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Sahihi M, Fayon P, Nauton L, Goujon F, Devémy J, Dequidt A, Hauret P, Malfreyt P. Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability. J Chem Inf Model 2024; 64:4112-4120. [PMID: 38703106 DOI: 10.1021/acs.jcim.4c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
Understanding the mechanisms influencing poly(ethylene terephthalate) (PET) biodegradation is crucial for developing innovative strategies to accelerate the breakdown of this persistent plastic. In this study, we employed all-atom molecular dynamics simulation to investigate the adsorption process of the LCC-ICCG cutinase enzyme onto the PET surface. Our results revealed that hydrophobic, π-π, and H bond interactions, specifically involving aliphatic, aromatic, and polar uncharged amino acids, were the primary driving forces for the adsorption of the cutinase enzyme onto PET. Additionally, we observed a negligible change in the enzyme's tertiary structure during the interaction with PET (RMSD = 1.35 Å), while its secondary structures remained remarkably stable. Quantitative analysis further demonstrated that there is about a 24% decrease in the number of enzyme-water hydrogen bonds upon adsorption onto the PET surface. The significance of this study lies in unraveling the molecular intricacies of the adsorption process, providing valuable insights into the initial steps of enzymatic PET degradation.
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Affiliation(s)
- Mehdi Sahihi
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Pierre Fayon
- CHU Clermont Ferrand, Clermont Auvergne INP, CNRS, ICCF, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Lionel Nauton
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Florent Goujon
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Julien Devémy
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Alain Dequidt
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Patrice Hauret
- Manufacture Francaise des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
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Gao L, Xu Z, Zhou J. Simulation Study of Polyethylene Terephthalate Hydrolase Adsorption on Self-Assembled Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7225-7233. [PMID: 38501967 DOI: 10.1021/acs.langmuir.4c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Polyethylene terephthalate (PET) hydrolase, discovered in Ideonella sakaiensis (IsPETase), is a promising agent for the biodegradation of PET under mild reaction conditions, yet the thermal stability is poor. The efficient immobilization and orientation of IsPETase on different solid substrates are essential for its application. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of IsPETase adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (SCDs). The results show that the protein adsorption orientation was determined not only by attraction interactions but also by repulsion interactions. IsPETase is adsorbed on the COOH-SAM surface with an "end-on" orientation, which favors the exposure of the catalyzed triplet to the solution. In addition, the entrance to the catalytic active center is larger on the COOH-SAM surface with a low SCD. This work reveals the controlled orientation and conformational information on IsPETase on charged surfaces at the atomistic level. This study would certainly promote our understanding of the mechanism of IsPETase adsorption and provide theoretical support for the design of substrates for IsPETase immobilization.
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Affiliation(s)
- Lijian Gao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Zhiyong Xu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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Barati F, Hosseini F, Vafaee R, Sabouri Z, Ghadam P, Arab SS, Shadfar N, Piroozmand F. In silico approaches to investigate enzyme immobilization: a comprehensive systematic review. Phys Chem Chem Phys 2024; 26:5744-5761. [PMID: 38294035 DOI: 10.1039/d3cp03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.
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Affiliation(s)
- Farzaneh Barati
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Fakhrisadat Hosseini
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Rayeheh Vafaee
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Sabouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Parinaz Ghadam
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Najmeh Shadfar
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Firoozeh Piroozmand
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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Kato T, Uchida J, Ishii Y, Watanabe G. Aquatic Functional Liquid Crystals: Design, Functionalization, and Molecular Simulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306529. [PMID: 38126650 PMCID: PMC10885670 DOI: 10.1002/advs.202306529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Aquatic functional liquid crystals, which are ordered molecular assemblies that work in water environment, are described in this review. Aquatic functional liquid crystals are liquid-crystalline (LC) materials interacting water molecules or aquatic environment. They include aquatic lyotropic liquid crystals and LC based materials that have aquatic interfaces, for example, nanoporous water treatment membranes that are solids preserving LC order. They can remove ions and viruses with nano- and subnano-porous structures. Columnar, smectic, bicontinuous LC structures are used for fabrication of these 1D, 2D, 3D materials. Design and functionalization of aquatic LC sensors based on aqueous/LC interfaces are also described. The ordering transitions of liquid crystals induced by molecular recognition at the aqueous interfaces provide distinct optical responses. Molecular orientation and dynamic behavior of these aquatic functional LC materials are studied by molecular dynamics simulations. The molecular interactions of LC materials and water are key of these investigations. New insights into aquatic functional LC materials contribute to the fields of environment, healthcare, and biotechnology.
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Affiliation(s)
- Takashi Kato
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Research Initiative for Supra-Materials, Shinshu University, Nagano, 380-8553, Japan
| | - Junya Uchida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshiki Ishii
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, 252-0373, Japan
| | - Go Watanabe
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, 252-0373, Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC), Ebina, 243-0435, Japan
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Yu H, Qin L, Zhou J. Effect of Oil Polarity on the Protein Adsorption at Oil-Water Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:10701-10710. [PMID: 37470337 DOI: 10.1021/acs.langmuir.3c01541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Protein adsorption at oil-water interfaces has received much attention in applications of food emulsion and biocatalysis. The protein activity is influenced by the protein orientation and conformation. The oil polarity is expected to influence the orientation and conformation of adsorbed proteins by modulating intermolecular interactions. Hence, it is possible to tune the protein emulsion stability and activity by varying the oil polarity. Martini v3.0-based coarse-grained molecular dynamics (CGMD) simulations were employed to investigate the effect of oil polarity on the orientation and conformation of hydrophobin (HFBI) and Candida antarctica lipase B (CALB) adsorbed at triolein-water, hexadecane-water, and octanol-water interfaces for the first time. The protein adsorption orientation was predicted through the hydrophobic dipole, indicating that protein adsorption exists in preferred orientations at hydrophobic oil interfaces. The conformation of the adsorbed HFBI is well conserved, whereas relatively larger conformational changes occur during the CALB adsorption as the oil hydrophobicity increases. Comparisons on the adsorption interaction energy of proteins with oils confirm the relationship between the oil polarity and the interaction strength of proteins with oils. In addition, CGMD simulations allow longer time scale simulations of the behaviors of protein adsorption at oil-water interfaces.
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Affiliation(s)
- Hai Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Lanlan Qin
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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Bhattacharjee N, Alonso-Cotchico L, Lucas MF. Enzyme immobilization studied through molecular dynamic simulations. Front Bioeng Biotechnol 2023; 11:1200293. [PMID: 37362217 PMCID: PMC10285225 DOI: 10.3389/fbioe.2023.1200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.
