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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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Huang M, Luo Z, Zhang Q, Zeng Q, Sun B, Li H, Zhang P, Tang K. Encapsulation of lipase in zeolitic imidazolate framework-8 induced by polyethyleneimine to form a honeycomb structure with enhanced activity. Int J Biol Macromol 2024; 254:127787. [PMID: 37924919 DOI: 10.1016/j.ijbiomac.2023.127787] [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: 09/23/2023] [Revised: 10/21/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023]
Abstract
Embedding an enzyme in the metal-organic frameworks (MOFs) gives good protection to the fragile enzyme. However, this may also restrain the enzyme activity because of the decreased substrate accessibility. Encapsulation of lipase AK from Pseudomonas fluorescens for preparing the enzyme-MOF composite (AK@ZIF-8-PEI) was performed through a new strategy based on polyethyleneimine and enzyme induced in-situ growth of zeolitic imidazolate framework-8 (ZIF-8). Characterizations indicate that AK@ZIF-8-PEI has a honeycomb structure and the hierarchical porosity formed during the preparation, which provides adequate mass transfer channels for catalytic applications. Activity evaluation shows that specific activity of AK@ZIF-8-PEI is 8-fold than the commercial lipase powder. AK@ZIF-8-PEI is demonstrated as an efficient catalyst in kinetic resolution of α-naphthol enantiomers through enantioselective transesterification. Within 12 h, the conversion and substrate enantiomeric excess (ees) reaches 49.8 % and 96.4 %, achieving an improved resolution than previous researches.
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Affiliation(s)
- Meiai Huang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Zhuolin Luo
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Qian Zhang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Quan Zeng
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Bizhu Sun
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
| | - Hao Li
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China.
| | - Panliang Zhang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China.
| | - Kewen Tang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, Hunan, China
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3
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Li H, Pan Y, Li C, Yang Z, Rao J, Chen B. Lysozyme-phenolics bioconjugates with antioxidant and antibacterial bifunctionalities: Structural basis underlying the dual-function. Food Chem 2023; 406:135070. [PMID: 36462353 DOI: 10.1016/j.foodchem.2022.135070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/26/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
This work aims at adopting an Electron Paramagnetic Resonance (EPR) spectroscopic technique to help understanding protein-phenolic conjugation and final functionalities relationship as well as the underlying structural basis of antioxidant and antibacterial dual functionalities. Specifically, lysozyme (Lys) was conjugated with two natural phenolic acids, i.e. rosmarinic acid (RA) and gentisic acid (GA, our previous work) with obviously different molecular features. Lys-RA displayed 8.6- and 4.0-times enhanced antioxidant stoichiometry compared to the native Lys and ones with GA, respectively, due to the stronger antioxidant activity of RA. However, RA conjugation mitigated both enzymatic and antibacterial activities of Lys-RA conjugates. Such inhibition effect is attributed to the greater structural and surface property changes of Lys upon conjugating with RA. Furthermore, the polyphenol conjugation related structural basis of disturbance, reactivity and selectivity were explored via site-directed spin labeling (SDSL)-EPR. A dynamic picture of reactivity and selectivity of phenolics conjugation on Lys was proposed.
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Affiliation(s)
- Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, United States
| | - Chun Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, United States.
| | - Jiajia Rao
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States.
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Pan Y, Li Q, Liu W, Armstrong Z, MacRae A, Feng L, McNeff C, Zhao P, Li H, Yang Z. Unveiling the orientation and dynamics of enzymes in unstructured artificial compartments of metal-organic frameworks (MOFs). NANOSCALE 2023; 15:2573-2577. [PMID: 36655708 DOI: 10.1039/d2nr06659a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Confining enzymes in well-shaped MOF compartments is a promising approach to mimic the cellular environment of enzymes and determine enzyme structure-function relationship therein. Under the cellular crowding, however, enzymes can also be confined in unstructured spaces that are close to the shapes/outlines of the enzyme. Therefore, for a better understanding of enzymes in their physiological environments, it is necessary to study enzymes in these unstructured spaces. However, practically it is challenging to create compartments that are close to the outline of an enzyme and probe enzyme structural information therein. Here, for proof-of-principle, we confined a model enzyme, lysozyme, in the crystal defects of a MOF via co-crystallization, where lysozyme served as the nuclei for MOF crystal scaffolds to grow on so that unstructured spaces close to the outline of lysozyme are created, and determined enzyme relative orientation and dynamics. This effort is important for understanding enzymes in near-native environments and guiding the rational design of biocatalysts that mimic how nature confines enzymes.
