Protein-x of hepatitis B virus in interaction with CCAAT/enhancer-binding protein α (C/EBPα) - an in silico analysis approach

<p>Abstract</p> <p>Background</p> <p>Even though many functions of protein-x from the Hepatitis B virus (HBV) have been revealed, the nature of protein-x is yet unknown. This protein is well-known for its transactivation activity through interaction with several cellular transcription factors, it is also known as an oncogene. In this work, we have presented computational approaches to design a model to show the structure of protein-x and its respective binding sites associated with the CCAAT/enhancer-binding protein α (C/EBPα). C/EBPα belongs to the bZip family of transcription factors, which activates transcription of several genes through its binding sites in liver and fat cells. The C/EBPα has been shown to bind and modulate enhancer I and the enhancer II/core promoter of HBV. In this study using the bioinformatics tools we tried to present a reliable model for the protein-x interaction with C/EBPα.</p> <p>Results</p> <p>The amino acid sequence of protein-x was extracted from UniProt [UniProt:Q80IU5] and the x-ray crystal structure of the partial CCAAT-enhancer α [PDB:<ext-link ext-link-id="1NWQ" ext-link-type="pdb">1NWQ</ext-link>] was retrieved from the Protein Data Bank (PDB). Similarity search for protein-x was carried out by psi-blast and bl2seq using NCBI [GenBank: <ext-link ext-link-id="BAC65106.1" ext-link-type="gen">BAC65106.1</ext-link>] and Local Meta-Threading-Server (LOMETS) was used as a threading server for determining the maximum tertiary structure similarities. Advanced MODELLER was implemented to design a comparative model, however, due to the lack of a suitable template, Quark was used for <it>ab initio </it>tertiary structure prediction.</p> <p>The PDB-blast search indicated a maximum of 23% sequence identity and 33% similarity with crystal structure of the porcine reproductive and respiratory syndrome virus leader protease Nsp1α [PDB:<ext-link ext-link-id="3IFU" ext-link-type="pdb">3IFU</ext-link>]. This meant that protein-x does not have a suitable template to predict its tertiary structure using comparative modeling tools, therefore we used QUARK as an <it>ab initio </it>3D prediction approach. Docking results from the <it>ab initio </it>tertiary structure of protein-x and crystal structure of the C/EBPα- DNA region [PDB:<ext-link ext-link-id="1NWQ" ext-link-type="pdb">1NWQ</ext-link>] illustrated the protein-binding site interactions. Indeed, the N-terminal part of 1NWQ has a high affinity for certain regions in protein-x (e.g. from Ala76 to Ser101 and Thr105 to Glu125).</p> <p>Conclusion</p> <p>In this study, we predicted the structure of protein-x of HBV in interaction with C/EBPα. The docking results showed that protein-x has an interaction synergy with C/EBPα. However, despite previous experimental data, protein-x was found to interact with DNA. This can lead to a better understanding of the function of protein-x and may provide an opportunity to use it as a therapeutic target.</p

Computational study of SENP1 in cancer by novel natural compounds and ZINC database screening

Introduction: Sentrin-specific protease 1 (SENP1) is a protein whose main function is deSUMOylation. SENP1 inhibits apoptosis, and increases angiogenesis, estrogen and androgen receptor transcription and c-Jun transcription factor, proliferation, growth, cell migration, and invasion of cancer. The in vivo and in vitro studies also demonstrated which natural compounds, especially phytochemicals, minerals, and vitamins, prevent cancer. More than 3,000 plant species have been reported in modern medicine. Natural compounds have many anti-cancerous andanti-turmeric properties such as antioxidative, antiangiogenic, antiproliferative, and pro-apoptotic properties.Methods: In this study, we investigated the interaction of some natural compounds with SENP1 to inhibit its activity. We also screened the ZINC database including natural compounds. Molecular docking was performed, and toxicity of compounds was determined; then, molecular dynamics simulation (MDS) and essential dynamics (ED) were performed on natural compounds with higher free binding energies and minimal side effects. By searching in a large library, virtual screening of the ZINC database was performed using LibDock and CDOCKER, and the final top 20 compounds were allowed for docking against SENP1. According to the docking study, the top three leading molecules were selected and further analyzed by MDS and ED.Results: The results suggest that resveratrol (from the selected compounds) and ZINC33916875 (from the ZINC database) could be more promising SENP1 inhibitory ligands.Discussion: Because these compounds can inhibit SENP1 activity, then they can be novel candidates for cancer treatment. However, wet laboratory experiments are needed to validate their efficacy as SENP1 inhibitors

