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In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51.

ABSTRACT: The envelope glycoprotein 51 (gp51) is essential for bovine leukaemia virus (BLV) entry to bovine B-lymphocytes. Although the bovine adaptor protein 3 complex subunit delta-1 (boAP3D1) has been proposed as the potential receptor, the specific ligand-receptor interaction has not yet been completely defined and boAP3D1 receptor and gp51 3D structures have not been determined. This study was thus aimed at a functional annotation of boAP3D1 cellular adaptor protein and BLV gp51 and, proposing a reliable model for gp51-AP3D1 interaction using bioinformatics tools. The boAP3D1 receptor interaction patterns were calculated based on models of boAP3D1 receptor and gp51 complexes' 3D structures, which were constructed using homology techniques and data-driven docking strategy. The results showed that the participation of 6 key amino acids (aa) on gp51 (Asn170, Trp127, His115, Ala97, Ser98 and Glu128) and 4 aa on AP3D1 (Lys925, Asp807, Asp695 and Arg800) was highly probable in the interaction between gp51 and BLVR domains. Three gp51 recombinant peptides were expressed and purified to validate these results: the complete domain (rgp51), the N-terminal portion (rNgp51) and the C-terminal fragment (rCgp51); and binding assays to Madin-Darby bovine kidney (MDBK) cells were then carried out with each recombinant. It was found that rNgp51 preferentially bound to MDBK cells, suggesting this domain's functional role during invasion. The rNgp51-MDBK cell interaction was sensitive to trypsin (98% reduction) and chymotrypsin treatment (80% reduction). These results highlighted that the N-terminal portion of gp51 interacted in vitro with the AP3D1 receptor and provides a plausible in silico interaction model.

SUBMITTER: Corredor AP

PROVIDER: S-EPMC6013181 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51.

Corredor Adriana Patricia AP González Janneth J Baquero Luis Alfredo LA Curtidor Hernando H Olaya-Galán Nury Nathalia NN Patarroyo Manuel Alfonso MA Gutiérrez María Fernanda MF

PloS one 20180621 6

The envelope glycoprotein 51 (gp51) is essential for bovine leukaemia virus (BLV) entry to bovine B-lymphocytes. Although the bovine adaptor protein 3 complex subunit delta-1 (boAP3D1) has been proposed as the potential receptor, the specific ligand-receptor interaction has not yet been completely defined and boAP3D1 receptor and gp51 3D structures have not been determined. This study was thus aimed at a functional annotation of boAP3D1 cellular adaptor protein and BLV gp51 and, proposing a reli ...[more]

PMID: 29928016

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Project description:The bovine leukaemia virus (BLV) is a retrovirus responsible for enzootic bovine leukaemia (EBL) disease, the most common cattle disease leading to high annual economic losses to the cattle breeding industry. Virus monitoring among the sheep and cattle herds is usually done by vaccination. Inactivated virus vaccines can partially protect the livestock from viral challenge. However, vaccinated animals are likely to be infected. So, there is an essential need for producing vaccine by other methods. Gp60 SU, encoded by Env gene, is the surface glycoprotein of BLV detected to be the major target for the host immunity against the virus. Different stages were performed to predict the potential B and T-helper cell epitopes. The general framework of the method includes retrieving the amino acid sequence of gp60 SU, conducting the sequence alignment, getting the entropy plot, retrieving the previously found epitopes, predicting the hydropathy parameters, modelling the tertiary structure of the glycoprotein, minimizing the structure energy, validating the model by Ramachandran plot, predicting the linear and discontinuous epitopes by various servers and eventually choosing the consensus immunogenic regions. Ramachandran plot scrutiny has demonstrated that the modelled prediction is accurate and suitable. By surveying overlaps of various results, 4 and 2 immunogenic regions were selected as linear and conformational epitopes respectively. Amino acids 35-53, 67-97, 288-302 and 410-421 and those of numbers 37-58 and 72-100 were the regions selected as linear and conformational epitopes respectively. The tertiary structure of the final epitope was modelled as well. A comparison of the predicted epitopes structure with that of gp60 SU envelope, illustrated that the tertiary structure of these epitopes does not change after being separated from the primary complete one. The present achievements will lead to a better interpretation of the antigen-antibody interactions against gp60 in the designing process of safe and efficient vaccines.

Project description:BACKGROUND: 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 ? (C/EBP?). C/EBP? 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/EBP? 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/EBP?. RESULTS: The amino acid sequence of protein-x was extracted from UniProt [UniProt:Q80IU5] and the x-ray crystal structure of the partial CCAAT-enhancer ? [PDB:1NWQ] was retrieved from the Protein Data Bank (PDB). Similarity search for protein-x was carried out by psi-blast and bl2seq using NCBI [GenBank: BAC65106.1] 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 ab initio tertiary structure prediction.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 Nsp1? [PDB:3IFU]. 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 ab initio 3D prediction approach. Docking results from the ab initio tertiary structure of protein-x and crystal structure of the C/EBP?- DNA region [PDB:1NWQ] 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). CONCLUSION: In this study, we predicted the structure of protein-x of HBV in interaction with C/EBP?. The docking results showed that protein-x has an interaction synergy with C/EBP?. 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.

Dataset Information

In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51.

Publications

In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51.

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