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Free Energy Decomposition of CarO Outer Membrane Protein of Acinetobacter baumannii

Year 2022, Volume: 43 Issue: 1, 20 - 26, 30.03.2022

Emrah Sarıyer

https://doi.org/10.17776/csj.1022384

Abstract

The increase in the number of antibiotic-resistant microorganisms reported today has made this issue one of the main topics of all institutes. Acineteobacter baumanni is a species that is on the list of the WHO and plays an important role, especially in hospital-acquired infections. CarO outer membrane protein, which regulates the passage of small molecules and some antibiotics into the periplasmic space and is associated with carbapenem resistance, has been identified in A. baumannii. In this study, residues that contribute to the binding energy of imipenem to different types of CarO proteins were identified. In addition, energy decomposition was compared when Biapenem, Ertapenem, Imipenem, Faropenem, and Meropenem were docked to ATCC-17978 CarO protein separately. As a result of this study, it was determined that generally charged residues had a negative effect on binding affinity, but hydrophobic and uncharged residues had a positive effect. In addition, in ertapenem, faropenem, and meropenem-bound complexes, charged residues increased the affinity and caused the interaction between carbapenems and CarO to be continuous and tight. It was predicted that the residues determined in this study would be precursors to mutagenesis studies and could also be an example for similar studies.

Keywords

Acinetobacter baumannii CarO Imipenem Binding affinity Energy decomposition

Supporting Institution

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Project Number

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Thanks

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References

  • [1] Eliopoulos G. M., Maragakis L. L., Perl T. M., Acinetobacter baumannii: epidemiology, antimicrobial resistance, and treatment options, Clinical Infectious Diseases, 46 (2008) 1254-1263.
  • [2] Chen L.K., Kuo S.C., Chang K.C., Cheng C.C., Yu P.Y., Chang C.H., Clinical antibiotic-resistant Acinetobacter baumannii strains with higher susceptibility to environmental phages than antibiotic-sensitive strains, Scientific Reports, 7 (2017) 1-10.
  • [3] Lee C.-R., Lee J. H., Park M., Park K. S., Bae I. K., Kim Y. B. et al, Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options, Frontiers in Cellular and Infection Microbiology, 7 (2017) 55.
  • [4] Kyriakidis I., Vasileiou E., Pana Z. D., Tragiannidis A., Acinetobacter baumannii Antibiotic Resistance Mechanisms, Pathogens, 10 (2021) 373.
  • [5] Kamischke C., Fan J., Bergeron J., Kulasekara H. D., Dalebroux Z. D., Burrell A. et al, The Acinetobacter baumannii Mla system and glycerophospholipid transport to the outer membrane, Elife, 8 (2019) e40171.
  • [6] Hua M., Liu J., Du P., Liu X., Li M., Wang H., The novel outer membrane protein from OprD/Occ family is associated with hypervirulence of carbapenem resistant Acinetobacter baumannii ST2/KL22, Virulence, 12 (2021) 1-11.
  • [7] Nie D., Hu Y., Chen Z., Li M., Hou Z., Luo X., Outer membrane protein A (OmpA) as a potential therapeutic target for Acinetobacter baumannii infection, Journal of Biomedical Science, 27 (2020) 1-8.
  • [8] Vila-Farrés X., Ferrer-Navarro M., Callarisa A. E., Martí S., Espinal P., Gupta S., Loss of LPS is involved in the virulence and resistance to colistin of colistin-resistant Acinetobacter nosocomialis mutants selected in vitro, Journal of Antimicrobial Chemotherapy, 70 (2015) 2981-2986.
  • [9] Zahn M., D'agostino T., Eren E., Baslé A., Ceccarelli M., Van Den Berg B., Small-molecule transport by CarO, an abundant eight-stranded β-barrel outer membrane protein from Acinetobacter baumannii, Journal of Molecular Biology, 427 (2015) 2329-2339.
  • [10] Siroy A., Molle V., Lemaître-Guillier C., Vallenet D., Pestel-Caron M., Cozzone A. J., Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii, Antimicrobial Agents and Chemotherapy, 49 (2005) 4876-4883.
  • [11] Uppalapati S. R., Sett A., Pathania R., The outer membrane proteins OmpA, CarO, and OprD of Acinetobacter baumannii confer a two-pronged defense in facilitating its success as a potent human pathogen, Frontiers in Microbiology, 11 (2020).
  • [12] Zhu L. J., Chen X. Y., Hou P. F., Mutation of CarO participates in drug resistance in imipenem‐resistant Acinetobacter baumannii, Journal of Clinical Laboratory Analysis, 33 (2019) e22976.
  • [13] Baxevanis A. D., Bader G. D., Wishart D. S., Bioinformatics. John Wiley & Sons, (2020).
  • [14] Morris G. M., Huey R., Olson A. J., Using autodock for ligand‐receptor docking, Current Protocols in Bioinformatics, 24 (2008) 8.14. 11-18.14. 40.
  • [15] Gotz A. W., Williamson M. J., Xu D., Poole D., Le Grand S., Walker R. C., Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born, Journal of Chemical Theory and Computation, 8 (2012) 1542-1555.
  • [16] Genheden S., Ryde U., The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities, Expert Opinion on Drug Discovery, 10 (2015) 449-461.
  • [17] Ylilauri M., Pentikäinen O. T., MMGBSA as a tool to understand the binding affinities of filamin–peptide interactions, Journal of Chemical Information and Modeling, 53 (2013) 2626-2633.
  • [18] Miller III B. R., McGee Jr T. D., Swails J. M., Homeyer N., Gohlke H., Roitberg A. E., MMPBSA. py: an efficient program for end-state free energy calculations, Journal of Chemical Theory and Computation, 8 (2012) 3314-3321.
  • [19] Catel-Ferreira M., Coadou G., Molle V., Mugnier P., Nordmann P., Siroy A. et al, Structure–function relationships of CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii, Journal of Antimicrobial Chemotherapy, 66 (2011) 2053-2056.