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A combined computational and experimental approach predicts thrombin adsorption to zeolites. Colloids Surf B Biointerfaces 2023; 221:113007. [DOI: 10.1016/j.colsurfb.2022.113007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/08/2022]
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Xu Z, Yang S, Xie Y, Yu H, Zhou J. Modulating the adsorption orientation of methionine-rich laccase by tailoring the surface chemistry of single-walled carbon nanotubes. Colloids Surf B Biointerfaces 2022; 217:112660. [PMID: 35777167 DOI: 10.1016/j.colsurfb.2022.112660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022]
Abstract
Achieving fast electron transfer process between oxidoreductase and electrodes is pivotal for the biocathode of enzymatic biofuel cells (EBFCs). However, in-depth understanding of the interplay mechanism between enzymes and electrode materials remains challenging when designing and constructing EBFCs. Herein, atomic-scale insight into the direct electron transfer (DET) behavior of Thermus thermophilus laccase (TtLac) with a special methionine-rich β-hairpin motif adsorbed on the carboxyl-functionalized carbon nanotube (COOH-CNT) and amino-functionalized carbon nanotube (NH2-CNT) surfaces were disclosed by multi-scale molecular simulations. Simulation results reveal that electrostatic modification is an effective way to tune the DET behavior for TtLac on the modified-CNTs electrode surface. Surprisingly, the positively charged TtLac can be attracted by both negatively charged COOH-CNT and positively charged NH2-CNT surfaces, yet only the latter is capable to trigger the DET process due to the 'lying-on' adsorption orientation. Specifically, the T1 copper site is near the methionine-rich β-hairpin motif, which is the key binding site for TtLac binding onto the NH2-CNT surface via electrostatic interaction, π-π stacking and cation-π interaction. Moreover, TtLac on the NH2-CNT surface undergoes less conformational changes than those on the COOH-CNT surface, which allows the laccase stability and catalytic efficiency to be well preserved. These findings provide a fundamental guidance for future design and fabrication of methionine-rich laccase-based EBFCs with high power output and long lifespan.
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Affiliation(s)
- Zhiyong Xu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, PR China
| | - Shengjiang Yang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, PR China
| | - Yun Xie
- Guangdong Provincial Key Laboratory of Electronic Functional Materials and Devices, Huizhou University, Huizhou, PR China
| | - Hai Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, PR China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, PR China.
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Godoy CA, Pardo-Tamayo JS, Barbosa O. Microbial Lipases and Their Potential in the Production of Pharmaceutical Building Blocks. Int J Mol Sci 2022; 23:9933. [PMID: 36077332 PMCID: PMC9456414 DOI: 10.3390/ijms23179933] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Processes involving lipases in obtaining active pharmaceutical ingredients (APIs) are crucial to increase the sustainability of the industry. Despite their lower production cost, microbial lipases are striking for their versatile catalyzing reactions beyond their physiological role. In the context of taking advantage of microbial lipases in reactions for the synthesis of API building blocks, this review focuses on: (i) the structural origins of the catalytic properties of microbial lipases, including the results of techniques such as single particle monitoring (SPT) and the description of its selectivity beyond the Kazlauskas rule as the "Mirror-Image Packing" or the "Key Region(s) rule influencing enantioselectivity" (KRIE); (ii) immobilization methods given the conferred operative advantages in industrial applications and their modulating capacity of lipase properties; and (iii) a comprehensive description of microbial lipases use as a conventional or promiscuous catalyst in key reactions in the organic synthesis (Knoevenagel condensation, Morita-Baylis-Hillman (MBH) reactions, Markovnikov additions, Baeyer-Villiger oxidation, racemization, among others). Finally, this review will also focus on a research perspective necessary to increase microbial lipases application development towards a greener industry.
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Affiliation(s)
- César A. Godoy
- Laboratorio de Investigación en Biocatálisis y Biotransformaciones (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Departamento de Química, Universidad del Valle, Cali 76001, Colombia
| | - Juan S. Pardo-Tamayo
- Laboratorio de Investigación en Biocatálisis y Biotransformaciones (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Departamento de Química, Universidad del Valle, Cali 76001, Colombia
| | - Oveimar Barbosa
- Grupo de Investigación de Materiales Porosos (GIMPOAT), Departamento de Química, Universidad del Tolima, Ibague 730001, Colombia
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Zhang J, Wang Z, Zhuang W, Rabiee H, Zhu C, Deng J, Ge L, Ying H. Amphiphilic Nanointerface: Inducing the Interfacial Activation for Lipase. ACS APPLIED MATERIALS & INTERFACES 2022; 14:39622-39636. [PMID: 35980131 DOI: 10.1021/acsami.2c11500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Graphene-based materials are widely used in the field of immobilized enzymes due to their easily tunable interfacial properties. We designed amphiphilic nanobiological interfaces between graphene oxide (GO) and lipase TL (Thermomyces lanuginosus) with tunable reduction degrees through molecular dynamics simulations and a facile chemical modulation, thus revealing the optimal interface for the interfacial activation of lipase TL and addressing the weakness of lipase TL, which exhibits weak catalytic activity due to an inconspicuous active site lid. It was demonstrated that the reduced graphene oxide (rGO) after 4 h of ascorbic acid reduction could boost the relative enzyme activity of lipase TL to reach 208%, which was 48% higher than the pristine GO and 120% higher than the rGO after 48 h of reduction. Moreover, TL-GO-4 h's tolerance against heat, organic solvent, and long-term storage environment was higher than that of free TL. The drawbacks of strong hydrophobic nanomaterials on lipase production were explored in depth with the help of molecular dynamics simulations, which explained the mechanism of enzyme activity enhancement. We demonstrated that nanomaterials with certain hydrophilicity could facilitate the lipase to undergo interfacial activation and improve its stability and protein loading rate, displaying the potential of the extensive application.
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Affiliation(s)
- Jihang Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Zhaoxin Wang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Hesamoddin Rabiee
- Centre for Future Materials, University of Southern Queensland, Springfield, QLD 4300, Australia
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chenjie Zhu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jiawei Deng
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Lei Ge
- Centre for Future Materials, University of Southern Queensland, Springfield, QLD 4300, Australia
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
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Du J, Yang C, Ma X, Li Q. Insights into the conformation changes of SARS-CoV-2 spike receptor-binding domain on graphene. APPLIED SURFACE SCIENCE 2022; 578:151934. [PMID: 34866721 PMCID: PMC8627288 DOI: 10.1016/j.apsusc.2021.151934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/24/2021] [Accepted: 11/14/2021] [Indexed: 05/13/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread in the world, causing more than two million deaths and seriously threatening human life. Effective protection measures are important to prevent the infection and spreading of the virus. To explore the effects of graphene on the virus adsorption and its biological properties, the adsorption process of the receptor binding domain (RBD) of SARS-CoV-2 on graphene has been investigated by molecular dynamics simulations in this paper. The results show that RBD can be quickly adsorbed onto the surface of graphene due to π - π stacking and hydrophobic interactions. Residue PHE486 with benzene ring has stronger adsorption force and the maximum contact area with graphene. Graphene significantly affects the secondary structure of RBD area, especially on the three key sites of binding with human ACE2, GLY476, PHE486 and ASN487. The binding free energy of RBD and graphene shows that the adsorption is irreversible. Undoubtedly, these changes will inevitably affect the pathogenicity of the virus. Therefore, this study provides a theoretical basis for the application of graphene in the protection of SARS-CoV-2, and also provides a reference for the potential application of graphene in the biomedical field.
