Showing papers in "Amino Acids in 2007"
TL;DR: It is demonstrated that, using SVM (support vector machine) classifier, the AAP antigenicity scale approach has much better performance than the existing scales based on the single amino acid propensity, which is the essence why the new approach is superior to the existing ones.
Abstract: Identification of antigenic sites on proteins is of vital importance for developing synthetic peptide vaccines, immunodiagnostic tests and antibody production. Currently, most of the prediction algorithms rely on amino acid propensity scales using a sliding window approach. These methods are oversimplified and yield poor predicted results in practice. In this paper, a novel scale, called the amino acid pair (AAP) antigenicity scale, is proposed that is based on the finding that B-cell epitopes favor particular AAPs. It is demonstrated that, using SVM (support vector machine) classifier, the AAP antigenicity scale approach has much better performance than the existing scales based on the single amino acid propensity. The AAP antigenicity scale can reflect some special sequence-coupled feature in the B-cell epitopes, which is the essence why the new approach is superior to the existing ones. It is anticipated that with the continuous increase of the known epitope data, the power of the AAP antigenicity scale approach will be further enhanced.
509 citations
TL;DR: The increase in TWD with supplementation followed the increase in muscle carnosine, which was significantly increased by +58.8% and +80.1% after 4 and 10 wks β-alanine supplementation.
Abstract: Muscle carnosine synthesis is limited by the availability of β-alanine. Thirteen male subjects were supplemented with β-alanine (CarnoSyn™) for 4 wks, 8 of these for 10 wks. A biopsy of the vastus lateralis was obtained from 6 of the 8 at 0, 4 and 10 wks. Subjects undertook a cycle capacity test to determine total work done (TWD) at 110% (CCT110%) of their maximum power (Wmax). Twelve matched subjects received a placebo. Eleven of these completed the CCT110% at 0 and 4 wks, and 8, 10 wks. Muscle biopsies were obtained from 5 of the 8 and one additional subject. Muscle carnosine was significantly increased by +58.8% and +80.1% after 4 and 10 wks β-alanine supplementation. Carnosine, initially 1.71 times higher in type IIa fibres, increased equally in both type I and IIa fibres. No increase was seen in control subjects. Taurine was unchanged by 10 wks of supplementation. 4 wks β-alanine supplementation resulted in a significant increase in TWD (+13.0%); with a further +3.2% increase at 10 wks. TWD was unchanged at 4 and 10 wks in the control subjects. The increase in TWD with supplementation followed the increase in muscle carnosine.
430 citations
TL;DR: The pathological consequences of the presence of excessive concentrations of These compounds are related to the short- and, most important, long-term effects of these compounds on the rapid colonic epithelium renewing and homeostasis.
Abstract: Depending on the amount of alimentary proteins, between 6 and 18 g nitrogenous material per day enter the large intestine lumen through the ileocaecal junction. This material is used as substrates by the flora resulting eventually in the presence of a complex mixture of metabolites including ammonia, hydrogen sulfide, short and branched-chain fatty acids, amines; phenolic, indolic and N-nitroso compounds. The beneficial versus deleterious effects of these compounds on the colonic epithelium depend on parameters such as their luminal concentrations, the duration of the colonic stasis, the detoxication capacity of epithelial cells in response to increase of metabolite concentrations, the cellular metabolic utilization of these metabolites as well as their effects on colonocyte intermediary and oxidative metabolism. Furthermore, the effects of metabolites on electrolyte movements through the colonic epithelium must as well be taken into consideration for such an evaluation. The situation is further complicated by the fact that other non-nitrogenous compounds are believed to interfere with these various phenomenons. Finally, the pathological consequences of the presence of excessive concentrations of these compounds are related to the short- and, most important, long-term effects of these compounds on the rapid colonic epithelium renewing and homeostasis.
350 citations
TL;DR: L-tyrosine and L-Dopa had an effect on DPPH radical scavenging, ABTS radical scavenming, superoxide anion radical scaventing, H2O2 scavenging), total ferric ions reducing power and metal chelating on ferrous ions activities.
Abstract: Phenolic compounds are interesting because of their antioxidant properties. In the present study, the antioxidant properties of L-tyrosine as a monophenolic and L-Dopa as a diphenolic amino acid were investigated by using different antioxidant assays: (i) 1,1-diphenyl-2-picryl-hydrazyl free radical (DPPH*) scavenging; (ii) 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical cation decolorization assay; (iii) total antioxidant activity by ferric thiocyanate method; (iv) ferric ions (Fe3+) reducing power; (v) superoxide anion radical (O2*-) scavenging; (vi) hydrogen peroxide (H2O2) scavenging, and (vii) ferrous ions (Fe2+) chelating activities. Butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), alpha-tocopherol and trolox, a water-soluble analogue of tocopherol, were used as the reference antioxidant compounds. At the same concentration (20 microg/mL), L-tyrosine and L-Dopa showed 30.6 and 67.9% inhibition of lipid peroxidation of linoleic acid emulsion, respectively. On the other hand, BHA, BHT, alpha-tocopherol and trolox indicated inhibitions of 74.4, 71.2, 54.7 and 20.1% on the peroxidation of linoleic acid emulsion, respectively, at the above-mentioned concentration. In addition, L-tyrosine and L-Dopa had an effect on DPPH radical scavenging, ABTS radical scavenging, superoxide anion radical scavenging, H2O2 scavenging, total ferric ions reducing power and metal chelating on ferrous ions activities.
