scholarly journals A Multifeatures Fusion and Discrete Firefly Optimization Method for Prediction of Protein Tyrosine Sulfation Residues

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Song Guo ◽  
Chunhua Liu ◽  
Peng Zhou ◽  
Yanling Li
Keyword(s):  
Feature Selection ◽  
Posttranslational Modifications ◽  
Optimization Method ◽  
Tyrosine Sulfation ◽  
Selection Scheme ◽  
Protein Tyrosine ◽  
Research Fields ◽  
Physiological Processes ◽  
Novel Method ◽  
Protein Posttranslational Modifications

Tyrosine sulfation is one of the ubiquitous protein posttranslational modifications, where some sulfate groups are added to the tyrosine residues. It plays significant roles in various physiological processes in eukaryotic cells. To explore the molecular mechanism of tyrosine sulfation, one of the prerequisites is to correctly identify possible protein tyrosine sulfation residues. In this paper, a novel method was presented to predict protein tyrosine sulfation residues from primary sequences. By means of informative feature construction and elaborate feature selection and parameter optimization scheme, the proposed predictor achieved promising results and outperformed many other state-of-the-art predictors. Using the optimal features subset, the proposed method achieved mean MCC of 94.41% on the benchmark dataset, and a MCC of 90.09% on the independent dataset. The experimental performance indicated that our new proposed method could be effective in identifying the important protein posttranslational modifications and the feature selection scheme would be powerful in protein functional residues prediction research fields.

scholarly journals Histone deacetylase (HDAC) 9: versatile biological functions and emerging roles in human cancer

2021 ◽  
Author(s):  
Chun Yang ◽  
Stéphane Croteau ◽  
Pierre Hardy
Keyword(s):  
Histone Deacetylase ◽  
Posttranslational Modifications ◽  
Histone Deacetylases ◽  
Muscle Development ◽  
Target Genes ◽  
Human Cancer ◽  
Expression Patterns ◽  
Aberrant Expression ◽  
Physiological Processes ◽  
Cancer Pathogenesis

Abstract Background HDAC9 (histone deacetylase 9) belongs to the class IIa family of histone deacetylases. This enzyme can shuttle freely between the nucleus and cytoplasm and promotes tissue-specific transcriptional regulation by interacting with histone and non-histone substrates. HDAC9 plays an essential role in diverse physiological processes including cardiac muscle development, bone formation, adipocyte differentiation and innate immunity. HDAC9 inhibition or activation is therefore a promising avenue for therapeutic intervention in several diseases. HDAC9 overexpression is also common in cancer cells, where HDAC9 alters the expression and activity of numerous relevant proteins involved in carcinogenesis. Conclusions This review summarizes the most recent discoveries regarding HDAC9 as a crucial regulator of specific physiological systems and, more importantly, highlights the diverse spectrum of HDAC9-mediated posttranslational modifications and their contributions to cancer pathogenesis. HDAC9 is a potential novel therapeutic target, and the restoration of aberrant expression patterns observed among HDAC9 target genes and their related signaling pathways may provide opportunities to the design of novel anticancer therapeutic strategies.

scholarly journals E3 ligase Nedd4l promotes antiviral innate immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Peng Gao ◽  
Xianwei Ma ◽  
Ming Yuan ◽  
Yulan Yi ◽  
Guoke Liu ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Type I Interferon ◽  
Zinc Fingers ◽  
E3 Ligase ◽  
Type I ◽  
E3 Ligases ◽  
Protein Posttranslational Modifications ◽  
Antiviral Innate Immunity

AbstractUbiquitination is one of the most prevalent protein posttranslational modifications. Here, we show that E3 ligase Nedd4l positively regulates antiviral immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3. Deficiency of Nedd4l significantly impairs type I interferon and proinflammatory cytokine production induced by virus infection both in vitro and in vivo. Nedd4l deficiency inhibits virus-induced ubiquitination of TRAF3, the binding between TRAF3 and TBK1, and subsequent phosphorylation of TBK1 and IRF3. Nedd4l directly interacts with TRAF3 and catalyzes K29-linked ubiquitination of Cys56 and Cys124, two cysteines that constitute zinc fingers, resulting in enhanced association between TRAF3 and E3 ligases, cIAP1/2 and HECTD3, and also increased K48/K63-linked ubiquitination of TRAF3. Mutation of Cys56 and Cys124 diminishes Nedd4l-catalyzed K29-linked ubiquitination, but enhances association between TRAF3 and the E3 ligases, supporting Nedd4l promotes type I interferon production in response to virus by catalyzing ubiquitination of the cysteines in TRAF3.

scholarly journals An Adaptive Unsupervised Feature Selection Algorithm Based on MDS for Tumor Gene Data Classification

Sensors ◽  
2021 ◽  
Vol 21 (11) ◽  
pp. 3627
Author(s):  
Bo Jin ◽  
Chunling Fu ◽  
Yong Jin ◽  
Wei Yang ◽  
Shengbin Li ◽  
...  
Keyword(s):  
Feature Selection ◽  
Local Structure ◽  
Gene Selection ◽  
Dimensional Space ◽  
Original Data ◽  
Global Structure ◽  
Biological Data ◽  
Special Treatment ◽  
Selection Scheme ◽  
Unsupervised Feature Selection

