Molecular simulations of myoglobin adsorbed on rutile (110) and (001) surfaces

Yang, Chuan; Chen, Peng; Zhao, Daohui; Liao, Chenyi; Jian, Zhou; Lü, Xiaohua

doi:10.1016/j.fluid.2013.10.052

Cited by 19 publications

(22 citation statements)

References 42 publications

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“…71 The interfacial water structure plays a major role in dictating the orientation and conformation of the adsorbed peptides and has been reported by previous simulation results. [72][73][74][75] In this sense, the interfacial water structure may also serve as a sensitive probe of adsorption events and adsorbed structure. Therefore, it is necessary to understand the effect of water on lipase adsorption on different surfaces.…”

Section: Interfacial Water Behaviorsmentioning

confidence: 99%

Lipase adsorption on different nanomaterials: a multi-scale simulation study

Zhao

Chen

Jian

2015

Phys. Chem. Chem. Phys.

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Candida antarctica lipase B (CalB) is an efficient biocatalyst for hydrolysis and esterification, which plays an important role in the production of biodiesel in the bioenergy industries. The ordered immobilisation of lipases on different supports would be significant for its enzymatic catalysis in some biodiesel production processes; however, the underlying mechanisms and the preferred lipase orientation are not well understood yet. In this work, a fundamental understanding of the orientation and adsorption mechanism of lipase on four different nanomaterial surfaces with different surface chemistry are explored in detail by a combination of parallel tempering Monte Carlo (PTMC) and molecular dynamics (MD) simulations. Simulation results show that lipase is strongly adsorbed onto the hydrophobic graphite surface, as reflected by the large contact area and interaction energy; while the adsorption onto the hydrophilic TiO2 surface is weak due to two strongly adhered water layers; meanwhile lipase undergoes desorption and reorientation processes. For CalB adsorption on positively and negatively charged surfaces (NH2-SAM and COOH-SAM), the orientation distributions of lipase are narrow, and opposite orientations are obtained. CalB adsorbed on NH2-SAM has its catalytic centre oriented towards the surface, which is not conducive to the substrate binding; while the catalytic centre faces toward the solution when it is adsorbed on the COOH-SAM. Besides, the native structures of CalB adsorbed on different surfaces are preserved, which indicates lipase as a robust enzyme. The simulation results will promote our understanding on how surface properties of nanomaterials, such as charge or hydrophobicity, will affect lipase immobilisation, and help us in the rational design and development of immobilised lipase carriers.

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Section: Interfacial Water Behaviorsmentioning

confidence: 99%

Lipase adsorption on different nanomaterials: a multi-scale simulation study

Zhao

Chen

Jian

2015

Phys. Chem. Chem. Phys.

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“…The mechanism of protein interplaying with the solid support has been described using molecular dynamic methods, which can provide information such as orientation, conformational changes or key adsorbing residues. These methods have been applied to understand immobilization mechanism via the adsorption process of cytochrome C onto carboxyl-terminated self-assembled monolayer or graphene oxide [45], myoglobin onto rutile (110) and (001) surfaces [46], ribonuclease A [47], lysozyme [48] as well as laccase [49][50][51]. To date, the mechanism of the immobilization process has not been described by density functional theory (DFT) methods.…”

Section: Introductionmentioning

confidence: 99%

Theoretical insight into plasma deposition of laccase bio-coating formation

Malinowski

Jaroszyńska-Wolińska

Herbert³

2019

J Mater Sci

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Development of new techniques for deposition of biologically active coatings in the form of bio-recognition layers in biosensor construction is a current technological challenge. Biosensors are widely applied in environmental protection in determination of hazardous materials, e.g., catechol, hydrochinon or resorcinol. Application of a soft plasma polymerization (SPP) technique by lowenergy-density corona discharge has allowed significant simplification of the deposition process of bio-recognition layers. However, the mechanism of the SPP process is by no means fully understood. This paper presents insights into the mechanism of binding laccase enzyme onto graphene oxide (GO) and multiwalled carbon nanotubes (MWCNT) through analysis carried out by density functional theory (DFT) methods and Fourier transform infrared spectroscopy (FTIR). The objective was to examine the mechanism on the basis of binding energies and electrostatic interactions between laccase and carbon nanomaterials as well as enzyme structure after cold plasma deposition. The lowest binding energies have been calculated for the ON bond between the arginine amino acid of laccase and the hydroxyl group of GO and the CO bond between the serine molecule of laccase and the carboxyl groups of GO and MWCNT. FTIR and DFT studies showed that the chemical structures of the laccase enzyme and carbon nanomaterials after corona jet plasma treatment are not substantially changed. Preliminary recognition of the mechanism of biosensing layer deposition by the SPP technique opens the way to application of this innovative technique to the construction of other biosensors such as for determination of pollutants in water samples.