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Affiliation(s)
- Jianbin Du
- College of Science, Langfang Normal University, Langfang 065000, China
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Chunmei Yang
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xiangyun Ma
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Qifeng Li
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
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Wang J, Dong H, Leng T, Yu Y, Li Y. Turning the structure of the Aβ 42 peptide by different functionalized carbon nanotubes: a molecular dynamics simulation study. Phys Chem Chem Phys 2022; 24:4270-4279. [PMID: 35107452 DOI: 10.1039/d1cp04278e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functionalized carbon nanotubes (CNTs) can inhibit the self-assembly of amyloid-beta (Aβ) peptides. Under abnormal conditions, the structure of the Aβ peptides undergoes a fundamental transformation, and this transformation will induce conformational conversions of other polymerized Aβ peptides. Here, we explore the interactions between different functionalized CNTs and Aβ42 peptides by molecular dynamics simulations. Our results show that compared to the original CNTs, the highly functionalized CNTs induce different adsorption patterns of the peptides. This adsorption pattern destroys the α-helix structure and increases the β-turn and random coil content significantly. The hydrogen bonds formed by the peptide and water molecules or CNTs further reveal the reasons for the structural transformation of the peptide. Due to electrostatic interactions and π-π stacking interactions, some amino acids (such as Phe4, Lys16, Phe20, and Lys28) are tightly fixed on the surfaces, and other amino acids move around these amino acids to accelerate the unfolding and denaturation of the peptide. Our research shows that functionalized CNTs have excellent potential to inhibit the abnormal aggregation of Aβ42 peptides. Our research also provides theoretical guidance in the design and synthesis of carbon nanomedicines for protein conformation diseases.
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Affiliation(s)
- Jiawen Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China.
| | - Huilong Dong
- School of Materials Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Tianle Leng
- Dougherty Valley High School, 10550 Albion Rd, San Ramon, CA 94582, USA
| | - Yi Yu
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China.
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China. .,Macao Institute of Materials Science and Engineering, Macau University of Science and Technology, Taipa 999078, Macau SAR, China
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Simulating and Predicting Adsorption of Organic Pollutants onto Black Phosphorus Nanomaterials. NANOMATERIALS 2022; 12:nano12040590. [PMID: 35214919 PMCID: PMC8875661 DOI: 10.3390/nano12040590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 02/02/2023]
Abstract
Layered black phosphorus (BP) has exhibited exciting application prospects in diverse fields. Adsorption of organics onto BP may influence environmental behavior and toxicities of both organic pollutants and BP nanomaterials. However, contributions of various intermolecular interactions to the adsorption remain unclear, and values of adsorption parameters such as adsorption energies (Ead) and adsorption equilibrium constants (K) are lacking. Herein, molecular dynamic (MD) and density functional theory (DFT) was adopted to calculate Ead and K values. The calculated Ead and K values for organics adsorbed onto graphene were compared with experimental ones, so as to confirm the reliability of the calculation methods. Polyparameter linear free energy relationship (pp-LFER) models on Ead and logK were developed to estimate contributions of different intermolecular interactions to the adsorption. The adsorption in the gaseous phase was found to be more favorable than in the aqueous phase, as the adsorbates need to overcome cohesive energies of water molecules onto BP. The affinity of the aromatics to BP was comparable to that of graphene. The pp-LFER models performed well for predicting the Ead and K values, with external explained variance ranging from 0.90 to 0.97, and can serve as effective tools to rank adsorption capacities of organics onto BP.
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Yang S, Zhao D, Xu Z, Yu H, Zhou J. Molecular understanding of acetylcholinesterase adsorption on functionalized carbon nanotubes for enzymatic biosensors. Phys Chem Chem Phys 2022; 24:2866-2878. [PMID: 35060980 DOI: 10.1039/d1cp04997f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The immobilization of acetylcholinesterase on different nanomaterials has been widely used in the field of amperometric organophosphorus pesticide (OP) biosensors. However, the molecular adsorption mechanism of acetylcholinesterase on a nanomaterial's surface is still unclear. In this work, multiscale simulations were utilized to study the adsorption behavior of acetylcholinesterase from Torpedo californica (TcAChE) on amino-functionalized carbon nanotube (CNT) (NH2-CNT), carboxyl-functionalized CNT (COOH-CNT) and pristine CNT surfaces. The simulation results show that the active center and enzyme substrate tunnel of TcAChE are both close to and oriented toward the surface when adsorbed on the positively charged NH2-CNT, which is beneficial to the direct electron transfer (DET) and accessibility of the substrate molecule. Meanwhile, the NH2-CNT can also reduce the tunnel cost of the enzyme substrate of TcAChE, thereby further accelerating the transfer rate of the substrate from the surface or solution to the active center. However, for the cases of TcAChE adsorbed on COOH-CNT and pristine CNT, the active center and substrate tunnel are far away from the surface and face toward the solution, which is disadvantageous for the DET and transportation of enzyme substrate. These results indicate that NH2-CNT is more suitable for the immobilization of TcAChE. This work provides a better molecular understanding of the adsorption mechanism of TcAChE on functionalized CNT, and also provides theoretical guidance for the ordered immobilization of TcAChE and the design, development and improvement of TcAChE-OPs biosensors based on functionalized carbon nanomaterials.
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Affiliation(s)
- Shengjiang Yang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
| | - Daohui Zhao
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P. R. China
| | - Zhiyong Xu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
| | - Hai Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
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15
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Wang S, Ou X, Yi M, Li J. Spontaneous desorption of protein from self-assembled monolayer (SAM)-coated gold nanoparticles induced by high temperature. Phys Chem Chem Phys 2022; 24:2363-2370. [PMID: 35018922 DOI: 10.1039/d1cp04000f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nonspecific binding of proteins with nanomaterials (NMs) is a dynamic reversible process including both protein adsorption and desorption parts, which is crucial for controlled release of protein drug loaded by nanocarriers. The nonspecific binding of proteins is susceptible to high temperature, whereas its underlying mechanism still remains elusive. Here, the binding behavior of human serum albumin (HSA) with an amino-terminated self-assembled monolayer (SAM)-coated gold (111) surface was investigated by using molecular dynamics (MD) simulations. HSA binds to the SAM surface through salt bridges at 300 K. As the temperature increases to 350 K, HSA maintains its native structure, while the salt bridges largely diminish owing to the considerable lateral diffusion of HSA on the SAM. Moreover, the interfacial water located between HSA and the SAM gets increased and prevents the reformation of the salt bridges of HSA with the SAM, which reduces the binding affinity of HSA. And HSA eventually desorbs from the SAM. The depiction of thermally induced spontaneous protein desorption enriches our understanding of reversible binding behavior of protein with NMs, and may provide new insights into the controlled release of protein drugs delivered by using nanocarriers under the regulation of high temperature.
