1
|
Ye J, Fan M, Zhan J, Zhang X, Lu S, Chai M, Zhang Y, Zhao X, Li S, Zhang D. In silico bioactivity prediction of proteins interacting with graphene-based nanomaterials guides rational design of biosensor. Talanta 2024; 277:126397. [PMID: 38865956 DOI: 10.1016/j.talanta.2024.126397] [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: 11/10/2023] [Revised: 05/24/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024]
Abstract
Graphene-based nanomaterials have attracted significant attention for their potentials in biomedical and biotechnology applications in recent years, owing to the outstanding physical and chemical properties. However, the interaction mechanism and impact on biological activity of macro/micro biomolecules still require more concerns and further research in order to enhance their applicability in biosensors, etc. Herein, an integrated method has been developed to predict the protein bioactivity performance when interacting with nanomaterials for protein-based biosensor. Molecular dynamics simulation and molecular docking technique were consolidated to investigate several nanomaterials: C60 fullerene, single-walled carbon nanotube, pristine graphene and graphene oxide, and their effect when interacting with protein. The adsorption behavior, secondary structure changes and protein bioactivity changes were simulated, and the results of protein activity simulation were verified in combination with atomic force spectrum, circular dichroism spectrum fluorescence and electrochemical experiments. The best quantification alignment between bioactivity obtained by simulation and experiment measurements was further explored. The two proteins, RNase A and Exonuclease III, were regarded as analysis model for the proof of concept, and the prediction accuracy of protein bioactivity could reach up to 0.98. The study shows an easy-to-operate and systematic approach to predict the effects of graphene-based nanomaterials on protein bioactivity, which holds guiding significance for the design of protein-related biosensors. In addition, the proposed prediction model is not limited to carbon-based nanomaterials and can be extended to other types of nanomaterials. This facilitates the rapid, simple, and low-cost selection of efficient and biosafe nanomaterials candidates for protein-related applications in biosensing and biomedical systems.
Collapse
Affiliation(s)
- Jing Ye
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Minzhi Fan
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Jie Zhan
- Research Center for New Materials Computation, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Xiaoyu Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Shasha Lu
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Mengyao Chai
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Yunshan Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Xiaoyu Zhao
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China; College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Diming Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China.
| |
Collapse
|
2
|
Ye J, Fan M, Zhang X, Liang Q, Zhang Y, Zhao X, Lin CT, Zhang D. A novel biomimetic electrochemical taste-biosensor based on conformational changes of the taste receptor. Biosens Bioelectron 2024; 249:116001. [PMID: 38199084 DOI: 10.1016/j.bios.2024.116001] [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: 07/20/2023] [Revised: 11/06/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
Taste sensor, a useful tool which could detect and identify thousands of different chemical substances in liquid environments, has attracted continuous concern from beverage and foodstuff industry and its consumers. Although many taste sensing methods have been extensively developed, the assessment of tastant content remains challenging due to the limitations of sensor selectivity and sensitivity. Here we present a novel biomimetic electrochemical taste-biosensor based on bioactive sensing elements and immune amplification with nanomaterials carrier to address above concerns, while taking sweet taste perception as a model. The proposed biosensor based on ligand binding domain (T1R2 VFT) of human sweet taste receptor protein showed human mimicking character and initiated the application of immune recognition in gustation biosensor, which can precisely and sensitively distinguish sweet substances against other related gustation substances with detection limit of 5.1 pM, far less than that of taste sensors without immune amplification whose detection limit was 0.48 nM. The performance test demonstrated the biosensor has the capacity of monitoring the response of sweet substances in real food environments, which is crucial in practical. This biomimetic electrochemical taste-biosensor can work as a new screening platform for newly developed tastants and disclose sweet perception mechanism.
Collapse
Affiliation(s)
- Jing Ye
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Minzhi Fan
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Xiaoyu Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Qi Liang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China; College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Yunshan Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Xiaoyu Zhao
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China; College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Cheng-Te Lin
- Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
| | - Diming Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China.
| |
Collapse
|
3
|
Mukhopadhyay T, Ghosh A, Datta A. Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook. ACS PHYSICAL CHEMISTRY AU 2024; 4:97-121. [PMID: 38560753 PMCID: PMC10979489 DOI: 10.1021/acsphyschemau.3c00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 04/04/2024]
Abstract
Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.
Collapse
Affiliation(s)
- Titas
Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Anupam Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| |
Collapse
|
4
|
Panigrahi AR, Sahu A, Yadav P, Beura SK, Singh J, Mondal K, Singh SK. Nanoinformatics based insights into the interaction of blood plasma proteins with carbon based nanomaterials: Implications for biomedical applications. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:263-288. [PMID: 38448137 DOI: 10.1016/bs.apcsb.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
In the past three decades, interest in using carbon-based nanomaterials (CBNs) in biomedical application has witnessed remarkable growth. Despite the rapid advancement, the translation of laboratory experimentation to clinical applications of nanomaterials is one of the major challenges. This might be attributed to poor understanding of bio-nano interface. Arguably, the most significant barrier is the complexity that arises by interplay of several factors like properties of nanomaterial (shape, size, surface chemistry), its interaction with suspending media (surface hydration and dehydration, surface reconstruction and release of free surface energy) and the interaction with biomolecules (conformational change in biomolecules, interaction with membrane and receptor). Tailoring a nanomaterial that minimally interacts with protein and lipids in the medium while effectively acts on target site in biological milieu has been very difficult. Computational methods and artificial intelligence techniques have displayed potential in effectively addressing this problem. Through predictive modelling and deep learning, computer-based methods have demonstrated the capability to create accurate models of interactions between nanoparticles and cell membranes, as well as the uptake of nanomaterials by cells. Computer-based simulations techniques enable these computational models to forecast how making particular alterations to a material's physical and chemical properties could enhance functional aspects, such as the retention of drugs, the process of cellular uptake and biocompatibility. We review the most recent progress regarding the bio-nano interface studies between the plasma proteins and CBNs with a special focus on computational simulations based on molecular dynamics and density functional theory.
Collapse
Affiliation(s)
| | - Abhinandana Sahu
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Pooja Yadav
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Samir Kumar Beura
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Jyoti Singh
- Department of Applied Agriculture, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | | | - Sunil Kumar Singh
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India; Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India.
| |
Collapse
|
5
|
Wang Y, Zhang X, Yue H. Two-dimensional nanomaterials induced nano-bio interfacial effects and biomedical applications in cancer treatment. J Nanobiotechnology 2024; 22:67. [PMID: 38369468 PMCID: PMC10874567 DOI: 10.1186/s12951-024-02319-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/26/2024] [Indexed: 02/20/2024] Open
Abstract
Two-dimensional nanomaterials (2D NMs), characterized by a large number of atoms or molecules arranged in one dimension (typically thickness) while having tiny dimensions in the other two dimensions, have emerged as a pivotal class of materials with unique properties. Their flat and sheet-like structure imparts distinctive physical, chemical, and electronic attributes, which offers several advantages in biomedical applications, including enhanced surface area for efficient drug loading, surface-exposed atoms allowing precise chemical modifications, and the ability to form hierarchical multilayer structures for synergistic functionality. Exploring their nano-bio interfacial interactions with biological components holds significant importance in comprehensively and systematically guiding safe applications. However, the current lack of in-depth analysis and comprehensive understanding of interfacial effects on cancer treatment motivates our ongoing efforts in this field. This study provides a comprehensive survey of recent advances in utilizing 2D NMs for cancer treatment. It offers insights into the structural characteristics, synthesis methods, and surface modifications of diverse 2D NMs. The investigation further delves into the formation of nano-bio interfaces during their in vivo utilization. Notably, the study discusses a wide array of biomedical applications in cancer treatment. With their potential to revolutionize therapeutic strategies and outcomes, 2D NMs are poised at the forefront of cancer treatment, holding the promise of transformative advancements.
