Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations
Abstract A carbon nanotube (CNT) can affect biological systems, ranging from toxicity to changes in functionality. Here, a series of long-scale (1–2 µs) molecular dynamics simulations were conducted to investigate the adsorption and interaction of lysozyme with the CNT, a possible mechanism for alte...
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Nature Portfolio
2025-04-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-96435-3 |
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| author | S. Mehdi Vaez Allaei Mehriar Amininasab Hrachya Ishkhanyan Armen H. Poghosyan |
| author_facet | S. Mehdi Vaez Allaei Mehriar Amininasab Hrachya Ishkhanyan Armen H. Poghosyan |
| author_sort | S. Mehdi Vaez Allaei |
| collection | DOAJ |
| description | Abstract A carbon nanotube (CNT) can affect biological systems, ranging from toxicity to changes in functionality. Here, a series of long-scale (1–2 µs) molecular dynamics simulations were conducted to investigate the adsorption and interaction of lysozyme with the CNT, a possible mechanism for altering protein flexibility and function. Four systems were examined: native lysozyme/CNT, denatured lysozyme/CNT, and both systems post-docking. Our results indicate that native lysozyme does not undergo conformational changes when initially captured by a CNT. However, after docking, the native lysozyme/CNT complex exhibits conformational changes. In contrast, the denatured lysozyme binds more effectively to the CNT in both pre- and post-docking scenarios. Key amino acid residues, arginine and tryptophan, have been identified as crucial for lysozyme/CNT interactions. The surface of the CNT adsorbs lysozyme through π-π stacking and van der Waals interactions, with these multimodal interactions serving as the main driving force for protein anchoring to the nanotube. These results also underscore the significance of docking in the simulation of protein/nanoparticle interactions, which can lead to entirely different conclusions regarding, for example, the toxicity or functionality of a given nanoparticle life. |
| format | Article |
| id | doaj-art-293e1ce4bb7d45c5bec9a58cf977f900 |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-293e1ce4bb7d45c5bec9a58cf977f9002025-08-20T03:07:41ZengNature PortfolioScientific Reports2045-23222025-04-0115111510.1038/s41598-025-96435-3Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulationsS. Mehdi Vaez Allaei0Mehriar Amininasab1Hrachya Ishkhanyan2Armen H. Poghosyan3Department of Physics, University of TehranDepartment of Cell and Molecular Biology, School of Biology, College of Science, University of TehranInstitute of Informatics and Automation ProblemsInstitute of Informatics and Automation ProblemsAbstract A carbon nanotube (CNT) can affect biological systems, ranging from toxicity to changes in functionality. Here, a series of long-scale (1–2 µs) molecular dynamics simulations were conducted to investigate the adsorption and interaction of lysozyme with the CNT, a possible mechanism for altering protein flexibility and function. Four systems were examined: native lysozyme/CNT, denatured lysozyme/CNT, and both systems post-docking. Our results indicate that native lysozyme does not undergo conformational changes when initially captured by a CNT. However, after docking, the native lysozyme/CNT complex exhibits conformational changes. In contrast, the denatured lysozyme binds more effectively to the CNT in both pre- and post-docking scenarios. Key amino acid residues, arginine and tryptophan, have been identified as crucial for lysozyme/CNT interactions. The surface of the CNT adsorbs lysozyme through π-π stacking and van der Waals interactions, with these multimodal interactions serving as the main driving force for protein anchoring to the nanotube. These results also underscore the significance of docking in the simulation of protein/nanoparticle interactions, which can lead to entirely different conclusions regarding, for example, the toxicity or functionality of a given nanoparticle life.https://doi.org/10.1038/s41598-025-96435-3Carbon nanotubeProteinDenaturationMolecular dynamics |
| spellingShingle | S. Mehdi Vaez Allaei Mehriar Amininasab Hrachya Ishkhanyan Armen H. Poghosyan Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations Scientific Reports Carbon nanotube Protein Denaturation Molecular dynamics |
| title | Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations |
| title_full | Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations |
| title_fullStr | Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations |
| title_full_unstemmed | Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations |
| title_short | Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations |
| title_sort | potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations |
| topic | Carbon nanotube Protein Denaturation Molecular dynamics |
| url | https://doi.org/10.1038/s41598-025-96435-3 |
| work_keys_str_mv | AT smehdivaezallaei potentialfunctionalchangesinnativelysozymeinducedbycarbonnanotubesstudiedbymoleculardynamicssimulations AT mehriaramininasab potentialfunctionalchangesinnativelysozymeinducedbycarbonnanotubesstudiedbymoleculardynamicssimulations AT hrachyaishkhanyan potentialfunctionalchangesinnativelysozymeinducedbycarbonnanotubesstudiedbymoleculardynamicssimulations AT armenhpoghosyan potentialfunctionalchangesinnativelysozymeinducedbycarbonnanotubesstudiedbymoleculardynamicssimulations |