Residual Participation and Thermodynamic Stability Due to Molecular Interactions in IL11, IL11R alpha and Gp130 from Homo sapiens: An In Silico Outlook for IL11 as a Therapeutic Remedy
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS
Authors: Banerjee, Arundhati; Dasgupta, Rakhi; Ray, Sujay
Abstract
An extensive problem after chemotherapy is "thrombocytopenia". It has been known (through protein assays only) to recover after the interaction of IL11 protein with IL11R alpha and gp130. Among the three proteins, gp130 is known as a predominant player as it interacts with several other proteins of IL6 cytokine family. This study focused to the structure and interaction pattern of the associated proteins through protein-protein docking and molecular dynamics simulation studies. The detailed stability parameters and conformational fluctuations due to interaction were analyzed. Delta G values and net solvent accessibility showed spontaneous interaction of gp130 with stronger residual participation. Conformational fluctuations in gp130 to adopt a higher percentage of residues in helical and beta-sheets make the protein stable with firmer interaction. All outcomes showed a P-value of less than 5% (statistically significant). Mainly, ionic-ionic, aromatic-aromatic and cation-pi interactions were observed to be predominant. Among 5 ionic interactions, (from gp130) three were by Lys551 and Asp552 with IL11R alpha protein, respectively. The other two ionic interactions were between IL11 and its receptor. Each of the aromatic interactions was formed mainly by Tyr95 (gp130 protein) while phenylalanine played an important role in cation-pi interactions. Residues from Ig-like domain of IL11R alpha were seen to interact directly. Altogether, a positive environment with cavity was formed to strongly accommodate IL11 and its receptor protein. This leads to infer IL11 as a therapeutic remedy for replenishing the loss of blood platelets. This study through detailed molecular and residual exposure instigates effective drug discovery and future studies of mutational impacts. [GRAPHICS] .
Identification of specific gene expression after exposure to low dose ionizing radiation revealed through integrative analysis of cDNA microarray data and the interactome
INTERNATIONAL JOURNAL OF RADIATION RESEARCH
Authors: Son, J. C.; Jeong, H. O.; Lee, E. K.; No, S. G.; Park, D.; Chung, H. Y.
Abstract
Background: Accumulating reports suggest that the biological effects of low- and high-dose ionizing radiation (LDIR and HDIR) are qualitatively different and might cause different effects in human skin. Materials and Methods: To better understand the potential risks of LDIR, we analyzed three cDNA microarray datasets from the Gene Expression Omnibus database. Results: A pathway analysis showed that genes in immune-associated pathways were upregulated while those in cancer-associated pathways were downregulated in skin exposed to LDIR as compared with non-irradiated control skin. Consistently, according to a comparative gene ontology analysis, "antigen presentation and processing" was the most different gene ontology between the LIDR and HDIR transcriptomes. To identify key molecules regulated by LDIR, we constructed a protein-protein interaction network analysis using topological metrics. One of the key molecules with a high network scores was E1A binding protein p300 (EP300), which is a potential target of a new therapeutic strategy to promote anti-tumor immunity. Conclusion: Our results showed that LDIR exposure mainly induced the upregulation of immune-related genes including chemokines (CXCL1, CXCL2, and CXCL5) and interleukins (IL1B, IL11, IL6, IL15, and IL7). Additionally, LDIR induced the upregulation of antigen processing and presentation-related genes including CIITA, HLA-DQB1, and KIF26A, but these genes were downregulated in HDIR-exposed skin. Our protein network interaction results indicated that EP300 is downregulated by the immune response in skin after LDIR exposure.