285
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

In silico study of interaction of (ZnO)12 nanocluster to glucose oxidase-FAD in absence and presence of glucose

, , &
Pages 15234-15242 | Received 17 Feb 2022, Accepted 26 Feb 2023, Published online: 13 Mar 2023

References

  • Alberto Flores-Hidalgo, M., Glossman-Mitnik, D., Galvan, D. H., & Barraza-Jimenez, D. (2013). Computational study of cage like (ZnO)12 cluster using hybrid and hybrid meta functionals. Journal of the Chinese Chemical Society, 60(8), 1082–1091. https://doi.org/10.1002/jccs.201200439
  • Aloraefy, M., Joshua Pfefer, T., Ramella-Roman, J. C., & Sapsford, K. E. (2014). In vitro evaluation of fluorescence glucose biosensor response. Sensors (Basel, Switzerland), 14(7), 12127–12148. https://doi.org/10.3390/s140712127
  • Amber v14. (n.d.). Retrieved November 27, 2018, from https://intranet.birmingham.ac.uk/it/teams/infrastructure/research/bear/bluebear/applications/amber-v14-0.aspx
  • Åqvist, J. (1996). Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. Journal of Computational Chemistry, 17(14), 1587–1597. https://doi.org/10.1002/(SICI)1096-987X(19961115)17:14<1587::AID-JCC1>3.0.CO;2-H
  • Bhunia, A. K. (2017). ZnO nanoparticles: Recent biomedical applications and interaction with proteins. Current Trends in Biomedical Engineering & Biosciences, 6(1), 10–13. https://doi.org/10.19080/CTBEB.2017.06.555676
  • BIOVIA - Scientific Enterprise Software for Chemical Research. (n.d.). Material science R&D. Retrieved November 27, 2018, from http://3dsbiovia.com/
  • Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham III, T. E., Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Ghoreishi, D., Gilson, M. K., Gohlke, H., Goetz, A. W., Greene, D., Harris, R., Homeyer, N., Izadi, S., Kovalenko, A., Kurtzman, T., Lee, T. S., LeGrand, S., … Li, P. (2018). AMBER 2018. University of California.
  • Chakraborti, S., Joshi, P., Chakravarty, D., Shanker, V., Ansari, Z. A., Singh, S. P., & Chakrabarti, P. (2012). Interaction of polyethyleneimine-functionalized ZnO nanoparticles with bovine serum albumin. Langmuir: The ACS Journal of Surfaces and Colloids, 28(30), 11142–11152. https://doi.org/10.1021/la3007603
  • Chen, L., Hwang, E., & Zhang, J. (2018). Fluorescent nanobiosensors for sensing glucose. Sensors (Switzerland), 18(5), 1–21. https://doi.org/10.3390/s18051440
  • Chomoucka, J., Drbohlavova, J., Ryvolova, M., Sobrova, P., Janu, L., Adam, V., Hubalek, J., & Kizek, R. (2013). Quantum dots: Biological and biomedical applications. Quantum Dots: Applications, Synthesis and Characterization, 2014, 193–215.
