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Bhattacharjee N, Alonso-Cotchico L, Lucas MF. Enzyme immobilization studied through molecular dynamic simulations. Front Bioeng Biotechnol 2023; 11:1200293. [PMID: 37362217 PMCID: PMC10285225 DOI: 10.3389/fbioe.2023.1200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.
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2
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A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:ijms221910813. [PMID: 34639151 PMCID: PMC8509277 DOI: 10.3390/ijms221910813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.
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3
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García-Hevia L, Saramiforoshani M, Monge J, Iturrioz-Rodríguez N, Padín-González E, González F, González-Legarreta L, González J, Fanarraga ML. The unpredictable carbon nanotube biocorona and a functionalization method to prevent protein biofouling. J Nanobiotechnology 2021; 19:129. [PMID: 33952241 PMCID: PMC8097984 DOI: 10.1186/s12951-021-00872-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/24/2021] [Indexed: 01/10/2023] Open
Abstract
Background The intrinsic physicochemical properties of carbon nanotubes (CNTs) make them unique tools in nanotechnology. Their elemental composition, resilience, thermal properties, and surface reactivity make CNTs also of undisputed interest in biotechnology. In particular, their extraordinary ability to capture biomolecules on their surface makes them essential in this field. The proteins adsorbed on the CNTs create a biological coating that endows them the ability to interact with some cell receptors, penetrate membranes or interfere with cell biomechanics, thus behaving as an active bio-camouflage. But some of these proteins unfold, triggering an immune response that unpredictably changes the biological activity of CNTs. For this reason, the control of the biocorona is fundamental in the nanobiotechnology of CNTs. Results Using TEM and AFM here we demonstrate a significant increase in CNTs diameter after protein functionalization. A quantitative analysis using TGA revealed that between 20 and 60% of the mass of functionalized nanotubes corresponds to protein, with single-walled CNTs capturing the highest amounts. To qualitatively/quantitatively characterize these biocoatings, we studied the biochemical "landscape" of the proteins captured by the different nanotubes after functionalization under various conditions. This study revealed a significant variability of the proteins in the corona as a function of the type of nanotube, the functionalization temperature, or the time after exposure to serum. Remarkably, the functionalization of a single type of CNT with sera from various human donors also resulted in different protein landscapes. Given the unpredictable assortment of proteins captured by the corona and the biological implications of this biocoating, we finally designed a method to genetically engineer and produce proteins to functionalize nanotubes in a controlled and customizable way. Conclusions We demonstrate the high unpredictability of the spontaneous protein corona on CNTs and propose a versatile functionalization technique that prevents the binding of nonspecific proteins to the nanotube to improve the use of CNTs in biomedical applications.
![]() Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-00872-x.
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Affiliation(s)
- Lorena García-Hevia
- The Nanomedicine Group, University of Cantabria-IDIVAL, 39011, Santander, Spain.
| | | | - Jorge Monge
- Osakidetza, Basque Center for Blood Transfusion and Human Tissues, Galdakao, Spain. Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Nerea Iturrioz-Rodríguez
- The Nanomedicine Group, University of Cantabria-IDIVAL, 39011, Santander, Spain.,Istituto Italiano Di Tecnologia, Smart Bio-Interfaces, Viale Rinaldo Piaggio 34, 56025, Pontedera, Italy
| | - Esperanza Padín-González
- The Nanomedicine Group, University of Cantabria-IDIVAL, 39011, Santander, Spain.,Department of Chemistry, Royal College of Surgeons in Ireland, Dublin, D02 YN77, Ireland
| | - Fernando González
- The Nanomedicine Group, University of Cantabria-IDIVAL, 39011, Santander, Spain.,Department of Chemistry and Process & Resource Engineering, University of Cantabria, Barakaldo, Spain
| | - Lorena González-Legarreta
- The Nanomedicine Group, University of Cantabria-IDIVAL, 39011, Santander, Spain.,Department of Chemistry and Process & Resource Engineering, University of Cantabria, Barakaldo, Spain
| | - Jesús González
- The Nanomedicine Group, University of Cantabria-IDIVAL, 39011, Santander, Spain
| | - Mónica L Fanarraga
- The Nanomedicine Group, University of Cantabria-IDIVAL, 39011, Santander, Spain
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4
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Pandey A, Nikam AN, Padya BS, Kulkarni S, Fernandes G, Shreya AB, García MC, Caro C, Páez-Muñoz JM, Dhas N, García-Martín ML, Mehta T, Mutalik S. Surface architectured black phosphorous nanoconstructs based smart and versatile platform for cancer theranostics. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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5
