Interaction of fullerenol with lysozyme investigated by experimental and computational approaches

Yang, Shengrong; Wang, Haifang; Guo, Lin; Gao, Yang; Liu, Yuanfang; Cao, Aoneng

doi:10.1088/0957-4484/19/39/395101

Cited by 70 publications

(80 citation statements)

References 45 publications

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“…Five other binding sites contain amino acid residues recognized as important for other ligand binding [72]; therefore, we considered them in the presented results. It was also experimentally proven that increasing concentration of fullerenol adsorbed to lysozyme decreases its enzymatic activity because of blocking a binding cleft [50]. Our computational results remain in an agreement with previous experimental and computational study data (see Table 1 and Fig.…”

Section: Binding Sites Analysissupporting

confidence: 92%

“…For two of the examined proteins, previously published data exist regarding fullerene or fullerenol binding sites: human serum albumin (HSA) [31,57,58] and hen-egg white lysozyme with fullerenol C 60 (OH)x (x≈24) [50] and pristine fullerene C60 [59]. Thus, albumin-C60 and lysozyme-C60 complexes were used as a validation set.…”

Section: Resultsmentioning

confidence: 99%

“…In the case of nonpolar residues, these are leucine and alanine (see Fig.6). With aromatic amino acid residues as tryptophan, phenylalanine, or tyrosine, fullerene C 60 used to create π-π stacking interactions [50] and we detected many of them in the computed models. Aromatic residues make about 12% of all residues found in binding sites (see Fig.…”

Section: Characterization Of the Observed Fullerene C 60 -Protein Intmentioning

confidence: 93%

“…The 3D structure of nonsubstituted fullerene C60 was received by using Avogadro 1.1.1 program library [43]. Docking procedure was performed by AUTODOCK 1.5.6 package [44] with AMBER force field [45] as default for AUTODOCK program [46], since it is commonly used and a very potent tool in structure-based virtual screening [47], and it was already previously used to study fullerene derivatives with proteins [48][49][50][51].…”

Section: Methodsmentioning

confidence: 99%

“…Five of them were taken into consideration as possible binding pockets for fullerene C 60 (see Table 1). The lowest protein-ligand interactions energy (2nd in an occupancy rank 26% of ligands) is located at the end of the active cleft of lysozyme and contains most of amino acid residues recognized previously as important for hen-egg white lysozyme original ligand binding [50,[69][70][71]79] (see Table 1 and Fig. 5).…”

Section: Binding Sites Analysismentioning

confidence: 99%

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Rapid insight into C60 influence on biological functions of proteins

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Experimental methods of investigations of nanoparticle (NP)-protein interactions are limited, because they require a high amount of samples and the NPs tend to interfere with spectral results. Therefore, molecular modeling is a commonly accepted tool in such kind of investigations. Examining the molecule toxicity on the molecular level, we usually want to know, mainly, the location of the ligand on the protein surface and what is an influence of such a contact on the biological functions of the protein. In the presented work, we demonstrate that multiple-docking of the ligand from a random start and with large grid volume, to let the ligand search the whole protein surface, allows to find the best binding sites and gives reliable results considering ligand-protein interactions. In the present work, we have constructed six models of bronchoalveolar lavage fluids proteins: α1-antitripsin, albumin, ceruloplasmin, lactoferrin, lysozyme, and transferrin with fullerene, C 60 utilizing molecular docking methods. The most probable results were examined with steered molecular dynamics (SMD) to see, if the simple docking method is able to predict the fullerene binding affinity. Albumin and lysozyme were already widely investigated and literature data is available for their complexes with fullerene C 60 and/or its derivatives. Thus, we used these two models as a reference set to validate the used molecular modeling methods. With our best knowledge, interactions of the remaining four proteins with NPs have never been investigated in detail before. Our results indicate that fullerene C 60 readily interacts with all studied proteins and may have a large impact on their biological functions.

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Section: Binding Sites Analysissupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Characterization Of the Observed Fullerene C 60 -Protein Intmentioning

confidence: 93%

Section: Methodsmentioning

confidence: 99%

Section: Binding Sites Analysismentioning

confidence: 99%

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Graphene and its derivatives have been considered intensively in the development and application of new types of adsorption and separation functional materials, due to its unique structure and superior performance. A comprehensive review on recent studies on adsorption and separation functional materials is given, including graphene, graphene oxide, graphene gel, graphene‐based sponge, graphene separation membrane as well as graphene continuous oil absorption and separation materials. Moreover, the preparation methods and application prospects are mainly utilized to illustrate the research progress. Especially, it is predicted that layered graphene membrane and graphene continuous oil absorption and separation materials may be the most research worthy.

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Many efforts have been made to develop inhibitors of MDM2 as potential drugs for cancer therapy. In this work, we use our previous developed conformational engineering technique to stabilize the binding conformation of the p53 transcription activation domain (TAD) peptide on gold nanoparticles (AuNPs), and create an AuNP‐based anti‐MDM2 artificial antibody, denoted as anti‐MDM2 Goldbody, that specifically binds MDM2. Though the free TAD peptide is unstructured, circular dichroism (CD) spectra confirm that its α‐helical conformation in the original p53 protein is restored on the anti‐MDM2 Goldbody, and surface plasmon resonance (SPR) experiments confirm that there is strong specific interaction between the anti‐MDM2 Goldbody and MDM2, demonstrating the anti‐MDM2 Goldbody as a potential inhibitor of MDM2. This work demonstrates that the conformational engineering technique is not limited to the antigen‐antibody systems, but can also be applied more widely in other protein‐protein interfaces to create increasingly more artificial proteins for various biomedical applications.

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Interaction of fullerenol with lysozyme investigated by experimental and computational approaches

Cited by 70 publications

References 45 publications

Rapid insight into C60 influence on biological functions of proteins

Rapid insight into C60 influence on biological functions of proteins

Graphene Adsorption and Separation Functional Materials

A Potential MDM2 Inhibitor Formed by Restoring the Native Conformation of the p53 α‐Helical Peptide on Gold Nanoparticles

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