Analysis of Paracoccidioides lutzii mitochondria: a proteomic approach.

The genus Paracoccidioides is composed of thermal dimorphic fungi, causative agents of paracoccidioidomycosis, one of the most frequent systemic mycoses in Latin America. Mitochondria have sophisticated machinery for ATP production, which involves metabolic pathways such as citric acid and glyoxylate cycles, electron transport chain and oxidative phosphorylation. In addition, this organelle performs a variety of functions in the cell, working as an exceptional metabolic signalling centre that contributes to cellular stress responses, as autophagy and apoptosis in eukaryotic organisms. The aim of this work was to perform a descriptive proteomic analysis of mitochondria in Paracoccidioides lutzii yeast cells. After mitochondria fractionation, samples enriched in mitochondrial proteins were digested with trypsin and analysed using a NanoUPLC-MSE system (Waters Corporation, Manchester, UK). Ours results revealed that the established protocol for purification of mitochondria was very effective for P. lutzii, and 298 proteins were identified as primarily mitochondrial, in our analysis. To our knowledge, this is the first compilation of mitochondrial proteins from P. lutzii, to date. Copyright © 2016 John Wiley & Sons, Ltd.

In silico characterization of hypothetical proteins from Paracoccidioides lutzii.

Nearly 60% of Paracoccidioides lutzii genes encode products annotated as hypothetical or predicted proteins (HPs). In this study, we describe the global detection and functional inference of HPs, using computational methods based on sequence similarity, identification of targeting signals, presence of known protein domains, and use of the Gene Ontology functional classification scheme. Our analysis enabled a high-throughput characterization of predicted cellular localization and presence of protein domains, clustering HPs into different functional categories including metabolism, localization, cell cycle, response to stimulus, and signaling. To investigate P. lutzii HP expression profiles, we used data obtained from the expressed sequence tag database (dbEST). These analyses revealed 2364 HPs expressed in different situations, namely in mycelial and yeast forms, during the transition from mycelium to yeast, and under conditions mimicking infection. Based on this transcriptomic data, we performed a functional enrichment analysis according to the domains present in the HPs expressed in each condition. The most overrepresented functional domains were those involved in the regulation of gene expression, suggesting important and as yet undescribed roles for these HPs in the adaptation of P. lutzii to environmental conditions. In addition, the expression profiles of six randomly selected HPs were analyzed by quantitative real-time polymerase chain reaction in order to verify their expression in the complementary DNA libraries analyzed in this investigation. The approach used in this study should improve functional characterization of P. lutzii HPs.

Ureia e glicerina bruta como aditivos na ensilagem de cana-de-açúcar / Urea and crude glycerin as additive in sugar cane silage

Objetivou-se avaliar a inclusão de ureia e glicerina bruta como aditivos na ensilagem da cana-de-açúcar, na composição químico-bromatológica, pH, N-amoniacal (N-NH3) e digestibilidade in vitro (DIV). Os tratamentos foram quatro doses de ureia, 0, 10, 20 e 30 g de ureia por kg de cana-de-açúcar na ensilagem, e cinco doses de glicerina bruta, 0, 10, 20, 30 e 40g de glicerina bruta por kg de cana-de-açúcar na ensilagem. As silagens foram armazenadas por 180 dias. O tratamento com ureia afetou a maioria das variáveis relacionadas ao valor nutritivo, aumentando os teores de matéria seca (MS) e proteína (PB) (2,58; 7,76; 18,70 e 19,31%), reduzindo os teores de fibra em detergente neutro (FDN) e melhorando a DIV da MS (42,61; 48,53; 50,69 e 51,18%) e FDN (38,81; 39,23; 41,06 e 43,46%), e as características fermentativas da silagem, apresentando valores de pH de 3,49; 3,86; 4,18 e 3,93 e de N-NH3 de 1,72; 3,80; 7,88 e 9,00, para as dose de 0, 10, 20 e 30 g, respectivamente. A glicerina bruta aumentou os teores de MS e extrato etéreo (1,45; 3,03; 3,62; 3,41 e 4,38%), melhorou a DIV da MS com valores de 49,61; 52,24; 53,28; 55,60 e 56,09% e reduziu perdas por gases durante o processo de fermentação, apresentando médias de 6,69; 5,97; 5,89; 5,51 e 5,48% da MS para as doses 0, 10, 20, 30 e 40g, respectivamente. Assim, a ureia e a glicerina bruta podem ser utilizadas como aditivos na ensilagem da cana-de-açúcar...