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Abdelsattar AS, Dawoud A, Helal MA. Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies. Nanotoxicology 2020; 15:66-95. [PMID: 33283572 DOI: 10.1080/17435390.2020.1842537] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The high frequency of using engineered nanoparticles in various medical applications entails a deep understanding of their interaction with biological macromolecules. Molecular docking simulation is now widely used to study the binding of different types of nanoparticles with proteins and nucleic acids. This helps not only in understanding the mechanism of their biological action but also in predicting any potential toxicity. In this review, the computational techniques used in studying the nanoparticles interaction with biological macromolecules are covered. Then, a comprehensive overview of the docking studies performed on various types of nanoparticles will be offered. The implication of these predicted interactions in the biological activity and/or toxicity is also discussed for each type of nanoparticles.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray and Determination of Structure of Matter, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Mohamed A Helal
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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6
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Park SJ. Protein-Nanoparticle Interaction: Corona Formation and Conformational Changes in Proteins on Nanoparticles. Int J Nanomedicine 2020; 15:5783-5802. [PMID: 32821101 PMCID: PMC7418457 DOI: 10.2147/ijn.s254808] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/21/2020] [Indexed: 12/11/2022] Open
Abstract
Nanoparticles (NPs) are highly potent tools for the diagnosis of diseases and specific delivery of therapeutic agents. Their development and application are scientifically and industrially important. The engineering of NPs and the modulation of their in vivo behavior have been extensively studied, and significant achievements have been made in the past decades. However, in vivo applications of NPs are often limited by several difficulties, including inflammatory responses and cellular toxicity, unexpected distribution and clearance from the body, and insufficient delivery to a specific target. These unfavorable phenomena may largely be related to the in vivo protein-NP interaction, termed "protein corona." The layer of adsorbed proteins on the surface of NPs affects the biological behavior of NPs and changes their functionality, occasionally resulting in loss-of-function or gain-of-function. The formation of a protein corona is an intricate process involving complex kinetics and dynamics between the two interacting entities. Structural changes in corona proteins have been reported in many cases after their adsorption on the surfaces of NPs that strongly influence the functions of NPs. Thus, understanding of the conformational changes and unfolding process of proteins is very important to accelerate the biomedical applications of NPs. Here, we describe several protein corona characteristics and specifically focus on the conformational fluctuations in corona proteins induced by NPs.
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Affiliation(s)
- Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon21936, Korea
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7
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Di Costanzo L, Geremia S. Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins. Molecules 2020; 25:E3555. [PMID: 32759758 PMCID: PMC7435792 DOI: 10.3390/molecules25153555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.
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Affiliation(s)
- Luigi Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, 100, 80055 Portici, Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
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8
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Noor M, Goswami J, Davis VA. Comparison of Attachment and Antibacterial Activity of Covalent and Noncovalent Lysozyme-Functionalized Single-Walled Carbon Nanotubes. ACS OMEGA 2020; 5:2254-2259. [PMID: 32064386 PMCID: PMC7016910 DOI: 10.1021/acsomega.9b03387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Carbon nanotube-lysozyme (LSZ) conjugates provide an attractive combination of high strength and antimicrobial activity. However, there has not been a direct comparison of the covalent and noncovalent methods for creating them. In this work, single-walled carbon nanotubes (SWNT) were functionalized with LSZ using both noncovalent adsorption and covalent attachment via N-ethyl-N-(3-dimethylamino-propyl) carbodiimide hydrochloride-N-hydroxysuccinimide (EDC-NHS) chemistry. The amount of attached lysozyme, dispersion stability, and antimicrobial activity was compared. In addition, the mechanical properties of LSZ-SWNT in poly(vinyl alcohol) (PVA) composite films were investigated. Dispersions of covalently bound LSZ-SWNT had better dispersion stability. This was attributed to covalent functionalization enabling sustained SWNT dispersion at a lower LSZ/SWNT ratio. The covalently bound LSZ-SWNT also exhibited a lower initial rate of antibacterial response but were active over a longer time scale. Composite films made from LSZ-SWNT maintained similar activity as the corresponding dispersions. However, the noncovalent LSZ-SWNT films were stronger and more hydrolytically stable than those made from covalent LSZ-SWNT.