Collapse
Affiliation(s)
- Yan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hua Yue
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
6
|
Zhang J, Pei R, Tan J, Ni Z, Ye S, Luo Y. Visualizing Water Monomers and Chiral OH -(H 2O) Complexes Infiltrated in a Macroscopic Hydrophobic Teflon Matrix. J Am Chem Soc 2023. [PMID: 38048434 DOI: 10.1021/jacs.3c09950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Insights into the interaction of fluoroalkyl groups with water are crucial to understanding the polar hydrophobicity of fluorinated compounds, such as Teflon. While an ordered hydrophobic-like 2D water layer has been demonstrated to be present on the surface of macroscopically hydrophobic fluorinated polymers, little is known about how the water infiltrates into the Teflon and what is the molecular structure of the water infiltrated into the Teflon. Using highly sensitive femtosecond sum frequency generation vibrational spectroscopy (SFG-VS), we observe for the first time that monomeric H2O and chiral OH-(H2O) complexes are present in macroscopically hydrophobic Teflon. The species are inhomogeneously distributed inside the Teflon matrix and at the Teflon surface. No water clusters or single-file water "wires" are observed in the matrix. SFG free induction decay (SFG-FID) experiments demonstrate that the OH oscillators of physically absorbed molecular water at the surface dephase on the time scale of <230 fs, whereas the water monomers and hydrated hydroxide ions infiltrated in the Teflon matrix dephase much more slowly (680-830 fs), indicating that the embedded monomeric H2O and OH-(H2O) complexes are decoupled from the outer environment. Our findings can well interpret ultrafast water permeation through fluorous nanochannels and the charging mechanism of Teflon, which may tailor the desired applications of organofluorines.
Collapse
Affiliation(s)
- Jiahui Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Ruoqi Pei
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Junjun Tan
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Zijian Ni
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Yi Luo
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| |
Collapse
|
7
|
Achôa GL, Mattos PA, Clements A, Roca Y, Brooks Z, Ferreira JRM, Canal R, Fernandes TL, Riera R, Amano MT, Hokugo A, Jarrahy R, Lenz E Silva GF, Bueno DF. A scoping review of graphene-based biomaterials for in vivo bone tissue engineering. J Biomater Appl 2023; 38:313-350. [PMID: 37493398 DOI: 10.1177/08853282231188805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The growing demand for more efficient materials for medical applications brought together two previously distinct fields: medicine and engineering. Regenerative medicine has evolved with the engineering contributions to improve materials and devices for medical use. In this regard, graphene is one of the most promising materials for bone tissue engineering and its potential for bone repair has been studied by several research groups. The aim of this study is to conduct a scoping review including articles published in the last 12 years (from 2010 to 2022) that have used graphene and its derivatives (graphene oxide and reduced graphene) in preclinical studies for bone tissue regeneration, searching in PubMed/MEDLINE, Embase, Web of Science, Cochrane Central, and clinicaltrials.gov (to confirm no study has started with clinical trial). Boolean searches were performed using the defined key words "bone" and "graphene", and manuscript abstracts were uploaded to Rayyan, a web-tool for systematic and scoping reviews. This scoping review was conducted based on Joanna Briggs Institute Manual for Scoping Reviews and the report follows the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses - Extension for Scoping Reviews (PRISMA-ScR) statement. After the search protocol and application of the inclusion criteria, 77 studies were selected and evaluated by five blinded researchers. Most of the selected studies used composite materials associated with graphene and its derivatives to natural and synthetic polymers, bioglass, and others. Although a variety of graphene materials were analyzed in these studies, they all concluded that graphene, its derivatives, and its composites improve bone repair processes by increasing osteoconductivity, osteoinductivity, new bone formation, and angiogenesis. Thus, this systematic review opens up new opportunities for the development of novel strategies for bone tissue engineering with graphene.
Collapse
Affiliation(s)
- Gustavo L Achôa
- Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | | | | | | | | | - Raul Canal
- Universidade Corporativa ANADEM, Brasília, Brazil
| | - Tiago L Fernandes
- Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Rachel Riera
- Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Mariane T Amano
- Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | | | | | - Daniela F Bueno
- Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, Brazil
- Engenharia Metalúrgica e de Materiais, USP, São Paulo, Brazil
- Universidade Corporativa ANADEM, Brasília, Brazil
| |
Collapse
|
8
|
Yang P, Guo W, Ramamoorthy A, Chen Z. Conformation and Orientation of Antimicrobial Peptides MSI-594 and MSI-594A in a Lipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5352-5363. [PMID: 37017985 DOI: 10.1021/acs.langmuir.2c03430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
There is significant interest in the development of antimicrobial compounds to overcome the increasing bacterial resistance to conventional antibiotics. Studies have shown that naturally occurring and de novo-designed antimicrobial peptides could be promising candidates. MSI-594 is a synthetic linear, cationic peptide that has been reported to exhibit a broad spectrum of antimicrobial activities. Investigation into how MSI-594 disrupts the cell membrane is important for better understanding the details of this antimicrobial peptide (AMP)'s action against bacterial cells. In this study, we used two different synthetic lipid bilayers: zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and anionic 7:3 POPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1'-rac-glycerol) (POPG). Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) were used to determine the orientations of MSI-594 and its analogue MSI-594A associated with zwitterionic POPC and anionic 7:3 POPC/POPG lipid bilayers. The simulated ATR-FTIR and SFG spectra using nuclear magnetic resonance (NMR)-determined structures were compared with experimental spectra to optimize the bent angle between the N- (1-11) and C- (12-24) termini helices and the membrane orientations of the helices; since the NMR structure of the peptide was determined from lipopolysaccharide (LPS) micelles, the optimization was needed to find the most suitable conformation and orientation in lipid bilayers. The reported experimental results indicate that the optimized MSI-594 helical hairpin structure adopts a complete lipid bilayer surface-bound orientation (denoted "face-on") in both POPC and 7:3 POPC/POPG lipid bilayers. The analogue peptide, MSI-584A, on the other hand, exhibited a larger bent angle between the N- (1-11) and C- (12-24) termini helices with the hydrophobic C-terminal helix inserted into the hydrophobic region of the bilayer (denoted "membrane-inserted") when interacting with both POPC and 7:3 POPC/POPG lipid bilayers. These experimental findings on the membrane orientations suggest that both peptides are likely to disrupt the cell membrane through the carpet mechanism.
Collapse
Affiliation(s)
- Pei Yang
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Wen Guo
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Zhan Chen
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
9
|
Lu T, Chen Z. Monitoring the Molecular Structure of Fibrinogen during the Adsorption Process at the Buried Silicone Oil Interface In Situ in Real Time. J Phys Chem Lett 2023; 14:3139-3145. [PMID: 36961304 DOI: 10.1021/acs.jpclett.3c00331] [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: 06/18/2023]
Abstract
Interfacial proteins play important roles in many research fields and applications, such as biosensors, biomedical implants, nonfouling coatings, etc. Directly probing interfacial protein behavior at buried solid/liquid and liquid/liquid interfaces is challenging. We used sum frequency generation vibrational spectroscopy and a Hamiltonian data analysis method to monitor the molecular structure of fibrinogen on silicone oil during the adsorption process in situ in real time. The results showed that the adsorbed fibrinogen molecules tend to adopt a bent structure throughout the entire adsorption process with the same orientation. This is different from the case of adsorbed fibrinogen on CaF2 with a linear structure or on polystyrene with a bent structure but a different orientation. The method introduced herein is generally applicable for following time-dependent molecular structures of many other proteins and peptides at interfaces in situ in real time at the molecular level.
Collapse
Affiliation(s)
- Tieyi Lu
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
10
|
Wang X, Yao C, Yao X, Lin J, Li R, Huang K, Lin W, Long X, Dai C, Dong J, Yu X, Huang W, Weng W, Wang Q, Ouyang H, Cheng K. Dynamic photoelectrical regulation of ECM protein and cellular behaviors. Bioact Mater 2023; 22:168-179. [PMID: 36203959 PMCID: PMC9529514 DOI: 10.1016/j.bioactmat.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 12/02/2022] Open
Abstract
Dynamic regulation of cell-extracellular matrix (ECM)-material interactions is crucial for various biomedical applications. In this study, a light-activated molecular switch for the modulation of cell attachment/detachment behaviors was established on monolayer graphene (Gr)/n-type Silicon substrates (Gr/Si). Initiated by light illumination at the Gr/Si interface, pre-adsorbed proteins (bovine serum albumin, ECM proteins collagen-1, and fibronectin) underwent protonation to achieve negative charge transfer to Gr films (n-doping) through π-π interactions. This n-doping process stimulated the conformational switches of ECM proteins. The structural alterations in these ECM interactors significantly reduced the specificity of the cell surface receptor-ligand interaction (e.g., integrin recognition), leading to dynamic regulation of cell adhesion and eventual cell detachment. RNA-sequencing results revealed that the detached bone marrow mesenchymal stromal cell sheets from the Gr/Si system manifested regulated immunoregulatory properties and enhanced osteogenic differentiation, implying their potential application in bone tissue regeneration. This work not only provides a fast and feasible method for controllable cells/cell sheets harvesting but also gives new insights into the understanding of cell-ECM-material communications. A light-activated molecular switch for regulation of cell attachment/detachment behaviors was established on (Gr/Si) substrates. Light-induced charge transfer from ECM protein to Gr/Si through π-π interactions, resulting in the conformational alteration of ECM proteins. Structural changes in ECM weakened the binding between RGD and integrin, inducing cell detachment. This work provides a feasible method for cell harvesting and improves the understanding of cell-ECM-material communications.