327 citations
TL;DR: This review provides an overview of homocysteine influence on endothelium function as well as on protein metabolism with a special respect to posttranslational modification of protein with homocy steine thiolactone.
Abstract: Homocysteine, a non-protein amino acid, is an important risk factor for ischemic heart disease and stroke in humans. This review provides an overview of homocysteine influence on endothelium function as well as on protein metabolism with a special respect to posttranslational modification of protein with homocysteine thiolactone. Homocysteine is a pro-thrombotic factor, vasodilation impairing agent, pro-inflammatory factor and endoplasmatic reticulum-stress inducer. Incorporation of Hcy into protein via disulfide or amide linkages (S-homocysteinylation or N-homocysteinylation) affects protein structure and function. Protein N-homocysteinylation causes cellular toxicity and elicits autoimmune response, which may contribute to atherogenesis.
278 citations
TL;DR: The growth and survival of mouse fibroblasts unable to synthesize spermine were compared to their normal counterparts in their native and polyamine-depleted states in response to oxidative stress, suggesting that polyamines not only play a role in protecting cells from oxidative stress but this role is distinct from that played by glutathione.
Abstract: The polyamines spermidine and spermine have been hypothesized to possess different functions in the protection of DNA from reactive oxygen species. The growth and survival of mouse fibroblasts unable to synthesize spermine were compared to their normal counterparts in their native and polyamine-depleted states in response to oxidative stress. The results of these studies suggest that when present at normal or supraphysiological concentrations, either spermidine or spermine can protect cells from reactive oxygen species. However, when polyamine pools are pharmacologically manipulated to produce cells with low levels of predominately spermine or spermidine, spermine appears to be more effective. Importantly, when cells are depleted of both glutathione and endogenous polyamines, they exhibit increased sensitivity to hydrogen peroxide as compared to glutathione depletion alone, suggesting that polyamines not only play a role in protecting cells from oxidative stress but this role is distinct from that played by glutathione.
254 citations
TL;DR: This review covers various biotechnology applications of amino acids, in particular arginine, which finds much wider applications than previously anticipated in the research and development of proteins, in particularly in pharmaceutical applications.
Abstract: Amino acids are widely used in biotechnology applications. Since amino acids are natural compounds, they can be safely used in pharmaceutical applications, e.g., as a solvent additive for protein purification and as an excipient for protein formulations. At high concentrations, certain amino acids are found to raise intra-cellular osmotic pressure and adjust to the high salt concentrations of the surrounding medium. They are called "compatible solutes", since they do not affect macromolecular function. Not only are they needed to increase the osmotic pressure, they are known to increase the stability of the proteins. Sucrose, glycerol and certain amino acids were used to enhance the stability of unstable proteins after isolation from natural environments. The mechanism of the action of these protein-stabilizing amino acids is relatively well understood. On the contrary, arginine was accidentally discovered as a useful reagent for assisting in the refolding of recombinant proteins. This effect of arginine was ascribed to its ability to suppress aggregation of the proteins during refolding, thereby increasing refolding efficiency. By the same mechanism, arginine now finds much wider applications than previously anticipated in the research and development of proteins, in particular in pharmaceutical applications. For example, arginine solubilizes proteins from loose inclusion bodies, resulting in efficient production of active proteins. Arginine suppresses protein-protein interactions in solution and also non-specific adsorption to gel permeation chromatography columns. Arginine facilitates elution of bound proteins from various column resins, including Protein-A or dye affinity columns and hydrophobic interaction columns. This review covers various biotechnology applications of amino acids, in particular arginine.
231 citations
TL;DR: The data show changes in antioxidants, neurotransmitters and their precursors, or FAA associated with urea metabolism in pAD compared with CT, and it is proposed that manipulation of these metabolic pathways may be important in preventing AD progression.
