Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12
Microbes have a proclivity for binding to cell surfaces and forming biofilms. The act of creating biofilms is the microbe’s social activity while they are under stress. In humans, this form of cell aggregation leads to biofilm, which often leads to an infection. Despite their ability to form adhesi...
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| Format: | Article |
| Language: | English |
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Tehran University of Medical Sciences
2023-01-01
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| Series: | Acta Medica Iranica |
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| Online Access: | https://acta.tums.ac.ir/index.php/acta/article/view/9784 |
| _version_ | 1797902823133806592 |
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| author | Rohit Pritam Das Banishree Sahoo Manoranjan Arakha Arun Kumar Pradhan |
| author_facet | Rohit Pritam Das Banishree Sahoo Manoranjan Arakha Arun Kumar Pradhan |
| author_sort | Rohit Pritam Das |
| collection | DOAJ |
| description |
Microbes have a proclivity for binding to cell surfaces and forming biofilms. The act of creating biofilms is the microbe’s social activity while they are under stress. In humans, this form of cell aggregation leads to biofilm, which often leads to an infection. Despite their ability to form adhesion to the cell surface, biofilm has also drawn attention due to its involvement in chronic disorders. Accumulation of biofilm leads to a serious health concern showing high resistance to antibiotics. In order to address this concern, there is a desperate need to find out natural bioproducts like biosurfactants which could be an alternative to synthetic compounds. In the current study, the inhibitory effect of rhamnolipid against E. coli k-12 proteins that are involved in biofilm formation was studied through various computational approaches. In the molecular docking approach, the interaction between rhamnolipid and targeted proteins has been recorded. Rhamnolipid interacts with pgaC with the total highest energy of -8.91 kcal/mol, indicating a tight ligand-protein interaction. Further, to validate the interaction, a 10-ns molecular dynamics simulation was performed for pgaC and with rhamnolipid bound complex. The stability of biosurfactant and biofilm-producing protein was investigated using the RMSD, RMSF, Rg, and SASA plots. As a comparison to only protein, a complex Binding with rhamnolipid shows a stable RMSD value with minimal RMSF and Rg values, which indicates the tight interaction between rhamnolipid and pgaC. This could be a leading novel in silico approach to studying the inhibitory effect of biosurfactants against biofilm formation proteins.
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| first_indexed | 2024-04-10T09:23:26Z |
| format | Article |
| id | doaj.art-8c6f21439e7241aea563674c2bffdce0 |
| institution | Directory Open Access Journal |
| issn | 0044-6025 1735-9694 |
| language | English |
| last_indexed | 2024-04-10T09:23:26Z |
| publishDate | 2023-01-01 |
| publisher | Tehran University of Medical Sciences |
| record_format | Article |
| series | Acta Medica Iranica |
| spelling | doaj.art-8c6f21439e7241aea563674c2bffdce02023-02-20T08:35:34ZengTehran University of Medical SciencesActa Medica Iranica0044-60251735-96942023-01-01601210.18502/acta.v60i12.11825Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12Rohit Pritam Das0Banishree Sahoo1Manoranjan Arakha2Arun Kumar Pradhan3Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, IndiaCentre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, IndiaCentre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, IndiaCentre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, India Microbes have a proclivity for binding to cell surfaces and forming biofilms. The act of creating biofilms is the microbe’s social activity while they are under stress. In humans, this form of cell aggregation leads to biofilm, which often leads to an infection. Despite their ability to form adhesion to the cell surface, biofilm has also drawn attention due to its involvement in chronic disorders. Accumulation of biofilm leads to a serious health concern showing high resistance to antibiotics. In order to address this concern, there is a desperate need to find out natural bioproducts like biosurfactants which could be an alternative to synthetic compounds. In the current study, the inhibitory effect of rhamnolipid against E. coli k-12 proteins that are involved in biofilm formation was studied through various computational approaches. In the molecular docking approach, the interaction between rhamnolipid and targeted proteins has been recorded. Rhamnolipid interacts with pgaC with the total highest energy of -8.91 kcal/mol, indicating a tight ligand-protein interaction. Further, to validate the interaction, a 10-ns molecular dynamics simulation was performed for pgaC and with rhamnolipid bound complex. The stability of biosurfactant and biofilm-producing protein was investigated using the RMSD, RMSF, Rg, and SASA plots. As a comparison to only protein, a complex Binding with rhamnolipid shows a stable RMSD value with minimal RMSF and Rg values, which indicates the tight interaction between rhamnolipid and pgaC. This could be a leading novel in silico approach to studying the inhibitory effect of biosurfactants against biofilm formation proteins. https://acta.tums.ac.ir/index.php/acta/article/view/9784RhamnolipidBiofilmIn silicoGlycolipidInteractionK-12 strain |
| spellingShingle | Rohit Pritam Das Banishree Sahoo Manoranjan Arakha Arun Kumar Pradhan Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12 Acta Medica Iranica Rhamnolipid Biofilm In silico Glycolipid Interaction K-12 strain |
| title | Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12 |
| title_full | Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12 |
| title_fullStr | Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12 |
| title_full_unstemmed | Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12 |
| title_short | Molecular Docking and Simulation Approach to Study the Inhibitory Effect of Rhamnolipid on Biofilm Producing Proteins in E. coli K12 |
| title_sort | molecular docking and simulation approach to study the inhibitory effect of rhamnolipid on biofilm producing proteins in e coli k12 |
| topic | Rhamnolipid Biofilm In silico Glycolipid Interaction K-12 strain |
| url | https://acta.tums.ac.ir/index.php/acta/article/view/9784 |
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