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Affiliation(s)
- Matthew
M. Noor
- Department of Chemical Engineering, Auburn University, 212 Ross Hal, Auburn, Alabama 36849, United States
| | - Joyanta Goswami
- Department of Chemical Engineering, Auburn University, 212 Ross Hal, Auburn, Alabama 36849, United States
| | - Virginia A. Davis
- Department of Chemical Engineering, Auburn University, 212 Ross Hal, Auburn, Alabama 36849, United States
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9
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Qu G, Xia T, Zhou W, Zhang X, Zhang H, Hu L, Shi J, Yu XF, Jiang G. Property-Activity Relationship of Black Phosphorus at the Nano-Bio Interface: From Molecules to Organisms. Chem Rev 2020; 120:2288-2346. [PMID: 31971371 DOI: 10.1021/acs.chemrev.9b00445] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a novel member of the two-dimensional nanomaterial family, mono- or few-layer black phosphorus (BP) with direct bandgap and high charge carrier mobility is promising in many applications such as microelectronic devices, photoelectronic devices, energy technologies, and catalysis agents. Due to its benign elemental composition (phosphorus), large surface area, electronic/photonic performances, and chemical/biological activities, BP has also demonstrated a great potential in biomedical applications including biosensing, photothermal/photodynamic therapies, controlled drug releases, and antibacterial uses. The nature of the BP-bio interface is comprised of dynamic contacts between nanomaterials (NMs) and biological systems, where BP and the biological system interact. The physicochemical interactions at the nano-bio interface play a critical role in the biological effects of NMs. In this review, we discuss the interface in the context of BP as a nanomaterial and its unique physicochemical properties that may affect its biological effects. Herein, we comprehensively reviewed the recent studies on the interactions between BP and biomolecules, cells, and animals and summarized various cellular responses, inflammatory/immunological effects, as well as other biological outcomes of BP depending on its own physical properties, exposure routes, and biodistribution. In addition, we also discussed the environmental behaviors and potential risks on environmental organisms of BP. Based on accumulating knowledge on the BP-bio interfaces, this review also summarizes various safer-by-design strategies to change the physicochemical properties including chemical stability and nano-bio interactions, which are critical in tuning the biological behaviors of BP. The better understanding of the biological activity of BP at BP-bio interfaces and corresponding methods to overcome the challenges would promote its future exploration in terms of bringing this new nanomaterial to practical applications.
