Study of Glucose Binding Protein Encapsulated Gold Nanoclusters by Molecular Dynamic Simulation

Abstract:

Protein encapsulated gold nanoclusters has attracted great attention for their excellent fluorescent properties and potential biomedical applications. Glucose Binding Protein (GBP) has a high sensitivity and selectivity to glucose binding that makes them ideal for biosensor development. It is anticipated that GBP encapsulated gold nanoclusters could be a promising glucose sensor. Here we investigated the growth of gold nanoclusters in GBP using Molecular Dynamics (MD) simulation. To facilitation the nucleation of gold nanoclusters at specific sites, cysteine mutations were introduced in GBP. It is found that the nucleation site of gold nanoclusters inside mutant GBP are different from those in native GBP. Gold nanoclusters were formed near the mutated cysteine and tyrosine residues. Glucose remained in the binding site of a mutant GBP with gold nanoclusters although no conformational change was observed in MD simulation, similar to a native GBP. This work suggests the possibility of growing gold nanoclusters in the designed site within GBP and a new glucose sensor based on mutated GBP protected gold nanoclusters.

• Periodical: Materials Science Forum (Volume 948)
• Pages: 133-139
• DOI: https://doi.org/10.4028/www.scientific.net/MSF.948.133
• Online since: March 2019
• Authors: Boy Marsaputra Panjaitan, Karina Kubiak-Ossowska, David Birch, Yu Chen
• Keywords: Glucose Binding Protein, Gold Nanoclusters, Molecular Dynamic Simulation

References

[1] WHO, Media Centre Diabetes, Diabetes, p.11–14, (2013).

[2] B. Zhou et al., Worldwide trends in diabetes since 1980: A pooled analysis of 751 population-based studies with 4.4 million participants, Lancet, vol. 387, no. 10027, p.1513–1530, (2016).

[3] C. D. Mathers and D. Loncar, Projections of global mortality and burden of disease from 2002 to 2030, PLoS Med., vol. 3, no. 11, p.2011–2030, (2006).

DOI: 10.1371/journal.pmed.0030442

[4] B. H. Ginsberg, Blood glucose monitoring: necessary and sufficient?, J. Diabetes Sci. Technol., vol. 1, no. 5, p.612, (2007).

[5] L. Zhang and E. Wang, Metal nanoclusters: New fluorescent probes for sensors and bioimaging, Nano Today, vol. 9, no. 1, p.132–157, (2014).

DOI: 10.1016/j.nantod.2014.02.010

[6] L. Shang, S. Dong, and G. U. Nienhaus, Ultra-small fluorescent metal nanoclusters: Synthesis and biological applications, Nano Today, vol. 6, no. 4, p.401–418, (2011).

DOI: 10.1016/j.nantod.2011.06.004

[7] L. L. Wang, J. Qiao, L. Qi, X. Z. Xu, and D. Li, Construction of OVA-stabilized fluorescent gold nanoclusters for sensing glucose, Sci. China Chem., vol. 58, no. 9, p.1508–1514, (2015).

DOI: 10.1007/s11426-015-5354-5

[8] J. Zhang et al., Fluorescent gold nanoclusters based photoelectrochemical sensors for detection of H2O2and glucose, Biosens. Bioelectron., vol. 67, p.296–302, (2015).

[9] V. Scognamiglio et al., D-galactose/D-glucose-binding Protein from Escherichia coli as Probe for a Non-consuming Glucose Implantable Fluorescence Biosensor, Sensors, vol. 7, no. 10, p.2484–2491, (2007).

DOI: 10.3390/s7102484

[10] K. Palani, D. Kumaran, S. K. Burley, and S. Swaminathan, Structure of a periplasmic glucose-binding protein from Thermotoga maritima, Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., vol. 68, no. 12, p.1460–1464, (2012).

DOI: 10.1107/s1744309112045241

[11] F. Khan, L. Gnudi, and J. C. Pickup, Fluorescence-based sensing of glucose using engineered glucose/galactose-binding protein: A comparison of fluorescence resonance energy transfer and environmentally sensitive dye labelling strategies, Biochem. Biophys. Res. Commun., vol. 365, no. 1, p.102–106, (2008).

DOI: 10.1016/j.bbrc.2007.10.129

[12] B. A. Russell, K. Kubiak-Ossowska, P. A. Mulheran, D. J. S. Birch, and Y. Chen, Locating the nucleation sites for protein encapsulated gold nanoclusters: a molecular dynamics and fluorescence study, Phys. Chem. Chem. Phys., vol. 17, no. 34, p.21935–21941, (2015).

DOI: 10.1039/c5cp02380g

[13] N. K. Vyas, M. N. Vyas, and F. A. Quiocho, Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein., Science, vol. 242, no. 4883, p.1290–5, (1988).

DOI: 10.1126/science.3057628

[14] N. Foloppe and A. D. MacKerell, All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data, J. Comput. Chem., vol. 21, no. 2, p.86–104, (2000).

DOI: 10.1002/(sici)1096-987x(20000130)21:2<86::aid-jcc2>3.0.co;2-g

[15] J. C. Phillips et al., Scalable molecular dynamics with NAMD, J. Comput. Chem., vol. 26, no. 16, p.1781–1802, (2005).

[16] S. Raut, R. Chib, S. Butler, J. Borejdo, Z. Gryczynski, and I. Gryczynski, Evidence of energy transfer from tryptophan to BSA/HSA protected gold nanoclusters, Methods Appl. Fluoresc., vol. 2, no. 3, (2014).

DOI: 10.1088/2050-6120/2/3/035004

[17] U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, A smooth particle mesh Ewald method, J. Chem. Phys., vol. 103, no. 19, p.8577–8593, (1995).

DOI: 10.1063/1.470117

[18] C. D. Geddes and J. R. Lakowicz, Glucose Sensing. (2006).

[19] M. J. Borrok, L.L. Kiessling, and K. T. Forest, Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures, Protein Sci., vol. 16, no. 6, p.1032–1041, (2007).

DOI: 10.1110/ps.062707807

[20] M.-L. Cui et al., Selective determination of cysteine using BSA-stabilized gold nanoclusters with red emission, Analyst, vol. 137, no. 22, p.5346, (2012).

DOI: 10.1039/c2an36284h

[21] J. Xie, Y. Zheng, and J. Y. Ying, Protein-Directed Synthesis of Highly Fluorescent Gold Nanoclusters, J. Agric. Food Chem., p.888–889, (2009).

DOI: 10.1021/ja806804u

[22] H. KAWASAKI, K. YOSHIMURA, K. HAMAGUCHI, and R. ARAKAWA, Trypsin-Stabilized Fluorescent Gold Nanocluster for Sensitive and Selective Hg2+ Detection, Anal. Sci., vol. 27, no. 6, p.591, (2011).

DOI: 10.2116/analsci.27.591