Collapse
Affiliation(s)
- Xiaozhao Wang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Cai Yao
- School of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Xudong Yao
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000, China
| | - Junxin Lin
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Rui Li
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Kun Huang
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Weiming Lin
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Xiaojun Long
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Chao Dai
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
| | - Jiajun Dong
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
| | - Xuegong Yu
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Wenwen Huang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Wenjian Weng
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Qi Wang
- School of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Hongwei Ouyang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
- Corresponding author. Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Kui Cheng
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
- Corresponding author.
| |
Collapse
|
11
|
Guo W, Lu T, Crisci R, Nagao S, Wei T, Chen Z. Determination of protein conformation and orientation at buried solid/liquid interfaces. Chem Sci 2023; 14:2999-3009. [PMID: 36937592 PMCID: PMC10016606 DOI: 10.1039/d2sc06958j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Protein structures at solid/liquid interfaces mediate interfacial protein functions, which are important for many applications. It is difficult to probe interfacial protein structures at buried solid/liquid interfaces in situ at the molecular level. Here, a systematic methodology to determine protein molecular structures (orientation and conformation) at buried solid/liquid interfaces in situ was successfully developed with a combined approach using a nonlinear optical spectroscopic technique - sum frequency generation (SFG) vibrational spectroscopy, isotope labeling, spectra calculation, and computer simulation. With this approach, molecular structures of protein GB1 and its mutant (with two amino acids mutated) were investigated at the polymer/solution interface. Markedly different orientations and similar (but not identical) conformations of the wild-type protein GB1 and its mutant at the interface were detected, due to the varied molecular interfacial interactions. This systematic strategy is general and can be widely used to elucidate protein structures at buried interfaces in situ.
Collapse
Affiliation(s)
- Wen Guo
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Tieyi Lu
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Ralph Crisci
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Satoshi Nagao
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Ako-gun Kamigouri-cho Hyogo 678-1297 Japan
| | - Tao Wei
- Department of Chemical Engineering, Howard University 2366 Sixth Street NW Washington 20059 DC USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| |
Collapse
|
12
|
Suo H, Geng H, Zhang L, Liu G, Yan H, Cao R, Zhu J, Hu Y, Xu L. Covalent immobilization of lipase on an ionic liquid-functionalized magnetic Cu-based metal-organic framework with boosted catalytic performance in flavor ester synthesis. J Mater Chem B 2023; 11:1302-1311. [PMID: 36651865 DOI: 10.1039/d2tb02246j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Enzymatic esterification plays an important role in the fields of chemistry and biotechnology. In this study, lipase was immobilized on an ionic liquid (IL)-modified magnetic metal-organic framework (MOF) and used to synthesize isoamyl acetate. The immobilized lipase (PPL-ILs/Fe3O4@MOF) showed 2.1-fold and 1.8-fold higher activity compared to the free and immobilized lipase without ILs (PPL-Fe3O4@MOF), respectively. In addition, the anti-denaturant ability and reusability of the PPL-ILs/Fe3O4@MOF were also higher than those of other samples. The ester yield reached 75.1% when the biocatalyst was used to synthesize isoamyl acetate in hexane. The synthesized supports supplied a good microenvironment for the immobilized lipase through multiple interactions. Results of the structural analysis showed that the conformation state of lipase molecules changed after immobilization. The magnetism of the prepared biocatalyst makes it easy to recycle so that PPL-ILs/Fe3O4@MOF maintained 70.2% of the initial activity after eight cycles. The prepared composite materials exhibited good potential in lipase immobilization with enhanced catalytic ability and stability.
Collapse
Affiliation(s)
- Hongbo Suo
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Huining Geng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Lu Zhang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Guoyun Liu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Rui Cao
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Jiahao Zhu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China.
| | - Lili Xu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| |
Collapse
|
13
|
Yang XG, Zhang JR, Tian XK, Qin JH, Zhang XY, Ma LF. Enhanced Activity of Enzyme Immobilized on Hydrophobic ZIF-8 Modified by Ni 2+ Ions. Angew Chem Int Ed Engl 2023; 62:e202216699. [PMID: 36536412 DOI: 10.1002/anie.202216699] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The development of efficient enzyme immobilization to promote their recyclability and activity is highly desirable. Zeolitic imidazolate framework-8 (ZIF-8) has been proved to be an effective platform for enzyme immobilization due to its easy preparation and biocompatibility. However, the intrinsic hydrophobic characteristic hinders its further development in this filed. Herein, a facile synthesis approach was developed to immobilize pepsin (PEP) on the ZIF-8 carrier by using Ni2+ ions as anchor (ZIF-8@PEP-Ni). By contrast, the direct coating of PEP on the surface of ZIF-8 (ZIF-8@PEP) generated significant conformational changes. Electrochemical oxygen evolution reaction (OER) was employed to study the catalytic activity of immobilized PEP. The ZIF-8@PEP-Ni composite attains remarkable OER performance with an ultralow overpotential of only 127 mV at 10 mA cm-2 , which is much lower than the 690 and 919 mV overpotential values of ZIF-8@PEP and PEP, respectively.
Collapse
Affiliation(s)
- Xiao-Gang Yang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang, 471934, P. R. China
| | - Ji-Rui Zhang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang, 471934, P. R. China
| | - Xu-Ke Tian
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang, 471934, P. R. China
| | - Jian-Hua Qin
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang, 471934, P. R. China
| | - Xin-Ya Zhang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang, 471934, P. R. China
| | - Lu-Fang Ma
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang, 471934, P. R. China
| |
Collapse
|
14
|
Suo H, Geng X, Sun Y, Zhang L, Yang J, Yang F, Yan H, Hu Y, Xu L. Surface Modification of Magnetic ZIF-90 Nanoparticles Improves the Microenvironment of Immobilized Lipase and Its Application in Esterification. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15384-15393. [PMID: 36448653 DOI: 10.1021/acs.langmuir.2c02672] [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
Interactions of enzymes with supports significantly affect the activity and stability of immobilized enzymes. Herein, amino-functionalized ionic liquid (IL)-grafted magnetic zeolitic imidazolate framework-90 (MZIF-90) was prepared and used to immobilize porcine pancreatic lipase (PPL). The nanocomposites were fully characterized; meanwhile, the interactions between ILs and ZIF-90 were calculated based on density functional theory. The prepared biocatalyst (PPL-ILs/MZIF-90) had a lipase loading of 178.3 mg/g and hydrolysis activity up to 287.5 U/g. When the biocatalyst was used to synthesize isoamyl acetate, the reaction media, molar ratio of alcohol/acid, temperature, and reaction time were optimized. Under the optimized reaction conditions (in hexane, alcohol/acid = 3:1, under 45 °C, reacted for 9 h), the ester yield reached 85.5%. The results of the stability test showed that PPL-ILs/MZIF-90 retained 88.7% of the initial activity after storing for 35 days and 92.5% of the initial activity after reusing for seven cycles for synthesizing isoamyl acetate. Moreover, the secondary structure analysis showed that the synthesized supports protected the active conformation of immobilized lipase, which lead to the enhanced catalytic performance. Additionally, the biocatalyst can be easily separated with a magnet, which facilitated the reusability. This study provides insights regarding the application of metal organic framework composites in the field of enzyme catalysis.