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Affiliation(s)
- Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences 100085 , Beijing , P.R. China.,Institute of Environment and Health , Jianghan University , Wuhan 430056 , China.,Institute of Environment and Health , Hangzhou Institute for Advanced Study, UCAS , Hangzhou 310000 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tian Xia
- Division of Nanomedicine, Department of Medicine , University of California Los Angeles California 90095 , United States
| | - Wenhua Zhou
- Materials Interfaces Center , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P.R. China
| | - Xue Zhang
- Materials Interfaces Center , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P.R. China
| | - Haiyan Zhang
- College of Environment , Zhejiang University of Technology , Hangzhou 310032 , China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences 100085 , Beijing , P.R. China.,Institute of Environment and Health , Jianghan University , Wuhan 430056 , China.,Institute of Environment and Health , Hangzhou Institute for Advanced Study, UCAS , Hangzhou 310000 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences 100085 , Beijing , P.R. China.,Institute of Environment and Health , Jianghan University , Wuhan 430056 , China.,Institute of Environment and Health , Hangzhou Institute for Advanced Study, UCAS , Hangzhou 310000 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xue-Feng Yu
- Materials Interfaces Center , Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055 , P.R. China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences 100085 , Beijing , P.R. China.,Institute of Environment and Health , Jianghan University , Wuhan 430056 , China.,Institute of Environment and Health , Hangzhou Institute for Advanced Study, UCAS , Hangzhou 310000 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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10
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Nanocatalysts Containing Direct Electron Transfer-Capable Oxidoreductases: Recent Advances and Applications. Catalysts 2019. [DOI: 10.3390/catal10010009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Direct electron transfer (DET)-capable oxidoreductases are enzymes that have the ability to transfer/receive electrons directly to/from solid surfaces or nanomaterials, bypassing the need for an additional electron mediator. More than 100 enzymes are known to be capable of working in DET conditions; however, to this day, DET-capable enzymes have been mainly used in designing biofuel cells and biosensors. The rapid advance in (semi) conductive nanomaterial development provided new possibilities to create enzyme-nanoparticle catalysts utilizing properties of DET-capable enzymes and demonstrating catalytic processes never observed before. Briefly, such nanocatalysts combine several cathodic and anodic catalysis performing oxidoreductases into a single nanoparticle surface. Hereby, to the best of our knowledge, we present the first review concerning such nanocatalytic systems involving DET-capable oxidoreductases. We outlook the contemporary applications of DET-capable enzymes, present a principle of operation of nanocatalysts based on DET-capable oxidoreductases, provide a review of state-of-the-art (nano) catalytic systems that have been demonstrated using DET-capable oxidoreductases, and highlight common strategies and challenges that are usually associated with those type catalytic systems. Finally, we end this paper with the concluding discussion, where we present future perspectives and possible research directions.
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11
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Chio L, Del Bonis-O'Donnell JT, Kline MA, Kim JH, McFarlane IR, Zuckermann RN, Landry MP. Electrostatic Assemblies of Single-Walled Carbon Nanotubes and Sequence-Tunable Peptoid Polymers Detect a Lectin Protein and Its Target Sugars. NANO LETTERS 2019; 19:7563-7572. [PMID: 30958010 DOI: 10.1021/acs.nanolett.8b04955] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A primary limitation to real-time imaging of metabolites and proteins has been the selective detection of biomolecules that have no naturally occurring or stable molecular recognition counterparts. We present developments in the design of synthetic near-infrared fluorescent nanosensors based on the fluorescence modulation of single-walled carbon nanotubes (SWNTs) with select sequences of surface-adsorbed N-substituted glycine peptoid polymers. We assess the stability of the peptoid-SWNT nanosensor candidates under variable ionic strengths, protease exposure, and cell culture media conditions and find that the stability of peptoid-SWNTs depends on the composition and length of the peptoid polymer. From our library, we identify a peptoid-SWNT assembly that can detect lectin protein wheat germ agglutinin (WGA) with a sensitivity comparable to the concentration of serum proteins. To demonstrate the retention of nanosensor-bound protein activity, we show that WGA on the nanosensor produces an additional fluorescent signal modulation upon exposure to the lectin's target sugars, suggesting the lectin protein remains active and selectively binds its target sugars through ternary molecular recognition interactions relayed to the nanosensor. Our results inform design considerations for developing synthetic molecular recognition elements by assembling peptoid polymers on SWNTs and also demonstrate these assemblies can serve as optical nanosensors for lectin proteins and their target sugars. Together, these data suggest certain peptoid sequences can be assembled with SWNTs to serve as versatile optical probes to detect proteins and their molecular substrates.