  • Dill, K. A. (1997). Additivity principles in biochemistry. The Journal of Biological Chemistry, 272(2), 701–704. https://doi.org/10.1074/jbc.272.2.701
  • Fu, Y.-S., Du, X.-W., Kulinich, S. A., Qiu, J.-S., Qin, W.-J., Li, R., Sun, J., & Liu, J. (2007). Stable aqueous dispersion of ZnO quantum dots with strong blue emission via simple solution route. Journal of the American Chemical Society, 129(51), 16029–16033. https://doi.org/10.1021/ja075604i
  • Garimella, L. B. V. S., Dhiman, T. K., Kumar, R., Singh, A. K., & Solanki, P. R. (2020). One-step synthesized ZnO np-based optical sensors for detection of aldicarb via a photoinduced electron transfer route. ACS Omega, 5(6), 2552–2560. https://doi.org/10.1021/acsomega.9b01987
  • Gaussian.com. (n.d.). | Expanding the limits of computational chemistry. Retrieved November 27, 2018, from http://gaussian.com/
  • Gavin, J. R. (2007). The importance of monitoring blood glucose. US Endocrinology, 2, 42–45. https://doi.org/10.17925/USE.2007.00.2.42
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Gulzar, M., Ali, S., Khan, F. I., Khan, P., Taneja, P., & Hassan, M. I. (2019). Binding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: a comparative docking and MD simulation studies. Journal of Biomolecular Structure & Dynamics, 37(16), 4327–4337. https://doi.org/10.1080/07391102.2018.1546621
  • Hu, L., Chen, W., Xie, X., Liu, N., Yang, Y., Wu, H., Yao, Y., Pasta, M., Alshareef, H. N., & Cui, Y. (2011). Symmetrical MnO2–carbon nanotube–textile nanostructures for wearable pseudocapacitors with high mass loading. ACS Nano, 5(11), 8904–8913. https://doi.org/10.1021/nn203085j
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Janati-Fard, F., Housaindokht, M. R., & Monhemi, H. (2016). Investigation of structural stability and enzymatic activity of glucose oxidase and its subunits. Journal of Molecular Catalysis B: Enzymatic, 134, 16–24. https://doi.org/10.1016/j.molcatb.2016.09.008
  • Jayaram, B. (1998). A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts. The Journal of Chemical Physics, 109(4), 1465. https://doi.org/10.1063/1.476697
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Joshi, P., Chakraborti, S., Chakrabarti, P., Singh, S.P., Ansari, Z.A., & Shankar V.(2011). Polyethyleneimine functionalized ZnO quantum dots and their binding interaction with bovine serum albumin protein. Materials Research Society Symposium Proceedings, 1316, 307. https://doi.org/10.1557/opl.2011
  • Joshi, P., Shewale, V., Pandey, R., Shanker, V., Hussain, S., & Karna, S. P. (2011). Site specific interaction between ZnO nanoparticles and tryptophan: A first principles quantum mechanical study. Physical Chemistry Chemical Physics: PCCP, 13(2), 476–479. https://doi.org/10.1039/c0cp01466d
  • Karplus, M., et al. (1981). Method for estimating the configurational entropy of macromolecules. Macromolecules, 14(2), 325–332. https://doi.org/10.1021/ma50003a019
  • Kommoju, P. R., Chen, Z. W., Bruckner, R. C., Mathews, F. S., & Jorns, M. S. (2011). Crystal structure of glucose oxidase for space group C2221 at 1.2 A resolution. Biochemistry, 50, 5521–5534. https://doi.org/10.2210/PDB3QVP/PDB
  • Kong, T., Chen, Y., Ye, Y., Zhang, K., Wang, Z., & Wang, X. (2009). An amperometric glucose biosensor based on the immobilization of glucose oxidase on the ZnO nanotubes. Sensors and Actuators, B: Chemical, 138(1), 344–350. https://doi.org/10.1016/j.snb.2009.01.002
  • Kumar, A., Mishra, A., Kumar, T., & Sardar, M. (2022). Experimental and In Silico interaction studies of Alpha Amylase-Silver nanoparticle: a nano-bio-conjugate. 1–17.
  • Kurkina, et al. (2010). Approximate atomic surfaces from linear combinations of. Sensors, 6(1), 413–419. https://doi.org/10.1021/ic201327n
  • Kutzner, C., et al. (n.d.). Performance tuning of molecular dynamics simulations using PME.
  • Lemak, A. S., & Balabaev, N. K. (1994). On the berendsen thermostat. Molecular Simulation, 13(3), 177–187. https://doi.org/10.1080/08927029408021981
  • Li, P., & Merz, K. M. (2016). MCPB.py: A Python based metal center parameter builder. Journal of Chemical Information and Modeling, 56(4), 599–604. https://doi.org/10.1021/acs.jcim.5b00674
  • Liu, H., Wang, S., Zhou, G., Wu, J., & Duan, W. (2006). Structural, electronic, and magnetic properties of manganese-doped Zn12O12 clusters: A first-principles study. The Journal of Chemical Physics, 124(17), 174705. https://doi.org/10.1063/1.2194015
  • Matxain, J. M., Mercero, J. M., Fowler, J. E., & Ugalde, J. M. (2003). Electronic excitation energies of ZniOi clusters. Journal of the American Chemical Society, 125(31), 9494–9499. https://doi.org/10.1021/ja0264504
  • Mcshane, M., & Stein, E. (2009). Fluorescence-based glucose sensors. Sensors, 74, 269–316.