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Affiliation(s)
- Yanxiong Pan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Wei Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| | - Zoe Armstrong
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Li Feng
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Charles McNeff
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Pinjing Zhao
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
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Li H, Pan Y, Lan Y, Yang Z, Rao J, Chen B. Molecular interaction mechanism and structure–activity relationships of protein–polyphenol complexes revealed by side-directed spin labeling-electron paramagnetic resonance (SDSL-EPR) spectroscopy. Food Chem 2023; 402:134354. [DOI: 10.1016/j.foodchem.2022.134354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/05/2022] [Accepted: 09/18/2022] [Indexed: 11/26/2022]
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Czarnecka J, Kwiatkowski M, Wiśniewski M, Roszek K. Protein Corona Hinders N-CQDs Oxidative Potential and Favors Their Application as Nanobiocatalytic System. Int J Mol Sci 2021; 22:ijms22158136. [PMID: 34360901 PMCID: PMC8347256 DOI: 10.3390/ijms22158136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023] Open
Abstract
The oxidative properties of nanomaterials arouse legitimate concerns about oxidative damage in biological systems. On the other hand, the undisputable benefits of nanomaterials promote them for biomedical applications; thus, the strategies to reduce oxidative potential are urgently needed. We aimed at analysis of nitrogen-containing carbon quantum dots (N-CQDs) in terms of their biocompatibility and internalization by different cells. Surprisingly, N-CQD uptake does not contribute to the increased oxidative stress inside cells and lacks cytotoxic influence even at high concentrations, primarily through protein corona formation. We proved experimentally that the protein coating effectively limits the oxidative capacity of N-CQDs. Thus, N-CQDs served as an immobilization support for three different enzymes with the potential to be used as therapeutics. Various kinetic parameters of immobilized enzymes were analyzed. Regardless of the enzyme structure and type of reaction catalyzed, adsorption on the nanocarrier resulted in increased catalytic efficiency. The enzymatic-protein-to-nanomaterial ratio is the pivotal factor determining the course of kinetic parameter changes that can be tailored for enzyme application. We conclude that the above properties of N-CQDs make them an ideal support for enzymatic drugs required for multiple biomedical applications, including personalized medical therapies.
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Affiliation(s)
- Joanna Czarnecka
- Department of Biochemistry, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Correspondence: (J.C.); (M.W.); (K.R.)
| | - Mateusz Kwiatkowski
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland;
| | - Marek Wiśniewski
- Physicochemistry of Carbon Materials Research Group, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Correspondence: (J.C.); (M.W.); (K.R.)
| | - Katarzyna Roszek
- Department of Biochemistry, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Correspondence: (J.C.); (M.W.); (K.R.)
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Pan Y, Li H, Li Q, Lenertz M, Schuster I, Jordahl D, Zhu X, Chen B, Yang Z. Protocol for resolving enzyme orientation and dynamics in advanced porous materials via SDSL-EPR. STAR Protoc 2021; 2:100676. [PMID: 34308381 PMCID: PMC8287244 DOI: 10.1016/j.xpro.2021.100676] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Enzyme encapsulation in metal-organic frameworks (MOFs)/covalent-organic frameworks (COFs) provides advancement in biocatalysis, yet the structural basis underlying the catalytic performance is challenging to probe. Here, we present an effective protocol to determine the orientation and dynamics of enzymes in MOFs/COFs using site-directed spin labeling and electron paramagnetic resonance spectroscopy. The protocol is demonstrated using lysozyme and can be generalized to other enzymes. For complete information on the generation and use of this protocol, please refer to Pan et al. (2021a). A protocol to resolve protein orientation/dynamics in porous materials is provided Site-directed spin labeling is combined with electron paramagnetic resonance Principles of protein labeling and key data acquisition steps are summarized Spectral simulation details with troubleshooting procedures are detailed
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Affiliation(s)
- Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Mary Lenertz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Isabelle Schuster
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Drew Jordahl
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Xiao Zhu
- Research Computing, Information Technology at Purdue (ITaP), Purdue University, West Lafayette, IN 47907, USA.,Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
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Emerging applications of site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) to study food protein structure, dynamics, and interaction. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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9
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Georgieva ER. Protein Conformational Dynamics upon Association with the Surfaces of Lipid Membranes and Engineered Nanoparticles: Insights from Electron Paramagnetic Resonance Spectroscopy. Molecules 2020; 25:E5393. [PMID: 33218036 PMCID: PMC7698768 DOI: 10.3390/molecules25225393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed study of conformational rearrangements and dynamics of proteins is central to our understanding of their physiological functions and the loss of function. This review outlines the applications of the electron paramagnetic resonance (EPR) technique to study the structural aspects of proteins transitioning from a solution environment to the states in which they are associated with the surfaces of biological membranes or engineered nanoobjects. In the former case these structural transitions generally underlie functional protein states. The latter case is mostly relevant to the application of protein immobilization in biotechnological industries, developing methods for protein purification, etc. Therefore, evaluating the stability of the protein functional state is particularly important. EPR spectroscopy in the form of continuous-wave EPR or pulse EPR distance measurements in conjunction with protein spin labeling provides highly versatile and sensitive tools to characterize the changes in protein local dynamics as well as large conformational rearrangements. The technique can be widely utilized in studies of both protein-membrane and engineered nanoobject-protein complexes.
