Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid
Abstract Background Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation product of HEV ORF2 has recently been demonstrated as a protein involved in multiple functions besides performing its major role of a viral capsid. As intrinsically disordered regions (IDRs) are...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43141-023-00477-x |
| _version_ | 1797204266271637504 |
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| author | Zoya Shafat Anwar Ahmed Mohammad K. Parvez Shama Parveen |
| author_facet | Zoya Shafat Anwar Ahmed Mohammad K. Parvez Shama Parveen |
| author_sort | Zoya Shafat |
| collection | DOAJ |
| description | Abstract Background Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation product of HEV ORF2 has recently been demonstrated as a protein involved in multiple functions besides performing its major role of a viral capsid. As intrinsically disordered regions (IDRs) are linked to various essential roles in the virus’s life cycle, we analyzed the disorder pattern distribution of the retrieved ORF2 protein sequences by employing different online predictors. Our findings might provide some clues on the disorder-based functions of ORF2 protein that possibly help us in understanding its behavior other than as a HEV capsid protein. Results The modeled three dimensional (3D) structures of ORF2 showed the predominance of random coils or unstructured regions in addition to major secondary structure components (alpha helix and beta strand). After initial scrutinization, the predictors VLXT and VSL2 predicted ORF2 as a highly disordered protein while the predictors VL3 and DISOPRED3 predicted ORF2 as a moderately disordered protein, thus categorizing HEV-ORF2 into IDP (intrinsically disordered protein) or IDPR (intrinsically disordered protein region) respectively. Thus, our initial predicted disorderness in ORF2 protein 3D structures was in excellent agreement with their predicted disorder distribution patterns (evaluated through different predictors). The abundance of MoRFs (disorder-based protein binding sites) in ORF2 was observed that signified their interaction with binding partners which might further assist in viral infection. As IDPs/IDPRs are targets of regulation, we carried out the phosphorylation analysis to reveal the presence of post-translationally modified sites. Prevalence of several disordered-based phosphorylation sites further signified the involvement of ORF2 in diverse and significant biological processes. Furthermore, ORF2 structure-associated functions revealed its involvement in several crucial functions and biological processes like binding and catalytic activities. Conclusions The results predicted ORF2 as a protein with multiple functions besides its role as a capsid protein. Moreover, the occurrence of IDPR/IDP in ORF2 protein suggests that its disordered region might serve as novel drug targets via functioning as potential interacting domains. Our data collectively might provide significant implication in HEV vaccine search as disorderness in viral proteins is related to mechanisms involved in immune evasion. |
| first_indexed | 2024-04-09T22:42:46Z |
| format | Article |
| id | doaj.art-8978cf74be66478485e1c8eb91aa5371 |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-04-24T08:32:30Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-8978cf74be66478485e1c8eb91aa53712024-04-16T18:57:48ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202023-03-0121113510.1186/s43141-023-00477-xIntrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsidZoya Shafat0Anwar Ahmed1Mohammad K. Parvez2Shama Parveen3Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia IslamiaCentre of Excellence in Biotechnology Research, College of Science, King Saud UniversityDepartment of Pharmacognosy, College of Pharmacy, King Saud UniversityCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia IslamiaAbstract Background Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation product of HEV ORF2 has recently been demonstrated as a protein involved in multiple functions besides performing its major role of a viral capsid. As intrinsically disordered regions (IDRs) are linked to various essential roles in the virus’s life cycle, we analyzed the disorder pattern distribution of the retrieved ORF2 protein sequences by employing different online predictors. Our findings might provide some clues on the disorder-based functions of ORF2 protein that possibly help us in understanding its behavior other than as a HEV capsid protein. Results The modeled three dimensional (3D) structures of ORF2 showed the predominance of random coils or unstructured regions in addition to major secondary structure components (alpha helix and beta strand). After initial scrutinization, the predictors VLXT and VSL2 predicted ORF2 as a highly disordered protein while the predictors VL3 and DISOPRED3 predicted ORF2 as a moderately disordered protein, thus categorizing HEV-ORF2 into IDP (intrinsically disordered protein) or IDPR (intrinsically disordered protein region) respectively. Thus, our initial predicted disorderness in ORF2 protein 3D structures was in excellent agreement with their predicted disorder distribution patterns (evaluated through different predictors). The abundance of MoRFs (disorder-based protein binding sites) in ORF2 was observed that signified their interaction with binding partners which might further assist in viral infection. As IDPs/IDPRs are targets of regulation, we carried out the phosphorylation analysis to reveal the presence of post-translationally modified sites. Prevalence of several disordered-based phosphorylation sites further signified the involvement of ORF2 in diverse and significant biological processes. Furthermore, ORF2 structure-associated functions revealed its involvement in several crucial functions and biological processes like binding and catalytic activities. Conclusions The results predicted ORF2 as a protein with multiple functions besides its role as a capsid protein. Moreover, the occurrence of IDPR/IDP in ORF2 protein suggests that its disordered region might serve as novel drug targets via functioning as potential interacting domains. Our data collectively might provide significant implication in HEV vaccine search as disorderness in viral proteins is related to mechanisms involved in immune evasion.https://doi.org/10.1186/s43141-023-00477-xHepatitis E virus (HEV)Open reading frame 2 (ORF2)Intrinsically disordered protein (IDP)Intrinsically disordered protein region (IDPR)Phosphorylation predictionMolecular function |
| spellingShingle | Zoya Shafat Anwar Ahmed Mohammad K. Parvez Shama Parveen Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid Journal of Genetic Engineering and Biotechnology Hepatitis E virus (HEV) Open reading frame 2 (ORF2) Intrinsically disordered protein (IDP) Intrinsically disordered protein region (IDPR) Phosphorylation prediction Molecular function |
| title | Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid |
| title_full | Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid |
| title_fullStr | Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid |
| title_full_unstemmed | Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid |
| title_short | Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid |
| title_sort | intrinsic disorder in the open reading frame 2 of hepatitis e virus a protein with multiple functions beyond viral capsid |
| topic | Hepatitis E virus (HEV) Open reading frame 2 (ORF2) Intrinsically disordered protein (IDP) Intrinsically disordered protein region (IDPR) Phosphorylation prediction Molecular function |
| url | https://doi.org/10.1186/s43141-023-00477-x |
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