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Murcko, M. A. (1995). Computational methods to predict binding free energy in ligand-receptor complexes. Journal of Medicinal Chemistry, 38(26), 4953–4967. https://doi.org/10.1021/jm00026a001
  • Naccess V2.1.1 - Solvent accessible area calculations. (n.d.). Retrieved November 27, 2018, from http://www.bioinf.manchester.ac.uk/naccess/nac_intro.html
  • Naqvi, A. A. T., Mohammad, T., Hasan, G. M., & Hassan, M. I. (2018). Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships. Current Topics in Medicinal Chemistry, 18(20), 1755–1768. https://doi.org/10.2174/1568026618666181025114157
  • Onufriev, A. V., & Case, D. A. (2019). Generalized born implicit solvent models for biomolecules. Annual Review of Biophysics, 48, 275–296. https://doi.org/10.1146/annurev-biophys-052118-115325
  • Perera, D. C., & Rasaiah, J. C. (2022). Exchange functionals and basis sets for density functional theory studies of water splitting on selected ZnO nanocluster catalysts. ACS Omega, 7(15), 12556–12569. https://doi.org/10.1021/acsomega.1c05666
  • Pickup, J. C., Hussain, F., Evans, N. D., Rolinski, O. J., & Birch, D. J. S. (2005). Fluorescence-based glucose sensors. Biosensors & Bioelectronics, 20(12), 2555–2565. https://doi.org/10.1016/j.bios.2004.10.002
  • Putzbach, W., & Ronkainen, N. J. (2013). Immobilization techniques in the fabrication of nanomaterial-based electrochemical biosensors: A review. Sensors (Basel, Switzerland), 13(4), 4811–4840. https://doi.org/10.3390/s130404811
  • PyMOL | pymol.org. (n.d.). Retrieved November 27, 2018, from https://pymol.org/2/
  • Rahman, M. M., Ahammad, A. J. S., Jin, J.-H., Ahn, S. J., & Lee, J.-J. (2010). A comprehensive review of glucose biosensors based on nanostructured metal-oxides. Sensors (Basel, Switzerland), 10(5), 4855–4886. https://doi.org/10.3390/s100504855
  • Reber, A. C., Khanna, S. N., Hunjan, J. S., & Beltrán, M. R. (2006). Cobalt doped rings and cages of ZnO clusters: Motifs for magnetic cluster-assembled materials. Chemical Physics Letters, 428(4), 376–380. https://doi.org/10.1016/j.cplett.2006.07.045
  • Repp, S., Weber, S., & Erdem, E. (2016). Defect evolution of nonstoichiometric ZnO Quantum Dots. Journal of Physical Chemistry C, 120(43), 25124–25130. https://doi.org/10.1021/acs.jpcc.6b09108
  • Rodriguez, J. A., Jirsak, T., Dvorak, J., Sambasivan, S., & Fischer, D. (2000). Reaction of NO2 with Zn and ZnO: Photoemission, XANES, and density functional studies on the formation of NO3. The Journal of Physical Chemistry B, 104(2), 319–328. https://doi.org/10.1021/jp993224g
  • Shamsazar, A., Shamsazar, F., Asadi, A., & Rezaei-Zarchi, S. (2016). A glucose biosensor based on glucose oxidase enzyme and ZnO nanoparticles modified carbon paste electrode. International Journal of Electrochemical Science, 11(12), 9891–9901. https://doi.org/10.20964/2016.12.33
  • Sharma, S., & Deep, S. (2020). pH effect on the dynamics of SARS-CoV-2 main protease (M pro). BioRxiv, 2020.11.30.404384.