Collapse
Affiliation(s)
- Hongbo Suo
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Xinyue Geng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Yinghui Sun
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Lu Zhang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Jie Yang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Fan Yang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China
| | - Lili Xu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| |
Collapse
|
15
|
Lu T, Fu L, Qiu Y, Zhang J, Chen Z. Probing Molecular Interactions of Antibody Drugs, Silicone Oil, and Surfactant at Buried Interfaces In Situ. Anal Chem 2022; 94:14761-14768. [PMID: 36215703 DOI: 10.1021/acs.analchem.2c03425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antibody drugs have been rapidly developed to cure many diseases including COVID-19 infection. Silicone oil is commonly used as a lubricant coating material for devices used in the pharmaceutical industry to store and administer antibody drug formulations. However, the interaction between silicone oil and antibody molecules could lead to the adsorption, denaturation, and aggregation of antibody molecules, impacting the efficacy of antibody drugs. Here, we studied the molecular interactions between antibodies and silicone oil in situ in real time. The effect of the surfactant on such interactions was also investigated. Specifically, the adsorption dynamics of a bispecific antibody (BsAb) onto a silicone oil surface without and with different concentrations of the surfactant PS80 in antibody solutions were monitored. Also the possible lowest effective PS80 concentrations that can prevent the adsorption of BsAb as well as a monoclonal antibody (mAb) onto silicone oil were measured. It was found that different concentrations of PS80 are required for preventing the adsorption of different antibodies. Both BsAB and mAB denature on silicone oil without a surfactant. However, for a low surfactant concentration in the solution, although the surfactant could not completely prevent the antibody from adsorption, it could maintain the native structures of adsorbed BsAb and mAb antibodies on silicone oil. This is important knowledge, showing that to prevent antibody aggregation on silicone oil it is not necessary to add surfactant to a concentration high enough to completely minimize protein adsorption.
Collapse
Affiliation(s)
- Tieyi Lu
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Li Fu
- Sanofi, 1 The Mountain Road, Framingham, Massachusetts 01701, United States
| | - Yu Qiu
- Sanofi, 350 Water St, Cambridge, Massachusetts 02141, United States
| | - Jifeng Zhang
- Sanofi, 1 The Mountain Road, Framingham, Massachusetts 01701, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
16
|
Chen J, Xu E, Wei Y, Chen M, Wei T, Zheng S. Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10817-10825. [PMID: 36001808 DOI: 10.1021/acs.langmuir.2c01331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding the interfacial behaviors of biomolecules is crucial to applications in biomaterials and nanoparticle-based biosensing technologies. In this work, we utilized autoencoder-based graph clustering to analyze discontinuous molecular dynamics (DMD) simulations of lysozyme adsorption on a graphene surface. Our high-throughput DMD simulations integrated with a Go̅-like protein-surface interaction model makes it possible to explore protein adsorption at a large temporal scale with sufficient accuracy. The graph autoencoder extracts a low-dimensional feature vector from a contact map. The sequence of the extracted feature vectors is then clustered, and thus the evolution of the protein molecule structure in the absorption process is segmented into stages. Our study demonstrated that the residue-surface hydrophobic interactions and the π-π stacking interactions play key roles in the five-stage adsorption. Upon adsorption, the tertiary structure of lysozyme collapsed, and the secondary structure was also affected. The folding stages obtained by autoencoder-based graph clustering were consistent with detailed analyses of the protein structure. The combination of machine learning analysis and efficient DMD simulations developed in this work could be an important tool to study biomolecules' interfacial behaviors.
Collapse
Affiliation(s)
- Jing Chen
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
| | | | - Yong Wei
- Department of Computer Science, High Point University, High Point, North Carolina 27268, United States
| | | | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Size Zheng
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Wu Y, Xu W, Jiao L, Gu W, Du D, Hu L, Lin Y, Zhu C. Nanobiocatalysis: a materials science road to biocatalysis. Chem Soc Rev 2022; 51:6948-6964. [PMID: 35894547 DOI: 10.1039/d1cs01106e] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With high activity and specificity to conduct catalysis under mild conditions, enzymes show great promise in many fields. However, they are not acclimatized to environments in practice after leaving the familiar biological conditions. Aiming at this issue, nanobiocatalysis, a fresh area integrating nanotechnology and enzymatic catalysis, is expected to design biocatalysis based on materials science. Specifically, nano-integrated biocatalysis and bio-inspired nanocatalysis are considered as two effective nanobiocatalytic systems to meet different design needs. Notably, both systems are not entirely separated, and the combination of both further sparks more possibilities. This review summarizes the type, construction, and function of nanobiocatalytic systems, analyzing the pros and cons of different strategies. Moreover, the corresponding applications in bioassay, biotherapy, and environmental remediation are highlighted. We hope that the advent of nanobiocatalysis will help in grasping the inherence of biocatalysis and propel biocatalytic applications.
Collapse
Affiliation(s)
- Yu Wu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Weiqing Xu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Lei Jiao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Wenling Gu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Dan Du
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164, USA.
| | - Liuyong Hu
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, Hubei Engineering Technology Research Center of Optoelectronic and New Energy Materials, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Yuehe Lin
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164, USA.
| | - Chengzhou Zhu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| |
Collapse
|
19
|
Chen SH, Bell DR, Luan B. Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes. Adv Drug Deliv Rev 2022; 186:114336. [PMID: 35597306 PMCID: PMC9212071 DOI: 10.1016/j.addr.2022.114336] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 12/28/2022]
Abstract
Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.
Collapse
Affiliation(s)
- Serena H Chen
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - David R Bell
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Binquan Luan
- IBM Thomas J. Watson Research, Yorktown Heights, New York 10598, USA.
| |
Collapse
|
20
|
Perets EA, Olesen KB, Yan ECY. Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5765-5778. [PMID: 35482888 DOI: 10.1021/acs.langmuir.2c00365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure-function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air-water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C-H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C-H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.
Collapse
Affiliation(s)
- Ethan A Perets
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kristian B Olesen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Elsa C Y Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| |
Collapse
|
21
|
Ren J, Andrikopoulos N, Velonia K, Tang H, Cai R, Ding F, Ke PC, Chen C. Chemical and Biophysical Signatures of the Protein Corona in Nanomedicine. J Am Chem Soc 2022; 144:9184-9205. [PMID: 35536591 DOI: 10.1021/jacs.2c02277] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An inconvenient hurdle in the practice of nanomedicine is the protein corona, a spontaneous collection of biomolecular species by nanoparticles in living systems. The protein corona is dynamic in composition and may entail improved water suspendability and compromised delivery and targeting to the nanoparticles. How much of this nonspecific protein ensemble is determined by the chemistry of the nanoparticle core and its surface functionalization, and how much of this entity is dictated by the biological environments that vary spatiotemporally in vivo? How do we "live with" and exploit the protein corona without significantly sacrificing the efficacy of nanomedicines in diagnosing and curing human diseases? This article discusses the chemical and biophysical signatures of the protein corona and ponders challenges ahead for the field of nanomedicine.
Collapse
Affiliation(s)
- Jiayu Ren
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nicholas Andrikopoulos
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Kelly Velonia
- Department of Materials Science and Technology, University of Crete, Heraklion 70013, Greece
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Rong Cai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Pu Chun Ke
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.,Nanomedicine Center, The GBA National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou 510700, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Nanomedicine Center, The GBA National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou 510700, China
| |
Collapse
|
22
|
Zhao L, Zhang J, Zhang Y, Ye S, Zhang G, Chen X, Jiang B, Jiang J. Accurate Machine Learning Prediction of Protein Circular Dichroism Spectra with Embedded Density Descriptors. JACS AU 2021; 1:2377-2384. [PMID: 34977905 PMCID: PMC8715543 DOI: 10.1021/jacsau.1c00449] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Indexed: 05/08/2023]
Abstract
A data-driven approach to simulate circular dichroism (CD) spectra is appealing for fast protein secondary structure determination, yet the challenge of predicting electric and magnetic transition dipole moments poses a substantial barrier for the goal. To address this problem, we designed a new machine learning (ML) protocol in which ordinary pure geometry-based descriptors are replaced with alternative embedded density descriptors and electric and magnetic transition dipole moments are successfully predicted with an accuracy comparable to first-principle calculation. The ML model is able to not only simulate protein CD spectra nearly 4 orders of magnitude faster than conventional first-principle simulation but also obtain CD spectra in good agreement with experiments. Finally, we predicted a series of CD spectra of the Trp-cage protein associated with continuous changes of protein configuration along its folding path, showing the potential of our ML model for supporting real-time CD spectroscopy study of protein dynamics.