The aim of this study was to evaluate the inclusion of urea and crude glycerin as an additive in ensiling of sugar cane, in chemical composition, pH, ammonia-N (N-NH3) and in vitro digestibility (IVD). The treatments were four doses of urea 0, 10, 20 and 30 g per kg of sugar cane ensiling and five doses of crude glycerin 0, 10, 20, 30 and 40g per kg of crude glycerin sugar cane ensiling. The silages were stored for 180 days. Treatment with urea affected most variables related to nutritional value, increasing the concentrations of dry matter (DM) and protein (CP) (2.58, 7.76, 18.70 and 19.31%) and reduced levels of neutral detergent fiber (NDF) and improved IVDDM (42.61, 48.53, 50.69 and 51.18%) and NDF (38.81, 39.23, 41.06 and 43.46%) and fermentation characteristics of silage, with pH values of 3.49, 3.86, 4.18 and 3.93 and NH3 1.72, 3.80, 7.88 and 9.00 for the dose of 0, 10, 20 and 30 g, respectively. The crude glycerin increased in DM and ether extract (1.45, 3.03, 3.62, 3.41 and 4.38%), improved IVDDM with values of 49.61, 52.24, 53 28; 55.60 and 56.09% and reduced gas losses during the fermentation process with mean of 6.69, 5.97, 5.89, 5.51 and 5.48% of DM for the doses 0, 10 , 20, 30 and 40g, respectively. Urea and crude glycerin can be used as an additive in ensiling of sugar cane...

Imunidade passiva, ingestão de colostro e mortalidade em cabritos Moxotó criados em sistemas extensivo e intensivo / Passive immunity, colostrum ingestion, and mortality of Moxotó kids raised under extensive and intensive breeding systems

Dosou-se a proteína sérica total para avaliar a aquisição de imunidade passiva em cabritos Moxotó. Para tal, formaram-se quatro grupos experimentais, sendo dois sistemas de criação, extensivo e intensivo, e dois manejos de colostro, ingestão natural e artificial. Tanto no sistema intensivo quanto no extensivo, os teores de proteína no soro foram significativamente mais altos nos animais com ingestão natural de colostro, 7,11±0,2g/dL, do que nos com ingestão artificial, 6,35±0,17g/dL. Independentemente da forma de ingestão de colostro, os cabritos do sistema intensivo tiveram teores de proteína sérica total, 7,21±0,19g/dL, mais elevados que os do sistema extensivo, 6,25±0,18g/dL, no entanto a imunidade passiva foi satisfatória nos dois grupos de animais. Ocorreu alta mortalidade de crias no sistema extensivo, 37 por cento, devido ao complexo hipotermia/inanição em decorrência dos baixos níveis de colostro ingeridos. No sistema intensivo de criação não ocorreu mortalidade de cabritos. A produção de colostro das cabras criadas intensivamente, 163,5±14,71mL, foi mais alta que das cabras criadas extensivamente, 53,75±19,12mL. O peso total dos cabritos foi semelhante nos dois sistemas de criação, 2881±252,78g no sistema extensivo, e 2297±194,59g no sistema intensivo. Conclui-se que a ingestão de colostro nos dois sistemas de produção permitiu adequada aquisição de imunidade em cabritos, porém o sistema extensivo determinou severa deficiência nutricional nas mães, com baixa produção de colostro e graves perdas de neonatos.