  • Sharma, S., & Deep, S. (2022). In-silico drug repurposing for targeting SARS-CoV-2 main protease (Mpro). Journal of Biomolecular Structure and Dynamics, 40(7), 3003–3010. https://doi.org/10.1080/07391102.2020.1844058
  • Szakacs, C., Merschrod S, E., & Poduska, K. (2013). Structural features that stabilize ZnO clusters: An electronic structure approach. Computation, 1(1), 16–26. https://doi.org/10.3390/computation1010016
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
  • Verma, A. K., & Ansari, Z. A. (2020). Fluorescent ZnO quantum dot probe to study glucose–glucose oxidase interaction via fluorescence resonance energy transfer. Sensor Letters, 18(5), 351–365. https://doi.org/10.1166/sl.2020.4232
  • VMD - Visual Molecular Dynamics. (n.d.). Retrieved February 16, 2022, from https://www.ks.uiuc.edu/Research/vmd/
  • Wang, B., Nagase, S., Zhao, J., & Wang, G. (2007). Structural growth sequences and electronic properties of zinc oxide clusters (ZnO)n (n = 2-18). The Journal of Physical Chemistry C, 111(13), 4956–4963. https://doi.org/10.1021/jp066548v
  • Wang, J. X., Sun, X. W., Wei, A., Lei, Y., Cai, X. P., Li, C. M., & Dong, Z. L. (2006). Zinc oxide nanocomb biosensor for glucose detection. Applied Physics Letters, 88(23), 10–13. https://doi.org/10.1063/1.2210078
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157-1174. https://doi.org/10.1002/jcc.20035
  • Wang, Z., He, H., Slough, W., Pandey, R., & Karna, S. P. (2015). Nature of interaction between semiconducting nanostructures and biomolecules: Chalcogenide QDs and BNNT with DNA molecules. Journal of Physical Chemistry C, 119(46), 25965–25973. https://doi.org/10.1021/acs.jpcc.5b08084
  • Wei, A., Sun, X. W., Wang, J. X., Lei, Y., Cai, X. P., Li, C. M., Dong, Z. L., & Huang, W. (2006). Enzymatic glucose biosensor based on ZnO nanorod array grown by hydrothermal decomposition. Applied Physics Letters, 89(12), 3–6. https://doi.org/10.1063/1.2356307
  • Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20(2), 217–230. https://doi.org/10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
  • Wu, Y. L. (2007). Surface modifications of ZnO quantum dots for bio-imaging. Iop Publishing Nanotechnology, 18, 215604–215613. https://doi.org/10.1088/0957-4484/18/21/215604
  • Xiang, X. U. C., et al. (2013). Nanostructured ZnO for biosensing applications. Chinese Science Bulletin, 58(21), 2563–2566. https://doi.org/10.1007/s11434-013-5714-5
  • Yadav, M. K., Ghosh, M., Biswas, R., Raychaudhuri, A. K., Mookerjee, A., & Datta, S. (2007). Band-gap variation in Mg- and Cd-doped ZnO nanostructures and molecular clusters. Physical Review B, 76(19), 195450. https://doi.org/10.1103/PhysRevB.76.195450
  • Zang, J., Chang, M. L., Cui, X., Wang, J., Sun, X., Dong, H., & Sun, C. Q. (2007). Tailoring zinc oxide nanowires for high performance amperometric glucose sensor. Electroanalysis, 19(9), 1008–1014. https://doi.org/10.1002/elan.200603808
  • Zhang, F., Wang, X., Ai, S., Sun, Z., Wan, Q., Zhu, Z., Xian, Y., Jin, L., & Yamamoto, K. (2004). Immobilization of uricase on ZnO nanorods for a reagentless uric acid biosensor. Analytica Chimica Acta, 519(2), 155–160. https://doi.org/10.1016/j.aca.2004.05.070
  • Zhu, H., Li, L., Zhou, W., Shao, Z., & Chen, X. (2016). Advances in non-enzymatic glucose sensors based on metal oxides. Journal of Materials Chemistry. B, 4(46), 7333–7349. https://doi.org/10.1039/C6TB02037B
  • Zhu, X., Yuri, I., Gan, X., Suzuki, I., & Li, G. (2007). Electrochemical study of the effect of nano-zinc oxide on microperoxidase and its application to more sensitive hydrogen peroxide biosensor preparation. Biosensors & Bioelectronics, 22(8), 1600–1604. https://doi.org/10.1016/j.bios.2006.07.007

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.