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Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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Farmakes J, Schuster I, Overby A, Alhalhooly L, Lenertz M, Li Q, Ugrinov A, Choi Y, Pan Y, Yang Z. Enzyme Immobilization on Graphite Oxide (GO) Surface via One-Pot Synthesis of GO/Metal-Organic Framework Composites for Large-Substrate Biocatalysis. ACS APPLIED MATERIALS & INTERFACES 2020; 12:23119-23126. [PMID: 32338863 DOI: 10.1021/acsami.0c04101] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Although enzyme immobilization has improved many areas, biocatalysis involving large-size substrates is still challenging for immobilization platform design because of the protein damage under the often "harsh" reaction conditions required for these reactions. Our recent efforts indicate the potential of using Metal-Organic Frameworks (MOFs) to partially confine enzymes on the surface of MOF-based composites while offering sufficient substrate contact. Still, improvements are required to expand the feasible pH range and the efficiency of contacting substrates. In this contribution, we discovered that Zeolitic Imidazolate Framework (ZIF) and a new calcium-carboxylate based MOF (CaBDC) can both be coprecipitated with a model large-substrate enzyme, lysozyme (lys), to anchor the enzyme on the surface of graphite oxide (GO). We observed lys activity against its native substrate, bacterial cell walls, indicating lys was confined on composite surface. Remarkably, lys@GO/CaBDC displayed a stronger catalytic efficiency at pH 6.2 as compared to pH 7.4, indicating CaBDC is a good candidate for biocatalysis under acidic conditions as compared to ZIFs which disassemble under pH < 7. Furthermore, to understand the regions of lys being exposed to the reaction medium, we carried out a site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy study. Our data showed a preferential orientation of lys in GO/ZIF composite, whereas a random orientation in GO/CaBDC. This is the first report on immobilizing solution-state large-substrate enzymes on GO surface using two different MOFs via one-pot synthesis. These platforms can be generalized to other large-substrate enzymes to carry out catalysis under the optimal buffer/pH conditions. The orientation of enzyme at the molecular level on composite surfaces is critical for guiding the rational design of new composites.
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Affiliation(s)
- Jasmin Farmakes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Isabelle Schuster
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Amanda Overby
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Lina Alhalhooly
- Department of Physics, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Mary Lenertz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
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Dosadina E, Agyeiwaa C, Ferreira W, Cutting S, Jibawi A, Ferrari E, Soloviev M. Oriented Immobilization on Gold Nanoparticles of a Recombinant Therapeutic Zymogen. Methods Mol Biol 2020; 2118:213-225. [PMID: 32152982 DOI: 10.1007/978-1-0716-0319-2_16] [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] [Indexed: 06/10/2023]
Abstract
Direct immobilization of functional proteins on gold nanoparticles (AuNPs) affects their structure and function. Changes may vary widely and range from strong inhibition to the enhancement of protein function. More often though the outcome of direct protein immobilization results in protein misfolding and the loss of protein activity. Additional complications arise when the protein being immobilized is a zymogen which requires and relies on additional protein-protein interactions to exert its function. Here we describe molecular design of a glutathione-S-transferase-Staphylokinase fusion protein (GST-SAK) and its conjugation to AuNPs. The multivalent AuNP-(GST-SAK)n complexes generated show plasminogen activation activity in vitro. The methods described are transferable and could be adapted for conjugation and functional analysis of other plasminogen activators, thrombolytic preparations or other functional enzymes.
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Affiliation(s)
- Elina Dosadina
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Celetia Agyeiwaa
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - William Ferreira
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Simon Cutting
- Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Abdullah Jibawi
- Ashford and St. Peter's Hospitals NHS Foundation Trust, Surrey, UK
| | - Enrico Ferrari
- College of Science, School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, Lincolnshire, UK
| | - Mikhail Soloviev
- Centre for Biomedical Sciences, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK.