The acquisition of passive immunity in Moxotó kids was determined by dosages of total serum proteins. Four experimental groups were formed in two breeding systems - extensive and intensive - and two managements of colostrum intake - suckling from the mother or supplying in bottles. In both breeding systems, the serum protein levels were significantly higher in kids with natural ingestion of colostrum, 7.11±0.2g/dL, than in kids with artificial ingestion, 6.35±0.17g/dL. The kids of the intensive system had levels of total serum protein of 7.21±0.19 g/dL which was higher than the one of the extensive breeding system, 6.25±0.18g/dL. However, the passive immunity was satisfactory in all groups. There was high mortality of kids, 37 percent, due to starvation/hypothermia, in the extensive breeding system. This mortality was apparently due to the low levels of colostrum ingestion, 55.83±8.7mL. The production of colostrum by does from intensive breeding sistem, 163.5±14.71mL, was significantly higher than those from extensive breeding system, 53.75±19.12mL. The total weight of the kids born in the extensive breeding system, 2,881±252.78g, was similar to those born in the intensive breeding system, 2,297±194.59g. The colostrum ingestion allowed appropriate immunity acquisition by kid raised under both systems. However, the extensive breeding system determined a severe nutritional deficiency in the does with low colostrum production and high neonatal losses.

Occurrence of group A rotavirus mixed P genotypes infections in children living in Goiânia-Goiás, Brazil.

Group A rotaviruses (RVA) are the main causing agents of acute gastroenteritis worldwide, having a great impact on childhood mortality in developing countries. The objective of this study was to identify RVA-positive fecal samples with mixed P genotypes by hemi-nested reverse transcriptase-polymerase chain reaction (RT-PCR), followed by sequencing confirmation. Our results showed that, from the 81 RVA-positive samples, 25 were positive for more than one P genotype by hemi-nested RT-PCR. Of these 25 samples, 12 (48%) had their mixed P genotypes confirmed by sequencing and, from these, 10 were identified as P[6]P[8], one as P[4]P[6], and one as P[4]P[6]P[8]. Our results confirm the occurrence of RVA mixed infections among children in Brazil and reinforce the importance of the constant monitoring of RVA circulating strains for the efficacy of control/prevention against these agents.

Comparative analyses of the structure of the 1,3-beta-glucan synthase gene in Paracoccidioides brasiliensis isolates.

The evolutionary origin and significance of spliceosomal introns have been the subject of many investigations. Two theories, "introns-early" theory and "introns-late" theory, have been proposed to explain the evolution of introns in eukaryotic genes. Intron position is generally conserved in paralogue and orthologue genes. Some introns occur at similar but not necessarily identical positions in homologous genes, which were separated by great evolutionary distances. This event can be explained by insertion, loss or movement of the intron over short distances. Intron loss and gain events are unique in evolution and can be useful as markers for phylogenetic analyses. The insertion of introns at an identical position suggests a common ancestor gene. Here we analyzed, using PCR and RT-PCR, the structure of the 1,3-beta-glucan synthase gene (FKS) in several clinical isolates of Paracoccidioides brasiliensis (Pb): isolates Pb 01, Pb 4940, Pb 8515, Pb 8311, Pb 8334, Pb 4268, Pb 1668, and Pb E. Our results showed that seven of the isolates examined showed identical structures concerning the position of introns in PbFKS1. PbFKS4940 showed the intron described at the 3' end and had lost that one at the 5' end. The presence of the PbFKS4940 transcript suggests that it could be a functional gene. These data suggest a divergent evolution for introns with regard to the 1,3-beta-glucan synthase gene in P. brasiliensis isolates.

Comparative analyses of the structure of the 1, 3-beta-glucan synthase gene in Paracoccidioides brasiliensis isolates