Collapse
Affiliation(s)
- Luyuan Zhao
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jinxiao Zhang
- Guangxi
Key Laboratory of Electrochemical and Magneto-chemical Functional
Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541006, P. R. China
| | - Yaolong Zhang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Sheng Ye
- School
of Artificial Intelligence, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Guozhen Zhang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xin Chen
- Gusu
Laboratory of Materials, Suzhou, Jiangsu 215123, P. R. China
| | - Bin Jiang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jun Jiang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| |
Collapse
|
23
|
Yu R, Zhang H, Guo B. Conductive Biomaterials as Bioactive Wound Dressing for Wound Healing and Skin Tissue Engineering. NANO-MICRO LETTERS 2021; 14:1. [PMID: 34859323 PMCID: PMC8639891 DOI: 10.1007/s40820-021-00751-y] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/29/2021] [Indexed: 05/06/2023]
Abstract
Conductive biomaterials based on conductive polymers, carbon nanomaterials, or conductive inorganic nanomaterials demonstrate great potential in wound healing and skin tissue engineering, owing to the similar conductivity to human skin, good antioxidant and antibacterial activities, electrically controlled drug delivery, and photothermal effect. However, a review highlights the design and application of conductive biomaterials for wound healing and skin tissue engineering is lacking. In this review, the design and fabrication methods of conductive biomaterials with various structural forms including film, nanofiber, membrane, hydrogel, sponge, foam, and acellular dermal matrix for applications in wound healing and skin tissue engineering and the corresponding mechanism in promoting the healing process were summarized. The approaches that conductive biomaterials realize their great value in healing wounds via three main strategies (electrotherapy, wound dressing, and wound assessment) were reviewed. The application of conductive biomaterials as wound dressing when facing different wounds including acute wound and chronic wound (infected wound and diabetic wound) and for wound monitoring is discussed in detail. The challenges and perspectives in designing and developing multifunctional conductive biomaterials are proposed as well.
Collapse
Affiliation(s)
- Rui Yu
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Hualei Zhang
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Baolin Guo
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| |
Collapse
|
24
|
Han Q, Pang J, Li Y, Sun B, Ibarlucea B, Liu X, Gemming T, Cheng Q, Zhang S, Liu H, Wang J, Zhou W, Cuniberti G, Rümmeli MH. Graphene Biodevices for Early Disease Diagnosis Based on Biomarker Detection. ACS Sens 2021; 6:3841-3881. [PMID: 34696585 DOI: 10.1021/acssensors.1c01172] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The early diagnosis of diseases plays a vital role in healthcare and the extension of human life. Graphene-based biosensors have boosted the early diagnosis of diseases by detecting and monitoring related biomarkers, providing a better understanding of various physiological and pathological processes. They have generated tremendous interest, made significant advances, and offered promising application prospects. In this paper, we discuss the background of graphene and biosensors, including the properties and functionalization of graphene and biosensors. Second, the significant technologies adopted by biosensors are discussed, such as field-effect transistors and electrochemical and optical methods. Subsequently, we highlight biosensors for detecting various biomarkers, including ions, small molecules, macromolecules, viruses, bacteria, and living human cells. Finally, the opportunities and challenges of graphene-based biosensors and related broad research interests are discussed.
Collapse
Affiliation(s)
- Qingfang Han
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan Xinzhuang, Jinan 250022, Shandong, China
| | - Jinbo Pang
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
| | - Yufen Li
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
| | - Baojun Sun
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan Xinzhuang, Jinan 250022, Shandong, China
| | - Bergoi Ibarlucea
- Dresden Center for Computational Materials Science, Technische Universität Dresden, Dresden 01062, Germany
- Dresden Center for Intelligent Materials (GCL DCIM), Technische Universität Dresden, Dresden 01062, Germany
| | - Xiaoyan Liu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
| | - Thomas Gemming
- Leibniz Institute for Solid State and Materials Research Dresden, Dresden D-01171, Germany
| | - Qilin Cheng
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
| | - Shu Zhang
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
| | - Hong Liu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
- State Key Laboratory of Crystal Materials, Center of Bio & Micro/Nano Functional Materials, Shandong University, 27 Shandanan Road, Jinan 250100, China
| | - Jingang Wang
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
| | - Weijia Zhou
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, Shandong, China
| | - Gianaurelio Cuniberti
- Dresden Center for Computational Materials Science, Technische Universität Dresden, Dresden 01062, Germany
- Dresden Center for Intelligent Materials (GCL DCIM), Technische Universität Dresden, Dresden 01062, Germany
- Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, Dresden 01069, Germany
- Center for Advancing Electronics Dresden, Technische Universität Dresden, Dresden 01069, Germany
| | - Mark H. Rümmeli
- Leibniz Institute for Solid State and Materials Research Dresden, Dresden D-01171, Germany
- College of Energy, Soochow, Institute for Energy and Materials Innovations, Soochow University, Suzhou 215006, China
- Key Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu Province, Soochow University, Suzhou 215006, China
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, M. Curie Sklodowskiej 34, Zabrze 41-819, Poland
- Institute of Environmental Technology (CEET), VŠB-Technical University of Ostrava, 17. Listopadu 15, Ostrava 708 33, Czech Republic
| |
Collapse
|
25
|
Zhang S, Hsu L, Toolis A, Li B, Zhou J, Lin T, Chen Z. Investigation of the Atmospheric Moisture Effect on the Molecular Behavior of an Isocyanate-Based Primer Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12705-12713. [PMID: 34668715 DOI: 10.1021/acs.langmuir.1c02135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A primer coating is engineered to facilitate compatibility between products like adhesives, sealants, and potting compounds and targeted substrates. Prolonged exposure of isocyanate-based primer surfaces to the environment is known to negatively affect the interfacial adhesion between itself and the products subsequently applied on top of it. However, the molecular behavior behind this observed phenomenon remained to be further investigated. In this study, sum frequency generation (SFG) vibrational spectroscopy, a nonlinear optical spectroscopic technique, was applied to study the surface of an isocyanate-based primer exposed to different environments at the molecular level. Atmospheric moisture was considered to be a potential factor in impairing the adhesion performance of the primer, and thus, time- and humidity-dependent experiments were executed to monitor the molecular behavior at the primer surface using SFG. In addition, 180° peel testing experiments were conducted to measure the adhesion properties of primers after being exposed to the corresponding conditions to correlate to SFG results and establish a chemical structure-macroscopic performance relationship. This study on the changes at the primer surface in different environments with varied humidity levels as a function of time aims to provide an in-depth understanding of the moisture effect on isocyanate-based primers. These learnings may also be helpful toward exploring a broader range of coatings and surface layers and improving customer product use guidelines.
Collapse
Affiliation(s)
| | - Lorraine Hsu
- Coatings and Innovation Center, PPG, 4325 Rosanna Drive, Allison Park, Pennsylvania 15101, United States
| | - Amy Toolis
- Coatings and Innovation Center, PPG, 4325 Rosanna Drive, Allison Park, Pennsylvania 15101, United States
| | | | | | | | | |
Collapse
|
26
|
Guo W, Lu T, Gandhi Z, Chen Z. Probing Orientations and Conformations of Peptides and Proteins at Buried Interfaces. J Phys Chem Lett 2021; 12:10144-10155. [PMID: 34637311 DOI: 10.1021/acs.jpclett.1c02956] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Molecular structures of peptides/proteins at interfaces determine their interfacial properties, which play important roles in many applications. It is difficult to probe interfacial peptide/protein structures because of the lack of appropriate tools. Sum frequency generation (SFG) vibrational spectroscopy has been developed into a powerful technique to elucidate molecular structures of peptides/proteins at buried solid/liquid and liquid/liquid interfaces. SFG has been successfully applied to study molecular interactions between model cell membranes and antimicrobial peptides/membrane proteins, surface-immobilized peptides/enzymes, and physically adsorbed peptides/proteins on polymers and 2D materials. A variety of other analytical techniques and computational simulations provide supporting information to SFG studies, leading to more complete understanding of structure-function relationships of interfacial peptides/proteins. With the advance of SFG techniques and data analysis methods, along with newly developed supplemental tools and simulation methodology, SFG research on interfacial peptides/proteins will further impact research in fields like chemistry, biology, biophysics, engineering, and beyond.
Collapse
Affiliation(s)
- Wen Guo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tieyi Lu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zahra Gandhi
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
27
|
Huang H, Zhang C, Crisci R, Lu T, Hung HC, Sajib MSJ, Sarker P, Ma J, Wei T, Jiang S, Chen Z. Strong Surface Hydration and Salt Resistant Mechanism of a New Nonfouling Zwitterionic Polymer Based on Protein Stabilizer TMAO. J Am Chem Soc 2021; 143:16786-16795. [PMID: 34582683 DOI: 10.1021/jacs.1c08280] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Zwitterionic polymers exhibit excellent nonfouling performance due to their strong surface hydrations. However, salt molecules may severely reduce the surface hydrations of typical zwitterionic polymers, making the application of these polymers in real biological and marine environments challenging. Recently, a new zwitterionic polymer brush based on the protein stabilizer trimethylamine N-oxide (TMAO) was developed as an outstanding nonfouling material. Using surface-sensitive sum frequency generation (SFG) vibrational spectroscopy, we investigated the surface hydration of TMAO polymer brushes (pTMAO) and the effects of salts and proteins on such surface hydration. It was discovered that exposure to highly concentrated salt solutions such as seawater only moderately reduced surface hydration. This superior resistance to salt effects compared to other zwitterionic polymers is due to the shorter distance between the positively and negatively charged groups, thus a smaller dipole in pTMAO and strong hydration around TMAO zwitterion. This results in strong bonding interactions between the O- in pTMAO and water, and weaker interaction between O- and metal cations due to the strong repulsion from the N+ and hydration water. Computer simulations at quantum and atomistic scales were performed to support SFG analyses. In addition to the salt effect, it was discovered that exposure to proteins in seawater exerted minimal influence on the pTMAO surface hydration, indicating complete exclusion of protein attachment. The excellent nonfouling performance of pTMAO originates from its extremely strong surface hydration that exhibits effective resistance to disruptions induced by salts and proteins.