Abstract: Our aim was to determine changes in free amino acid (FAA) and dipeptide (DP) concentrations in probable Alzheimer’s disease (pAD) subjects compared with control (CT) subjects using liquid chromatography and electrospray ionization tandem mass spectrometry (LCMS2). We recruited gender- and age-matched study participants based on neurological and neuropsychological assessments. We measured FAAs and DPs in cerebrospinal fluid (CSF), plasma and urine using LCMS2 with selected reaction monitoring (SRM). Imidazole-containing FAAs (histidine, methyl-histidine), catecholamines (L-DOPA and dopamine), citrulline, ornithine, glycine and antioxidant DPs (carnosine and anserine) accounted for the major changes between CT and pAD. Carnosine levels were significantly lower in pAD (328.4 ± 91.31 nmol/dl) than in CT plasma (654.23 ± 100.61 nmol/dl). In contrast, L-DOPA levels were higher in pAD (1400.84 ± 253.68) than CT (513.10 ± 121.61 nmol/dl) plasma. These data underscore the importance of FAA and DP metabolism in the pathogenesis of AD. Since our data show changes in antioxidants, neurotransmitters and their precursors, or FAA associated with urea metabolism in pAD compared with CT, we propose that manipulation of these metabolic pathways may be important in preventing AD progression.
217 citations
TL;DR: Ten-wks of resistance training with 20 g protein and amino acids ingested 1 h before and after exercise is more effective than carbohydrate placebo in up-regulating markers of muscle protein synthesis and anabolism along with subsequent improvements in muscle performance.
Abstract: This study examined 10 wks of resistance training and the ingestion of supplemental protein and amino acids on muscle performance and markers of muscle anabolism. Nineteen untrained males were randomly assigned to supplement groups containing either 20 g protein (14 g whey and casein protein, 6 g free amino acids) or 20 g dextrose placebo ingested 1 h before and after exercise for a total of 40 g/d. Participants exercised 4 times/wk using 3 sets of 6-8 repetitions at 85-90% of the one repetition maximum. Data were analyzed with two-way ANOVA (p < 0.05). The protein supplement resulted in greater increases in total body mass, fat-free mass, thigh mass, muscle strength, serum IGF-1, IGF-1 mRNA, MHC I and IIa expression, and myofibrillar protein. Ten-wks of resistance training with 20 g protein and amino acids ingested 1 h before and after exercise is more effective than carbohydrate placebo in up-regulating markers of muscle protein synthesis and anabolism along with subsequent improvements in muscle performance.
208 citations
TL;DR: β-alanine supplementation appears to improve submaximal cycle ergometry performance and time-to-exhaustion in young women, perhaps as a result of an increased buffering capacity due to elevated muscle carnosine concentrations.
Abstract: This study examined the effects of 28 days of β-alanine supplementation on the physical working capacity at fatigue threshold (PWCFT), ventilatory threshold (VT), maximal oxygen consumption (\(\dot{\rm V}\)O2-MAX), and time-to-exhaustion (TTE) in women. Twenty-two women (age ± SD 27.4 ± 6.1 yrs) participated and were randomly assigned to either the β-alanine (CarnoSyn™) or Placebo (PL) group. Before (pre) and after (post) the supplementation period, participants performed a continuous, incremental cycle ergometry test to exhaustion to determine the PWCFT, VT, \(\dot{\rm V}\)O2-MAX, and TTE. There was a 13.9, 12.6 and 2.5% increase (p 0.05). There were no changes for \(\dot{\rm V}\)O2-MAX (p > 0.05) in either group. Results of this study indicate that β-alanine supplementation delays the onset of neuromuscular fatigue (PWCFT) and the ventilatory threshold (VT) at submaximal workloads, and increase in TTE during maximal cycle ergometry performance. However, β-alanine supplementation did not affect maximal aerobic power (\(\dot{\rm V}\)O2-MAX). In conclusion, β-alanine supplementation appears to improve submaximal cycle ergometry performance and TTE in young women, perhaps as a result of an increased buffering capacity due to elevated muscle carnosine concentrations.
186 citations
TL;DR: The antiparasitic effects of inhibitors of polyamine and trypanothione formation, reviewed here, emphasize the relevance of these enzymes as drug targets.
Abstract: Trypanosomatids depend on spermidine for growth and survival. Consequently, enzymes involved in spermidine synthesis and utilization, i.e. arginase, ornithine decarboxylase (ODC), S-adenosylmethionine decarboxylase (AdoMetDC), spermidine synthase, trypanothione synthetase (TryS), and trypanothione reductase (TryR), are promising targets for drug development. The ODC inhibitor alpha-difluoromethylornithine (DFMO) is about to become a first-line drug against human late-stage gambiense sleeping sickness. Another ODC inhibitor, 3-aminooxy-1-aminopropane (APA), is considerably more effective than DFMO against Leishmania promastigotes and amastigotes multiplying in macrophages. AdoMetDC inhibitors can cure animals infected with isolates from patients with rhodesiense sleeping sickness and leishmaniasis, but have not been tested on humans. The antiparasitic effects of inhibitors of polyamine and trypanothione formation, reviewed here, emphasize the relevance of these enzymes as drug targets. By taking advantage of the differences in enzyme structure between parasite and host, it should be possible to design new drugs that can selectively kill the parasites.