The evolutionary origin and significance of spliceosomal introns have been the subject of many investigations. Two theories, [quot ]introns-early[quot ] theory and [quot ]introns-late[quot ] theory, have been proposed to explain the evolution of introns in eukaryotic genes. Intron position is generally conserved in paralogue and orthologue genes. Some introns occur at similar but not necessarily identical positions in homologous genes, which were separated by great evolutionary distances. This event can be explained by insertion, loss or movement of the intron over short distances. Intron loss and gain events are unique in evolution and can be useful as markers for phylogenetic analyses. The insertion of introns at an identical position suggests a common ancestor gene. Here we analyzed, using PCR and RT-PCR, the structure of the 1,3-beta-glucan synthase gene (FKS) in several clinical isolates of Paracoccidioides brasiliensis (Pb): isolates Pb 01, Pb 4940, Pb 8515, Pb 8311, Pb 8334, Pb 4268, Pb 1668, and Pb E. Our results showed that seven of the isolates examined showed identical structures concerning the position of introns in PbFKS1. PbFKS4940 showed the intron described at the 3' end and had lost that one at the 5' end. The presence of the PbFKS4940 transcript suggests that it could be a functional gene. These data suggest a divergent evolution for introns with regard to the 1,3-beta-glucan synthase gene in P. brasiliensis isolates.

Therapeutic targets in Paracoccidioides brasiliensis: post-transcriptome perspectives

The rise in antifungal resistance, observed as a result of the increasing numbers of immunocompromised patients, has made the discovery of new targets for drug therapy imperative. The description of the Paracoccidioides brasiliensis transcriptome has allowed us to find alternatives to refine current therapy against paracoccidioidomycosis. We used comparative analysis of expressed sequence tags to find promising drug targets that have been addressed in other pathogens. We divided the analysis into six different categories, based on the involvement of the targeted mechanisms in the cell: i) cell wall construction, ii) plasma membrane composition, iii) cellular machinery, iv) cellular metabolism, v) signaling pathways, and vi) other essential processes. Through this approach, it has been possible to infer strategies to develop alternative drugs against this pathogen.

Transcriptome overview of Paracoccidioides brasiliensis proteases

Proteases perform a wide variety of functions inside and outside cells, regulating many biological processes. Infectious microorganisms use proteases, either secreted or attached to their cell surface to weaken and invade their hosts. Therefore, proteases are targets for drugs against a diverse set of diseases. Paracoccidioides brasiliensis is the most prevalent fungal pathogen causing systemic mycosis in Latin America. The development of paracoccidioidomycosis depends on interactions between fungal and host components and proteases have been described as important factors implicated in the mechanism of host colonization by fungi. The primary goal for this study is to present an overview of the transcriptome sequences--identified cDNAs that encode proteases. We obtained a total of 53 cDNAs encoding proteases; 15 were classified as ATP-independent, 12 as ATP-dependent, 22 as proteasome subunits, and 4 as deubiquitinating proteases. The mechanisms and biological activity of these proteases differ in substrate specificity and in catalytic mechanisms.

Screening for glycosylphosphatidylinositol-anchored proteins in the Paracoccidioides brasiliensis transcriptome

Open reading frames in the transcriptome of Paracoccidioides brasiliensis were screened for potential glycosylphosphatidylinositol (GPI)-anchored proteins, which are a functionally and structurally diverse family of post-translationally modified molecules found in a variety of eukaryotic cells. Numerous studies have demonstrated that various GPI anchor sequences can affect the localization of these proteins in the plasma membrane or the cell wall. The GPI anchor core is produced in the endoplasmic reticulum by sequential addition of monosaccharides and phospho-ethanolamine to phosphatidylinositol. The complete GPI anchor is post-translationally attached to the protein carboxyl-terminus by GPI transamidases. Removal of this GPI lipid moiety by phospholipases generates a soluble form of the protein. The identification of putative GPI-attached proteins in the P. brasiliensis transcriptome was based on the following criteria: the presence of an N-terminal signal peptide for secretion and a hydrophobic region in the C-terminus presenting the GPI-attachment site. The proteins that were identified were in several functional categories: i) eight proteins were predicted to be enzymes (Gel1, Gel2, Gel3, alpha-amylase, aspartic proteinase, Cu-Zn SOD, DFG5, PLB); ii) Ag2/PRA, ELI-Ag1 and Gel1 are probably surface antigens; iii) Crh-like and the GPI-anchored cell wall protein have a putative structural role; iv) ECM33 and Gels (1, 2 and 3) are possibly involved in cell wall biosynthesis, and v) extracellular matrix protein is considered to be an adhesion protein. In addition, eight deduced proteins were predicted to localize in the plasma membrane and six in the cell wall. We also identified proteins involved in the synthesis, attachment and cleaving of the GPI anchor in the P. brasiliensis transcriptome.

