan Pan (pp. 565-572).

The rapidly increasing number of sequence entering into the genome databank has called for the need for developing automated methods to analyze them. Information on the subcellular localization of new found protein sequences is important for helping to reveal their functions in time and conducting the study of system biology at the cellular level. Based on the concept of Chou’s pseudo-amino acid composition, a series of useful information and techniques, such as residue conservation scores, von Neumann entropies, multi-scale energy, and weighted auto-correlation function were utilized to generate the pseudo-amino acid components for representing the protein samples. Based on such an infrastructure, a hybridization predictor was developed for identifying uncharacterized proteins among the following 12 subcellular localizations: chloroplast, cytoplasm, cytoskeleton, endoplasmic reticulum, extracell, Golgi apparatus, lysosome, mitochondria, nucleus, peroxisome, plasma membrane, and vacuole. Compared with the results reported by the previous investigators, higher success rates were obtained, suggesting that the current approach is quite promising, and may become a useful high-throughput tool in the relevant areas.

Keywords: Chou’s pseudo-amino acid composition; Residue evolutionary conservation; von Neumann entropies; Multi-scale energy; Weighted auto-correlation function

Hydrogen sulfide inhibits myocardial injury induced by homocysteine in rats by Lin Chang; Bin Geng; Fang Yu; Jing Zhao; Hongfeng Jiang; Junbao Du; Chaoshu Tang (pp. 573-585).

Hyperhomocysteinemia (HHcy) is a critical independent risk factor for cardiovascular diseases. However, to date, no satisfactory strategies to prevent HHcy exist. Since homocysteine (Hcy) and endogenous H₂S are both metabolites of sulfur-containing amino acids, we aimed to investigate whether a metabolic product of Hcy and H₂S, may antagonize in part the cardiovascular effects of Hcy. In the HHcy rat model injected subcutaneously with Hcy for 3 weeks, H₂S levels and the H₂S-generating enzyme cystathionine γ lyase (CSE) activity in the myocardium were decreased. The intraperitoneal injection of H₂S gas saturation solution significantly reduced plasma total Hcy (tHcy) concentration and decreased lipid peroxidation formation (i.e., lowered manodialdehyde and conjugated diene levels in myocardia and plasma). The activities of myocardial mitochondrial respiratory enzymes succinate dehydrogenase, cytochrome oxidase, and manganese superoxide dismutase, related to reactive oxygen species metabolism, were significantly dysfunctional in HHcy rats. The H₂S administration restored the level of enzyme activities and accelerated the scavenging of H₂O₂ and superoxide anion generated by Hcy in isolated mitochondria. The H₂S treatment also inhibited the expression of glucose-regulated protein 78, a marker of endoplasmic reticulum (ER) stress, induced by Hcy in vivo and in vitro. Thus, HHcy impaired the myocardial CSE/H₂S pathway, and the administration of H₂S protected the myocardium from oxidative and ER stress induced by HHcy, which suggests that an endogenous metabolic balance of sulfur-containing amino acids may be a novel strategy for treatment of HHcy.

Keywords: Homocysteine; Hydrogen sulfide; Sulfur containing amino acids; Oxidative stress; Endoplasmic reticulum stress

Application of the Phenomenex EZ:faast™ amino acid analysis kit for rapid gas-chromatographic determination of concentrations of plasma tryptophan and its brain uptake competitors by A. A.-B. Badawy; C. J. Morgan; J. A. Turner (pp. 587-596).

The Phenomenex EZ:faast™ amino acid analysis kit is available for gas (GC) or liquid (LC) chromatographic analysis of amino acids (AA) using mass spectrometry (MS) and other GC detectors. We used it for rapid GC determination of plasma tryptophan, its brain uptake competitors (Val, Leu, Ile, Phe and Tyr) and many other amino acids. Based on solid-phase extraction, this fast method enables one person to process two plasma samples in 8–10 min and six samples in ∼15 min up to GC injection and a 7-min GC run per plasma sample. Using a Perkin-Elmer Clarus 500 GC, a Total Chrome software, a flame-ionisation detector (FID) and norvaline as internal standard, we used this method to analyse ∼1,000 plasma samples from normal subjects undergoing acute tryptophan depletion and loading tests. The limit of detection for most amino acids is 1 nmol/ml (1 μM) and in many cases less. With manual injection, coefficients of variation for the above six amino acids were 1.5–6.2% (intra-assay) and 3.8–9.7% (inter-assay). This simple, rapid and elegant method will be valuable to the amino acid analyst and researcher, as it can save much manpower time and meet urgent emergency requests and the demands of a high-throughput laboratory.