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Affiliation(s)
- Shuai Wang
- College of informatics, Huazhong Agricultural University, Wuhan 430070, China.,Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Xinwen Ou
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China.
| | - Jingyuan Li
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
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16
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Wang J, Yu Y, Leng T, Li Y, Lee ST. The Inhibition of SARS-CoV-2 3CL M pro by Graphene and Its Derivatives from Molecular Dynamics Simulations. ACS APPLIED MATERIALS & INTERFACES 2022; 14:191-200. [PMID: 34933561 PMCID: PMC8713398 DOI: 10.1021/acsami.1c18104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
At present, the most powerful new drugs for COVID-19 are antibody proteins. In addition, there are some star small molecule drugs. However, there are few studies on nanomaterials. Here, we study the intact graphene (IG), defective graphene (DG), and graphene oxide (GO) interacting with COVID-19 protein. We find that they show progressive inhibition of COVID-19 protein. By using molecular dynamics simulations, we study the interactions between SARS-CoV-2 3CL Mpro and graphene-related materials (GRMs): IG, DG, and GO. The results show that Mpro can be absorbed onto the surfaces of investigated materials. DG and GO interacted with Mpro more intensely, causing the decisive part of Mpro to become more flexible. Further analysis shows that compared to IG and GO, DG can inactivate Mpro and inhibit its expression effectively by destroying the active pocket of Mpro. Our work not only provides detailed and reliable theoretical guidance for the application of GRMs in treating with SARS-CoV-2 but also helps in developing new graphene-based anti-COVID-19 materials.
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Affiliation(s)
- Jiawen Wang
- Institute of Functional Nano & Soft Materials
(FUNSOM), Soochow University, Suzhou, Jiangsu 215123,
China
| | - Yi Yu
- Institute of Functional Nano & Soft Materials
(FUNSOM), Soochow University, Suzhou, Jiangsu 215123,
China
| | - Tianle Leng
- Dougherty Valley High School,
10550 Albion Rd, San Ramon, California 94582, United States
| | - Youyong Li
- Institute of Functional Nano & Soft Materials
(FUNSOM), Soochow University, Suzhou, Jiangsu 215123,
China
- Macao Institute of Materials Science and Engineering,
Macau University of Science and Technology, Taipa, 999078
Macau, SAR, China
| | - Shuit-Tong Lee
- Institute of Functional Nano & Soft Materials
(FUNSOM), Soochow University, Suzhou, Jiangsu 215123,
China
- Macao Institute of Materials Science and Engineering,
Macau University of Science and Technology, Taipa, 999078
Macau, SAR, China
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17
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Gao F. Adsorption of Mussel Protein on Polymer Antifouling Membranes: A Molecular Dynamics Study. Molecules 2021; 26:5660. [PMID: 34577131 PMCID: PMC8468479 DOI: 10.3390/molecules26185660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Biofouling is one of the most difficult problems in the field of marine engineering. In this work, molecular dynamics simulation was used to study the adsorption process of mussel protein on the surface of two antifouling films-hydrophilic film and hydrophobic film-trying to reveal the mechanism of protein adsorption and the antifouling mechanism of materials at the molecular level. The simulated conclusion is helpful to design and find new antifouling coatings for the experiments in the future.
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Affiliation(s)
- Fengfeng Gao
- Department of Chemical Engineering, Zibo Vocational Institute, Zibo 255300, China
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18
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Morshed MN, Behary N, Bouazizi N, Guan J, Nierstrasz VA. An overview on biocatalysts immobilization on textiles: Preparation, progress and application in wastewater treatment. CHEMOSPHERE 2021; 279:130481. [PMID: 33894516 DOI: 10.1016/j.chemosphere.2021.130481] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/27/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
The immobilization of biocatalysts or other bioactive components often means their transformation from a soluble to an insoluble state by attaching them to a solid support material. Various types of fibrous textiles from both natural and synthetic sources have been studied as suitable support material for biocatalysts immobilization. Strength, inexpensiveness, high surface area, high porosity, pore size, availability in various forms, and simple preparation/functionalization techniques have made textiles a primary choice for various applications. This led to the concept of a new domain called-biocatalysts immobilization on textiles. By addressing the growing advancement in biocatalysts immobilization on textile, this study provides the first detailed overview on this topic based on the terms of preparation, progress, and application in wastewater treatment. The fundamental reason behind the necessity of biocatalysts immobilized textile as well as the potential preparation methods has been identified and discussed. The overall progress and performances of biocatalysts immobilized textile have been scrutinized and summarized based on the form of textile, catalytic activity, and various influencing factors. This review also highlighted the potential challenges and future considerations that can enhance the pervasive use of such immobilized biocatalysts in various sustainable and green chemistry applications.
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Affiliation(s)
- Mohammad Neaz Morshed
- Department of Textile Technology, The Swedish School of Textiles, Faculty of Textiles, Engineering and Business, University of Borås, SE-50190, Borås, Sweden; Ecole Nationale Supérieure des Arts et Industries Textiles (ENSAIT), GEMTEX Laboratory, 2 allée Louise et Victor Champier BP 30329, 59056, Roubaix, France; Université de Lille, Nord de France, F-59000, Lille, France; College of Textile and Clothing Engineering, Soochow University, 215006, Suzhou, China.
| | - Nemeshwaree Behary
- Ecole Nationale Supérieure des Arts et Industries Textiles (ENSAIT), GEMTEX Laboratory, 2 allée Louise et Victor Champier BP 30329, 59056, Roubaix, France; Université de Lille, Nord de France, F-59000, Lille, France.
| | - Nabil Bouazizi
- Ecole Nationale Supérieure des Arts et Industries Textiles (ENSAIT), GEMTEX Laboratory, 2 allée Louise et Victor Champier BP 30329, 59056, Roubaix, France; Université de Lille, Nord de France, F-59000, Lille, France.
| | - Jinping Guan
- College of Textile and Clothing Engineering, Soochow University, 215006, Suzhou, China.
| | - Vincent A Nierstrasz
- Department of Textile Technology, The Swedish School of Textiles, Faculty of Textiles, Engineering and Business, University of Borås, SE-50190, Borås, Sweden.
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19
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Jiaojiao X, Bin Z, Ruoyu Z, Onyinye AI. Lipase nanogel catalyzed synthesis of vitamin E succinate in non-aqueous phase. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:3186-3192. [PMID: 33216351 DOI: 10.1002/jsfa.10947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/21/2020] [Accepted: 11/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND In order to improve the stability of vitamin E and broaden its scope of application, an effective solution is to convert vitamin E into its derivatives. This work developed a new Candida rugosa lipase (CRL) nanogel based on modification of ionic liquid with vinyl functional groups. This novel CRL nanogel was used in the preparation process of vitamin E succinate based on the principle of non-aqueous enzymology. At the same time, various factors including enzyme concentration, substrate molar ratio, reaction temperature and reaction time, that affect the yield of vitamin E succinate were optimized and analyzed. RESULTS Different solvents with various hydrophobicity parameters (LogP values) from -1.3 to 3.5 were studied, it was found that dimethyl sulfoxide (DMSO) had the lowest LogP value among organic solvents but vitamin E succinate had the highest yield in DMSO. Furthermore, the effect of different operating conditions, such as molar ratios of substrate, enzyme concentration, reaction temperature and reaction time was studied. Under the optimal process conditions (enzyme concentration 6 mg mL-1 , substrate molar ratio 4:1, reaction temperature 55 °C and reaction time 15 h), the product yield was 62.58 ± 1.16%. CRL and CRL nanogel were characterized using Fourier-transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM). It was shown that CRL nanogel influenced the catalytic behavior of lipase significantly by changing the structure and surface properties of CRL. CONCLUSION Novel lipase nanogel was an excellent biocatalyst for enzymatic synthesis of vitamin E succinate. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Xia Jiaojiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Zou Bin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Zhou Ruoyu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Adesanya I Onyinye
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
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20
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Zhao D, Huang C, Quan X, Li L, Wang Y, Zhou J. Lysozyme Adsorption on Different Functionalized MXenes: A Multiscale Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5932-5942. [PMID: 33961443 DOI: 10.1021/acs.langmuir.1c00480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, MXenes, due to their abundant advantages, have been widely applied in energy storage, separation, catalysis, biosensing, et al. In this study, parallel tempering Monte Carlo and molecular dynamics methods were performed to investigate lysozyme adsorption on different functionalized Ti3C2Tx (-O, -OH, and -F). The simulation results show that lysozyme can adsorb effectively on Ti3C2Tx surfaces, and the order of interaction strength is Ti3C2O2 > Ti3C2F2 > Ti3C2(OH)2. Electrostatics together with van der Waals interactions control protein adsorption. The orientation distributions of lysozyme adsorbed on the Ti3C2O2 and Ti3C2F2 surfaces are more concentrated than that on the Ti3C2(OH)2 surface. During adsorption, the conformation of lysozyme remains stable, suggesting the good biocompatibility of Ti3C2Tx. Besides, the distribution of the interfacial water layer on the Ti3C2Tx surface has a certain impact on protein adsorption. This study provides theoretical insights for understanding the biocompatibility of 2D Ti3C2Tx materials and may help us evaluate the engineering of their surfaces for future biorelated applications.
