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Chin. Phys. B, 2024, Vol. 33(11): 118102    DOI: 10.1088/1674-1056/ad7af5
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

Unravelling biotoxicity of graphdiyne: Molecular dynamics simulation of the interaction between villin headpiece protein and graphdiyne

Bei-Wei Zhang(张贝薇)1, Bing-Quan Zhang(张兵权)2, Zhi-Gang Shao(邵志刚)1,2,†, and Xianqiu Wu(吴先球)1,2
1 Guangdong Basic Research Center of Excellence for Structure and Fundamental Interactions of Matter, Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics, South China Normal University, Guangzhou 510006, China;
2 Guangdong-Hong Kong Joint Laboratory of Quantum Matter, Frontier Research Institute for Physics, South China Normal University, Guangzhou 510006, China
Abstract  Recently, there has been a growing prevalence in the utilization of graphdiyne (GDY) in the field of biomedicine, attributed to its distinctive physical structure and chemical properties. Additionally, its biocompatibility has garnered increasing attention. However, there is a lack of research on the biological effects and physical mechanisms of GDY-protein interactions at the molecular scale. In this study, the villin headpiece subdomain (HP35) served as a representative protein model. Molecular dynamics simulations were employed to investigate the interaction process between the HP35 protein and GDY, as well as the structural evolution of the protein. The data presented in our study demonstrate that GDY can rapidly adsorb HP35 protein and induce denaturation to one of the $\alpha$-helix structures of HP35 protein. This implies a potential cytotoxicity concern of GDY for biological systems. Compared to graphene, GDY induced less disruption to HP35 protein. This can be attributed to the presence of natural triangular vacancies in GDY, which prevents $\pi$-$\pi$ stacking action and the limited interaction of GDY with HP35 protein is not conducive to the expansion of protein structures. These findings unveil the biological effects of GDY at the molecular level and provide valuable insights for the application of GDY in biomedicine.
Keywords:  graphdiyne      villin headpiece      molecular dynamics simulation      biotoxicity  
Received:  21 May 2024      Revised:  16 July 2024      Accepted manuscript online:  14 September 2024
PACS:  81.05.U- (Carbon/carbon-based materials)  
  87.10.Tf (Molecular dynamics simulation)  
  87.14.E- (Proteins)  
  87.15.bd (Secondary structure)  
Fund: Project supported by the National Natural Science Foundation of China (Grant No. 52072132).
Corresponding Authors:  Zhi-Gang Shao     E-mail:  zgshao@scnu.edu.cn

Cite this article: 

Bei-Wei Zhang(张贝薇), Bing-Quan Zhang(张兵权), Zhi-Gang Shao(邵志刚), and Xianqiu Wu(吴先球) Unravelling biotoxicity of graphdiyne: Molecular dynamics simulation of the interaction between villin headpiece protein and graphdiyne 2024 Chin. Phys. B 33 118102

[1] Yu J, Loh X J, Luo Y, Ge S, Fan X and Ruan J 2020 Biomater. Sci. 8 763
[2] Xie J, Gong L, Zhu S, Yong Y, Gu Z and Zhao Y 2019 Adv. Mater. 31 1802244
[3] Yang Z, Kang S and Zhou R 2014 Nanoscale 6 663
[4] Xu Y, Huang S W, Ding H M and Ma Y Q 2024 Chin. Phys. B 33 028701
[5] Luo Y, Gu Z, Liao W, Huang Y and Luo Y 2024 ACS Appl. Nano Mater. 7 3817
[6] Wu M, Ma H, Fang H, Yang L and Lei X 2023 Chin. Phys. B 32 018701
[7] Ma H, Chen J, Fang H and Lei X 2021 Chin. Phys. B 30 106806
[8] Zhang B Q and Shao Z G 2023 Physica E 146 115547
[9] Calvaresi M and Zerbetto F 2013 Acc. Chem. Res. 46 2454
[10] Zhang W, Huynh T, Xiu P, Zhou B, Ye C, Luan B and Zhou R 2015 Carbon 94 895
[11] Gu Z, Song W, Chen S H, Li B, Li W and Zhou R 2019 Nanoscale 11 19362
[12] Babadaei M M N, Moghaddam M F, Solhvand S, Alizadehmollayaghoob E, Attar F, Rajabbeigi E, Akhtari K, Sari S and Falahati M 2018 Int. J. Nanomedicine 13 6871
[13] Bayda S, Amadio E, Cailotto S, Frión-Herrera Y, Perosa A and Rizzolio F 2021 Nanoscale Adv. 3 5183
[14] Nel A, Xia T, Madler L and Li N 2006 Science 311 622
[15] Carneiro P G, Pereira D G, da Silva B M O, Ribeiro H, Barbosa L A, Villar J A F P and Schnitzler M C 2023 Surf. Interfaces 41 103211
[16] Albanese A, Tang P S and Chan W C 2012 Annu. Rev. Biomed. Eng. 14 1
[17] An D Y, Su J G, Li C H and Li J Y 2015 Chin. Phys. B 24 120504
[18] Wang J G, Shi X X, Liu Y R, Wang P Y, Chen H and Xie P 2022 Chin. Phys. B 31 058702
[19] Tang Y, Yang Z, Yao Y, Zhou Y, Tan Y, Wang Z, Pan T, Xiong R, Sun J and Wei G 2024 Chin. Phys. B 33 030701
[20] Jariwala D, Sangwan V K, Lauhon L J, Marks T J and Hersam M C 2013 Chem. Soc. Rev. 42 2824
[21] Rao N, Singh R and Bashambu L 2021 Mater. Today Proc. 44 608
[22] Hayashi T, Kim Y A, Natsuki T and Endo M 2007 Chemphyschem 8 999
[23] Choi H and Yoon H 2015 Nanomaterials 5 906
[24] Ispasoiu R G, Balogh L, Varnavski O P, Tomalia D A and Goodson 2000 J. Am. Chem. Soc. 122 11005
[25] Wu J, Pan Z, Zhang Y, Wang B and Peng H 2018 J. Mater. Chem. A 6 12932
[26] Qi X, Qin C, Zhong W, Au C, Ye X and Du Y 2010 Materials 3 4142
[27] Lacerda L, Bianco A, Prato M and Kostarelos K 2006 Adv. Drug. Deliv. Rev. 58 1460
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