Collapse
Affiliation(s)
| | | | | | | | - Hsiang-Chieh Hung
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Md Symon Jahan Sajib
- Department of Chemical Engineering, Howard University, Washington D.C. 20059, United States
| | - Pranab Sarker
- Department of Chemical Engineering, Howard University, Washington D.C. 20059, United States
| | - Jinrong Ma
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington D.C. 20059, United States
| | - Shaoyi Jiang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | | |
Collapse
|
28
|
Relaxation behavior of polymer thin films: Effects of free surface, buried interface, and geometrical confinement. Prog Polym Sci 2021. [DOI: 10.1016/j.progpolymsci.2021.101431] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
29
|
Lin L, Chowdhury AU, Ma YZ, Sacci RL, Katsaras J, Hong K, Collier CP, Carrillo JMY, Doughty B. Ion Pairing Mediates Molecular Organization Across Liquid/Liquid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:33734-33743. [PMID: 34235915 DOI: 10.1021/acsami.1c09763] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Liquid/liquid interfaces play a central role in scientific fields ranging from nanomaterial synthesis and soft matter electronics to nuclear waste remediation and chemical separations. This diversity of functions arises from an interface's ability to respond to changing conditions in its neighboring bulk phases. Understanding what drives this interfacial flexibility can provide novel avenues for designing new functional interfaces. However, limiting this progress is an inadequate understanding of the subtle intermolecular and interphase interactions taking place at the molecular level. Here, we use surface-specific vibrational sum frequency generation spectroscopy combined with atomistic molecular dynamics simulations to investigate the self-assembly and structure of model ionic oligomers consisting of an oligodimethylsiloxane (ODMS) tail covalently attached to a positively charged methyl imidazolium (MIM+) head group at buried oil/aqueous interfaces. We show how the presence of seemingly innocuous salts can impart dramatic changes to the ODMS tail conformations in the oil phase via specific ion effects and ion-pairing interactions taking place in the aqueous phase. These specific ion interactions are shown to drive enhanced amphiphile adsorption, induce morphological changes, and disrupt emergent hydrogen-bonding structures at the interface. Tuning these interactions allows for independent control over the oligomer structure in the oil phase versus interfacial population changes and represents key mechanistic insight that is needed to control chemical reactions at liquid/liquid interfaces.
Collapse
Affiliation(s)
- Lu Lin
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Azhad U Chowdhury
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Ying-Zhong Ma
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert L Sacci
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Kunlun Hong
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Benjamin Doughty
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| |
Collapse
|
30
|
Guo W, Zou X, Jiang H, Koebke KJ, Hoarau M, Crisci R, Lu T, Wei T, Marsh ENG, Chen Z. Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein. J Phys Chem B 2021; 125:7706-7716. [PMID: 34254804 DOI: 10.1021/acs.jpcb.1c03849] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.
Collapse
Affiliation(s)
- Wen Guo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Xingquan Zou
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Karl J Koebke
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Marie Hoarau
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Ralph Crisci
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Tieyi Lu
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Tao Wei
- Department of Chemical Engineering, Howard University, 2366 Sixth Street, NW, Washington, D.C. 20059, United States
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
31
|
Jia Y, Guo S, Han Q, Zhu J, Zhang X, Na N, Ouyang J. Target-triggered and controlled release plasmon-enhanced fluorescent AIE probe for conformational monitoring of insulin fibrillation. J Mater Chem B 2021; 9:5128-5135. [PMID: 34132315 DOI: 10.1039/d1tb00712b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, we constructed a target-triggered and controlled-release plasmon-enhanced fluorescent AIE probe to realize the purpose of conformational monitoring of insulin fibrillation. We synthesized a novel water-soluble anthracene derivative, 4,4',4'',4'''-(anthracene-9,10-diylbis(ethene-2,1,1-triyl))tetrakis(N,N,N-trimethylbenzenaminium) iodide (BDVAI), with AIE properties, high biocompatibility and good self-assembly effect. Gold nanocages (AuNCs) were selected as the substrate for PEF, and the inner space of hollow AuNCs was filled with BDVAI. Thiol-modified DNA chains were bonded to the surface of AuNCs by Au-S bonds, and an insulin aptamer was combined with the sulfhydryl chain to seal the AuNCs. This PEF-AIE sensor produces different fluorescence signals when interacting with native insulin and fibrillar insulin; thus, monitoring conformational changes in insulin can be realized by detecting fluorescence intensity changes during insulin fibrillation. Based on this design, this system realized sensitive detection of fibrillar insulin with a detection limit of 23.6 pM. This AIE molecular-based PEF fluorescence enhancement system improves the optical properties of fluorescent substances, which is of great significance in improving the detection sensitivity of amyloid fibrils conformational changes and providing a reliable basis for further understanding the pathogenesis of amyloidosis.
Collapse
Affiliation(s)
- Yijing Jia
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | | | | | | | | | | | | |
Collapse
|
32
|
Suo H, Li M, Liu R, Xu L. Enhancing bio-catalytic performance of lipase immobilized on ionic liquids modified magnetic polydopamine. Colloids Surf B Biointerfaces 2021; 206:111960. [PMID: 34224932 DOI: 10.1016/j.colsurfb.2021.111960] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/03/2021] [Accepted: 06/28/2021] [Indexed: 01/09/2023]
Abstract
In this study, imidazolium-based ionic liquid with [tf2N]- as the anion was successfully grafted to magnetic polydopamine nanoparticles (MPDA). The prepared materials were well characterized and used as supports for lipase immobilization. The immobilized lipase (PPL-ILs-MPDA) exhibited excellent activity and stability. The specific activity of PPL-ILs-MPDA was 2.15 and 1.49 folds higher than that of free PPL and PPL-MPDA. In addition, after 10 rounds of reuse, the residual activity of PPL-ILs-MPDA was 86.2 % higher than that of PPL-MPDA (75.4 %). Furthermore, the kinetic assay indicated that the affinity between PPL-ILs-MPDA and substrate had increased. Analysis of the secondary structure using circular dichroism was used to explain the mechanism underlying the improvement in the performance of PPL-ILs-MPDA. In addition, the immobilized lipase can be easily separated from the reaction system with a magnet. The observations regarding the development of new supports for lipase immobilization may provide new ideas regarding further studies in this field.
Collapse
Affiliation(s)
- Hongbo Suo
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China
| | - Moju Li
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China
| | - Renmin Liu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| | - Lili Xu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong, 252059, China.
| |
Collapse
|
33
|
Zhang C, Gao J, Hankett J, Varanasi P, Kerobo CO, Zhao S, Chen Z. Interfacial Structure and Interfacial Tension in Model Carbon Fiber-Reinforced Polymers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5311-5320. [PMID: 33880927 DOI: 10.1021/acs.langmuir.1c00403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Carbon fiber-reinforced plastics (CFRPs) are widely used materials with outstanding mechanical properties. The wettability between the polymer matrix and carbon fiber in the interphase region significantly influences the strength of the composite. Sizing agents consisting of multiple components are therefore frequently applied to improve wetting and interfacial adhesion between polymers and carbon fiber in CFRPs. However, the complex compositions of sizing solutions make detailed interpretations of their impacts on interfacial wetting difficult. In this work, surface-sensitive sum frequency generation (SFG) spectroscopy was utilized to characterize the sizing/polymer and sizing/carbon fiber interfacial structures to gain molecular-level understandings of the wetting improvements afforded by sizing. A mixture sizing solution containing polyethylenimine (PEI, adhesion promoter) and Lutensol (surfactant) was investigated when contacting nylon (model plastics), polypropylene (model plastics), and graphite (model carbon fiber). Our results demonstrated that although the addition of the surfactant led to an interfacial tension decrease (in comparison to pure PEI solution) on nylon and polypropylene, the interfacial tension was surprisingly increased on graphite, contrasting with the commonly accepted function of surfactants. SFG characterizations revealed the multilayer molecular structures at these buried interfaces. The peculiar interfacial tension increase at the graphite/sizing interface was then correlated to the strong amine-π interactions between PEI and graphite. PEI was therefore demonstrated to be an effective adhesion promoter for carbon fiber. This article reports the first investigation of (polymer + surfactant) complex structures at solid-liquid interfaces. The valuable structural insights obtained by SFG analysis enable more accurate understandings of the composition-wettability (structure-function) relationship. These detailed understandings of interactions between sizing and the substrates promote more informed and optimized selections of sizing formulae.