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Affiliation(s)
- Daohui Zhao
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Chu Huang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Libo Li
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yuqing Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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21
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Xu Z, He Z, Quan X, Sun D, Miao Z, Yu H, Yang S, Chen Z, Zeng J, Zhou J. Molecular simulations of charged complex fluids: A review. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Saeedimasine M, Brandt EG, Lyubartsev AP. Atomistic Perspective on Biomolecular Adsorption on Functionalized Carbon Nanomaterials under Ambient Conditions. J Phys Chem B 2021; 125:416-430. [PMID: 33373230 PMCID: PMC7871326 DOI: 10.1021/acs.jpcb.0c08622] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/03/2020] [Indexed: 01/23/2023]
Abstract
The use of carbon-based nanomaterials is tremendously increasing in various areas of technological, bioengineering, and biomedical applications. The functionality of carbon-based nanomaterials can be further broadened via chemical functionalization of carbon nanomaterial surfaces. On the other hand, concern is rising on possible adverse effects when nanomaterials are taken up by biological organisms. In order to contribute into understanding of interactions of carbon-based nanomaterials with biological matter, we have investigated adsorption of small biomolecules on nanomaterials using enhanced sampling molecular dynamics. The biomolecules included amino acid side chain analogues, fragments of lipids, and sugar monomers. The adsorption behavior on unstructured amorphous carbon, pristine graphene and its derivatives (such as few-layer graphene, graphene oxide, and reduced graphene oxide) as well as pristine carbon nanotubes, and those functionalized with OH-, COOH-, COO-, NH2-, and NH3+ groups was investigated with respect to surface concentration. An adsorption profile, that is, the free energy as a function of distance from the nanomaterial surfaces, was determined for each molecule and surface using the Metadynamics approach. The results were analyzed in terms of chemical specificity, surface charge, and surface concentration. It was shown that although morphology of the nanomaterial has a limited effect on the adsorption properties, functionalization of the surface by various molecular groups can drastically change the adsorption behavior that can be used in the design of nanosurfaces with highly selective adsorption properties and safe for human health and environment.
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Affiliation(s)
- Marzieh Saeedimasine
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Erik G. Brandt
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm 10691, Sweden
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23
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Zhao D, Wang Y, Su Q, Li L, Zhou J. Lysozyme Adsorption on Porous Organic Cages: A Molecular Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12299-12308. [PMID: 32988201 DOI: 10.1021/acs.langmuir.0c02233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Recently, porous organic cages (POCs) have emerged as a novel porous material with many merits and are widely utilized in many application fields. In this work, for the first time, molecular dynamics simulations were performed to investigate the mechanism of lysozyme adsorption onto the CC3 crystal, a kind of widely studied POC material. The simulation results show that lysozyme adsorbs onto the surface of CC3 with "top end-on," "back-on," or "side-on" orientations. It is found that the van der Waals interaction is the primary contribution to the binding; the conformation of the lysozyme is well preserved during the adsorption process. This provides some evidence for its biocompatibility and feasibility in biorelated applications. Arginine plays an important role in mediating the adsorption through nonpolar aliphatic chains. More importantly, the distribution and structure of the water layer on the POC surface has a significant impact on adsorption. This study provides insights into the development of POC materials with defined morphologies for the adsorption of biomolecules and may help the rational design of biorelated systems.
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Affiliation(s)
- Daohui Zhao
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yuqing Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Qianwen Su
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Libo Li
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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24
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Watanabe G, Eimura H, Abbott NL, Kato T. Biomolecular Binding at Aqueous Interfaces of Langmuir Monolayers of Bioconjugated Amphiphilic Mesogenic Molecules: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12281-12287. [PMID: 32970447 DOI: 10.1021/acs.langmuir.0c02191] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We report a molecular dynamics (MD) simulation study of protein binding at the aqueous-liquid crystal (LC) interfaces of bioconjugated mesogenic molecules. As a simple model of these interfaces, we use monolayers composed of biotin-conjugated or biotin-free amphiphilic mesogenic molecules and streptavidin in water. The all-atom MD simulations reveal that the binding of streptavidin to the biotin mesogenic monolayer is significantly stronger than that to biotin-free mesogenic monolayers. Although specific protein binding marginally increases the overall orientational order and the tilt of the biotin-conjugated mesogenic molecules of the monolayer, significant changes in tilt were observed near the bound protein (in contrast to the protein interaction with the monolayer without biotin). We also observe that specific protein binding changes the dynamic properties of the mesogens within the monolayer (e.g., lateral diffusion coefficients) and associated water. Overall, these MD simulations advance our understanding of the molecular-level phenomena involved in the binding of biomolecules and subsequent dynamic changes at the aqueous-LC interfaces. These results provide guidance to future molecular-level designs of biofunctional LC interfaces.