TL;DR: This review covers the chemistry of phosphohistidine in terms of its isomeric forms and chemical derivatives, how they can be synthesized, purified, identified and the relative stabilities of each of these forms.
Abstract: Phosphohistidine has been identified as an enzymic intermediate in numerous biochemical reactions and plays a functional role in many regulatory pathways. Unlike the phosphoester bond of its cousins (phosphoserine, phosphothreonine and phosphotyrosine), the phosphoramidate (P–N) bond of phosphohistidine has a high ΔG° of hydrolysis and is unstable under acidic conditions. This acid-lability has meant that the study of protein histidine phosphorylation and the associated protein kinases has been slower to progress than other protein phosphorylation studies. Histidine phosphorylation is a crucial component of cell signalling in prokaryotes and lower eukaryotes. It is also now becoming widely reported in mammalian signalling pathways and implicated in certain human disease states. This review covers the chemistry of phosphohistidine in terms of its isomeric forms and chemical derivatives, how they can be synthesized, purified, identified and the relative stabilities of each of these forms. Furthermore, we highlight how this chemistry relates to the role of phosphohistidine in its various biological functions.
TL;DR: A novel ensemble hybridization classifier was developed by fusing many basic individual classifiers through a voting system engineered by the KNN (K-Nearest Neighbor) principle, which resulted in a powerful predictor of subcellular location of eukaryotic proteins.
Abstract: With the avalanche of newly-found protein sequences emerging in the post genomic era, it is highly desirable to develop an automated method for fast and reliably identifying their subcellular locations because knowledge thus obtained can provide key clues for revealing their functions and understanding how they interact with each other in cellular networking. However, predicting subcellular location of eukaryotic proteins is a challenging problem, particularly when unknown query proteins do not have significant homology to proteins of known subcellular locations and when more locations need to be covered. To cope with the challenge, protein samples are formulated by hybridizing the information derived from the gene ontology database and amphiphilic pseudo amino acid composition. Based on such a representation, a novel ensemble hybridization classifier was developed by fusing many basic individual classifiers through a voting system. Each of these basic classifiers was engineered by the KNN (K-Nearest Neighbor) principle. As a demonstration, a new benchmark dataset was constructed that covers the following 18 localizations: (1) cell wall, (2) centriole, (3) chloroplast, (4) cyanelle, (5) cytoplasm, (6) cytoskeleton, (7) endoplasmic reticulum, (8) extracell, (9) Golgi apparatus, (10) hydrogenosome, (11) lysosome, (12) mitochondria, (13) nucleus, (14) peroxisome, (15) plasma membrane, (16) plastid, (17) spindle pole body, and (18) vacuole. To avoid the homology bias, none of the proteins included has ≥25% sequence identity to any other in a same subcellular location. The overall success rates thus obtained via the 5-fold and jackknife cross-validation tests were 81.6 and 80.3%, respectively, which were 40–50% higher than those performed by the other existing methods on the same strict dataset. The powerful predictor, named “Euk-PLoc”, is available as a web-server at http://202.120.37.186/bioinf/euk
. Furthermore, to support the need of people working in the relevant areas, a downloadable file will be provided at the same website to list the results predicted by Euk-PLoc for all eukaryotic protein entries (excluding fragments) in Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The large-scale results will be updated twice a year to include the new entries of eukaryotic proteins and reflect the continuous development of Euk-PLoc.
TL;DR: Evidence is provided to show that the existence of metal-catalyzed processes, the assistance of nitric oxide-dependent nitration steps and the facilitation by hydrophobic environments, provide individually and/or in combination, feasible scenarios for nitration in complex biological milieux.
Abstract: In this review we address current concepts on the biological occurrence, levels and consequences of protein tyrosine nitration in biological systems. We focused on mechanistic aspects, emphasizing on the free radical mechanisms of protein 3-nitrotyrosine formation and critically analyzed the restrictions for obtaining large tyrosine nitration yields in vivo, mainly due to the presence of strong reducing systems (e.g. glutathione) that can potently inhibit at different levels the nitration process. Evidence is provided to show that the existence of metal-catalyzed processes, the assistance of nitric oxide-dependent nitration steps and the facilitation by hydrophobic environments, provide individually and/or in combination, feasible scenarios for nitration in complex biological milieux. Recent studies using hydrophobic tyrosine analogs and tyrosine-containing peptides have revealed that factors controlling nitration in hydrophobic environments such as biomembranes and lipoproteins can differ to those in aqueous compartments. In particular, exclusion of key soluble reductants from the lipid phase will more easily allow nitration and lipid-derived radicals are suggested as important mediators of the one-electron oxidation of tyrosine to tyrosyl radical in proteins associated to hydrophobic environments. Development and testing of hydrophilic and hydrophobic probes that can compete with endogenous constituents for the nitrating intermediates provide tools to unravel nitration mechanisms in vitro and in vivo; additionally, they could also serve to play cellular and tissue protective functions against the toxic effects of protein tyrosine nitration.