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Affiliation(s)
- Linda Chio
- Department of Chemical and Biomolecular Engineering , University of California, Berkeley , Berkeley , California 94720 , United States
| | | | - Mark A Kline
- The Molecular Foundry , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Jae Hong Kim
- The Molecular Foundry , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Ian R McFarlane
- Department of Chemical and Biomolecular Engineering , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Ronald N Zuckermann
- The Molecular Foundry , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering , University of California, Berkeley , Berkeley , California 94720 , United States
- Chan-Zuckerberg Biohub , San Francisco , California 94158 , United States
- California Institute for Quantitative Biosciences (qb3) , University of California, Berkeley , Berkeley , California 94720 , United States
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12
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Antonucci A, Kupis-Rozmysłowicz J, Boghossian AA. Noncovalent Protein and Peptide Functionalization of Single-Walled Carbon Nanotubes for Biodelivery and Optical Sensing Applications. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11321-11331. [PMID: 28299937 DOI: 10.1021/acsami.7b00810] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The exquisite structural and optical characteristics of single-walled carbon nanotubes (SWCNTs), combined with the tunable specificities of proteins and peptides, can be exploited to strongly benefit technologies with applications in fields ranging from biomedicine to industrial biocatalysis. The key to exploiting the synergism of these materials is designing protein/peptide-SWCNT conjugation schemes that preserve biomolecule activity while keeping the near-infrared optical and electronic properties of SWCNTs intact. Since sp2 bond-breaking disrupts the optoelectronic properties of SWCNTs, noncovalent conjugation strategies are needed to interface biomolecules to the nanotube surface for optical biosensing and delivery applications. An underlying understanding of the forces contributing to protein and peptide interaction with the nanotube is thus necessary to identify the appropriate conjugation design rules for specific applications. This article explores the molecular interactions that govern the adsorption of peptides and proteins on SWCNT surfaces, elucidating contributions from individual amino acids as well as secondary and tertiary protein structure and conformation. Various noncovalent conjugation strategies for immobilizing peptides, homopolypeptides, and soluble and membrane proteins on SWCNT surfaces are presented, highlighting studies focused on developing near-infrared optical sensors and molecular scaffolds for self-assembly and biochemical analysis. The analysis presented herein suggests that though direct adsorption of proteins and peptides onto SWCNTs can be principally applied to drug and gene delivery, in vivo imaging and targeting, or cancer therapy, nondirect conjugation strategies using artificial or natural membranes, polymers, or linker molecules are often better suited for biosensing applications that require conservation of biomolecular functionality or precise control of the biomolecule's orientation. These design rules are intended to provide the reader with a rational approach to engineering biomolecule-SWCNT platforms, broadening the breadth and accessibility of both wild-type and engineered biomolecules for SWCNT-based applications.
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Affiliation(s)
- Alessandra Antonucci
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015-Lausanne, Switzerland
| | - Justyna Kupis-Rozmysłowicz
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015-Lausanne, Switzerland
| | - Ardemis A Boghossian
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015-Lausanne, Switzerland
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13
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Multi-walled carbon nanotubes increase antibody-producing B cells in mice immunized with a tetravalent vaccine candidate for dengue virus. J Nanobiotechnology 2016; 14:61. [PMID: 27465605 PMCID: PMC4964006 DOI: 10.1186/s12951-016-0196-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/23/2016] [Indexed: 12/25/2022] Open
Abstract
Background In recent times, studies have demonstrated that carbon nanotubes are good candidates for use as vehicles for transfection of exogenous material into the cells. However, there are few studies evaluating the behavior of carbon nanotubes as DNA vectors and few of these studies have used multi-walled carbon nanotubes (MWCNTs) or carboxylated MWCNTs. Thus, this study aims to assess the MWCNTs’ (carboxylated or not) efficiency in the increase in expression of the tetravalent vaccine candidate (TVC) plasmid vector for dengue virus in vitro using Vero cells, and in vivo, through the intramuscular route, to evaluate the immunological response profile. Results Multi-walled carbon nanotubes internalized by Vero cells, have been found in the cytoplasm and nucleus associated with the plasmid. However, it was not efficient to increase the messenger ribonucleic acid (mRNA) compared to the pure vaccine candidate associated with Lipofectamine® 2000. The in vivo experiments showed that the use of intramuscular injection of the TVC in combination with MWCNTs reduced the immune response compared to pure TVC, in a general way, although an increase was observed in the population of the antibody-producing B cells, as compared to pure TVC. Conclusions The results confirm the data found by other authors, which demonstrate the ability of nanotubes to penetrate target cells and reach both the cytoplasm and the cell nucleus. The cytotoxicity values are also in accordance with the literature, which range from 5 to 20 µg/mL. This has been found to be 10 µg/mL in this study. Although the expression levels are higher in cells that receive the pure TVC transfected using Lipofectamine® 2000, the nanotubes show an increase in B-cells producing antibodies. Electronic supplementary material The online version of this article (doi:10.1186/s12951-016-0196-7) contains supplementary material, which is available to authorized users.