The cell wall of Paracoccidioides brasiliensis: insights from its transcriptome

The cell wall of a human pathogenic fungus is in contact with the host, serves as a barrier against host defense mechanisms and harbors most fungal antigens. In addition, cell wall biosynthesis pathways have been recognized as essential to viability and as specific drug targets. Paracoccidioides brasiliensis is a dimorphic fungus that presents mycelium morphology in the free environment and causes infection in a yeast form. The morphogenetic conversion is correlated with changes in the cell wall composition, organization and structure. Based on transcriptome analysis, the enzymes involved in the biosynthesis and remodeling of cell wall polysaccharides, as well as several cell wall-associated molecules of P. brasiliensis, were identified and addressed in further detail.

Chemotaxis and flagellar genes of Chromobacterium violaceum

The availability of the complete genome of the Gram-negative beta-proteobacterium Chromobacterium violaceum has increasingly impacted our understanding of this microorganism. This review focuses on the genomic organization and structural analysis of the deduced proteins of the chemosensory adaptation system of C. violaceum. C. violaceum has multiple homologues of most chemotaxis genes, organized mostly in clusters in the bacterial genome. We found at least 67 genes, distributed in 10 gene clusters, involved in the chemotaxis of C. violaceum. A close examination of the chemoreceptors methyl-accepting chemotaxis proteins (MCPs), and the deduced sequences of the members of the two-component signaling system revealed canonical motifs, described as essential for the function of the deduced proteins. The chemoreceptors found in C. violaceum include the complete repertoire of such genes described in bacteria, designated as tsr, tar, trg, and tap; 41 MCP loci were found in the C. violaceum genome. Also, the C. violaceum genome includes a large repertoire of the proteins of the chemosensory transducer system. Multiple homologues of bacterial chemotaxis genes, including CheA, CheB, CheD, CheR, CheV, CheY, CheZ, and CheW, were found in the C. violaceum genome

Molecular and serological characterization of group a rotavirus isolates obtained from hospitalized children in Goiânia, Brazil, 1998-2000.

Fecal samples positive for rotavirus group A ( n=120) were analyzed by enzyme immunoassay-monoclonal antibody (EIA-MAb) serotyping and/or reverse transcription/multiplex polymerase chain reaction (PCR) amplification to determine the prevalence of the [P] and G genotypes. The most prevalent G genotype/serotype detected was G1 (76.7%), followed by G2 (5.0%). Six samples were characterized as G9 by multiplex PCR, and one sample was characterized as G3 by EIA-MAb. The combinations of [P] and G genotypes found were P[8] and G1 (20.8%), P[6] and G1 (10.8%), P[6] and G9 (4.2%), P[8] and G2 (1.7%), and P[6] and G2 (0.8%). The diversity of rotavirus group A [P] and G genotypes/serotypes reinforces the need for continuous characterization of rotaviruses circulating in populations in Brazil.

Transcriptome characterization of the dimorphic and pathogenic fungus Paracoccidioides brasiliensis by EST analysis.

Paracoccidioides brasiliensis is a pathogenic fungus that undergoes a temperature-dependent cell morphology change from mycelium (22 degrees C) to yeast (36 degrees C). It is assumed that this morphological transition correlates with the infection of the human host. Our goal was to identify genes expressed in the mycelium (M) and yeast (Y) forms by EST sequencing in order to generate a partial map of the fungus transcriptome. Individual EST sequences were clustered by the CAP3 program and annotated using Blastx similarity analysis and InterPro Scan. Three different databases, GenBank nr, COG (clusters of orthologous groups) and GO (gene ontology) were used for annotation. A total of 3,938 (Y = 1,654 and M = 2,274) ESTs were sequenced and clustered into 597 contigs and 1,563 singlets, making up a total of 2,160 genes, which possibly represent one-quarter of the complete gene repertoire in P. brasiliensis. From this total, 1,040 were successfully annotated and 894 could be classified in 18 functional COG categories as follows: cellular metabolism (44%); information storage and processing (25%); cellular processes-cell division, posttranslational modifications, among others (19%); and genes of unknown functions (12%). Computer analysis enabled us to identify some genes potentially involved in the dimorphic transition and drug resistance. Furthermore, computer subtraction analysis revealed several genes possibly expressed in stage-specific forms of P. brasiliensis. Further analysis of these genes may provide new insights into the pathology and differentiation of P. brasiliensis.

