Exploring the Potential of Structure-Based Deep Learning Approaches for T cell Receptor Design.

Deep learning methods, trained on the increasing set of available protein 3D structures and sequences, have substantially impacted the protein modeling and design field. These advancements have facilitated the creation of novel proteins, or the optimization of existing ones designed for specific functions, such as binding a target protein. Despite the demonstrated potential of such approaches in designing general protein binders, their application in designing immunotherapeutics remains relatively unexplored. A relevant application is the design of T cell receptors (TCRs). Given the crucial role of T cells in mediating immune responses, redirecting these cells to tumor or infected target cells through the engineering of TCRs has shown promising results in treating diseases, especially cancer. However, the computational design of TCR interactions presents challenges for current physics-based methods, particularly due to the unique natural characteristics of these interfaces, such as low affinity and cross-reactivity. For this reason, in this study, we explored the potential of two structure-based deep learning protein design methods, ProteinMPNN and ESM-IF, in designing fixed-backbone TCRs for binding target antigenic peptides presented by the MHC through different design scenarios. To evaluate TCR designs, we employed a comprehensive set of sequence- and structure-based metrics, highlighting the benefits of these methods in comparison to classical physics-based design methods and identifying deficiencies for improvement.

KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities.

Molecular interactions that modulate catalytic processes occur mainly in cavities throughout the molecular surface. Such interactions occur with specific small molecules due to geometric and physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: a RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web.

Session Frequency Matters in Neurofeedback Training of Athletes.

Neurofeedback training has been an increasingly used technique and is taking its first steps in sport. Being at an embryonic stage, it is difficult to find consensus regarding the applied methodology to achieve the best results. This study focused on understanding one of the major methodological issues-the training session frequency. The aim of the investigation was to understand if there are differences between performing two sessions or three sessions per week in enhancement of alpha activity and improvement of cognition; and in case there are differences, infer the best protocol. Forty-five athletes were randomly assigned to the three-session-training-per-week group, the two-session-training-per-week group and a control group. The results showed that neurofeedback training with three sessions per week was more effective in increase of alpha amplitude during neurofeedback training than two sessions per week. Furthermore, only the three-session-per-week group showed significant enhancement in N-back and oddball performance after training. The findings suggested more condensed training protocol lead to better outcomes, providing guidance on neurofeedback protocol design in order to optimize training efficacy.

First Nonphosphorylated Inhibitors of Phosphoglucose Isomerase Identified by Chemical Library Screening.

Human African trypanosomiasis, Chagas disease, and leishmaniasis are human infections caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania. Besides their severity and global impact, treatments are still challenging. Currently available drugs have important limitations, highlighting the urgent need to develop new drugs. Phosphoglucose isomerase (PGI) is considered a promising target for the development of antiparasitic drugs, as it acts on two essential metabolic pathways, glycolysis and gluconeogenesis. Herein, we describe the identification of new nonphosphorylated inhibitors of Leishmania mexicana PGI ( LmPGI), with the potential for the development of antiparasitic drugs. A fluorescence-based high-throughput screening (HTS) assay was developed by coupling the activities of recombinant LmPGI with glucose-6-phosphate dehydrogenase and diaphorase. This coupled assay was used to screen 42,720 compounds from ChemBridge and TimTec commercial libraries. After confirmatory assays, selected LmPGI inhibitors were tested against homologous Trypanosoma cruzi and humans. The PGI hits are effective against trypanosomatid PGIs, with IC50 values in the micromolar range, and also against the human homologous enzyme. A computational analysis of cavities present on PGI's crystallographic structure suggests a potential binding site for the proposed mixed-type inhibition mechanism.

Avaliação de IFN-γ e IL-10 em cães naturalmente infectados com Leishmania (Leishmania) chagasi com e sem manifestações clínicas / Evaluation of INF-γ and IL-10 in dogs naturally infected by Leishmania (Leishmania) chagasi with and without clinic events

As leishmanioses têm como agentes etiológicos parasitas intracelulares obrigatórios pertencentes ao gênero Leishmania capazes de infectar diferentes espécies de mamíferos e nestes se reproduzirem dentro do sistema fagocítico mononuclear. Os cães domésticos são os principais responsáveis pela manutenção da cadeia epidemiológica da doença, podendo apresentar uma grande variedade de perfis clínicos, desde aparentemente sadios a severamente acometidos. Avaliou-se a expressão das citocinas de cães naturalmente infectados com Leishmania (Leishmania) chagasi. Foram coletadas 50 amostras, sendo 20 de animais positivos e sintomáticos para Leishmaniose Visceral Canina (LVC), 20 de animais positivos e assintomáticos e 10 de animais sabidamente negativos para a LVC. As amostras foram analisadas pelo teste imunocromatográfico rápido Dual Path Platform (DPP/Biomanguinhos®) e pelo ELISA (EIE/Biomanguinhos®) indireto para detecção de anticorpos anti-Leishmania. Após as confirmações dos testes, foi realizado o ELISA de captura (R & D Systems) para quantificação das citocinas IL-10 e IFN-γ. Houve diferença estatística entre os grupos observando um aumento nos níveis de IFN-γ nos animais assintomáticos e um aumento de IL-10 nos sintomáticos.(AU)