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14
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Iwashita K, Shiraki K, Ishii R, Tanaka T, Hirano A. Liquid Chromatographic Analysis of the Interaction between Amino Acids and Aromatic Surfaces Using Single-Wall Carbon Nanotubes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015. [PMID: 26208035 DOI: 10.1021/acs.langmuir.5b02500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins have nonspecific adsorption capacities for solid surfaces. Although the nonspecific adsorption capacities are generally understood to be related to the hydrophobicity or charge density of the surfaces, little is known at the amino acid level about the interaction between proteins and polyaromatic surfaces such as carbon nanotubes, which have recently been used for biotechnology applications. In this study, we investigated the interaction between proteinogenic amino acids and carbon nanotubes using high-performance liquid chromatography on silica matrices coated by single-wall carbon nanotubes (SWCNTs). Among the amino acids used in this study, tryptophan, tyrosine, and phenylalanine showed exceptional affinity for the matrices. The characteristic affinities of these amino acids were ascribed to their unique interactions with the large polyaromatic surfaces of the SWCNTs. These results are useful for understanding and controlling protein adsorption onto aromatic surfaces.
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Affiliation(s)
- Kazuki Iwashita
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kentaro Shiraki
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Rieko Ishii
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Takeshi Tanaka
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Atsushi Hirano
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
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15
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Yao K, Tan P, Luo Y, Feng L, Xu L, Liu Z, Li Y, Peng R. Graphene Oxide Selectively Enhances Thermostability of Trypsin. ACS APPLIED MATERIALS & INTERFACES 2015; 7:12270-12277. [PMID: 25985836 DOI: 10.1021/acsami.5b03118] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the past few years, graphene and its derivative, graphene oxide (GO), have been extensively studied for their applications in biotechnology. In our previous work, we reported certain PEGylated GOs (GO-PEGs) can selectively promote trypsin activity and enhance its thermostability. To further explore this, here we synthesized a series of GO-PEGs with varying PEGylation degrees. Enzymatic activity assay shows that both GO and GO-PEGs can protect trypsin, but not chymotrypsin, from thermal denaturation at high temperature. Surprisingly, the lower the PEGylation degree, the better the protection, and GO as well as the GO-PEG with the lowest PEGylation degree show the highest protection efficiency (∼70% retained activity at 70 °C). Fluorescence spectroscopy analysis shows that GO/GO-PEGs have strong interactions with trypsin. Molecular Dynamics (MD) simulation results reveal that trypsin is adsorbed onto the surface of GO through its cationic residues and hydrophilic residues. Different from chymotrypsin adsorbed on GO, the active site of trypsin is covered by GO. MD simulation at high temperature shows that, through such interaction with GO, trypsin's active site is therefore stabilized and protected by GO. Our work not only illustrates the promising potential of GO/GO-PEGs as efficient, selective modulators for trypsin, but also provides the interaction mechanism of GO with specific proteins at the nano-bio interface.
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16
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Bhakta SA, Benavidez TE, Garcia CD. Immobilization of glucose oxidase to nanostructured films of polystyrene-block-poly(2-vinylpyridine). J Colloid Interface Sci 2014; 430:351-6. [PMID: 24980481 DOI: 10.1016/j.jcis.2014.05.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 05/29/2014] [Accepted: 05/31/2014] [Indexed: 12/31/2022]
Abstract
A critical step for the development of biosensors is the immobilization of the biorecognition element to the surface of a substrate. Among other materials that can be used as substrates, block copolymers have the untapped potential to provide significant advantages for the immobilization of proteins. To explore such possibility, this manuscript describes the fabrication and characterization of thin-films of polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP). These films were then used to investigate the immobilization of glucose oxidase, a model enzyme for the development of biosensors. According to the results presented, the nanoporous films can provide significant increases in surface area of the substrate and the immobilization of larger amounts of active enzyme. The characterization of the substrate-enzyme interface discussed in the manuscript aims to provide critical information about relationship between the surface (material, geometry, and density of pores), the protein structure, and the immobilization conditions (pH, and protein concentration) required to improve the catalytic activity and stability of the enzymes. A maximum normalized activity of 3300±700 U m(-2) was achieved for the nanoporous film of PS-b-P2VP.