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“…It has been successfully used in some of our previous works [34][35][36][37][38][39] to quickly obtain the preferential adsorption orientations. With these preliminarily optimized orientations from PTMC as the initial orientations, MD simulations were performed by using the GolP-CHARMM force field 32 to explore the adsorption behavior of Cyt-c on Au (111) surface.…”

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confidence: 99%

Molecular Simulations of Cytochrome c Adsorption on a Bare Gold Surface: Insights for the Hindrance of Electron Transfer

2015

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Experimental studies have shown that the adsorption of horse heart Cytochrome c (Cyt-c) on a bare gold surface leads to the hindrance of electron transfer (ET).The underlying mechanism remains controversial. In this work, the adsorption orientation and conformation of Cyt-c on Au (111) surface were investigated by performing Monte Carlo and molecular dynamics simulations. The results show that the most favorable binding mode of Cyt-c to gold agrees with the results characterized by SEIRA spectroscopy. The adsorption is mainly contributed by the strong van der Waals interactions between the surface and residues that have long side chains, which leads to the helix A and Ω1 loop of Cyt-c being in contact with the surface and most of the α-helixes being nearly parallel to the surface. The native structure of Cyt-c is well preserved during the adsorption and only the flexible Ω1 loop and the N-terminal show a relatively larger mobility. The hindrance of ET is ascribed to the confined rotation of the heme prosthetic group and the farther positioning of the central iron to the surface (about 12.9 Å). group was near and almost vertical to the negatively charged surface while far away from the positively charged surface. 17 However, Cyt-c had a random or relatively flat orientation on the bare gold nanohole surface. 17 Lin et al. 15 probed the adsorption of Cyt-c on a bare gold surface by surface-enhanced infrared absorption (SEIRA) spectroscopy. The results showed that Cyt-c kept its native structure when adsorbed on the bare gold, with most of the α-helixes running parallel to the surface. 15 They ascribed the hindrance of ET to the adsorption orientation and suppressed rotation of the adsorbed Cyt-c. However, the adsorption orientations of Cyt-c on bare gold surface characterized by SERS and SEIRA are quite different. What is the cause of the hindrance of ET? Although some experiments can provide structural, electronic and dynamic information simultaneously, in situ detection of the orientation and conformation changes of proteins emerging at the molecular level is still technically challenging. 15 Molecular simulations are very suitable to study the behavior of protein adsorption on surfaces at the molecular level. 18 So far, a few molecular dynamics (MD) simulation studies of Cyt-c adsorption on solid surfaces have been reported. 18-25 Zhou et al. 18 studied the adsorption of Cyt-c on carboxyl-terminated SAMs (COOH-SAM) by performing Monte Carlo and MD simulations. They showed that the heme ring was near and almost vertical to the COOH-SAM surface. 18 Alvarez-Paggi et al. 21-23 employed MD simulations and electron pathway analyses to investigate the ET properties of Cyt-c adsorbed on gold functionalized by COOH-SAM. Their findings demonstrated that the ET between the adsorbed Cyt-c and the electrode was determined by the interplay between protein dynamics and tunneling probabilities. 21 Hung et al. 24 investigated the adsorption of Cyt-c on monolayer-protected metal nanoparticles (MPMNs) through a combinedIn this wor...

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Molecular simulations of myoglobin adsorbed on rutile (110) and (001) surfaces

Cited by 19 publications

References 42 publications

Lipase adsorption on different nanomaterials: a multi-scale simulation study

Lipase adsorption on different nanomaterials: a multi-scale simulation study

Theoretical insight into plasma deposition of laccase bio-coating formation

Molecular Simulations of Cytochrome c Adsorption on a Bare Gold Surface: Insights for the Hindrance of Electron Transfer

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