Leishmaniasis has as obligatory intracellular parasitic etiological agents belonging to the genus Leishmania capable of infecting different species of mammals and reproducing them within the mononuclear phagocytic system. Domestic dogs are the main responsible for maintaining the epidemiological chain of the disease, presenting a wide variety of clinical profiles, from apparently healthy to severely affected. The expression of the cytokines from dogs naturally infected with Leishmania (Leishmania) chagasi was evaluated. Blood samples were collected from 50 animals, 20 from positive and symptomatic dogs for Leishmaniasis Canine (CVL), 20 from positive asymptomatic animals and 10 negative. Samples were analyzed by immunochromatographic test Dual Path Platform (DPP/Biomanguinhos®) and by indirect ELISA (EIE/Biomanguinhos®) for detection of anti-Leishmania antibodies. There was statistical difference between the groups observing an increase in IFN-γ levels in asymptomatic animals and an IL-10 increase in symptomatic.(AU)

Quantificação da IL-10 e do INF-γ em cães com ou sem sinais clínicos de infecção com Leishmania (Leishmania) chagasi / Quantification of IL-10 and IFN-γ in dogs with or without clinical signs of Leishmania (Leishmania) chagasi infection

As leishmanioses compreendem um complexo de doenças causadas por parasitos intracelulares obrigatórios pertencentes ao gênero Leishmania. Consideradas como importante problema de saúde pública, sendo os cães domésticos os principais responsáveis pela manutenção da cadeia epidemiológica da doença, estima-se que mais da metade dos cães infectados não manifestam sinais clínicos da enfermidade. Avaliou-se o perfil de IL-10 e INF- γ de cães naturalmente infectados com Leishmania (Leishmania) chagasi no município de São Luís-MA. Foram coletadas 50 amostras, sendo 20 de animais positivos e sintomáticos para Leishmaniose Visceral Canina (LVC), 20 de animais positivos e assintomáticos e 10 de animais sabidamente negativos para a LVC. As amostras foram analisadas pelo teste imunocromatográfico rápido Dual Path Platform (DPP/Biomanguinhos®) e pelo ELISA (EIE/Biomanguinhos®) indireto para detecção de anticorpos anti-Leishmania. Após as confirmações dos testes, foi realizado o ELISA de captura para quantificação das citocinas IL-10 e INF-γ através do kit Milliplex MAP. Houve diferença estatística entre os grupos, observando um aumento de IL-10 em soros de cães sintomáticos para LVC, comparado com o grupo de animais assintomáticos, sugerindo que animais com essa expressão de IL-10 podem estar associados à susceptibilidade a doença. Assim como o aumento dos níveis de INF-γ observados em cães assintomáticos, comparado com o grupo de cães sintomáticos, poderiam estar relacionados à cronicidade da doença.(AU)

Leishmaniasis comprise a complex of diseases caused by intracellular mandatory parasites belonging to the genus Leishmania. Considered as an important public health problem, and domestic dogs are primarily responsible for maintaining the epidemiological chain of the disease, it is estimated that more than the half of the dogs infected do not show clinical signs of the disease. The profile of IL-10 and IFN-γ dogs naturally infected with Leishmania (Leishmania) chagasi in São Luís/MA was evaluated. Blood samples were collected from 50 animals, 20 from positive and symptomatic dogs for leishmaniasis canine (CVL), 20 from positive asymptomatic animals and 10 negative. Samples were analyzed by immunochromatographic test Dual Path Platform (DPP/Biomanguinhos®) and by indirect ELISA (EIE/Biomanguinhos®) for detection of anti-Leishmania antibodies. After the confirmation of the tests, the capture ELISA was performed for quantification of IL-10 and IFN-γ cytokines through the Milliplex MAP kit. There was a statistical difference between the groups, observing an increase of IL-10 in blood of symptomatic dogs for CVL, compared to the group of asymptomatic animals, suggesting that animals with this expression of IL-10 may be associated with susceptibility to disease. As well as the increase in IFN-γ levels in asymptomatic dogs, compared to the symptomatic dog group, could be related to chronicity of the disease.(AU)