Keywords: Analysis; EZ:faast; Gas chromatography; Isoleucine; Leucine; Phenylalanine; Tryptophan; Tyrosine; Valine

Expression profiles of the organic acid metabolism-associated genes during rat liver regeneration by G. B. Guo; C. S. Xu (pp. 597-604).

In this study, 55 of the organic acid metabolism-involved genes were primarily confirmed to be associated with liver regeneration (LR) by bioinformatics and gene expression profiling analysis. Number of the initially and totally expressed genes occurring in initiation phase of LR, G₀/G₁, cell proliferation, cell differentiation and liver tissue structure-function reconstruction were 21, 5, 33, 1 and 40, 20, 174, 44, respectively, illustrating that genes were initially expressed mainly in initiation stage, and worked in different phases. 151 times up-regulation and 114 times down-regulation as well as 14 types of expression patterns showed the diversification and complication of genes expression changes. It is inferred from the above gene expression changes and patterns that acetate biosynthesis enhanced at forepart, propionate biosynthesis at forepart, prophase and early metaphase, pyruvate biosynthesis at forepart, metaphase and anaphase, succinate biosynthesis at forepart and anaphase; malate biosynthesis in metaphase and N-acetylneuraminate biosynthesis at 36, 66 and 96 h. Whereas, carnitine biosynthsis attenuates at forepart and prophase, enhancement at middle metaphase; isocitrate in the forepart, quinolinate at forepart and early metaphase, creatine at early metaphase and fumarate at anaphase perform the restrained biosynthesis, respectively; catabolisms of propionate and pyruvate were depressed in metaphase.

Keywords: Partial hepatectomy; Rat genome 230 2.0 array; Organic acid metabolism; Genes associated with liver regeneration

Near infrared spectroscopy compared to liquid chromatography coupled to mass spectrometry and capillary electrophoresis as a detection tool for peptide reaction monitoring by Christine H. Petter; Nico Heigl; Stefan Bachmann; Verena A. C. Huck-Pezzei; Muhammad Najam-ul-Haq; Rania Bakry; Andreas Bernkop-Schnürch; Günther K. Bonn; Christian W. Huck (pp. 605-616).

Peptide interaction is normally monitored by liquid chromatography (LC), liquid chromatography coupled to mass spectrometry (LC-MS), mass spectrometric (MS) methods such as MALDI-TOF/MS or capillary electrophoresis (CE). These analytical techniques need to apply either high pressure or high voltages, which can cause cleavage of newly formed bondages. Therefore, near infrared reflectance spectroscopy (NIRS) is presented as a rapid alternative to monitor the interaction of glutathione and oxytocin, simulating physiological conditions. Thereby, glutathione can act as a nucleophile with oxytocin forming four new conjugates via a disulphide bondage. Liquid chromatography coupled to UV (LC-UV) and mass spectrometry via an electrospray ionisation interface (LC-ESI-MS) resulted in a 82% and a 78% degradation of oxytocin at pH 3 and a 5% and a 7% degradation at pH 6.5. Capillary electrophoresis employing UV-detection (CE-UV) showed a 44% degradation of oxytocin. LC and CE in addition to the NIRS are found to be authentic tools for quantitative analysis. Nevertheless, NIRS proved to be highly suitable for the detection of newly formed conjugates after separating them on a thin layer chromatography (TLC) plate. The recorded fingerprint in the near infrared region allows for a selective distinct qualitative identification of conjugates without the need for expensive instrumentation such as quadrupole or MALDI-TOF mass spectrometers. The performance of the established NIRS method is compared to LC and CE; its advantages are discussed in detail.

Keywords: Near infrared spectroscopy; Peptides; Reaction monitoring; Liquid chromatography; Mass spectrometry; Capillary electrophoresis

Strong and weak hydrogen bonds in protein-ligand complexes of kinases: a comparative study by Sunil K. Panigrahi (pp. 617-633).

Strong and weak hydrogen bonds between protein and ligand are analyzed in a group of 233 X-ray crystal structures of the kinase family. These kinases are from both eukaryotic and prokaryotic organisms. The dataset comprises of 44 sub-families, out of which 35 are of human origin and the rest belong to other organisms. Interaction analysis was carried out in the active sites, defined here as a sphere of 10 Å radius around the ligand. A majority of the interactions are observed between the main chain of the protein and the ligand atoms. As a donor, the ligand frequently interacts with amino acid residues like Leu, Glu and His. As an acceptor, the ligand interacts often with Gly, and Leu. Strong hydrogen bonds N–H···O, O–H···O, N–H···N and weak bonds C–H···O, C–H···N are common between the protein and ligand. The hydrogen bond donor capacity of Gly in N–H···O and C–H···O interactions is noteworthy. Similarly, the acceptor capacity of main chain Glu is ubiquitous in several kinase sub-families. Hydrogen bonds between protein and ligand form characteristic hydrogen bond patterns (supramolecular synthons). These synthon patterns are unique to each sub-family. The synthon locations are conserved across sub-families due to a higher percentage of conserved sequences in the active sites. The nature of active site water molecules was studied through a novel classification scheme, based on the extent of exposure of water molecules. Water which is least exposed usually participates in hydrogen bond formation with the ligand. These findings will help structural biologists, crystallographers and medicinal chemists to design better kinase inhibitors.

