Molecular dynamics study of laccase immobilized on self-assembled monolayer-modified Au
Source abstract
Abstract
Molecular dynamics simulations of laccase immobilized by 4-aminothiophenol (4-ATP) were performed to understand the origin of the enhanced catalytic activity at 350 K of laccase immobilized by self-assembled monolayers. The simulation showed that laccase was stabilized by bonding with 4-ATP. In addition, docking simulation of 2, 6-dimethoxyphenol (DMP) to laccase revealed that the hydrophobic interaction energy was increased by bonding with 4-ATP. The variations of docking site size were minor considering the dimensions of DMP molecule. Therefore, it is suggested that the enhanced catalytic activity of laccase with 4-ATP is attributed to the high hydrophobic interaction energy between laccase and DMP.
Source: openaire · Quality: candidate unverified · Source record ↗
Research context
OpenAlex topics: Gold and Silver Nanoparticles Synthesis and Applications · Nanocluster Synthesis and Applications · Advanced biosensing and bioanalysis techniques
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (27)
Show source-provided references
1. Hakamada M, Takahashi M, Furukawa T, Tajima K, Yoshimura K, Chino Y, Mabuchi M (2011) Electrochemical stability of self-assembled monolayers on nanoporous Au. Phys Chem Chem Phys 13:12277–1228410.1039/c0cp02553d ↗
2. Shulga OV, Jefferson K, Khan AR, D’Souza VT, Liu J, Demchenko AV, Stine KJ (2007) Preparation and characterization of porous gold and its application as a platform for immobilization of acetylcholine esterase. Chem Mater 19:3902–391110.1021/cm070238n ↗
3. Qin H, Xu C, Huang X, Ding Y, Qu Y, Gao P (2009) Immobilization of laccase on nanoporous gold: comparative studies on the immobilization strategies and the particle size effect. J Phys Chem C 113:2521–252510.1021/jp8090304 ↗
4. Tielens F, Santos E (2010) AuS and SH bond formation/breaking during the formation of alkanethiol SAMs on Au (111): a theoretical study. J Phys Chem C 114:9444–945210.1021/jp102036r ↗
5. Hakamada M, Takahashi M, Mabuchi M (2012) Enhanced thermal stability of laccase immobilized on monolayer-modified nanoporous Au. Mater Lett 66:4–610.1016/j.matlet.2011.08.017 ↗
6. Yaropolov A, Skorobogat’ko OV, Vartanov SS, Varfolomeyev SD (1994) Laccase properties, catalytic mechanism, and applicability. Appl Biochem Biotechnol 49:257–28010.1007/BF02783061 ↗
7. Gupta G, Rajendran V, Atanassov P (2003) Laccase biosensor on monolayer-modified gold electrode. Electroanalysis 20:1577–158310.1002/elan.200302724 ↗
8. Mena ML, Carralero V, González-Cortés A, Yáñez-Sedeño P, Pingarrón JM (2005) Laccase biosensor based on N-succinimidyl-3-thiopropionate-functionalized gold electrodes. Electroanalysis 23:2147–215510.1002/elan.200503345 ↗
9. Deng L, Wang F, Chen H, Shang L, Wang L, Wang T, Shaojun D (2008) A biofuel cell with enhanced performance by multilayer biocatalyst immobilized on highly ordered macroporous electrode. Biosens Bioelectron 24:329–33310.1016/j.bios.2008.04.006 ↗
10. Miyazaki K (2005) A hyperthermophilic laccase from Thermus thermophilus HB27. Extremophiles 9:415–42510.1007/s00792-005-0458-z ↗
11. MacJerell AD Jr, Bashford D, Bellott M et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–361610.1021/jp973084f ↗
12. Garavaglia S, Cambria MT, Miglio M, Ragusa S, Lacobazzi V, Palmieri F, D’Ambrosio C, Scaloni A, Rizzi M (2004) The structure of Rigidoporus lignosus laccase containing a full complement of copper ions, reveals an asymmetrical arrangement for the T3 copper pair. J Mol Biol 342:1519–153110.1016/j.jmb.2004.07.100 ↗
13. Berman HM, Westbrook J, Feng Z, Gilliland G et al (2000) The protein data bank. Nucleic Acids Res 28:235–24210.1093/nar/28.1.235 ↗
14. Berendsen HJC, Postma JPM, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–369010.1063/1.448118 ↗
15. Dominguez CV, Pita M, De Lacey AL, Shleev S, Cuesta A (2012) Combined ATR-SEIRAS and EC-STM study of the immobilization of laccase on chemically modified Au electrodes. J Phys Chem C 116:16532–1654010.1021/jp303818p ↗
16. Gupta G, Rajendran V, Atanassov P (2004) Bioelectrocatalysis of oxygen reduction reaction by laccase on gold electrodes. Electroanalysis 16:1182–118510.1002/elan.200403010 ↗
17. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Oison AJ (2009) AutoDock4 and AutodockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:1639–166210.1002/jcc.21256 ↗
18. Martinez-Sotres C, Rutiaga-Quinones JG, Herrera-Bucio R, Gallo G, Lopez-Albarran P (2015) Molecular docking insights into the inhibition of laccase activity by medicarpin. Wood Sci Technol 49:857–86810.1007/s00226-015-0734-8 ↗
19. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate—DNA helices. J Am Chem Soc 120:9401–940910.1021/ja981844+ ↗
20. Trevino SR, Schaefer S, Scholtz JM, Pace CN (2007) Increasing protein conformational stability by optimizing beta-turn sequence. J Mol Biol 373:211–21810.1016/j.jmb.2007.07.061 ↗
21. Fu H, Grimsley GR, Razvi A, Scholtz JM, Pace CN (2009) Increasing protein stability by improving beta-turns. Proteins 77:491–49810.1002/prot.22509 ↗
22. Wang F, Guo C, Liu H-Z, Liu C-Z (2008) Immobilization of Pycnoporous sanguineus laccase by metal affinity adsorption on magnetic chelator particles. J Chem Technol Biotech 83:97–10410.1002/jctb.1793 ↗
23. Bayramoglu G, Yilmaz M, Arica MY (2010) Preparation and characterization of epoxy-functionalized magnetic chitosan beads: laccase immobilized for degradation of reactive dyes. Bioprocess Biosyst Eng 33:439–44810.1007/s00449-009-0345-6 ↗
24. Fernandes RA, Daniel-da-Silva AL, Tavares APM, Xavier AMRB (2017) EDTA-Cu(II) chelating magnetic nanoparticles as a support for laccase immobilization. Chem Eng Sci 158:599–60510.1016/j.ces.2016.11.011 ↗
25. Autore F, Del Vecchio C, Fraternali F, Giardina P, Sannia G, Faraco V (2009) Molecular determinants of peculiar properties of a Pleurotus ostreatus laccase: analysis by site-directed mutagenesis. Enzyme Microb Technol 45:507–51310.1016/j.enzmictec.2009.08.004 ↗
26. Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65:1–4310.1128/MMBR.65.1.1-43.2001 ↗
27. Tokuriki N, Stricher F, Serrano L, Tawfik DS (2008) How protein stability and new functions trade off. PLoS Comput Biol 4:e100000210.1371/journal.pcbi.1000002 ↗