A protein complex recognition method based on spatial-temporal graph convolution neural network / 南方医科大学学报

OBJECTIVE@#To propose a new method for mining complexes in dynamic protein network using spatiotemporal convolution neural network.@*METHODS@#The edge strength, node strength and edge existence probability are defined for modeling of the dynamic protein network. Based on the time series information and structure information on the graph, two convolution operators were designed using Hilbert-Huang transform, attention mechanism and residual connection technology to represent and learn the characteristics of the proteins in the network, and the dynamic protein network characteristic map was constructed. Finally, spectral clustering was used to identify the protein complexes.@*RESULTS@#The simulation results on several public biological datasets showed that the F value of the proposed algorithm exceeded 90% on DIP dataset and MIPS dataset. Compared with 4 other recognition algorithms (DPCMNE, GE-CFI, VGAE and NOCD), the proposed algorithm improved the recognition efficiency by 34.5%, 28.7%, 25.4% and 17.6%, respectively.@*CONCLUSION@#The application of deep learning technology can improve the efficiency in analysis of dynamic protein networks.

Network prediction of the potential molecular mechanisms in birds of prey exposed to organochlorine pesticides / Red de predicción de potenciales mecanismos moleculares en aves de presa expuestas a pesticidas organoclorados

Abstract In the 1960s, organochlorine compounds were responsible for the decline of birds of prey populations such as Haliaee- tus leucocephalus and Falco peregrinus. Pesticides similar to DDT cause bioaccumulation in birds, affecting their eggshell com- position and compromising their development. Using system biology tools, the goal of this study was to better comprehend how organochlorines act on birds. We performed a literature review, using the STITCH 5.0 platform, searching for the terms DDT and TCDD. The sub-networks were amplified in 100 interactions in STRING 10.5 and joined by the Cytoscape 3.4.0 Merge software, using the experimental animal model Gallus gallus. Clusterization, gene ontology, and centrality were the parameters evaluated in the resulting network. The resulting network had 1,417 interactions and 137 nodes. The clusterization indicated four clusters and the gene ontology pointed to biological processes related to cell signaling and morphological development. The centrality analysis indicated ESR1 and HSP90AB1 as hub/bottleneck proteins involved in the estrogen pathway and calcium transport. Therefore, it is possible that HSP90 proteins have increased expression in birds contaminated with organochlorine pesticides, favoring ESRI-organochlorines interaction and disturbing the calcium availability related to the eggshell formation. The presence or absence of heat shock proteins, such as HSP90, influences several aspects of reproduction in many species. Therefore, the relationship between the HSP90 protein expression and thin-shell syndrome was identified for the first time in this in silico study.

Resumen En los años 60, los organoclorados fueron responsables del declive de aves de rapiña como Haliaeetus leucocephalus y Falco peregrinus. Pesticidas como el DDT, causan biomagnificación en las aves, afectando las cáscaras de los huevos y dañando su desarrollo. El objetivo de este trabajo fue, a través de herramientas de biología de sistemas, comprender cómo los organoclorados actúan en el organismo de las aves. A través de una revisión bibliográfica se incluyeron dos compuestos, DDT y TCDD. Estos fue ron prospectos en la plataforma STITCH 5.0. Las subredes encontradas fueron aumentadas en 100 interacciones en la plataforma STRING 10.5 y unidas por la herramienta Merge del programa Cytoscape 3.4.0, usando el modelo experimental Gallus gallus. En la red resultante se analizaron la clusterización, la ontología génica y la centralidad. La red resultante presentó 137 nudos y 1.417 interacciones. El análisis de clusterización indicó 4 clusters, siendo que el análisis y ontología génica apuntó procesos biológicos ligados a la señalización y al desarrollo morfológico. El estudio de centralidad apuntó a ESR1 y HSP90AB1 como los hubs-bottle- neck proteínas que estaban involucradas en la vía de recepción de estrógeno y en el transporte de calcio. De acuerdo con los resultados podemos inferir que las proteínas HSP90 tienen su expresión aumentada, en aves contaminadas con pesticidas organoclo rados, favoreciendo la interacción entre ESRI y DDT / TCDD. Con ello, la interacción ESRI y la hormona estrógeno se compromete perjudicando el transporte de calcio y consecuentemente la formación de la cáscara del huevo en aves expuestas. La expresión de proteínas de choque térmico ha sido asociada a varios aspectos de la reproducción en muchas especies, sin embargo, una asociación entre HSP90 y el síndrome de la cáscara fina del huevo fue identificada por primera vez en este experimento in silico.

A Combination of Molecular Simulation and Network Methods for Analysis of Conformation Variation in Activation Process of β2 Adrenergic Receptor / 分析化学

To fill the urgent need of researches on the structure and function of proteins to obtain conformation information, we combined targeted molecular dynamics ( TMD) simulation with protein network methods to analyze conformation variations in the activation process of β2 adrenergic receptor. First, targeted MD was used to obtain the conformation resembles in the activation process, and then the protein network method was applied to identify the key residues and pathways in the activation process. The results indicate that the activa-tion process of β2 adrenergic receptor involves in the cooperation of all regions and the connector region of transmembrane helices is signaling hubs. In addition, the helix ends, including intracellular and extracellular loops, are the core areas. The pathway analysis reveals that there is more than one signaling pathway. All the pathways start from Ser204 of the ligand pocket and finally transmit to NPxxY or ICL2 region, which are depended on the different pathways. While the helix TMIII, TMV, TMVI are the important areas in all the pathways. The observations from the work provide valuable information at molecular level for unraveling the signal transduction mechanism associated with the activation process.

Hemostatic potential of the sap of Musa sapientum L. (Musaceae).

In Benin, Musa sapientum is one of the most important medicinal species used in the treatment of bleeding. In this study, hemostatic properties of M. sapientium sapand its mechanism of action have been identified through hematologic tests such as Clotting Time, Prothrombin Time, Activated Partial Thromboplastin Time and Milk Precipitation Test; biochemical test (total proteins); macroscopic and microscopic tests performed on different blood products before and after addition of sap. The results obtained showed that Musa sapientum reduced significantly clotting Time. However, it has no effect on the individual factors of coagulation. Its mechanism of action results from its ability to form a protein network which is a basis for cellular aggregation stopping bleeding. Moreover, Milk Precipitation Test showed astringent properties of Musa sapientum and therefore its vasoconstrictors properties. Phytochemical analyses revealed the presence of alkaloids, tannins, coumarins, reducing compounds, anthocyanins and leucoantocyanes. . M. sapientumis great on treatment of bleeding and could help to elaborate new drugs.