TL;DR: The unique feature of the hypusine modification is the strict specificity of the enzymes toward its substrate protein, eIF5A, which presents new potential targets for intervention in aberrant cell proliferation.
Abstract: A naturally occurring unusual amino acid, hypusine [N
ɛ-(4-amino-2-hydroxybutyl)-lysine] is a component of a single cellular protein, eukaryotic translation initiation factor 5A (eIF5A). It is a modified lysine with structural contribution from the polyamine spermidine. Hypusine is formed in a novel posttranslational modification that involves two enzymes, deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). eIF5A and deoxyhypusine/hypusine modification are essential for growth of eukaryotic cells. The hypusine synthetic pathway has evolved in eukaryotes and eIF5A, DHS and DOHH are highly conserved, suggesting maintenance of a fundamental cellular function of eIF5A through evolution. The unique feature of the hypusine modification is the strict specificity of the enzymes toward its substrate protein, eIF5A. Moreover, DHS exhibits a narrow specificity toward spermidine. In view of the extraordinary specificity and the requirement for hypusine-containing eIF5A for mammalian cell proliferation, eIF5A and the hypusine biosynthetic enzymes present new potential targets for intervention in aberrant cell proliferation.
TL;DR: This paper focuses on human serum albumin (HSA), the most abundant plasma protein, proposed to serve antioxidant functions in the vascular compartment, supporting a role of HSA-Cys34 as an important redox regulator in extracellular compartments.
Abstract: Sulfenic acid (RSOH) is a central intermediate in both the reversible and irreversible redox modulation by reactive species of an increasing number of proteins involved in signal transduction and enzymatic pathways. In this paper we focus on human serum albumin (HSA), the most abundant plasma protein, proposed to serve antioxidant functions in the vascular compartment. Sulfenic acid in HSA has been previously detected using different methods after oxidation of its single free thiol Cys34 through one- or two-electron mechanisms. Since recent evidence suggests that sulfenic acid in HSA is stabilized within the protein environment, this derivative represents an appropriate model to examine protein sulfenic acid biochemistry, structure and reactivity. Sulfenic acid in HSA could be involved in mixed disufide formation, supporting a role of HSA-Cys34 as an important redox regulator in extracellular compartments.
TL;DR: Quite promising results were obtained, indicating that MSE is quite effective in reflecting the sequence-order effects and might become a useful tool for predicting the other attributes of proteins as well.
Abstract: As more and more genomes have been discovered in recent years, there is an urgent need to develop a reliable method to predict the subcellular localization for the explosion of newly found proteins. However, many well-known prediction methods based on amino acid composition have problems utilizing the sequence-order information. Here, based on the concept of Chou's pseudo amino acid composition (PseAA), a new feature extraction method, the multi-scale energy (MSE) approach, is introduced to incorporate the sequence-order information. First, a protein sequence was mapped to a digital signal using the amino acid index. Then, by wavelet transform, the mapped signal was broken down into several scales in which the energy factors were calculated and further formed into an MSE feature vector. Following this, combining this MSE feature vector with amino acid composition (AA), we constructed a series of MSEPseAA feature vectors to represent the protein subcellular localization sequences. Finally, according to a new kind of normalization approach, the MSEPseAA feature vectors were normalized to form the improved MSEPseAA vectors, named as IEPseAA. Using the technique of IEPseAA, C-support vector machine (C-SVM) and three multi-class SVMs strategies, quite promising results were obtained, indicating that MSE is quite effective in reflecting the sequence-order effects and might become a useful tool for predicting the other attributes of proteins as well.
TL;DR: The underlying mechanisms of TG2 up-regulation induced by various stimuli including glutamate exposure, calcium influx, oxidative stress, UV, and inflammatory cytokines are discussed, agreeing with a postulated role for transglutaminases in molecular mechanisms involved in several diseases.
Abstract: The expression of the protein crosslinking enzyme tissue transglutaminase (TG2, tTG), the ubiquitous member of transglutaminase family, can be regulated by multiple factors Although it has been suggested that TG2 can be involved in apoptotic cell death, high levels of enzyme have also been associated with cell survival in response to different stimuli Furthermore, evidence indicates that increases in TG2 production cause enzyme translocation to cell membrane Cell stress can also lead to TG2 accumulation on the cell surface and in the extracellular matrix resulting in changes in cell-matrix interactions
TL;DR: An efficient and simple method of producing various γ-glutamyl compounds, especiallyγ- glutamymyl amino acids, using bacterial ε-glUTamyltranspeptidase has been developed, and a wide-range of γ -glut amyl compounds can be synthesized.