Year 2022, Volume: 43 Issue: 1, 20 - 26, 30.03.2022

Emrah Sarıyer

https://doi.org/10.17776/csj.1022384

Abstract

Project Number

-

References

  • [1] Eliopoulos G. M., Maragakis L. L., Perl T. M., Acinetobacter baumannii: epidemiology, antimicrobial resistance, and treatment options, Clinical Infectious Diseases, 46 (2008) 1254-1263.
  • [2] Chen L.K., Kuo S.C., Chang K.C., Cheng C.C., Yu P.Y., Chang C.H., Clinical antibiotic-resistant Acinetobacter baumannii strains with higher susceptibility to environmental phages than antibiotic-sensitive strains, Scientific Reports, 7 (2017) 1-10.
  • [3] Lee C.-R., Lee J. H., Park M., Park K. S., Bae I. K., Kim Y. B. et al, Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options, Frontiers in Cellular and Infection Microbiology, 7 (2017) 55.
  • [4] Kyriakidis I., Vasileiou E., Pana Z. D., Tragiannidis A., Acinetobacter baumannii Antibiotic Resistance Mechanisms, Pathogens, 10 (2021) 373.
  • [5] Kamischke C., Fan J., Bergeron J., Kulasekara H. D., Dalebroux Z. D., Burrell A. et al, The Acinetobacter baumannii Mla system and glycerophospholipid transport to the outer membrane, Elife, 8 (2019) e40171.
  • [6] Hua M., Liu J., Du P., Liu X., Li M., Wang H., The novel outer membrane protein from OprD/Occ family is associated with hypervirulence of carbapenem resistant Acinetobacter baumannii ST2/KL22, Virulence, 12 (2021) 1-11.
  • [7] Nie D., Hu Y., Chen Z., Li M., Hou Z., Luo X., Outer membrane protein A (OmpA) as a potential therapeutic target for Acinetobacter baumannii infection, Journal of Biomedical Science, 27 (2020) 1-8.
  • [8] Vila-Farrés X., Ferrer-Navarro M., Callarisa A. E., Martí S., Espinal P., Gupta S., Loss of LPS is involved in the virulence and resistance to colistin of colistin-resistant Acinetobacter nosocomialis mutants selected in vitro, Journal of Antimicrobial Chemotherapy, 70 (2015) 2981-2986.
  • [9] Zahn M., D'agostino T., Eren E., Baslé A., Ceccarelli M., Van Den Berg B., Small-molecule transport by CarO, an abundant eight-stranded β-barrel outer membrane protein from Acinetobacter baumannii, Journal of Molecular Biology, 427 (2015) 2329-2339.
  • [10] Siroy A., Molle V., Lemaître-Guillier C., Vallenet D., Pestel-Caron M., Cozzone A. J., Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii, Antimicrobial Agents and Chemotherapy, 49 (2005) 4876-4883.
  • [11] Uppalapati S. R., Sett A., Pathania R., The outer membrane proteins OmpA, CarO, and OprD of Acinetobacter baumannii confer a two-pronged defense in facilitating its success as a potent human pathogen, Frontiers in Microbiology, 11 (2020).
  • [12] Zhu L. J., Chen X. Y., Hou P. F., Mutation of CarO participates in drug resistance in imipenem‐resistant Acinetobacter baumannii, Journal of Clinical Laboratory Analysis, 33 (2019) e22976.
  • [13] Baxevanis A. D., Bader G. D., Wishart D. S., Bioinformatics. John Wiley & Sons, (2020).
  • [14] Morris G. M., Huey R., Olson A. J., Using autodock for ligand‐receptor docking, Current Protocols in Bioinformatics, 24 (2008) 8.14. 11-18.14. 40.
  • [15] Gotz A. W., Williamson M. J., Xu D., Poole D., Le Grand S., Walker R. C., Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born, Journal of Chemical Theory and Computation, 8 (2012) 1542-1555.
  • [16] Genheden S., Ryde U., The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities, Expert Opinion on Drug Discovery, 10 (2015) 449-461.
  • [17] Ylilauri M., Pentikäinen O. T., MMGBSA as a tool to understand the binding affinities of filamin–peptide interactions, Journal of Chemical Information and Modeling, 53 (2013) 2626-2633.
  • [18] Miller III B. R., McGee Jr T. D., Swails J. M., Homeyer N., Gohlke H., Roitberg A. E., MMPBSA. py: an efficient program for end-state free energy calculations, Journal of Chemical Theory and Computation, 8 (2012) 3314-3321.
  • [19] Catel-Ferreira M., Coadou G., Molle V., Mugnier P., Nordmann P., Siroy A. et al, Structure–function relationships of CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii, Journal of Antimicrobial Chemotherapy, 66 (2011) 2053-2056.
There are 19 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Natural Sciences
Authors

Emrah Sarıyer 0000-0003-1721-0314

Project Number -
Publication Date March 30, 2022
Submission Date November 11, 2021
Acceptance Date March 14, 2022
Published in Issue Year 2022Volume: 43 Issue: 1

Cite

APA Sarıyer, E. (2022). Free Energy Decomposition of CarO Outer Membrane Protein of Acinetobacter baumannii. Cumhuriyet Science Journal, 43(1), 20-26. https://doi.org/10.17776/csj.1022384
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