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Sharifi M, Sohrabi MJ, Hosseinali SH, Hasan A, Kani PH, Talaei AJ, Karim AY, Nanakali NMQ, Salihi A, Aziz FM, Yan B, Khan RH, Saboury AA, Falahati M. Enzyme immobilization onto the nanomaterials: Application in enzyme stability and prodrug-activated cancer therapy. Int J Biol Macromol 2020; 143:665-676. [DOI: 10.1016/j.ijbiomac.2019.12.064] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/05/2019] [Accepted: 12/08/2019] [Indexed: 01/04/2023]
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13
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Sun Q, Pan Y, Wang X, Li H, Farmakes J, Aguila B, Yang Z, Ma S. Mapping out the Degree of Freedom of Hosted Enzymes in Confined Spatial Environments. Chem 2019. [DOI: 10.1016/j.chempr.2019.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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Li H, Pan Y, Farmakes J, Xiao F, Liu G, Chen B, Zhu X, Rao J, Yang Z. A sulfonated mesoporous silica nanoparticle for enzyme protection against denaturants and controlled release under reducing conditions. J Colloid Interface Sci 2019; 556:292-300. [DOI: 10.1016/j.jcis.2019.08.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/23/2023]
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15
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Neupane S, Patnode K, Li H, Baryeh K, Liu G, Hu J, Chen B, Pan Y, Yang Z. Enhancing Enzyme Immobilization on Carbon Nanotubes via Metal-Organic Frameworks for Large-Substrate Biocatalysis. ACS APPLIED MATERIALS & INTERFACES 2019; 11:12133-12141. [PMID: 30839195 DOI: 10.1021/acsami.9b01077] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biocatalysis of large-sized substrates finds wide applications. Immobilizing the involved enzymes on solid supports improves biocatalysis yet faces challenges such as enzyme structural perturbation, leaching, and low cost-efficiencies, depending on immobilization strategies/matrices. Carbon nanotubes (CNTs) are attractive matrices but challenged by enzyme leaching (physical adsorption) or perturbation (covalent linking). Zeolitic imidazolate frameworks (ZIFs) overcome these issues. However, our recent study [ J. Am. Chem. Soc., 2018, 140, 16032-16036] showed reduced cost-efficiency as enzymes trapped below the ZIF surfaces cannot participate in biocatalysis; the enzyme-ZIF composites are also unstable under acidic conditions. In this work, we demonstrate the feasibility of using ZIFs to immobilize enzymes on CNT surfaces on two model enzymes, T4 lysozyme and amylase, both of which showed negligible leaching and retained catalytic activity under neutral and acidic conditions. To better understand the behavior of enzymes on CNTs and CNT-ZIF, we characterized enzyme orientation on both matrices using site-directed spin-labeling (SDSL)-electron paramagnetic resonance (EPR), which is immune to the complexities caused by CNT and ZIF background signals and enzyme-matrix interactions. Our structural investigations showed enhanced enzyme exposure to the solvent compared to enzymes in ZIFs alone; orientation of enzymes in matrices itself is directly related to substrate accessibility and, therefore, essential for understanding and improving catalytic efficiency. To the best of our knowledge, this is the first time ZIFs and one-pot synthesis are employed to anchor large-substrate enzymes on CNT surfaces for biocatalysis. This is also the first report of enzyme orientation on the CNT surface and upon trapping in CNT-ZIF composites. Our results are essential for guiding the rational design of CNT-ZIF combinations to improve enzyme stabilization, loading capacity, and catalytic efficiency.
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Affiliation(s)
| | | | | | | | | | - Jinlian Hu
- Institute of Textiles and Clothing , The Hong Kong Polytechnic University , Kowloon 999077 , Hong Kong , China
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Hosseinali SH, Boushehri ZP, Rasti B, Mirpour M, Shahpasand K, Falahati M. Biophysical, molecular dynamics and cellular studies on the interaction of nickel oxide nanoparticles with tau proteins and neuron-like cells. Int J Biol Macromol 2018; 125:778-784. [PMID: 30528999 DOI: 10.1016/j.ijbiomac.2018.12.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/28/2018] [Accepted: 12/06/2018] [Indexed: 01/15/2023]
Abstract
Nickel oxide nanoparticles (NiO NPs) have been used in the biological and medical sciences. However, their toxic effects against biological systems such as nervous system have not been well studied. Therefore, the adverse effect of NiO NPs on tau structure was investigated by fluorescence and CD spectroscopic methods as well as TEM study. Also, molecular dynamic study was run to extend the experimental data. Cytotoxic activity of NiO NPs against SH-SY5Y cell was determined by trypan blue exclusion, cell morphology, ROS, and apoptosis assays. ANS, Nile red, ThT assays and electron micrograph investigation revealed that NiO NPs can increase the hydrophobic portions of tau and induce the formation of amorphous tau aggregates. Far and near CD spectroscopic methods revealed that NiO NPs can change the secondary and tertiary structure of tau, respectively. Theoretical studies depicted that NiO NPs lead to folding of tau structure. In the cellular view, NiO NPs induced significant mortality and morphological effects against SH-SY5Y cells. NiO NPs also provided a significant impact on generating intracellular ROS and apoptosis induction. This study determined that NiO NPs could mediate the induction of some undesired effects on the nervous system.