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Affiliation(s)
- Samir A Bhakta
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle, San Antonio, TX 78249, USA
| | - Tomas E Benavidez
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle, San Antonio, TX 78249, USA
| | - Carlos D Garcia
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle, San Antonio, TX 78249, USA.
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17
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Jimenez-Cruz CA, Kang SG, Zhou R. Large scale molecular simulations of nanotoxicity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014; 6:329-43. [PMID: 24894909 DOI: 10.1002/wsbm.1271] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/02/2014] [Accepted: 05/19/2014] [Indexed: 12/25/2022]
Abstract
The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini-review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon-based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so-called π-π stacking (between aromatic rings), while for the noble metal nanoparticles the long-range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C₈₂(OH)₂₂ is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP-9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells.
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Affiliation(s)
- Camilo A Jimenez-Cruz
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, USA
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18
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Zhong ED, Shirts MR. Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4952-4961. [PMID: 24716898 DOI: 10.1021/la500511p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A better understanding of changes in protein stability upon adsorption can improve the design of protein separation processes. In this study, we examine the coupling of the folding and the adsorption of a model protein, the B1 domain of streptococcal protein G, as a function of surface attraction using a hybrid Monte Carlo (HMC) approach with temperature replica exchange and umbrella sampling. In our HMC implementation, we are able to use a molecular dynamics (MD) time step that is an order of magnitude larger than in a traditional MD simulation protocol and observe a factor of 2 enhancement in the folding and unfolding rate. To demonstrate the convergence of our systems, we measure the travel of our order parameter the fraction of native contacts between folded and unfolded states throughout the length of our simulations. Thermodynamic quantities are extracted with minimum statistical variance using multistate reweighting between simulations at different temperatures and harmonic distance restraints from the surface. The resultant free energies, enthalpies, and entropies of the coupled unfolding and absorption processes are in qualitative agreement with previous experimental and computational observations, including entropic stabilization of the adsorbed, folded state relative to the bulk on surfaces with low attraction.
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Affiliation(s)
- Ellen D Zhong
- Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States
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19
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Protein structure preservation by MWCNTs/RTIL nano-composite. Int J Biol Macromol 2013; 56:169-74. [DOI: 10.1016/j.ijbiomac.2013.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 11/18/2022]
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20
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Hung A, Mager M, Hembury M, Stellacci F, Stevens MM, Yarovsky I. Amphiphilic amino acids: a key to adsorbing proteins to nanopatterned surfaces? Chem Sci 2013. [DOI: 10.1039/c2sc21639f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Holt BD, McCorry MC, Boyer PD, Dahl KN, Islam MF. Not all protein-mediated single-wall carbon nanotube dispersions are equally bioactive. NANOSCALE 2012; 4:7425-7434. [PMID: 23086474 DOI: 10.1039/c2nr31928d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-wall carbon nanotubes (SWCNTs) have been dispersed with proteins to increase biocompatibility and specificity, but examinations of dispersion parameters on functional cellular uptake are required for utilization of SWCNTs in biological applications. Here we correlate conditions of SWCNT dispersion with various proteins to uptake these SWCNTs in NIH-3T3 fibroblasts and J774A.1 macrophage-like cells. We varied protein types (bovine serum albumin - BSA, lysozyme - LSZ, and γ-globulins - γG), protein : SWCNT ratio and sonication time. Each protein created stable, high yield (~25%) dispersions in water while preserving intrinsic SWCNT fluorescence, but SWCNT-LSZ flocculated in media and SWCNT-γG formed clusters in both water and media, drastically altering cellular internalization. Dispersion quality and yield improved with increased protein : SWCNT - without substantial effects from depletion attraction, even at 100 : 1 protein : SWCNT - and slightly increased internalized SWCNTs for both NIH-3T3 and J774A.1 cells. Longer sonication time (12 versus 2 h) improved the dispersion yield and quality but caused minor damage to SWCNTs and altered protein structure. Cell association of SWCNT-BSA was homogenous and unaltered by sonication time. Bulk assay showed that cell association of SWCNT-LSZ and SWCNT-γG was altered with 12 versus 2 h sonication, but imaging of individual cells showed that these differences are likely from precipitation of clusters of SWCNT-LSZ and SWCNT-γG in media onto cells. Hence, the quality of SWCNT-protein dispersions in water does not necessarily correlate with bulk cellular uptake, and quantification at the level of individual cells is required to determine delivery efficacy.
