Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses
Abstract Zika virus (ZIKV) and dengue virus (DENV) share a lot of similarities being both phylogenetically closely related, share the same insect vector passage for reaching the host, affinity for the same carbohydrate receptor domains (CRDs), indicating feasible competition between them on the natu...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | Virology Journal |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12985-023-02251-4 |
| _version_ | 1827590779408744448 |
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| author | Bruno Stein Barbosa Menechino Rodrigo Bentes Kato Helena Cristina Ferreira Franz Pedro Eduardo Almeida da Silva Marcus Corat Daniel Ferreira de Lima Neto |
| author_facet | Bruno Stein Barbosa Menechino Rodrigo Bentes Kato Helena Cristina Ferreira Franz Pedro Eduardo Almeida da Silva Marcus Corat Daniel Ferreira de Lima Neto |
| author_sort | Bruno Stein Barbosa Menechino |
| collection | DOAJ |
| description | Abstract Zika virus (ZIKV) and dengue virus (DENV) share a lot of similarities being both phylogenetically closely related, share the same insect vector passage for reaching the host, affinity for the same carbohydrate receptor domains (CRDs), indicating feasible competition between them on the natural field. Here, we prospected interactions of both envelope proteins with a DC-SIGN, a transmembrane c-type lectine receptor with the most implicated CRD with the Flavivirus infection presents on dendritic cells involved in viruses replication processes into the host, and among rares CRD receptors susceptible to interacting with a broad of subtypes of DENV. Protein–protein docking procedures produced structures for molecular dynamics experiments, suggesting the most energetically favorable complex. The difference found in the deltaG results prompted the experimentation with molecular dynamics. To investigate further specific residues involved with such interactions we produced a decomposition analysis using molecular dynamics of the docked proteins evaluated afterward with the Generalized Born Surface Area method. Solvent-accessible surface area (SASA) analysis for both showed very similar but with a slight reduction for ZIKV_E, which agreed with residues SASA analysis highlighting regions more exposed in the ZIVK protein than in DENV. Despite residues PHE313 is reponsible for most of the interactions with the envelope of these arboviruses, ZIKV interacted with this residue in DC-SIGN with lower energies and using more interactions with not expexted residues GLU241 and ARG386. Taken together these results suggest better competitive interaction of ZIKV with the DC-SIGN receptor, particularly in the CRD portion. |
| first_indexed | 2024-03-09T01:21:34Z |
| format | Article |
| id | doaj.art-8755172b2cdf42f4af0a4ad5aff6103b |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-03-09T01:21:34Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-8755172b2cdf42f4af0a4ad5aff6103b2023-12-10T12:07:30ZengBMCVirology Journal1743-422X2023-12-012011810.1186/s12985-023-02251-4Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analysesBruno Stein Barbosa Menechino0Rodrigo Bentes Kato1Helena Cristina Ferreira Franz2Pedro Eduardo Almeida da Silva3Marcus Corat4Daniel Ferreira de Lima Neto5Multidisciplinary Center for Biological Research - Laboratory for the Development of Biological Models, University of CampinasGeneral-Coordination of Public Health Laboratories, Department of Strategic Articulation in Health and Ambient, Ministry of HealthGeneral-Coordination of Public Health Laboratories, Department of Strategic Articulation in Health and Ambient, Ministry of HealthGeneral-Coordination of Public Health Laboratories, Department of Strategic Articulation in Health and Ambient, Ministry of HealthMultidisciplinary Center for Biological Research - Laboratory for the Development of Biological Models, University of CampinasGeneral-Coordination of Public Health Laboratories, Department of Strategic Articulation in Health and Ambient, Ministry of HealthAbstract Zika virus (ZIKV) and dengue virus (DENV) share a lot of similarities being both phylogenetically closely related, share the same insect vector passage for reaching the host, affinity for the same carbohydrate receptor domains (CRDs), indicating feasible competition between them on the natural field. Here, we prospected interactions of both envelope proteins with a DC-SIGN, a transmembrane c-type lectine receptor with the most implicated CRD with the Flavivirus infection presents on dendritic cells involved in viruses replication processes into the host, and among rares CRD receptors susceptible to interacting with a broad of subtypes of DENV. Protein–protein docking procedures produced structures for molecular dynamics experiments, suggesting the most energetically favorable complex. The difference found in the deltaG results prompted the experimentation with molecular dynamics. To investigate further specific residues involved with such interactions we produced a decomposition analysis using molecular dynamics of the docked proteins evaluated afterward with the Generalized Born Surface Area method. Solvent-accessible surface area (SASA) analysis for both showed very similar but with a slight reduction for ZIKV_E, which agreed with residues SASA analysis highlighting regions more exposed in the ZIVK protein than in DENV. Despite residues PHE313 is reponsible for most of the interactions with the envelope of these arboviruses, ZIKV interacted with this residue in DC-SIGN with lower energies and using more interactions with not expexted residues GLU241 and ARG386. Taken together these results suggest better competitive interaction of ZIKV with the DC-SIGN receptor, particularly in the CRD portion.https://doi.org/10.1186/s12985-023-02251-4DC-SIGNDengueZikaMolecular dynamicsMM/GBSA |
| spellingShingle | Bruno Stein Barbosa Menechino Rodrigo Bentes Kato Helena Cristina Ferreira Franz Pedro Eduardo Almeida da Silva Marcus Corat Daniel Ferreira de Lima Neto Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses Virology Journal DC-SIGN Dengue Zika Molecular dynamics MM/GBSA |
| title | Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses |
| title_full | Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses |
| title_fullStr | Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses |
| title_full_unstemmed | Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses |
| title_short | Interactions between DC-SIGN and the envelope protein from Dengue and Zika viruses: a structural perspective based on molecular dynamics and MM/GBSA analyses |
| title_sort | interactions between dc sign and the envelope protein from dengue and zika viruses a structural perspective based on molecular dynamics and mm gbsa analyses |
| topic | DC-SIGN Dengue Zika Molecular dynamics MM/GBSA |
| url | https://doi.org/10.1186/s12985-023-02251-4 |
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