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Affiliation(s)
- Sara Haji Hosseinali
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Pourmokhtar Boushehri
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Behnam Rasti
- Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University (IAU), Lahijan, Guilan, Iran
| | - Mirsasan Mirpour
- Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University (IAU), Lahijan, Guilan, Iran
| | - Koorosh Shahpasand
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran..
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17
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Pan Y, Li H, Farmakes J, Xiao F, Chen B, Ma S, Yang Z. How Do Enzymes Orient When Trapped on Metal–Organic Framework (MOF) Surfaces? J Am Chem Soc 2018; 140:16032-16036. [DOI: 10.1021/jacs.8b09257] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Hui Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Jasmin Farmakes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Feng Xiao
- Department of Civil Engineering, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Shengqian Ma
- Department of Chemistry and Biochemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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18
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Pan Y, Neupane S, Farmakes J, Oh M, Bentz K, Choi Y, Yang Z. Insights on the Structure, Molecular Weight and Activity of an Antibacterial Protein-Polymer Hybrid. Chemphyschem 2018; 19:651-658. [PMID: 29131929 PMCID: PMC6122959 DOI: 10.1002/cphc.201701097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Indexed: 12/11/2022]
Abstract
Protein-polymer conjugates are attractive biomaterials which combine the functions of both proteins and polymers. The bioactivity of these hybrid materials, however, is often reduced upon conjugation. It is important to determine and monitor the protein structure and active site availability in order to optimize the polymer composition, attachment point, and abundance. The challenges in probing these insights are the large size and high complexity in the conjugates. Herein, we overcome the challenges by combining electron paramagnetic resonance (EPR) spectroscopy and atomic force microscopy (AFM) and characterize the structure of antibacterial hybrids formed by polyethylene glycol (PEG) and an antibacterial protein. We discovered that the primary reasons for activity loss were PEG blocking the substrate access pathway and/or altering protein surface charges. Our data indicated that the polymers tended to stay away from the protein surface and form a coiled conformation. The structural insights are meaningful for and applicable to the rational design of future hybrids.
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Affiliation(s)
- Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, 1231 Albrecht Blvd, Fargo, ND, 58108 (USA),
| | - Sunanda Neupane
- Department of Chemistry and Biochemistry, North Dakota State University, 1231 Albrecht Blvd, Fargo, ND, 58108 (USA),
| | - Jasmin Farmakes
- Department of Chemistry and Biochemistry, North Dakota State University, 1231 Albrecht Blvd, Fargo, ND, 58108 (USA),
| | - Myungkeun Oh
- Materials and Nanotechnology Program, North Dakota State University, 251 Batcheller Technology Center, Fargo, ND 58105
| | - Kylie Bentz
- Department of Chemistry and Biochemistry, North Dakota State University, 1231 Albrecht Blvd, Fargo, ND, 58108 (USA),
| | - Yongki Choi
- Materials and Nanotechnology Program, North Dakota State University, 251 Batcheller Technology Center, Fargo, ND 58105
- Department of Physics, North Dakota State University, 1211 Albrecht Blvd, Fargo, ND, 58108 (USA),
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, 1231 Albrecht Blvd, Fargo, ND, 58108 (USA),
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19
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Chen M, Zeng G, Xu P, Lai C, Tang L. How Do Enzymes ‘Meet’ Nanoparticles and Nanomaterials? Trends Biochem Sci 2017; 42:914-930. [DOI: 10.1016/j.tibs.2017.08.008] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
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20
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Chang KJ, Kuo YH, Chiang YW. Study of Protein Dynamics under Nanoconfinement by Spin-Label ESR: A Case of T4 Lysozyme Protein. J Phys Chem B 2017; 121:4355-4363. [DOI: 10.1021/acs.jpcb.7b00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kuo-Jung Chang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Hsuan Kuo
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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