Estudo histológico e histoquímico da pele de jurará Kinosternon scorpioides scorpioides (Testudines: Kinosternidae) / Histological and histochemical study of the skin of the muçuã Kinosternon scorpioides scorpioides (Testudines: Kinosternidae)

O objetivo do presente trabalho foi analisar histológica e histo- químicamente a pele do jurará (Kinosternon scorpioides scorpioides). Foram utilizados seis animais (três machos e três fêmeas). Os animais foram eutanasiados com dose letal de tiopental sódico a 2,5%, para colheita de fragmentos de pele mole das patas e pescoço do animal, que após a fixação em líquido de Bouin, foram incluídos em parafina e corados pelas técnicas de hematoxilina-eosina, Giemsa, Sirius red, Reticulina de Gomori e Fucsina-resorcina de Weigert. Os resultados revelaram que a pele do jurará é delgada e composta de epiderme e derme. A epiderme é formada por estrato germinativo constituído por uma única camada de células cilíndricas; estrato espinhoso apresentando duas ou três camadas de células poliédricas; o estrato granuloso não foi observado nos exemplares estudados O estrato córneo apresenta uma delgada camada de queratina mole. Na derme, os fibroblastos foram as células mais freqüentes e as fibras colágenas formavam feixes espessos dispostos em várias direções. No método do Picro Sirius Red sob luz polarizada observou-se que, independente da região analisada, há predomínio de fibras colágenas tipo I em relação ao colágeno tipo III. Foi também observados mastócitos em pequena quantidade e fibras elásticas na região subepidérmica. Concluiu-se que a pele de Kinosternon scorpioides scorpioides possui características semelhantes a dos demais vertebrados (anfíbios, aves e mamíferos), apresenta peculiaridades, como por exemplo, a ausência de papilas dérmicas e glândulas...

The aim of this paper was to study the histology and histochemistry of the skin of six specimens of muçuã (three males and three females). The animals were euthanized through a lethal dose of sodium thiopental at 2.5%. Fragments of the soft skin were fixed in Bouin's solution and processed for inclusion in paraffin. The sections were stained with hematoxylin-eosin, Giemsa, Sirius red, Gomori's reticulin and Weigert's fuchsin-resorcin. The results revealed that the skin is thin and constituted by epidermis and dermis. The epidermis is made up by one layer of cylindrical cells of stratum germinativum, two or three layers of poliedric cells of stratum spinosum, but without stratum granular. The stratum corneum consists of a thin layer of soft keratin. In the dermis, the fibroblasts were the most frequent cells and collagen fibers formed a thick bound displayed in several directions. The Sirius red under polarized light showed that type I collagen was predominant when compared with the occurrence of type III collagen. Mast cells were also found, and elastic fibers were seen in the subepidermic layer. We concluded that the skin of Kinosternon scorpioides scorpioides has histological features similar to other vertebrates (amphibia, aves, mammalia), however without dermal papillae and glands...

Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages.

Protein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR classification performance. Also, we found that the addition of an amino acid conservation attribute did not improve the classification prediction. This result indicates that the increase in predictive power associated with amino acid conservation is exhausted by adequate use of an extensive list of independent physicochemical and structural parameters that, by themselves, fully describe the nano-environment at protein-protein interfaces. The IFR classifier developed in this study is now integrated into the BlueStar STING suite of programs. Consequently, the prediction of protein-protein interfaces for all proteins available in the PDB is possible through STING_interfaces module, accessible at the following website: (http://www.cbi.cnptia.embrapa.br/SMS/predictions/index.html).

Effects of fasting and refeeding on the metabolic functions of the turtle Kinosternon scorpioides (Linnaeus, 1766) raised in captivity / Efeitos do jejum e da realimentação sobre as funções metabólicas da tartaruga Kinosternon scorpioides (Linnaeus, 1766) criada em cativeiro

The metabolic responses of adult and young freshwater Kinosternon scorpioides turtles raised in captivity were evaluated. Two experiments were performed: a) blood metabolite changes caused by food deprivation, and b) liver and muscle glycogen and total lipid differences after fasting and refeeding. Blood glucose concentration of young animals was susceptible to food deprivation. In both groups this metabolite decreased after 30 days of fasting. Feeding for 15 days did not recover blood glucose. Total seric proteins were not affected by food deprivation. Fasting decreased blood urea nitrogen and the highest difference was found around 30 days. Uric acid increased in young animals after 60 days of fasting. Triacylglicerol decreased after 15 days of fasting and refeeding for 15 days recovered the pre-fasting levels. Free fatty acid plasma tended to increase around 15 days of fasting. Liver glycogen decreased at day 15 of fasting, being stable thereafter while muscle glycogen decreased at a slower rate. Total liver lipid stabilized after 30 days and then decreased 70% after 60 days of fasting. Muscle lipids remained stable throughout fasting. It could be concluded that fasting of Kinosternon scorpioides led to metabolic adaptations similar to the one reported from reptiles and fish.