Keywords: Hydrogen bond; Kinase; Protein Data Bank; Supramolecular synthon; Water

Combing ontologies and dipeptide composition for predicting DNA-binding proteins by Loris Nanni; Alessandra Lumini (pp. 635-641).

Given a novel protein it is very important to know if it is a DNA-binding protein, because DNA-binding proteins participate in the fundamental role to regulate gene expression. In this work, we propose a parallel fusion between a classifier trained using the features extracted from the gene ontology database and a classifier trained using the dipeptide composition of the protein. As classifiers the support vector machine (SVM) and the 1-nearest neighbour are used. Matthews’s correlation coefficient obtained by our fusion method is ≈0.97 when the jackknife cross-validation is used; this result outperforms the best performance obtained in the literature (0.924) using the same dataset where the SVM is trained using only the Chou’s pseudo amino acid based features. In this work also the area under the ROC-curve (AUC) is reported and our results show that the fusion permits to obtain a very interesting 0.995 AUC. In particular we want to stress that our fusion obtains a 5% false negative with a 0% of false positive. Matthews’s correlation coefficient obtained using the single best GO-number is only 0.7211 and hence it is not possible to use the gene ontology database as a simple lookup table. Finally, we test the complementarity of the two tested feature extraction methods using the Q-statistic. We obtain the very interesting result of 0.58, which means that the features extracted from the gene ontology database and the features extracted from the amino acid sequence are partially independent and that their parallel fusion should be studied more.

Keywords: DNA-binding proteins; Gene ontology; Dipeptide composition; Chou’s pseudo amino acid composition; Multi-classifier

Robustness of the residue conservation score reflecting both frequencies and physicochemistries by X.-S. Liu; W.-L. Guo (pp. 643-652).

Measuring residue conservation at aligned positions has many applications in biology. Recently, a new conservation score has been defined. Unlike the previous methods, the new approach considers both residue frequencies and physicochemistries. Specifically, it measures physicochemistries based on BLOSUM matrices disregarding the meaning of the entries in such matrices, which may involve the problem of log–log probability. In this paper we present a conservation measure that also reflects both frequencies and physicochemistries while considering the fact that the entries of BLOSUM matrices are already interpreted as log probability. When the supposed score is applied to 14 protein examples, the results show that these two conservation scores are equivalent aside from the different score ranges. The method is also used to score the functional sites of three protein families. Compared with the widely used entropy-based methods, the resulting scores are more robust and consistent in the sense that the functional sites are much more conserved because of functional constraints.

Keywords: Conservation score; Physicochemistry; Multiple sequence alignment; Functional site; Protein folding nucleus

Genetic programming for creating Chou’s pseudo amino acid based features for submitochondria localization by Loris Nanni; Alessandra Lumini (pp. 653-660).

Given a protein that is localized in the mitochondria it is very important to know the submitochondria localization of that protein to understand its function. In this work, we propose a submitochondria localizer whose feature extraction method is based on the Chou’s pseudo-amino acid composition. The pseudo-amino acid based features are obtained by combining pseudo-amino acid compositions with hundreds of amino-acid indices and amino-acid substitution matrices, then from this huge set of features a small set of 15 “artificial” features is created. The feature creation is performed by genetic programming combining one or more “original” features by means of some mathematical operators. Finally, the set of combined features are used to train a radial basis function support vector machine. This method is named GP-Loc. Moreover, we also propose a very few parameterized method, named ALL-Loc, where all the “original” features are used to train a linear support vector machine. The overall prediction accuracy obtained by GP-Loc is 89% when the jackknife cross-validation is used, this result outperforms the performance obtained in the literature (85.2%) using the same dataset. While the overall prediction accuracy obtained by ALL-Loc is 83.9%.

Keywords: Submitochondria localization; Chou’s pseudo amino acid; Genetic programming

Codon evolution is governed by linear formulas by K. Sorimachi; T. Okayasu (pp. 661-668).

