Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i>
The function of chaperones is to correct or degrade misfolded proteins inside the cell. Classic molecular chaperones such as GroEL and DnaK have not been found in the periplasm of <i>Yersinia pseudotuberculosis</i>. Some periplasmic substrate-binding proteins could be bifunctional, such...
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MDPI AG
2023-02-01
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| Series: | International Journal of Molecular Sciences |
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| author | Mirian Becerril Ramírez Lucía Soto Urzúa María de los Ángeles Martínez Martínez Luis Javier Martínez Morales |
| author_facet | Mirian Becerril Ramírez Lucía Soto Urzúa María de los Ángeles Martínez Martínez Luis Javier Martínez Morales |
| author_sort | Mirian Becerril Ramírez |
| collection | DOAJ |
| description | The function of chaperones is to correct or degrade misfolded proteins inside the cell. Classic molecular chaperones such as GroEL and DnaK have not been found in the periplasm of <i>Yersinia pseudotuberculosis</i>. Some periplasmic substrate-binding proteins could be bifunctional, such as OppA. Using bioinformatic tools, we try to elucidate the nature of the interactions between OppA and ligands from four proteins with different oligomeric states. Using the crystal structure of the proteins Mal12 alpha-glucosidase from <i>Saccharomyces cerevisiae</i> S288C, LDH rabbit muscle lactate dehydrogenase, <i>Eco</i>RI endonuclease from <i>Escherichia coli</i> and THG <i>Geotrichum candidum</i> lipase, a hundred models were obtained in total, including five different ligands from each enzyme with five conformations of each ligand. The best values for Mal12 stem from ligands 4 and 5, with conformation 5 for both; for LDH, ligands 1 and 4, with conformations 2 and 4, respectively; for <i>Eco</i>RI, ligands 3 and 5, with conformation 1 for both; and for THG, ligands 2 and 3, with conformation 1 for both. The interactions were analyzed with LigProt, and the length of the hydrogen bridges has an average of 2.8 to 3.0 Å. The interaction within the OppA pocket is energetically favored due to the formation of hydrogen bonds both of OppA and of the selected enzymes. The Asp 419 residue is important in these junctions. |
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| language | English |
| last_indexed | 2024-03-11T08:40:51Z |
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| spelling | doaj.art-6a2c300c27c84ee7b2d290ca97835d392023-11-16T21:08:24ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-02-01244402310.3390/ijms24044023Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i>Mirian Becerril Ramírez0Lucía Soto Urzúa1María de los Ángeles Martínez Martínez2Luis Javier Martínez Morales3Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla CP 72570, MexicoCentro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla CP 72570, MexicoFacultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla CP 72410, MexicoCentro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla CP 72570, MexicoThe function of chaperones is to correct or degrade misfolded proteins inside the cell. Classic molecular chaperones such as GroEL and DnaK have not been found in the periplasm of <i>Yersinia pseudotuberculosis</i>. Some periplasmic substrate-binding proteins could be bifunctional, such as OppA. Using bioinformatic tools, we try to elucidate the nature of the interactions between OppA and ligands from four proteins with different oligomeric states. Using the crystal structure of the proteins Mal12 alpha-glucosidase from <i>Saccharomyces cerevisiae</i> S288C, LDH rabbit muscle lactate dehydrogenase, <i>Eco</i>RI endonuclease from <i>Escherichia coli</i> and THG <i>Geotrichum candidum</i> lipase, a hundred models were obtained in total, including five different ligands from each enzyme with five conformations of each ligand. The best values for Mal12 stem from ligands 4 and 5, with conformation 5 for both; for LDH, ligands 1 and 4, with conformations 2 and 4, respectively; for <i>Eco</i>RI, ligands 3 and 5, with conformation 1 for both; and for THG, ligands 2 and 3, with conformation 1 for both. The interactions were analyzed with LigProt, and the length of the hydrogen bridges has an average of 2.8 to 3.0 Å. The interaction within the OppA pocket is energetically favored due to the formation of hydrogen bonds both of OppA and of the selected enzymes. The Asp 419 residue is important in these junctions.https://www.mdpi.com/1422-0067/24/4/4023<i>Yersinia pseudotuberculosis</i>OppA proteininteractions between OppA and ligandschaperones |
| spellingShingle | Mirian Becerril Ramírez Lucía Soto Urzúa María de los Ángeles Martínez Martínez Luis Javier Martínez Morales Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i> International Journal of Molecular Sciences <i>Yersinia pseudotuberculosis</i> OppA protein interactions between OppA and ligands chaperones |
| title | Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i> |
| title_full | Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i> |
| title_fullStr | Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i> |
| title_full_unstemmed | Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i> |
| title_short | Computational Analysis of the Ligand-Binding Sites of the Molecular Chaperone OppA from <i>Yersinia pseudotuberculosis</i> |
| title_sort | computational analysis of the ligand binding sites of the molecular chaperone oppa from i yersinia pseudotuberculosis i |
| topic | <i>Yersinia pseudotuberculosis</i> OppA protein interactions between OppA and ligands chaperones |
| url | https://www.mdpi.com/1422-0067/24/4/4023 |
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