Abstract: Some amino acids and peptides, which have low solubility in water, become much more soluble following γ-glutamylation. Compounds become more stable in the blood stream with γ-glutamylation. Several γ-glutamyl compounds are known to have favorable physiological effects on mammals. γ-Glutamylation can improve taste and can stabilize glutamine in aqueous solution. Because of such favorable features, γ-glutamyl compounds are very attractive. However, only a small number of γ-glutamyl amino acids have been studied although many other γ-glutamyl compounds may have characteristics that will benefit humans. This is mainly because γ-glutamyl compounds have not been readily available. An efficient and simple method of producing various γ-glutamyl compounds, especially γ-glutamyl amino acids, using bacterial γ-glutamyltranspeptidase has been developed. With this method, modifications of reactive groups of the substrate and energy source such as ATP are not required, and a wide-range of γ-glutamyl compounds can be synthesized. Moreover, bacterial γ-glutamyltranspeptidase, a catalyst for this method, is readily available from the strain over-producing this enzyme. The superiority of producing γ-glutamyl compounds with bacterial γ-glutamyltranspeptidase over other methods of production is discussed.
TL;DR: In this paper, a novel classifier, the so-called “ensemble classifier”, was introduced, formed by fusing a set of nearest neighbor (NN) classifiers, each of which is defined in a different pseudo amino acid composition space.
Abstract: Predicting membrane protein type is both an important and challenging topic in current molecular and cellular biology. This is because knowledge of membrane protein type often provides useful clues for determining, or sheds light upon, the function of an uncharacterized membrane protein. With the explosion of newly-found protein sequences in the post-genomic era, it is in a great demand to develop a computational method for fast and reliably identifying the types of membrane proteins according to their primary sequences. In this paper, a novel classifier, the so-called "ensemble classifier", was introduced. It is formed by fusing a set of nearest neighbor (NN) classifiers, each of which is defined in a different pseudo amino acid composition space. The type for a query protein is determined by the outcome of voting among these constituent individual classifiers. It was demonstrated through the self-consistency test, jackknife test, and independent dataset test that the ensemble classifier outperformed other existing classifiers widely used in biological literatures. It is anticipated that the idea of ensemble classifier can also be used to improve the prediction quality in classifying other attributes of proteins according to their sequences.
TL;DR: Data suggest that CrBA may potentially enhance endurance performance, and within groups, a significant time effect was observed for CrBa on 5 of the 8 parameters measured.
Abstract: The effect of beta-alanine (beta-Ala) alone or in combination with creatine monohydrate (Cr) on aerobic exercise performance is unknown. The purpose of this study was to examine the effects of 4 weeks of beta-Ala and Cr supplementation on indices of endurance performance. Fifty-five men (24.5 +/- 5.3 yrs) participated in a double-blind, placebo-controlled study and randomly assigned to one of 4 groups; placebo (PL, n = 13), creatine (Cr, n = 12), beta-alanine (beta-Ala, n = 14), or beta-alanine plus creatine (CrBA, n = 16). Prior to and following supplementation, participants performed a graded exercise test on a cycle ergometer to determine VO(2peak), time to exhaustion (TTE), and power output, VO(2), and percent VO(2peak) associated with VT and LT. No significant group effects were found. However, within groups, a significant time effect was observed for CrBa on 5 of the 8 parameters measured. These data suggest that CrBA may potentially enhance endurance performance.
TL;DR: Two recently discovered mechanisms regulating neuronal excitability in the BLA by modulating GABAergic inhibitory transmission are described, which may underlie the hyperexcitability of the amygdala in certain stress-related affective disorders, and may explain the stress-induced exacerbation of seizure activity in epileptic patients.
Abstract: The amygdala, a temporal lobe structure that is part of the limbic system, has long been recognized for its central role in emotions and emotional behavior. Pathophysiological alterations in neuronal excitability in the amygdala are characteristic features of certain psychiatric illnesses, such as anxiety disorders and depressive disorders. Furthermore, neuronal excitability in the amygdala, and, in particular, excitability of the basolateral nucleus of the amygdala (BLA) plays a pivotal role in the pathogenesis and symptomatology of temporal lobe epilepsy. Here, we describe two recently discovered mechanisms regulating neuronal excitability in the BLA, by modulating GABAergic inhibitory transmission. One of these mechanisms involves the regulation of GABA release via kainate receptors containing the GluR5 subunit (GluR5KRs). In the rat BLA, GluR5KRs are present on both somatodendritic regions and presynaptic terminals of GABAergic interneurons, and regulate GABA release in an agonist concentration-dependent, bidirectional manner. The relevance of the GluR5KR function to epilepsy is suggested by the findings that GluR5KR agonists can induce epileptic activity, whereas GluR5KR antagonists can prevent it. Further support for an important role of GluR5KRs in epilepsy comes from the findings that antagonism of GluR5KRs is a primary mechanism underlying the antiepileptic properties of the anticonvulsant topiramate. Another mechanism regulating neuronal excitability in the BLA by modulating GABAergic synaptic transmission is the facilitation of GABA release via presynaptic α1A adrenergic receptors. This mechanism may significantly underlie the antiepileptic properties of norepinephrine. Notably, the α1A adrenoceptor-mediated facilitation of GABA release is severely impaired by stress. This stress-induced impairment in the noradrenergic facilitation of GABA release in the BLA may underlie the hyperexcitability of the amygdala in certain stress-related affective disorders, and may explain the stress-induced exacerbation of seizure activity in epileptic patients.