Collapse
Affiliation(s)
- Chengcheng Zhang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Jinpeng Gao
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Jeanne Hankett
- BASF Corporation, 1609 Biddle Avenue, Wyandotte, Michigan 48192, United States
| | - Prabodh Varanasi
- BASF Corporation, 1609 Biddle Avenue, Wyandotte, Michigan 48192, United States
| | - Charles O Kerobo
- BASF Corporation, 1609 Biddle Avenue, Wyandotte, Michigan 48192, United States
| | - Shouxun Zhao
- BASF Corporation, 1609 Biddle Avenue, Wyandotte, Michigan 48192, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
34
|
Pushpavanam K, Ma J, Cai Y, Naser NY, Baneyx F. Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication. Annu Rev Chem Biomol Eng 2021; 12:333-357. [PMID: 33852353 DOI: 10.1146/annurev-chembioeng-102020-015923] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is considerable interest in the development of hybrid organic-inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Here, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.
Collapse
Affiliation(s)
- Karthik Pushpavanam
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
| | - Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Nada Y Naser
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA; .,Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
| |
Collapse
|
35
|
Ramadan S, Lobo R, Zhang Y, Xu L, Shaforost O, Kwong Hong Tsang D, Feng J, Yin T, Qiao M, Rajeshirke A, Jiao LR, Petrov PK, Dunlop IE, Titirici MM, Klein N. Carbon-Dot-Enhanced Graphene Field-Effect Transistors for Ultrasensitive Detection of Exosomes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:7854-7864. [PMID: 33560115 DOI: 10.1021/acsami.0c18293] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Graphene field-effect transistors (GFETs) are suitable building blocks for high-performance electrical biosensors, because graphene inherently exhibits a strong response to charged biomolecules on its surface. However, achieving ultralow limit-of-detection (LoD) is limited by sensor response time and screening effect. Herein, we demonstrate that the detection limit of GFET biosensors can be improved significantly by decorating the uncovered graphene sensor area with carbon dots (CDs). The developed CDs-GFET biosensors used for exosome detection exhibited higher sensitivity, faster response, and three orders of magnitude improvements in the LoD compared with nondecorated GFET biosensors. A LoD down to 100 particles/μL was achieved with CDs-GFET sensor for exosome detection with the capability for further improvements. The results were further supported by atomic force microscopy (AFM) and fluorescent microscopy measurements. The high-performance CDs-GFET biosensors will aid the development of an ultrahigh sensitivity biosensing platform based on graphene for rapid and early diagnosis of diseases.
Collapse
Affiliation(s)
- Sami Ramadan
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Richard Lobo
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Yuanzhou Zhang
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lizhou Xu
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Olena Shaforost
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Jingyu Feng
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Tianyi Yin
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mo Qiao
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Anvesh Rajeshirke
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Long R Jiao
- Department of Hepatobiliary Surgery, Division of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Peter K Petrov
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Iain E Dunlop
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Maria-Magdalena Titirici
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Norbert Klein
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
36
|
Zheng S, Sajib MSJ, Wei Y, Wei T. Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface. J Chem Theory Comput 2021; 17:1874-1882. [PMID: 33586958 DOI: 10.1021/acs.jctc.0c01172] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fundamental understanding of biomolecular interfacial behavior, such as protein adsorption at the microscopic scale, is critical to broad applications in biomaterials, nanomedicine, and nanoparticle-based biosensing techniques. The goal of achieving both computational efficiency and accuracy presents a major challenge for simulation studies at both atomistic and molecular scales. In this work, we developed a unique, accurate, high-throughput simulation method which, by integrating discontinuous molecular dynamics (DMD) simulations with the Go-like protein-surface interaction model, not only solves the dynamics efficiently, but also describes precisely the protein intramolecular and intermolecular interactions at the atomistic scale and the protein-surface interactions at the coarse-grained scale. Using our simulation method and in-house developed software, we performed a systematic study of α-helical ovispirin-1 peptide adsorption on a graphene surface, and our study focused on the effect of surface hydrophobic interactions and π-π stacking on protein adsorption. Our DMD simulations were consistent with full-atom molecular dynamics simulations and showed that a single ovispirin-1 peptide lay down on the flat graphene surface with randomized secondary structure due to strong protein-surface interactions. Peptide aggregates were formed with an internal hydrophobic core driven by strong interactions of hydrophobic residues in the bulk environment. However, upon adsorption, the hydrophobic graphene surface can break the hydrophobic core by denaturing individual peptide structures, leading to disassembling the aggregate structure and further randomizing the ovispirin-1 peptide's secondary structures.
Collapse
Affiliation(s)
- Size Zheng
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
| | - Md Symon Jahan Sajib
- Chemical Engineering Department, Howard University, Washington, D.C. 20059, United States
| | - Yong Wei
- Department of Computer Science and Information Systems, University of North Georgia, Dahlonega, Georgia 30597, United States
| | - Tao Wei
- Chemical Engineering Department, Howard University, Washington, D.C. 20059, United States
| |
Collapse
|
37
|
Badhe Y, Gupta R, Rai B. In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection. RSC Adv 2021; 11:3816-3826. [PMID: 35424358 PMCID: PMC8694220 DOI: 10.1039/d0ra09123e] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people across the globe and created not only a health emergency but also a financial crisis. This virus attacks the angiotensin-converting enzyme 2 (ACE2) receptor situated on the surface of the host cell membrane. The spike protein of the virus binds to this receptor which is a critical step in infection. A molecule which can specifically stop this binding could be a potential therapeutic agent. In this study, we have tested 12 potential peptides which can bind to the receptor binding domain (RBD) of the spike protein of the virus and thus can potentially inhibit the binding of the latter on ACE2 receptors. These peptides are screened based on their binding with the RBD of the spike protein and aqueous stability, obtained using several atomistic molecular dynamic simulations. The potential of mean force calculation of peptides confirmed their binding to the RBD of the spike protein. Furthermore, two potential peptides were tested for use in a biosensing application for SARS-CoV-2 detection. Two types of biosensing platforms, a graphene sheet and a carbon nano tube (CNT) were tested. The peptides were modified in order to functionalize the graphene and CNT. Based on the interaction between the substrate, peptide and spike protein, the utility of the screened peptide for a given bio sensing platform is discussed and recommended. The protocol for peptide design and testing for its usage as a sensor.![]()
Collapse
Affiliation(s)
- Yogesh Badhe
- Physical Science Research Area
- Tata Research Development and Design Centre
- TCS Research
- Tata Consultancy Services
- Pune-411013
| | - Rakesh Gupta
- Physical Science Research Area
- Tata Research Development and Design Centre
- TCS Research
- Tata Consultancy Services
- Pune-411013
| | - Beena Rai
- Physical Science Research Area
- Tata Research Development and Design Centre
- TCS Research
- Tata Consultancy Services
- Pune-411013
| |
Collapse
|
38
|
Zhang S, Andre JS, Hsu L, Toolis A, Esarey SL, Li B, Chen Z. Nondestructive In Situ Detection of Chemical Reactions at the Buried Interface between Polyurethane and Isocyanate-Based Primer. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01862] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shuqing Zhang
- Department of Macromolecular Science and Engineering, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - John S Andre
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Lorraine Hsu
- Coatings and Innovation Center, PPG, 4325 Rosanna Drive, Allison Park, Pennsylvania 15101, United States
| | - Amy Toolis
- Coatings and Innovation Center, PPG, 4325 Rosanna Drive, Allison Park, Pennsylvania 15101, United States
| | - Samuel L Esarey
- Coatings and Innovation Center, PPG, 4325 Rosanna Drive, Allison Park, Pennsylvania 15101, United States
| | - Bolin Li
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- Department of Macromolecular Science and Engineering, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
39
|
Wang X, Lan PC, Ma S. Metal-Organic Frameworks for Enzyme Immobilization: Beyond Host Matrix Materials. ACS CENTRAL SCIENCE 2020; 6:1497-1506. [PMID: 32999925 PMCID: PMC7517118 DOI: 10.1021/acscentsci.0c00687] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 05/15/2023]
Abstract
Enzyme immobilization in metal-organic frameworks (MOFs) as a promising strategy is attracting the interest of scientists from different disciplines with the expansion of MOFs' development. Different from other traditional host materials, their unique strengths of high surface areas, large yet adjustable pore sizes, functionalizable pore walls, and diverse architectures make MOFs an ideal platform to investigate hosted enzymes, which is critical to the industrial and commercial process. In addition to the protective function of MOFs, the extensive roles of MOFs in the enzyme immobilization are being well-explored by making full use of their remarkable properties like well-defined structure, high porosity, and tunable functionality. Such development shifts the focus from the exploration of immobilization strategies toward functionalization. Meanwhile, this would undoubtedly contribute to a better understanding of enzymes in regards to the structural transformation after being hosted in a confinement environment, particularly to the orientation and conformation change as well as the interplay between enzyme and matrix MOFs. In this Outlook, we target a comprehensive review of the role diversities of the host matrix MOF based on the current enzyme immobilization research, along with proposing an outlook toward the future development of this field, including the representatives of potential techniques and methodologies being capable of studying the hosted enzymes.