Neste trabalho foi avaliada as respostas metabólicas da tartaruga Kinosternon scorpioides criada em cativeiro, nas fases, adultos e jovens nos estados: alimentado, jejuado e realimentado. O estudo compreendeu dois experimentos: (a) mudanças metabólicas no sangue causadas por privação alimentar e realimentação e (b) diferenças nas concentrações de glicogênio e lipídeos totais no fígado e no músculo após jejum e realimentação. No experimento dos animais jovens a concentração de glicose no sangue apresentou mudanças significativas. Entretanto, nos dois experimentos esse metabólito reduziu significativamente aos 30 dias de jejum. Realimentados por um período de 15 dias foi observado que a concentração de glicose não recuperou os níveis de pré-jejum. Concentração de glicose no sangue de animais jovens foi mais suscetível à privação de alimentos. Em ambos os grupos os metabólitos analisados decresceu após 30 dias de jejum. Retomando a alimentação por 15 dias foi observado que a concentração de glicose não recuperou. As concentrações de proteínas séricas totais não foram afetadas pela privação alimentar. O jejum decresceu a concentração de uréia no sangue e a maior diferença ocorreu aos 30 dias. O ácido úrico decresceu nos animais jovens após 60 dias de jejum. O triacilglicerol diminuiu após 15 dias de jejum e a realimentação por 15 dias recuperou os níveis de pré-jejum. O glicogênio hepático diminuiu aos 15 dias de jejum, e estabilizou a partir daí, enquanto o glicogênio muscular diminuiu a um ritmo mais lento. O lipídio total hepático total se manteve estável até os 30 dias de jejum, diminuindo até 70% aos 60 dias de jejum. E, em seguida, diminuiu 70% após 60 dias de jejum. Os lipídeos musculares permaneceram estáveis durante o jejum. Conclui-se que o jejum na espécie Kinosternon scorpioides apresentou adaptações metabólicas semelhantes aos relatados para outros répteis e peixes.

High resolution analysis of snake venom metalloproteinase (SVMP) peptide bond cleavage specificity using proteome based peptide libraries and mass spectrometry.

Both serine and metalloproteinases have been shown to play the role of toxins in the venoms of many snakes. Determination of the natural protein substrates of these toxins is an important feature in the toxinological characterization of these proteinases. Furthermore, characterization of their peptide bond specificity is of value for understanding active site preference of the proteinase associated with effective proteolysis as well as of use in the design of peptide substrates and inhibitor lead compounds. Typically the determination of peptide bond cleavage specificity of snake venom serine proteinases (SVSPs) and snake venom metalloproteinases (SVMPs) has been performed using limited sets of peptides or small oligopeptides as experimental substrates. Although this approach has yielded valuable data it is generally limited in scope due to the relatively small sets of substrates used to generate the consensus specificity sequences for these proteinases. In this study we use a large, plasma based, proteome-derived peptide library as substrates along with mass spectrometry to explore the peptide bond specificity of three PI SVMPs and one PIII SVMP to determine their individual peptide cleavage consensus sequences. All of the proteinases assayed displayed a clear preference for a leucine residue in the P1' site. Careful analysis of the specificity profiles of the SVMPs examined showed interesting differences in the preferences at the other P and P' sites suggesting functional differences between these proteinases. The PI SVMPs, leucurolysin-a, atrolysin C, and BaP1, showed preferences across the full P4 to P4' range whereas the PIII SVMP bothropasin showed a narrower range of preferences across the sites. In silico docking experiments with the experimentally derived consensus sequences as well as with comparison of the results to those in the literature regarding peptide bond specificity based on both peptide and protein substrates give rise to a fresh understanding of the specificity of these SVMPS and may serve as a foundation for future experiments to better elucidate their mechanism of action in the complex pathophysiology of snakebite envenomation.

