scholarly journals Amplification and Detection of Single-Molecule Conformational Fluctuation through a Protein Interaction Network with Bimodal Distributions

2009 ◽  
Vol 113 (36) ◽  
pp. 12375-12381 ◽  
Author(s):  
Zhanghan Wu ◽  
Vlad Elgart ◽  
Hong Qian ◽  
Jianhua Xing
Keyword(s):  
Single Molecule ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Conformational Fluctuation

Analysis and Prediction of Protein Interaction Network ofRalstonia solanacearum

2012 ◽  
Vol 18 (1) ◽  
pp. 139
Author(s):  
Chunlei JIANG ◽  
rui ZHAO ◽  
Lingfeng Lü ◽  
Dairong QIAO ◽  
Yi CAO
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network

scholarly journals Diabetic Retinopathy and Laser Therapy in Rats: A Protein-Protein Interaction Network Analysis

2017 ◽  
Vol 8 (Suppl 1) ◽  
pp. S20-S21 ◽  
Author(s):  
Akram Safaei ◽  
Mostafa Rezaei Tavirani ◽  
Mona Zamanian Azodi ◽  
Alireza Lashay ◽  
Seyed Farzad Mohammadi ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Network Analysis ◽  
Laser Therapy ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

scholarly journals Potential treatment for chronic myeloid leukemia using microRNA: in silico comparison between plants and human microRNAs in targeting BCR-ABL1 gene

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Syarifah Faezah Syed Mohamad ◽  
Marjanu Hikmah Elias
Keyword(s):  
Targeted Therapy ◽  
Chronic Myeloid Leukemia ◽  
Tyrosine Kinase ◽  
Pathway Analysis ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
In Silico ◽  
Myeloid Leukemia ◽  
Interaction Network ◽  
Folding Energy

Abstract Background Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by the expression of the BCR-ABL1 fusion gene. Tyrosine kinase inhibitors (TKI) are used to treat CML, but mutations in the tyrosine kinase domain contribute to CML chemo-resistance. Therefore, finding alternative molecular-targeted therapy is important for the comprehensive treatment of CML. MicroRNAs (miRNA) are small non-coding regulatory RNAs which suppress the expression of their target genes by binding to the 3′ untranslated region (3′UTR) of the target mRNA. Hypothetically, the miRNA-mRNA interaction would suppress BCR-ABL1 expression and consequently reduce and inhibit CML cell proliferation. Thus, our objective was to determine the target interaction of human and plant miRNAs targeting the 3′UTR region of BCR-ABL1 in terms of miRNA binding conformity, protein interaction network, and pathways using in silico analysis. The 3′UTR sequence of BCR-ABL1 is obtained from Ensembl Genome Browser while the binding conformity was determined using the PsRNATarget Analysis Server, RNA22, Target Rank Server, and DIANA TOOLS. Protein-protein interaction network and pathway analysis are determined using STRING, Cytoscape, and KEGG pathway analysis. Results Five plants and five human miRNAs show strong binding conformity with 3′UTR of BCR-ABL1. The strongest binding conformity was shown by Oryza sativa’s Osa-miR1858a and osa-miR1858b with −24.4 kcal/mol folding energy and a p value of 0.0077. Meanwhile, in human miRNA, the hsa-miR-891a-3p shows the highest miTG score of 0.99 with −12 kcal/mol folding energy and a p value of 0.037. Apart from ABL1, osa-miR1858a/osa-miR1858b and hsa-miR891a-3p also target other 720 and 645 genes, respectively. The interaction network of Osa-miR1858a/osa-miR1858b and hsa-miR891a-3p identifies nineteen and twelve ABL1’s immediate neighboring proteins, respectively. The pathways analysis focuses on the RAS, MAPK, CML, and hematopoietic cell lineage pathway. Conclusion Both plant and human miRNAs tested in this study could be a potential therapeutic prospect in CML treatment, but thermodynamically, osa-miR1858a/osa-miR1858b binding to ABL1 is more favorable. However, it is important to carry out more research in vitro and in vivo and clinical studies to assess its efficacy as a targeted therapy for CML. Graphical abstract

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