When nucleotide (G, C, T and A) contents were plotted against each nucleotide, their relationships were clearly expressed by a linear formula, y = αx + β in the coding and non-coding regions. This linear relationship was obtained from the complete single-stranded DNA. Similarly, nucleotide contents at all three codon positions were expressed by linear regression lines based on the content of each nucleotide. In addition, 64 codon usages were also expressed by linear formulas against nucleotide content. Thus, the nucleotide content not only in coding sequence but also in non-coding sequence can be expressed by a linear formula, y = αx + β, in 145 organisms (112 bacteria, 15 archaea and 18 eukaryotes). Based on these results, the ratio of C/T, G/T, C/A or G/A one can essentially estimate all four nucleotide contents in the complete single-stranded DNA, and the determination of any ratio of two kinds of nucleotides can essentially estimate four nucleotide contents, nucleotide contents at the three different codon positions and codon distributions at 64 codons in the coding region. The maximum and minimum values of G content were ∼0.35 and ∼0.15, respectively, among various organisms examined. Codon evolution occurs according to linear formulas between these two values.

Keywords: Codon evolution; Nucleotide content; Linear empirical formula; Codon usage; Amino acid composition; Genome

Using Chou’s pseudo amino acid composition based on approximate entropy and an ensemble of AdaBoost classifiers to predict protein subnuclear location by Xiaoying Jiang; Rong Wei; Yanjun Zhao; Tongliang Zhang (pp. 669-675).

The knowledge of subnuclear localization in eukaryotic cells is essential for understanding the life function of nucleus. Developing prediction methods and tools for proteins subnuclear localization become important research fields in protein science for special characteristics in cell nuclear. In this study, a novel approach has been proposed to predict protein subnuclear localization. Sample of protein is represented by Pseudo Amino Acid (PseAA) composition based on approximate entropy (ApEn) concept, which reflects the complexity of time series. A novel ensemble classifier is designed incorporating three AdaBoost classifiers. The base classifier algorithms in three AdaBoost are decision stumps, fuzzy K nearest neighbors classifier, and radial basis-support vector machines, respectively. Different PseAA compositions are used as input data of different AdaBoost classifier in ensemble. Genetic algorithm is used to optimize the dimension and weight factor of PseAA composition. Two datasets often used in published works are used to validate the performance of the proposed approach. The obtained results of Jackknife cross-validation test are higher and more balance than them of other methods on same datasets. The promising results indicate that the proposed approach is effective and practical. It might become a useful tool in protein subnuclear localization. The software in Matlab and supplementary materials are available freely by contacting the corresponding author.

Keywords: Protein subnuclear localization; Pseudo amino acid composition; Approximate entropy; Ensemble classifier; AdaBoost algorithm

A new selective pre-column ninhydrin-based derivatization for a RP-HPLC determination of plasma asymmetric dimethyl-l-arginine (ADMA) by fluorescence detection by Salvatore Sotgia; Angelo Zinellu; Gerard Aime Pinna; Luca Deiana; Ciriaco Carru (pp. 677-682).

We report a new selective and direct pre-column ninhydrin-based derivatization reaction for determination of plasma ADMA levels. This original derivatization procedure matched to a validated and rapid RP-HPLC method can be a useful alternative to other assays in which time consuming and expensive extraction and/or purification steps are required.

Keywords: ADMA; Homoarginine; Ninhydrin; Fluorescence

Glutamine enhances glucose-induced mesangial cell proliferation by Claudia J. Lagranha; Sonia Q. Doi; Tania C. Pithon-Curi; Rui Curi; Donald F. Sellitti (pp. 683-685).

The proliferation of mesangial cells (MC) in the presence of glutamine (0–20 mM) was determined in both low (5 mM) and high (25 mM) glucose-containing medium. Glutamine in a high glucose (HG) environment increased cell proliferation in a dose-dependent manner. Inhibition of glutamine:fructose 6-phosphate amidotransferase (GFAT) and of phosphodiesterase significantly reduced glutamine-induced proliferation. Supraphysiologic levels of glutamine increase MC proliferation in a HG milieu via GFAT and cAMP-dependent pathways, suggesting that glutamine could pose a risk for diabetic nephropathy.

Keywords: Glutamine; Supplementation; Kidney disease; Mesangial cell; Cell proliferation

Hydrogen sulfide inhibits myocardial injury induced by homocysteine in rats by Lin Chang; Bin Geng; Fang Yu; Jing Zhao; Hongfeng Jiang; Junbao Du; Chaoshu Tang (pp. 687-687).

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Amino Acids: The Forum for Amino Acid, Peptide and Protein Research (v.34, #4)