Identification of differentially expressed transcripts in the human pathogenic fungus Paracoccidioides brasiliensis by differential display.

Paracoccidioides brasiliensis is a dimorphic human pathogenic fungus that is the causal agent of paracoccidioidomycosis, a systemic disease that predominantly affects rural communities in South and Central America. Dimorphism is a common characteristic of systemic human pathogenic fungi. Here we describe the use of differential display (DD) to isolate and identify differentially expressed genes of P. brasiliensis, in the two cell types, yeast (Y) and mycelium (M), as well as at different time intervals during temperature-induced M to Y transition. Using two oligo-deoxythymidine-anchored primers combined with 10 arbitrary ones, we were able to detect the presence of at least 20 differentially transcribed cDNA fragments. Some of these fragments were further analysed by reverse-northern blot and northern blot in order to confirm their differential expression. The M32, M51 and M73 cDNA fragments were specific for the mycelial form of P. brasiliensis. Furthermore, we found two cDNA fragments (M-Y1 and M-Y2) that were upregulated during M-Y transition. This method was efficient and useful in the detection of differentially expressed genes in P. brasiliensis.

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

The Atomic Solvation Parameter (ASP) model is one of the simplest models of solvation, in which the solvation free energy of a molecule is proportional to the solvent accessible surface area (SAS) of its atoms. However, until now this model had not been incorporated into the Self-Consistent Mean Field Theory (SCMFT) method for modelling sidechain conformations in proteins. The reason for this is that SAS is a many-body quantity and, thus, it is not obvious how to define it within the Mean Field (MF) framework, where multiple copies of each sidechain exist simultaneously. Here, we present a method for incorporating an SAS-based potential, such as the ASP model, into SCMFT. The theory on which the method is based is exact within the MF framework, that is, it does not depend on a pairwise or any other approximation of SAS. Therefore, SAS can be calculated to arbitrary accuracy. The method is computationally very efficient: only 7.6% slower on average than the method without solvation. We applied the method to the prediction of sidechain conformation, using as a test set high-quality solution structures of 11 proteins. Solvation was found to substantially improve the prediction accuracy of well-defined surface sidechains. We also investigated whether the methodology can be applied to prediction of folding free energies of protein mutants, using a set of barnase mutants. For apolar mutants, the modest correlation observed between calculated and observed folding free energies without solvation improved substantially when solvation was included, allowing the prediction of trends in the folding free energies of this type of mutants. For polar mutants, correlation was not significant even with solvation. Several other factors also responsible for the correlation were identified and analysed. From this analysis, future directions for applying and improving the present methodology are discussed.

Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome.

Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. There is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates. Tetraheme cytochrome c(3) is a small soluble and monomeric protein that performs a central step in the bioenergetic metabolism of sulfate reducing bacteria, termed "proton-thrusting," linking the oxidation of molecular hydrogen with the reduction of sulfate. The mechano-chemical coupling involved in the transfer of multiple electrons and protons in cytochrome c(3) from Desulfovibrio desulfuricans ATCC 27774 is described using results derived from the microscopic thermodynamic characterization of the redox and acid-base centers involved, crystallographic studies in the oxidized and reduced states of the cytochrome, and theoretical studies of the redox and acid-base transitions. This proton-assisted two-electron step involves very small, localized structural changes that are sufficient to generate the complex network of functional cooperativities leading to energy transduction, while using molecular mechanisms distinct from those established for other Desulfovibrio sp. cytochromes from the same structural family.

The mechanism of superoxide scavenging by Archaeoglobus fulgidus neelaredoxin.