High resolution analysis of snake venom metalloproteinase (SVMP) peptide bond cleavage specificity using proteome based peptide libraries and mass spectrometry. (AU)

Both serine and metalloproteinases have been shown to play the role of toxins in the venoms of many snakes. Determination of the natural protein substrates of these toxins is an important feature in the toxinological characterization of these proteinases. Furthermore, characterization of their peptide bond specificity is of value for understanding active site preference of the proteinase associated with effective proteolysis as well as of use in the design of peptide substrates and inhibitor lead compounds. Typically the determination of peptide bond cleavage specificity of snake venom serine proteinases (SVSPs) and snake venom metalloproteinases (SVMPs) has been performed using limited sets of peptides or small oligopeptides as experimental substrates. Although this approach has yielded valuable data it is generally limited in scope due to the relatively small sets of substrates used to generate the consensus specificity sequences for these proteinases. In this study we use a large, plasma based, proteome-derived peptide library as substrates along with mass spectrometry to explore the peptide bond specificity of three PI SVMPs and one PIII SVMP to determine their individual peptide cleavage consensus sequences. All of the proteinases assayed displayed a clear preference for a leucine residue in the P1Œ site. Careful analysis of the specificity profiles of the SVMPs examined showed interesting differences in the preferences at the other P and PŒ sites suggesting functional differences between these proteinases.

The origin of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase): luciferin stereoselectivity as a switch for the oxygenase activity.

Beetle luciferases evolved from AMP/CoA-ligases. However, it is unclear how the new luciferase activity evolved. In order to clarify this question, we compared the luminescence and catalytic properties of a recently cloned luciferase-like enzyme from Zophobas mealworm, an AMP/CoA-ligase displaying weak luminescence activity, with those of cloned luciferases from the three main families of luminescent beetles: Phrixthrix hirtus railroad worm; Pyrearinus termitilluminans click beetle and Photinus pyralis firefly. The catalytic constant of the mealworm enzyme was 2-4 orders of magnitude lower than that of beetle luciferases, but 3 orders of magnitude above the non-catalyzed chemiluminescence of luciferyl-adenylate in buffer. Studies with D- and L-luciferin and their adenylates show that the luminescence reaction of the luciferase-like enzyme and beetle luciferases are stereoselective for D-luciferin and its adenylate, and that the selectivity is determined mainly at the adenylation step. Modelling studies showed that the luciferin binding site cavity of this enzyme is smaller and more hydrophobic than that of beetle luciferases. Therefore Zophobas mealworm enzyme displays true luciferase activity, keeping the attributes of an ancient protoluciferase. These results suggest that stereoselectivity for D-luciferin may have been a key event for the origin of oxygenase/luciferase activity in AMP/CoA-ligases, and that efficient luciferase activity may have further evolved mainly by increasing the catalytic constant of the oxidative reaction and the quantum yield of bioluminescence.

Estudo histológico e histoquímico do esôfago do muçuã Kinosternon scorpioides Linnaeus, 1766 (Reptilia, Chelonia, Kinosternidae) / Histological and Histochemical Studies of the Esophagus of the Muçuã Kinosternon Scorpioides Linnaeus, 1766 (Reptilia, Chelonia, Kinosternidae) / Estudios histológicos e histoquímicos del esófago del muçuã kinosternon scorpioides linnaeus, 1766 (reptilia, chelonia, kinosternidae)

No estudo histológico e histoquímico do esôfago de Kinosternon scorpioides, foram utilizados 12 exemplares capturados em Santa Rita, Maranhão, submetidos à eutanásia com solução saturada de hidrato de cloral. Fragmentos do esôfago foram fixados em líquido de Bouin e em formol a 10, incluídos em parafina, seccionados a 4 µm e corados em H.E., P.A.S., Tricrômico de Gomori, Masson-Fontana modificada e Grimelius. O esôfago foi dividido em regiões cranial, média e caudal, constituídas pelas túnicas mucosa, submucosa, muscular, adventícia ou serosa. A mucosa das duas primeiras regiões é revestida por epitélio pseudoestratificado prismático ciliado com células caliciformes, e na última, os cílios estão ausentes. A lâmina própria do esôfago constituída de conjuntivo frouxo vascularizado e tecido linfóide é desprovida de glândulas. A muscular da mucosa é formada por camadas musculares lisas, circular interna e longitudinal externa, apenas na região caudal. A submucosa de conjuntivo frouxo com fibras colágenas é infiltrada por linfócitos, vascularizada e inervada, sem glândulas esofágicas. A túnica muscular das três regiões é composta por músculo liso disposto em camadas circular interna e longitudinal externa, a primeira, espessa, nas regiões cranial e média e delgada, na região caudal. A túnica adventícia, constituída de conjuntivo frouxo, células adiposas, vasos sangüíneos e terminações nervosas, é substituída pela serosa na região caudal do esôfago, quando este é revestido pelo mesotélio pleuroperitoneal. Células argirófilas e argentafins foram observadas entre células epiteliais ao longo do esôfago, com prolongamentos citoplasmáticos em direção ao lúmen.