Study of the association of DFNB3 locus with autosomal recessive non-syndromic hearing loss in iranian deaf population using genetic linkage analysis

Background: Hearing loss is a common sensory disorder that typically illustrates genetic heterogeneity in human populations. The incidence of congenital hearing loss is estimated at 1 in 500 births of which approximately 70 of cases are attributed to genetic factors. Genetic hearing impairment can be classified as either syndromic or non-syndromic and among non-syndromic hearing loss autosomal recessive (ALNSHL) accounts for approximately 75-80 of cases. This type of hearing loss is extremely heterogeneous and includes over 100 loci. For recessive deafness, most frequent genes are GJB2, SLC26A4, MYO15A, OTOF, and CDH23 in worldwide. This study aimed to determine the role of MYO15A (DFNB3) gene mutations in Iranian deaf population using linkage analysis. Methods: To investigate the frequency of DFNB3 gene mutation, linkage analysis was performed in 30 Iranian families with over three deaf child and negative GJB2. The negative mutations pedigrees for these gene mutations were then tested for the linkage to DFNB3 (MYO15A) locus, using short tandem repeat (STR) markers. Findings: Mutation 35delG was identified in 5 families out of 30 by sequencing the coding region of GJB2 gene. One family showed linkage to DFNB3 locus. Conclusion: Based on the results of this study, DFNB3 locus is the third cause of deafness after DFNB1 (GJB2) and DFNB4 (SLC26A4). © 2014, Isfahan University of Medical Sciences(IUMS). All rights reserved

MiRNAs which target CD3 subunits could be potential biomarkers for cancers.

BACKGROUND: T-cells play an important role in the immune response and are activated in response to the presentation of antigens bound to major histocompatibility complex (MHC) molecules participating with the T-cell receptor (TCR). T-cell receptor complexes also contain four CD3 (cluster of differentiation 3) subunits. The TCR-CD3 complex is vital for T-cell development and plays an important role in intervening cell recognition events. Since microRNAs (miRNAs) are highly stable in blood serum, some of which may target CD3 molecules, they could serve as good biomarkers for early cancer detection. The aim of this study was to see whether there is a relationship between cancers and the amount of miRNAs -targeted CD3 molecules. METHODS: Bioinformatics tools were used in order to predict the miRNA targets for these genes. Subsequently, these highly conserved miRNAs were evaluated to see if they are implicated in various kinds of cancers. Consequently, human disease databases were used. According to the latest research, this study attempted to investigate the possible down- or upregulation of miRNAs cancer patients. RESULTS: We identified miRNAs which target genes producing CD3 subunit molecules. The most conserved miRNAs were identified for the CD3G gene, while CD247 and CD3EAP genes had the least number and there were no conserved miRNA associated with the CD3D gene. Some of these miRNAs were found to be responsible for different cancers, following a certain pattern. CONCLUSIONS: It is highly likely that miRNAs affect the CD3 molecules, impairing the immune system, recognizing and destroying cancer tumor; hence, they can be used as suitable biomarkers in distinguishing cancer in the very early stages of its development

miRNAs which were predicted to target CD3G (broadly conserved).

<p>miRNAs which were predicted to target CD3G (broadly conserved).</p

miRNAs which were predicted to target CD3EAP (broadly conserved).

<p>miRNAs which were predicted to target CD3EAP (broadly conserved).</p

The status of miRNAs from the first group which affect the CD3G gene responsible for the CD3-gamma subunit in cancer tissues relative to adjacent normal tissues.

<p>The status of miRNAs from the first group which affect the CD3G gene responsible for the CD3-gamma subunit in cancer tissues relative to adjacent normal tissues.</p

The status of miRNA from the second group which affect the CD3EAP gene responsible for the CD3-epsilon subunit in cancer tissues relative to adjacent normal tissues.

<p>The status of miRNA from the second group which affect the CD3EAP gene responsible for the CD3-epsilon subunit in cancer tissues relative to adjacent normal tissues.</p

The status of miRNAs from the third group which affect the CD247 gene responsible for the CD3-zeta subunit in cancer tissues relative to adjacent normal tissues.

<p>The status of miRNAs from the third group which affect the CD247 gene responsible for the CD3-zeta subunit in cancer tissues relative to adjacent normal tissues.</p