Interaction of c(60)-fullerene and carboxyfullerene with proteins: docking and binding site alignment
- PMID: 16536469
- DOI: 10.1021/bc050299g
Interaction of c(60)-fullerene and carboxyfullerene with proteins: docking and binding site alignment
Abstract
The unique properties of fullerenes have raised the interest of using them for biomedical applications. Within this framework, the interactions of fullerenes with proteins have been an exciting research target, yet little is known about how native proteins can bind fullerenes, and what is the nature of these interactions. Moreover, though some proteins have been shown to interact with fullerenes, up to date, no crystal structure of such complexes was obtained. Here we report docking studies aimed at examining the interactions of fullerene in two forms (C60 nonsubstituted fullerene and carboxyfullerene) with four proteins that are known to bind fullerene derivatives: HIV protease, fullerene-specific antibody, human serum albumin, and bovine serum albumin. Our work provides docking models with detailed binding pockets information, which closely match available experimental data. We further compare the predicted binding sites using a novel multiple binding site alignment method. A high similarity between the physicochemical properties and surface geometry was found for fullerene's binding sites of HIV protease and the human and bovine serum albumins.
Similar articles
-
Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations.Bioorg Med Chem. 2008 Dec 1;16(23):9957-74. doi: 10.1016/j.bmc.2008.10.039. Epub 2008 Oct 22. Bioorg Med Chem. 2008. PMID: 18996019
-
Baiting proteins with C60.ACS Nano. 2010 Apr 27;4(4):2283-99. doi: 10.1021/nn901809b. ACS Nano. 2010. PMID: 20359241
-
Formation of a soluble stable complex between pristine C60-fullerene and a native blood protein.Chembiochem. 2006 Nov;7(11):1783-9. doi: 10.1002/cbic.200600237. Chembiochem. 2006. PMID: 16933357
-
Synthesis and biological properties of fullerene-containing amino acids and peptides.Mini Rev Med Chem. 2004 Sep;4(7):805-14. Mini Rev Med Chem. 2004. PMID: 15379647 Review.
-
The biological mechanisms and physicochemical characteristics responsible for driving fullerene toxicity.Toxicol Sci. 2010 Apr;114(2):162-82. doi: 10.1093/toxsci/kfp265. Epub 2009 Nov 9. Toxicol Sci. 2010. PMID: 19901017 Review.
Cited by
-
Enhanced Uptake and Phototoxicity of C60@albumin Hybrids by Folate Bioconjugation.Nanomaterials (Basel). 2022 Oct 6;12(19):3501. doi: 10.3390/nano12193501. Nanomaterials (Basel). 2022. PMID: 36234629 Free PMC article.
-
Application of non-metal nanoparticles, as a novel approach, for improving the stability of blood products: 2011-2021.Prog Biomater. 2022 Jun;11(2):137-161. doi: 10.1007/s40204-022-00188-5. Epub 2022 May 10. Prog Biomater. 2022. PMID: 35536502 Free PMC article. Review.
-
Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C60-Lysozyme Model.ACS Omega. 2018 Oct 22;3(10):13782-13789. doi: 10.1021/acsomega.8b01888. eCollection 2018 Oct 31. ACS Omega. 2018. PMID: 31458078 Free PMC article.
-
Distinct Binding Dynamics, Sites and Interactions of Fullerene and Fullerenols with Amyloid-β Peptides Revealed by Molecular Dynamics Simulations.Int J Mol Sci. 2019 Apr 25;20(8):2048. doi: 10.3390/ijms20082048. Int J Mol Sci. 2019. PMID: 31027286 Free PMC article.
-
Good's Buffer Ionic Liquids as Relevant Phase-Forming Components of Self-Buffered Aqueous Biphasic Systems.J Chem Technol Biotechnol. 2017 Sep;92(9):2287-2299. doi: 10.1002/jctb.5222. Epub 2017 Feb 1. J Chem Technol Biotechnol. 2017. PMID: 30270960 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