TL;DR: A 46-D (dimensional) PseAA was formulated to represent the sample of a protein and a new approach based on binary-tree support vector machines (BTSVMs) was proposed to predict the protein structural class.
Abstract: Compared with the conventional amino acid composition (AA), the pseudo amino acid composition (PseAA) as originally introduced by Chou can incorporate much more information of a protein sequence; this remarkably enhances the power to use a discrete model for predicting various attributes of a protein. In this study, based on the concept of Chou's PseAA, a 46-D (dimensional) PseAA was formulated to represent the sample of a protein and a new approach based on binary-tree support vector machines (BTSVMs) was proposed to predict the protein structural class. BTSVMs algorithm has the capability in solving the problem of unclassifiable data points in multi-class SVMs. The results by both the 10-fold cross-validation and jackknife tests demonstrate that the predictive performance using the new PseAA (46-D) is better than that of AA (20-D), which is widely used in many algorithms for protein structural class prediction. The results obtained by the new approach are quite encouraging, indicating that it can at least play a complimentary role to many of the existing methods and is a useful tool for predicting many other protein attributes as well.
TL;DR: The putative translation factor eIF5A is essential for cell viability and is highly conserved from archaebacteria to mammals and has also been implicated in nuclear export of HIV-1 Rev and mRNA decay, but these findings are controversial in the literature and may reflect secondary effects of eIF-5A function.
Abstract: The putative translation factor eIF5A is essential for cell viability and is highly conserved from archaebacteria to mammals. This factor is the only cellular protein that undergoes an essential posttranslational modification dependent on the polyamine spermidine, called hypusination. This review focuses on the functional characterization of eIF5A. Although this protein was originally identified as a translation initiation factor, subsequent studies did not support a role for eIF5A in general translation initiation. eIF5A has also been implicated in nuclear export of HIV-1 Rev and mRNA decay, but these findings are controversial in the literature and may reflect secondary effects of eIF-5A function. Next, the involvement of eIF5A and hypusination in the control of the cell cycle and proliferation in various organisms is reviewed. Finally, recent evidence in favor of reconsidering the role of eIF5A as a translation factor is discussed. Future studies may reveal the specific mechanism by which eIF5A affects protein synthesis.
TL;DR: The ODC irreversible inactivator DFMO has proven to be not only a valuable tool in the study of ODC in cancer, but also shows promise as a chemopreventive and chemotherapeutic agent in certain types of malignancies.
Abstract: The activity of ornithine decarboxylase (ODC(1)), the first enzyme in polyamine biosynthesis, is induced during carcinogenesis by a variety of oncogenic stimuli. Intracellular levels of ODC and the polyamines are tightly controlled during normal cell growth, and regulation occurs at the levels of transcription, translation and protein degradation. Several known proto-oncogenic pathways appear to control ODC transcription and translation, and dysregulation of pathways downstream of ras and myc result in the constitutive elevation of ODC activity that occurs with oncogenesis. Inhibition of ODC activity reverts the transformation of cells in vitro and reduces tumor growth in several animal models, suggesting high levels of ODC are necessary for the maintenance of the transformed phenotype. The ODC irreversible inactivator DFMO has proven to be not only a valuable tool in the study of ODC in cancer, but also shows promise as a chemopreventive and chemotherapeutic agent in certain types of malignancies.
TL;DR: A PRD associated with intermittent PIITD is a safe and well observed nutritional regimen and long term observance is possible, and performance status and pain scores were relatively stable during the trial.
Abstract: Polyamine contents were assessed by mass spectrometry in 233 current foods and beverages. In order to reduce gut polyamine uptake, a polyamine reduced diet (PRD) and partial intermittent intestinal tract decontamination (PIITD) with neomycin or nifuroxazide was proposed as nutritional therapy to 33 prostate carcinoma patients, 30 of whom with hormone refractory prostate cancer (HRPC). Mean PRD observance was 22 ± 19 (median: 16; range: 3–72) months. 10, 8 and 3 patients were respectively on PRD for more than 30, 36 and 64 months. No diet toxicity was observed. 8 patients had moderate intestinal intolerance due to PIITD which was interrupted. No significant differences in body weight, blood counts or serum protein levels were observed during the follow-up of patients under PRD. Performance status and pain scores were relatively stable during the trial with improved pain scores at 6 months. A PRD associated with intermittent PIITD is a safe and well observed nutritional regimen and long term observance is possible.