Collapse
Affiliation(s)
- Xiaoliang Wang
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Pui Ching Lan
- Department
of Chemistry, University of North Texas, 1508 West Mulberry Street, Denton, Texas 76201, United States
| | - Shengqian Ma
- Department
of Chemistry, University of North Texas, 1508 West Mulberry Street, Denton, Texas 76201, United States
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
- E-mail:
| |
Collapse
|
40
|
Zheng H, Yang SJ, Zheng YC, Cui Y, Zhang Z, Zhong JY, Zhou J. Electrostatic Effect of Functional Surfaces on the Activity of Adsorbed Enzymes: Simulations and Experiments. ACS APPLIED MATERIALS & INTERFACES 2020; 12:35676-35687. [PMID: 32649833 DOI: 10.1021/acsami.0c08080] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The efficient immobilization of haloalkane dehalogenase (DhaA) on carriers with retaining of its catalytic activity is essential for its application in environmental remediation. In this work, adsorption orientation and conformation of DhaA on different functional surfaces were investigated by computer simulations; meanwhile, the mechanism of varying the catalytic activity was also probed. The corresponding experiments were then carried out to verify the simulation results. (The simulations of DhaA on SAMs provided parallel insights into DhaA adsorption in carriers. Then, the theory-guided experiments were carried out to screen the best surface functional groups for DhaA immobilization.) The electrostatic interaction was considered as the main impact factor for the regulation of enzyme orientation, conformation, and enzyme bioactivity during DhaA adsorption. The synergy of overall conformation, enzyme substrate tunnel structural parameters, and distance between catalytic active sites and surfaces codetermined the catalytic activity of DhaA. Specifically, it was found that the positively charged surface with suitable surface charge density was helpful for the adsorption of DhaA and retaining its conformation and catalytic activity and was favorable for higher enzymatic catalysis efficiency in haloalkane decomposition and environmental remediation. The neutral, negatively charged surfaces and positively charged surfaces with high surface charge density always caused relatively larger DhaA conformation change and decreased catalytic activity. This study develops a strategy using a combination of simulation and experiment, which can be essential for guiding the rational design of the functionalization of carriers for enzyme adsorption, and provides a practical tool to rationally screen functional groups for the optimization of adsorbed enzyme functions on carriers. More importantly, the strategy is general and can be applied to control behaviors of different enzymes on functional carrier materials.
Collapse
Affiliation(s)
- He Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Sheng-Jiang Yang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yong-Chao Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Yan Cui
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Zhe Zhang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Jin-Yi Zhong
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| |
Collapse
|
41
|
Tiwari S, Patil R, Dubey SK, Bahadur P. Graphene nanosheets as reinforcement and cell-instructive material in soft tissue scaffolds. Adv Colloid Interface Sci 2020; 281:102167. [PMID: 32361407 DOI: 10.1016/j.cis.2020.102167] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/11/2022]
Abstract
Mechanical strength of polymeric scaffolds deteriorates quickly in the physiological mileu. This can be minimized by reinforcing the polymeric matrix with graphene, a planar two-dimensional material with unique physicochemical and biological properties. Association between the sheet and polymer chains offers a range of porosity commensurate with tissue requirements. Besides, studies suggest that corrugated structure of graphene offers desirable bio-mechanical cues for tissue regeneration. This review covers three important aspects of graphene-polymer composites, (a) the opportunity on reinforcing the polymer matrix with graphene, (b) challenges associated with limited aqueous processability of graphene, and (c) physiological signaling in the presence of graphene. Among numerous graphene materials, our discussion is limited to graphene oxide (GO) and reduced graphene oxide (rGO) nanosheets. Challenges associated with limited dispersity of hydrophobic sheets within the polymeric matrix have been discussed at molecular level.
Collapse
|
42
|
Wang W, Tan J, Ye S. Unsaturated Lipid Accelerates Formation of Oligomeric β-Sheet Structure of GP41 Fusion Peptide in Model Cell Membrane. J Phys Chem B 2020; 124:5169-5176. [PMID: 32453953 DOI: 10.1021/acs.jpcb.0c02464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Membrane fusion of the viral and host cell membranes is the initial step of virus infection and is catalyzed by fusion peptides. Although the β-sheet structure of fusion peptides has been proposed to be the most important fusion-active conformation, it is still very challenging to experimentally identify different types of β-sheet structures at the cell membrane surface in situ and in real time. In this work, we demonstrate that the interface-sensitive amide II spectral signals of protein backbones, generated by the sum frequency generation vibrational spectroscopy, provide a sensitive probe for directly capturing the formation of oligomeric β-sheet structure of fusion peptides. Using human immunodeficiency virus (HIV) glycoprotein GP41 fusing peptide (FP23) as the model, we find that formation speed of oligomeric β-sheet structure depends on lipid unsaturation. The unsaturated lipid such as POPG can accelerate formation of oligomeric β-sheet structure of FP23. The β-sheet structure is more deeply inserted into the hydrophobic region of the POPG bilayer than the α-helical segment. This work will pave the way for future researches on capturing intermediate structures during membrane fusion processes and revealing the fusion mechanism.
Collapse
Affiliation(s)
- Wenting Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Junjun Tan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shuji Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| |
Collapse
|
43
|
Zhang L, Ying Y, Li Y, Fu Y. Integration and synergy in protein-nanomaterial hybrids for biosensing: Strategies and in-field detection applications. Biosens Bioelectron 2020; 154:112036. [DOI: 10.1016/j.bios.2020.112036] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
|
44
|
Zhang J, Tan J, Pei R, Ye S. Acidic Environment Significantly Alters Aggregation Pathway of Human Islet Amyloid Polypeptide at Negative Lipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1530-1537. [PMID: 31995712 DOI: 10.1021/acs.langmuir.9b03623] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The misfolding and aggregation of human islet amyloid polypeptide (hIAPP) at cell membrane has a close relationship with the development of type 2 diabetes (T2DM). This aggregation process is susceptible to various physiologically related factors, and systematic studies on condition-mediated hIAPP aggregation are therefore essential for a thorough understanding of the pathology of T2DM. In this study, we combined surface-sensitive amide I and amide II spectral signals from the protein backbone, generated simultaneously in a highly sensitive femtosecond broad-band sum frequency generation vibrational spectroscopy system, to examine the effect of environmental pH on the dynamical structural changes of hIAPP at membrane surface in situ and in real time. Such a combination can directly discriminate the formation of β-hairpin-like monomer and oligomer/fibril at the membrane surface. It is evident that, in an acidic milieu, hIAPP slows down its conformational evolution and alters its aggregation pathway, leading to the formation of off-pathway oligomers. When matured hIAPP aggregates are exposed to basic subphase, partial conversion from β-sheet oligomers into ordered β-sheet fibrillar structures is observed. When exposed to acidic environment, however, hIAPP fibrils partially converse into more loosely patterned β-sheet oligomeric structures.
Collapse
Affiliation(s)
- Jiahui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Junjun Tan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Ruoqi Pei
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Shuji Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
| |
Collapse
|