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Affiliation(s)
- Go Watanabe
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Hiroki Eimura
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Nicholas L Abbott
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Takashi Kato
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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25
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Cerofolini L, Fragai M, Luchinat C, Ravera E. Orientation of immobilized antigens on common surfaces by a simple computational model: Exposition of SARS-CoV-2 Spike protein RBD epitopes. Biophys Chem 2020; 265:106441. [PMID: 32745829 PMCID: PMC7387289 DOI: 10.1016/j.bpc.2020.106441] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
The possibility of immobilizing a protein with antigenic properties on a solid support offers significant possibilities in the development of immunosensors and vaccine formulations. For both applications, the orientation of the antigen should ensure ready accessibility of the antibodies to the epitope. However, an experimental assessment of the orientational preferences necessarily proceeds through the preparation/isolation of the antigen, the immobilization on different surfaces and one or more biophysical characterization steps. To predict a priori whether favorable orientations can be achieved or not would allow one to select the most promising experimental routes, partly mitigating the time cost towards the final product. In this manuscript, we apply a simple computational model, based on united-residue modelling, to the prediction of the orientation of the receptor binding domain of the SARS-CoV-2 spike protein on surfaces commonly used in lateral-flow devices. These calculations can account for the experimental observation that direct immobilization on gold gives sufficient exposure of the epitope to obtain a response in immunochemical assays.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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26
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Chronopoulou L, Scaramuzzo FA, Fioravanti R, di Nitto A, Cerra S, Palocci C, Fratoddi I. Noble metal nanoparticle-based networks as a new platform for lipase immobilization. Int J Biol Macromol 2020; 146:790-797. [DOI: 10.1016/j.ijbiomac.2019.10.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/24/2019] [Accepted: 10/04/2019] [Indexed: 01/29/2023]
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27
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Yang S, Liu J, Zheng H, Zhong J, Zhou J. Simulated revelation of the adsorption behaviours of acetylcholinesterase on charged self-assembled monolayers. NANOSCALE 2020; 12:3701-3714. [PMID: 32022070 DOI: 10.1039/c9nr10123c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An acetylcholinesterase (AChE)-based electrochemical biosensor, as a promising alternative to detect organophosphates (OPs) and carbamate pesticides, has gained considerable attention in recent years, due to the advantages of simplicity, rapidity, reliability and low cost. The bio-activity of AChE immobilized on the surface and the direct electron transfer (DET) rate between an enzyme and an electrode directly determined the analytical performances of the AChE-based biosensor, and experimental studies have shown that the charged surfaces have a strong impact on the detectability of the AChE-based biosensor. Therefore, it is very important to reveal the behaviour of AChE in bulk solution and on charged surfaces at the molecular level. In this work, the adsorption orientation and conformation of AChE from Torpedo californica (TcAChE) on oppositely charged self-assembled monolayers (SAMs), COOH-SAM and NH2-SAM with different surface charge densities, were investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics simulations (AAMD). Simulation results show that TcAChE could spontaneously and stably adsorb on two oppositely charged surfaces by the synergy of an electric dipole and charged residue patch, and opposite orientations were observed. The active-site gorge of TcAChE is oriented toward the surface with the "end-on" orientation and the active sites are close to the surface when it is adsorbed on the positively charged surface and the tunnel cost for the substrate is lower than that on the negatively charged surface and in bulk solution, while for TcAChE adsorbed on the negatively charged surface, the active site of TcAChE is far away from the surface and the active-site gorge is oriented toward the solution with a "back-on" orientation. It suggests that the positively charged surface could provide a better microenvironment for the efficient bio-catalytic reaction and quick DET between TcAChE and the electrode surface. Moreover, the RMSD, RMSF, dipole moment, gyration radius, eccentricity and superimposed structures show that only a slight conformational change occurred on the relatively flexible structure of TcAChE during simulations, and the native conformation is well preserved after adsorption. This work helps us better comprehend the adsorption mechanism of TcAChE on charged surfaces and might provide some guidelines for the development of new TcAChE-based amperometric biosensors for the detection of organophosphorus pesticides.
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Affiliation(s)
- Shengjiang Yang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
| | - Jie Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, P. R. China
| | - He Zheng
- State Key Laboratory of NBC Protection for Civilian, Research Institute of Chemical Defense, Academy of Military Science, Beijing 102205, P. R. China
| | - Jinyi Zhong
- State Key Laboratory of NBC Protection for Civilian, Research Institute of Chemical Defense, Academy of Military Science, Beijing 102205, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.
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Dong L, Lv M, Gao X, Zhang L, Rogers M, Cao Y, Lan Y. In vitrogastrointestinal digestibility of phytosterol oleogels: influence of self-assembled microstructures on emulsification efficiency and lipase activity. Food Funct 2020; 11:9503-9513. [DOI: 10.1039/d0fo01642j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The objective of this study was to investigate the influence of a self-assembled microstructure on lipid digestibility of phytosterol (γ-oryzanol and β-sitosterol) oleogels, including the oil emulsification process and further lipolysis.
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Affiliation(s)
- Lulu Dong
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods
- College of Food Sciences
- South China Agricultural University
- Guangzhou
- P.R. China
| | - Muwen Lv
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods
- College of Food Sciences
- South China Agricultural University
- Guangzhou
- P.R. China
| | - Xiangyang Gao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods
- College of Food Sciences
- South China Agricultural University
- Guangzhou
- P.R. China
| | - Luping Zhang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods
- College of Food Sciences
- South China Agricultural University
- Guangzhou
- P.R. China
| | - Michael Rogers
- Department of Food Science
- University of Guelph
- Guelph
- Canada
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods
- College of Food Sciences
- South China Agricultural University
- Guangzhou
- P.R. China
| | - Yaqi Lan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods
- College of Food Sciences
- South China Agricultural University
- Guangzhou
- P.R. China
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30
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Molecular simulation of protein adsorption and conformation at gas-liquid, liquid–liquid and solid–liquid interfaces. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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Zhou W, Zhuang W, Ge L, Wang Z, Wu J, Niu H, Liu D, Zhu C, Chen Y, Ying H. Surface functionalization of graphene oxide by amino acids for Thermomyces lanuginosus lipase adsorption. J Colloid Interface Sci 2019; 546:211-220. [DOI: 10.1016/j.jcis.2019.03.066] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 12/13/2022]
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32
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Quan X, Liu J, Zhou J. Multiscale modeling and simulations of protein adsorption: progresses and perspectives. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Habibzadeh Mashatooki M, Rastkar Ebrahimzadeh A, Jahanbin Sardroodi J, Abbasi A. Investigation of TiO2 anatase (1 0 1), (1 0 0) and (1 1 0) facets as immobilizer for a potential anticancer RNA aptamer: a classical molecular dynamics simulation. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1605601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mohaddeseh Habibzadeh Mashatooki
- Molecular Simulation laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran
- Computational Nanomaterials Research Group (CNRG), Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Simulation laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran
- Computational Nanomaterials Research Group (CNRG), Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Physics, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran
- Computational Nanomaterials Research Group (CNRG), Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Amirali Abbasi
- Molecular Simulation laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran
- Computational Nanomaterials Research Group (CNRG), Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
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Park C, Lee SW, Kim J, Song EH, Jung HD, Park JU, Kim HE, Kim S, Jang TS. Reduced fibrous capsule formation at nano-engineered silicone surfaces via tantalum ion implantation. Biomater Sci 2019; 7:2907-2919. [DOI: 10.1039/c9bm00427k] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nano-engineered surface of silicone implant improves the biocompatibility and suppresses the fibrous capsule formation which is the most common side effect of polymeric implants.