Identifying the key genes related to tumors from gene expression data with a large number of features is important for the accurate classification of tumors and to make special treatment decisions. In recent years, unsupervised feature selection algorithms have attracted considerable attention in the field of gene selection as they can find the most discriminating subsets of genes, namely the potential information in biological data. Recent research also shows that maintaining the important structure of data is necessary for gene selection. However, most current feature selection methods merely capture the local structure of the original data while ignoring the importance of the global structure of the original data. We believe that the global structure and local structure of the original data are equally important, and so the selected genes should maintain the essential structure of the original data as far as possible. In this paper, we propose a new, adaptive, unsupervised feature selection scheme which not only reconstructs high-dimensional data into a low-dimensional space with the constraint of feature distance invariance but also employs ℓ2,1-norm to enable a matrix with the ability to perform gene selection embedding into the local manifold structure-learning framework. Moreover, an effective algorithm is developed to solve the optimization problem based on the proposed scheme. Comparative experiments with some classical schemes on real tumor datasets demonstrate the effectiveness of the proposed method.

Targeted proteomics of myofilament phosphorylation and other protein posttranslational modifications

2014 ◽  
Vol 8 (7-8) ◽  
pp. 543-553 ◽  
Author(s):  
Genaro A. Ramirez-Correa ◽  
Maria Isabel Martinez-Ferrando ◽  
Pingbo Zhang ◽  
Anne M. Murphy
Keyword(s):  
Posttranslational Modifications ◽  
Targeted Proteomics ◽  
Protein Posttranslational Modifications

Posttranslational modifications of recombinant myotube-synthesized human factor IX

Blood ◽  
2001 ◽  
Vol 97 (1) ◽  
pp. 130-138 ◽  
Author(s):  
Valder R. Arruda ◽  
James N. Hagstrom ◽  
Jeffrey Deitch ◽  
Terry Heiman-Patterson ◽  
Rodney M. Camire ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Posttranslational Modifications ◽  
Half Life ◽  
Specific Activity ◽  
Factor Ix ◽  
Serine Phosphorylation ◽  
Hemophilia B ◽  
Tyrosine Sulfation ◽  
Aav Vector ◽  
Carbohydrate Analysis

Abstract Recent data demonstrate that the introduction into skeletal muscle of an adeno-associated viral (AAV) vector expressing blood coagulation factor IX (F.IX) can result in long-term expression of the transgene product and amelioration of the bleeding diathesis in animals with hemophilia B. These data suggest that biologically active F.IX can be synthesized in skeletal muscle. Factor IX undergoes extensive posttranslational modifications in the liver, the normal site of synthesis. In addition to affecting specific activity, these posttranslational modifications can also affect recovery, half-life in the circulation, and the immunogenicity of the protein. Before initiating a human trial of an AAV-mediated, muscle-directed approach for treating hemophilia B, a detailed biochemical analysis of F.IX synthesized in skeletal muscle was carried out. As a model system, human myotubes transduced with an AAV vector expressing F.IX was used. F.IX was purified from conditioned medium using a novel strategy designed to purify material representative of all species of rF.IX in the medium. Purified F.IX was analyzed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), N-terminal sequence analysis, chemical γ-carboxyglutamyl analysis, carbohydrate analysis, assays for tyrosine sulfation, and serine phosphorylation, and for specific activity. Results show that myotube-synthesized F.IX has specific activity similar to that of liver-synthesized F.IX. Posttranslational modifications critical for specific activity, including removal of the signal sequence and propeptide, and γ-carboxylation of the N-terminal glutamic acid residues, are also similar, but carbohydrate analysis and assessment of tyrosine sulfation and serine phosphorylation disclose differences. In vivo experiments in mice showed that these differences affect recovery but not half-life of muscle-synthesized F.IX.

scholarly journals Decentralized Optimization for a Novel Control Structure of HVAC System

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Shiqiang Wang ◽  
Jianchun Xing ◽  
Ziyan Jiang ◽  
Juelong Li
Keyword(s):  
Control System ◽  
Decentralized Control ◽  
Control Structure ◽  
Optimization Method ◽  
Labor Cost ◽  
Smart Device ◽  
Hvac System ◽  
Decentralized Optimization ◽  
System A ◽  
Novel Method

A decentralized control structure is introduced into the heating, ventilation, and air conditioning (HVAC) system to solve the high maintenance and labor cost problem in actual engineering. Based on this new control system, a decentralized optimization method is presented for sensor fault repair and optimal group control of HVAC equipment. Convergence property of the novel method is theoretically analyzed considering both convex and nonconvex systems with constraints. In this decentralized control system, traditional device is fitted with a control chip such that it becomes a smart device. The smart device can communicate and operate collaboratively with the other devices to accomplish some designated tasks. The effectiveness of the presented method is verified by simulations and hardware tests.

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