TL;DR: The analogues are multi-site inhibitors affecting multiple reactions in the pathway and thus prevent the up-regulation of compensatory reactions that have been the downfall of DFMO in anticancer chemotherapy.
Abstract: The polyamines are growth factors in both normal and cancer cells. As the intracellular polyamine content correlates positively with the growth potential of that cell, the idea that depletion of polyamine content will result in inhibition of cell growth and, particularly tumour cell growth, has been developed over the last 15 years. The polyamine pathway is therefore a target for development of rationally designed, antiproliferative agents. Following the lessons from the single enzyme inhibitors (α-difluoromethylornithine DFMO), three generations of polyamine analogues have been synthesised and tested in vitro and in vivo. The analogues are multi-site inhibitors affecting multiple reactions in the pathway and thus prevent the up-regulation of compensatory reactions that have been the downfall of DFMO in anticancer chemotherapy. Although the initial concept was that the analogues may provide novel anticancer drugs, it now seems likely that the analogues will have wider applications in diseases involving hyperplasia.
TL;DR: The pentapeptide unit is reported as a common minimal amino acid sequence critically involved in peptide-protein interaction and immune recognition and may have implications in defining the dimensional module for peptides-based therapeutical approaches such as the development of novel antibiotics, enzyme inhibitors/activators, mimetic agonists/antagonists of neuropeptides, thrombolitic agents, specific anti-viral agents, etc.
Abstract: Short amino acid motifs, either linear sequences or discontinuous amino acid groupings, can interact with specific protein domains, so exerting a central role in cell adhesion, signal transduction, hormone activity, regulation of transcript expression, enzyme activity, and antigen-antibody interaction. Here, we analyze the literature for such critical short amino acid motifs to determine the minimal peptide length involved in biologically important interactions. We report the pentapeptide unit as a common minimal amino acid sequence critically involved in peptide-protein interaction and immune recognition. The present survey may have implications in defining the dimensional module for peptide-based therapeutical approaches such as the development of novel antibiotics, enzyme inhibitors/activators, mimetic agonists/antagonists of neuropeptides, thrombolitic agents, specific anti-viral agents, etc. In such a therapeutical context, it is of considerable interest that low molecular weight peptides can easily cross biological barriers, are less susceptible to protease attacks, and can be administered at high concentrations. In addition, small peptides are a rational target for strategies aimed at antigen-specific immunotherapeutical intervention. As an example, specific short peptide fragments might be used to elicit antibodies capable of reacting with the full-length proteins containing the peptide fragment's amino acid sequence, so abolishing the risk of cross-reactivity.
TL;DR: The effect of different doses of cadmium and copper was studied in relation to growth and polyamine (Pas) metabolism in shoots of sunflower plants to determine the role of Pas as markers of Cd or Cu toxicity.
Abstract: The effect of different doses of cadmium and copper was studied in relation to growth and polyamine (Pas) metabolism in shoots of sunflower plants. Cadmium accumulated to higher levels than copper and shoot length was reduced by 0.5 and 1 mM Cd, but only by 1 mM Cu. At 1 mM of Cd or Cu, Put content increased 270% and 160% with Cd2+ and Cu2+, respectively. Spermidine (Spd) was modified only by 1 mM Cd, while spermine (Spm) declined after seeds germinated, increasing thereafter but only with 1 mM Cd or Cu (273% over the controls for Cd and 230% for Cu at day 16). Both ADC and ODC activities were increased by 1 mM Cd, whereas 1 mM Cu enhanced ADC activity, but reduced ODC activity at every concentration used. The role of Pas as markers of Cd or Cu toxicity is discussed.
TL;DR: R reverse genetic studies indicated that the unique polyamines are synthesized from spermidine, and longer polyamines efficiently stabilized double stranded nucleic acids and a branched polyamine, tetrakis(3-aminropyl)ammonium, stabilized stem-and-loop structures.
Abstract: Recent research progress on polyamines in extreme thermophiles is reviewed. Extreme thermophiles produce two types of unique polyamines; one is longer polyamines such as caldopentamine and caldohexamine, and the other is branched polyamines such as tetrakis(3-aminopropyl)ammonium. The protein synthesis catalyzed by a cell-free extract of Thermus thermophilus, an extreme thermophile, required the presence of a polyamine and the highest activity was found in the presence of tetrakis(3-aminopropyl)ammonium. In vitro experiments, longer polyamines efficiently stabilized double stranded nucleic acids and a branched polyamine, tetrakis(3-aminropyl)ammonium, stabilized stem-and-loop structures. In T. thermophilus, polyamines are synthesized from arginine by a new metabolic pathway; arginine is converted to agmatine and then agmatine is aminopropylated to N1-aminopropylagmatine which is converted to spermidine by an enzyme coded by a gene homologous to speB (a gene for agmatinase). In this new pathway spermidine is not synthesized from putrescine. Reverse genetic studies indicated that the unique polyamines are synthesized from spermidine.