Neelaredoxin is a mononuclear iron protein widespread among prokaryotic anaerobes and facultative aerobes, including human pathogens. It has superoxide scavenging activity, but the exact mechanism by which this process occurs has been controversial. In this report, we present the study of the reaction of superoxide with the reduced form of neelaredoxin from the hyperthermophilic archaeon Archaeoglobus fulgidus by pulse radiolysis. This protein reduces superoxide very efficiently (k = 1.5 x 10(9) m(-1)s(-1)), and the dismutation activity is rate-limited, in steady-state conditions, by the much slower superoxide oxidation step. These data show unambiguously that the superfamily of neelaredoxin-like proteins (including desulfoferrodoxin) presents a novel type of reactivity toward superoxide, a result of particular relevance for the understanding of both oxygen stress response mechanisms and, in particular, how pathogens may respond to the oxidative burst produced by the defense cells in eukaryotes. The actual in vivo functioning of these enzymes will depend strongly on the cell redox status. Further insight on the catalytic mechanism was obtained by the detection of a transient intermediate ferric species upon oxidation of neelaredoxin by superoxide, detectable by visible spectroscopy with an absorption maximum at 610 nm, blue-shifted approximately 50 nm from the absorption of the resting ferric state. The role of the iron sixth ligand, glutamate-12, in the reactivity of neelaredoxin toward superoxide was assessed by studying two site-directed mutants: E12Q and E12V.

Two-dimensional electrophoresis and characterization of antigens from Paracoccidioides brasiliensis.

Paracoccidioides brasiliensis is a fungal pathogen of humans. To identify antigens from P. brasiliensis we fractionated a crude preparation of proteins from the fungus and detected the IgG reactive proteins by immunoblot assays of yeast cellular extracts with sera of patients with paracoccidioidomycosis (PCM). We identified and characterized six new antigens by amino acid sequencing and homology search analyses with other proteins deposited in a database. The newly characterized antigens were highly homologous to catalase, fructose-1,6-biphosphate aldolase (aldolase), glyceraldehyde-3-phosphate dehydrogenase, malate dehydrogenase and triosephosphate isomerase from several sources. The characterized antigens presented preferential synthesis in yeast cells, the host fungus phase.

Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.

The performance of the self-consistent mean field theory (SCMFT) method for side-chain modeling, employing rotamer energies calculated with the flexible rotamer model (FRM), is evaluated in the context of comparative modeling of protein structure. Predictions were carried out on a test set of 56 model backbones of varying accuracy, to allow side-chain prediction accuracy to be analyzed as a function of backbone accuracy. A progressive decrease in the accuracy of prediction was observed as backbone accuracy decreased. However, even for very low backbone accuracy, prediction was substantially higher than random, indicating that the FRM can, in part, compensate for the errors in the modeled tertiary environment. It was also investigated whether the introduction in the FRM-SCMFT method of knowledge-based biases, derived from a backbone-dependent rotamer library, could enhance its performance. A bias derived from the backbone-dependent rotamer conformations alone did not improve prediction accuracy. However, a bias derived from the backbone-dependent rotamer probabilities improved prediction accuracy considerably. This bias was incorporated through two different strategies. In one (the indirect strategy), rotamer probabilities were used to reject unlikely rotamers a priori, thus restricting prediction by FRM-SCMFT to a subset containing only the most probable rotamers in the library. In the other (the direct strategy), rotamer energies were transformed into pseudo-energies that were added to the average potential energies of the respective rotamers, thereby creating hybrid energy-based/knowledge-based average rotamer energies, which were used by the FRM-SCMFT method for prediction. For all degrees of backbone accuracy, an optimal strength of the knowledge-based bias existed for both strategies for which predictions were more accurate than pure energy-based predictions, and also than pure knowledge-based predictions. Hybrid knowledge-based/energy-based methods were obtained from both strategies and compared with the SCWRL method, a hybrid method based on the same backbone-dependent rotamer library. The accuracy of the indirect method was approximately the same as that of the SCWRL method, but that of the direct method was significantly higher.