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Affiliation(s)
- Cheonil Park
- Department of Materials Science and Engineering
- Seoul National University
- Seoul
- Korea
| | - Si-Woo Lee
- Department of Plastic and Reconstructive Surgery
- Seoul National University College of Medicine
- Seoul
- Korea
| | - Jinyoung Kim
- Department of Materials Science and Engineering
- Seoul National University
- Seoul
- Korea
| | - Eun-Ho Song
- Department of Materials Science and Engineering
- Seoul National University
- Seoul
- Korea
| | - Hyun-Do Jung
- Research Institute of Advanced Manufacturing Technology
- Korea Institute of Industrial Technology
- Incheon
- Korea
| | - Ji-Ung Park
- Department of Plastic and Reconstructive Surgery
- Seoul National University Boramae Medical Center
- Seoul
- Korea
| | - Hyoun-Ee Kim
- Department of Materials Science and Engineering
- Seoul National University
- Seoul
- Korea
| | - Sukwha Kim
- Department of Plastic and Reconstructive Surgery
- Seoul National University College of Medicine
- Seoul
- Korea
| | - Tae-Sik Jang
- Research Institute of Advanced Manufacturing Technology
- Korea Institute of Industrial Technology
- Incheon
- Korea
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Luo M, Gao Y, Yang S, Quan X, Sun D, Liang K, Li J, Zhou J. Computer simulations of the adsorption of an N-terminal peptide of statherin, SN15, and its mutants on hydroxyapatite surfaces. Phys Chem Chem Phys 2019; 21:9342-9351. [PMID: 30994664 DOI: 10.1039/c9cp01638d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Salt-bridge adsorption of the SN15 peptide and its mutants on the HAP(001) surface.
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Affiliation(s)
- Muzhong Luo
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangdong 510640
- People's Republic of China
| | - Yuan Gao
- State Key Laboratory of Oral Diseases
- West China Hospital of Stomatology
- Sichuan University
- Chengdu 610041
- China
| | - Shengjiang Yang
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangdong 510640
- People's Republic of China
| | - Xuebo Quan
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangdong 510640
- People's Republic of China
| | - Delin Sun
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangdong 510640
- People's Republic of China
| | - Kunneng Liang
- State Key Laboratory of Oral Diseases
- West China Hospital of Stomatology
- Sichuan University
- Chengdu 610041
- China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases
- West China Hospital of Stomatology
- Sichuan University
- Chengdu 610041
- China
| | - Jian Zhou
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangdong 510640
- People's Republic of China
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Arana-Peña S, Lokha Y, Fernández-Lafuente R. Immobilization on octyl-agarose beads and some catalytic features of commercial preparations of lipase a from Candida antarctica (Novocor ADL): Comparison with immobilized lipase B from Candida antarctica. Biotechnol Prog 2018; 35:e2735. [PMID: 30341806 DOI: 10.1002/btpr.2735] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/16/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022]
Abstract
Lipase A from Candida antarctica (CALA, commercialized as Novocor ADL) was immobilized on octyl-agarose, which is a very useful support for lipase immobilization, and coated with polyethylenimine to improve the stability. The performance was compared to that of the form B of the enzyme (CALB) immobilized on the same support, as both enzymes are among the most popular ones used in biocatalysis. CALA immobilization produced a significant increase in enzyme activity vs. p-nitrophenyl butyrate (pNPB) (by a factor of seven), and the coating with PEI did not have a significant effect on enzyme activity. CALB reduced its activity slightly after enzyme immobilization. Octyl-CALA was less stable than octyl-CALB at pH 9 and more stable at pH 5 and, more clearly, at pH 7. PEI coating only increased octyl-CALA stability at pH 9. In organic solvents, CALB had much better stability in methanol and was similarly stable in acetonitrile or dioxane. In these systems, the PEI coating of octyl-CALA permitted some stabilization. While octyl-CALA was more active vs. pNPB, octyl-CALB was much more active vs. mandelic esters or triacetin. Thus, depending on the specific reaction and the conditions, CALA or CALB may offer different advantages and drawbacks. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2735, 2019.
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Affiliation(s)
- Sara Arana-Peña
- Dept. de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, Madrid, Spain
| | - Yuliya Lokha
- Dept. de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, Madrid, Spain
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37
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Yang S, Liu J, Quan X, Zhou J. Bilirubin Oxidase Adsorption onto Charged Self-Assembled Monolayers: Insights from Multiscale Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9818-9828. [PMID: 30044918 DOI: 10.1021/acs.langmuir.8b01974] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The efficient immobilization and orientation of bilirubin oxidase (BOx) on different solid substrates are essential for its application in biotechnology. The T1 copper site within BOx is responsible for the electron transfer. In order to obtain quick direct electron transfer (DET), it is important to keep the distance between the T1 copper site and electrode surface small and to maintain the natural structure of BOx at the same time. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of BOx from Myrothecium verrucaria (MvBOx) adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (±0.05 and ±0.19 C·m-2). The results show that MvBOx adsorbs on negatively charged surfaces with a "back-on" orientation, whereas on positively charged surfaces, MvBOx binds with a "lying-on" orientation. The locations of the T1 copper site are closer to negatively charged surfaces. Furthermore, for negatively charged surfaces, the T1 copper site prefers to orient closer to the surface with lower surface charge density. Therefore, the negatively charged surface with low surface charge density is more suitable for the DET of MvBOx on electrodes. Besides, the structural changes primarily take place on the relatively flexible turns, coils, and α-helix. The native structure of MvBOx is well preserved when it adsorbs on both charged surfaces. This work sheds light on the controlling orientation and conformational information on MvBOx on charged surfaces at the atomistic level. This understanding would certainly promote our understanding of the mechanism of MvBOx immobilization and provide theoretical support for BOx-based bioelectrode design.
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Affiliation(s)
- Shengjiang Yang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640 , P. R. China
| | - Jie Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology , Wuhan 430073 , P. R. China
| | - Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640 , P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640 , P. R. China
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38
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Faccio G. From Protein Features to Sensing Surfaces. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1204. [PMID: 29662030 PMCID: PMC5948494 DOI: 10.3390/s18041204] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/08/2018] [Accepted: 04/12/2018] [Indexed: 12/25/2022]
Abstract
Proteins play a major role in biosensors in which they provide catalytic activity and specificity in molecular recognition. However, the immobilization process is far from straightforward as it often affects the protein functionality. Extensive interaction of the protein with the surface or significant surface crowding can lead to changes in the mobility and conformation of the protein structure. This review will provide insights as to how an analysis of the physico-chemical features of the protein surface before the immobilization process can help to identify the optimal immobilization approach. Such an analysis can help to preserve the functionality of the protein when on a biosensor surface.
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Affiliation(s)
- Greta Faccio
- Independent Scientist, St. Gallen 9000, Switzerland.
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39
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Yu G, Zhou J. Understanding the curvature effect of silica nanoparticles on lysozyme adsorption orientation and conformation: a mesoscopic coarse-grained simulation study. Phys Chem Chem Phys 2018; 18:23500-7. [PMID: 27465065 DOI: 10.1039/c6cp01478j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In nanobiotechnology applications, curvature of nanoparticles has a significant effect on protein activities. In this work, lysozyme adsorption on different-sized silica nanoparticles (SNPs) was simulated at the microsecond timescale by using mesoscopic coarse-grained molecular dynamics simulations. It is found that, with the increase of nanoparticle size, which indicates a decrease of surface curvature, adsorbed lysozyme shows a narrower orientation distribution and a greater conformation change, as the electrostatic attraction dominates lysozyme adsorption, and this trend is more pronounced on larger SNPs. Interestingly, the effect induced by different SNP surface curvatures is not related to the direct contact area between lysozyme and SNPs, but to the interfacial hydration layer above the silica surface, since a smaller curvature can lead to a stronger interfacial hydration and make the distribution of interfacial water molecules more ordered. Besides, at higher ionic strength, lysozyme conformation is less affected by strongly negatively charged SNPs, especially for larger nanoparticles. This work might shed some light on how to prepare protein coronas with higher bioactivities in nanobiotechnology.
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Affiliation(s)
- Gaobo Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
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40
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Tian R, Luo M, Li J. Spontaneous protein desorption from self-assembled monolayer (SAM)-coated gold nanoparticles. Phys Chem Chem Phys 2018; 20:68-74. [DOI: 10.1039/c7cp05515c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Interfacial water molecules and lateral diffusion of protein reduce the adsorption affinity of protein and promote protein desorption.
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Affiliation(s)
- Ranran Tian
- Department of Physics
- Zhejiang University
- Hangzhou
- China
| | - Mengbo Luo
- Department of Physics
- Zhejiang University
- Hangzhou
- China
| | - Jingyuan Li
- Department of Physics
- Zhejiang University
- Hangzhou
- China
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41
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Liu J, Xie Y, Peng C, Yu G, Zhou J. Molecular Understanding of Laccase Adsorption on Charged Self-Assembled Monolayers. J Phys Chem B 2017; 121:10610-10617. [DOI: 10.1021/acs.jpcb.7b08738] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Liu
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
- Key
Laboratory for Green Chemical Process of Ministry of Education, School
of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, P. R. China
| | - Yun Xie
- Huizhou University, Huizhou 516007, P. R. China
| | - Chunwang Peng
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Gaobo Yu
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
- School
of Materials and Chemical Engineering, Hainan University, Haikou 570228, P. R. China
| | - Jian Zhou
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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43
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Lysozyme orientation and conformation on MoS 2 surface: Insights from molecular simulations. Biointerphases 2017; 12:02D416. [PMID: 28576080 DOI: 10.1116/1.4984803] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Two-dimensional molybdenum disulfide (MoS2) has attracted intense interest owing to its unique properties and promising biosensor applications. To develop effective biocompatible platforms, it is crucial to understand the interactions between MoS2 and biological molecules such as proteins, but little knowledge exists on the orientation and conformation of proteins on the MoS2 surface at the molecular level. In this work, the lysozyme adsorption on the MoS2 surface was studied by molecular dynamics simulations, wherein six different orientations were selected based on the different faces of lysozyme. Simulation results showed that lysozyme tends to adsorb on the MoS2 surface in an "end-on" orientation, indicating that orientations within this range are favorable for stable adsorption. The end-on orientation could be further categorized into "bottom end-on" and "top end-on" orientations. The driving forces responsible for the adsorption were dominated by van der Waals interactions and supplemented by electrostatic interactions. Further, the conformations of the lysozyme adsorbed on the MoS2 surface were basically preserved. This simulation study promotes the fundamental understanding of interactions between MoS2 and proteins and can guide the development of future biomedical applications of MoS2.
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44
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Shuai W, Das RK, Naghdi M, Brar SK, Verma M. A review on the important aspects of lipase immobilization on nanomaterials. Biotechnol Appl Biochem 2017; 64:496-508. [DOI: 10.1002/bab.1515] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/27/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Weitao Shuai
- College of Environmental Sciences and Engineering; Peking University; Beijing People's Republic of China
- INRS-ETE; Université du Québec; Québec Canada
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45
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Cheng G, Liao M, Zhao D, Zhou J. Molecular Understanding on the Underwater Oleophobicity of Self-Assembled Monolayers: Zwitterionic versus Nonionic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1732-1741. [PMID: 28122450 DOI: 10.1021/acs.langmuir.6b03988] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular dynamics simulations are conducted to investigate the underwater oleophobicity of self-assembled monolayers (SAMs) with different head groups. Simulation results show that the order of underwater oleophobicity of SAMs is methyl < amide < oligo(ethylene glycol) (OEG) < ethanolamine (ETA) < hydroxyl < mixed-charged zwitterionic. The underwater-oil contact angles (OCAs) are <133° for all nonionic hydrophilic SAMs, while the mixed-charged zwitterionic SAMs are underwater superoleophobic (OCA can reach 180°). It appears that surfaces with stronger underwater oleophobicity have better antifouling performance. Further study on the effect of different alkyl ammonium ions on mixed-charged SAMs reveals that the underwater OCAs are >143.6° for all SAMs; mixed-charged SAMs containing primary alkyl ammonium ion are likely to possess the best underwater oleophobicity for its strong hydration capacity. It seems that alkyl sulfonate anion (SO3-) is more hydrophilic than alkyl trimethylammonium ion (NC3+) for the hydrophobic methyl groups on nitrogen atoms and that the hydration of SO3- in mixed-charged SAMs can be seriously blocked by NC3+. The monomer of SO3- should be slightly longer than that of NC3+ to obtain better underwater oleophobicity in NC3+-/SO3--SAMs. In addition, the underwater oleophobicity of SAMs might become worse at low grafting densities. This work systematically proves that a zwitterionic surface is more underwater oleophobic than a nonionic surface. These results will help for the design and development of superoleophobic surfaces.
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Affiliation(s)
- Gang Cheng
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
| | - Mingrui Liao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
| | - Daohui Zhao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, China
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46
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Bohinc K, Reščič J, May S. Electrostatic adsorption and orientational order of inhomogeneously charged particles on flat surfaces. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.10.087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Hoarau M, Badieyan S, Marsh ENG. Immobilized enzymes: understanding enzyme – surface interactions at the molecular level. Org Biomol Chem 2017; 15:9539-9551. [DOI: 10.1039/c7ob01880k] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Interactions between immobilized enzymes and supporting surfaces are complex and context-dependent and can significantly alter enzyme structure, stability and activity.
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Affiliation(s)
- Marie Hoarau
- Department of Chemistry
- University of Michigan
- Ann Arbor
- USA
| | | | - E. Neil G. Marsh
- Department of Chemistry
- University of Michigan
- Ann Arbor
- USA
- Department of Biological Chemistry
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48
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Zhao D, Zhou J. Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes. Phys Chem Chem Phys 2017; 19:986-995. [DOI: 10.1039/c6cp04962a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes.
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Affiliation(s)
- Daohui Zhao
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
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49
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Chen CT, Dutta S, Wang ZY, Chen JE, Ahamad T, Alshehri SM, Yamauchi Y, Lee YF, Wu KCW. An unique approach of applying magnetic nanoparticles attached commercial lipase acrylic resin for biodiesel production. Catal Today 2016. [DOI: 10.1016/j.cattod.2015.12.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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50
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Yorulmaz S, Jackman JA, Hunziker W, Cho NJ. Influence of membrane surface charge on adsorption of complement proteins onto supported lipid bilayers. Colloids Surf B Biointerfaces 2016; 148:270-277. [DOI: 10.1016/j.colsurfb.2016.08.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/29/2016] [Accepted: 08/21/2016] [Indexed: 10/21/2022]
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