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Affiliation(s)
- Brian D Holt
- Department of Biomedical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
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22
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Kubiak-Ossowska K, Mulheran PA. Protein diffusion and long-term adsorption states at charged solid surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15577-15585. [PMID: 23062108 DOI: 10.1021/la303323r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The diffusion pathways of lysozyme adsorbed to a model charged ionic surface are studied using fully atomistic steered molecular dynamics simulation. The simulations start from existing protein adsorption trajectories, where it has been found that one particular residue, Arg128 at the N,C-terminal face, plays a crucial role in anchoring the lysozyme to the surface [Langmuir 2010 , 26 , 15954 - 15965]. We first investigate the desorption pathway for the protein by pulling the Arg128 side chain away from the surface in the normal direction, and its subsequent readsorption, before studying diffusion pathways by pulling the Arg128 side chain parallel to the surface. We find that the orientation of this side chain plays a decisive role in the diffusion process. Initially, it is oriented normal to the surface, aligning in the electrostatic field of the surface during the adsorption process, but after resorption it lies parallel to the surface, being unable to return to its original orientation due to geometric constraints arising from structured water layers at the surface. Diffusion from this alternative adsorption state has a lower energy barrier of ∼0.9 eV, associated with breaking hydrogen bonds along the pathway, in reasonable agreement with the barrier inferred from previous experimental observation of lysozyme surface clustering. These results show the importance of studying protein diffusion alongside adsorption to gain full insight into the formation of protein clusters and films, essential steps in the future development of functionalized surfaces.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow, United Kingdom
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23
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Chen R, Radic S, Choudhary P, Ledwell KG, Huang G, Brown JM, Chun Ke P. Formation and cell translocation of carbon nanotube-fibrinogen protein corona. APPLIED PHYSICS LETTERS 2012; 101:133702. [PMID: 23093808 PMCID: PMC3470598 DOI: 10.1063/1.4756794] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 09/17/2012] [Indexed: 06/01/2023]
Abstract
The binding of plasma fibrinogen with both single-walled and multi-walled carbon nanotubes (SWNTs and MWNTs) has been examined. Specifically, our absorbance study indicated that MWNTs were coated with multi-layers of fibrinogen to render a "hard protein corona," while SWNTs were adsorbed with thin layers of the protein to precipitate out of the aqueous phase. In addition, static quenching as a result of energy transfer from fluorescently labeled fibrinogen to their nanotube substrates was revealed by Stern-Volmer analysis. When exposed to HT-29 cells, the nanotubes and fibrinogen could readily dissociate, possibly stemming from their differential affinities for the amphiphilic membrane bilayer.
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Affiliation(s)
- Ran Chen
- Nano-Biophysics and Soft Matter Laboratory, COMSET, Clemson University, Clemson, South Carolina 29634, USA
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24
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Calvaresi M, Hoefinger S, Zerbetto F. Probing the Structure of Lysozyme-Carbon-Nanotube Hybrids with Molecular Dynamics. Chemistry 2012; 18:4308-13. [DOI: 10.1002/chem.201102703] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Indexed: 11/09/2022]
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25
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Yang Z, Wang Z, Tian X, Xiu P, Zhou R. Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations. J Chem Phys 2012; 136:025103. [DOI: 10.1063/1.3675486] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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26
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Tian J, Garcia AE. Simulation Studies of Protein Folding/Unfolding Equilibrium under Polar and Nonpolar Confinement. J Am Chem Soc 2011; 133:15157-64. [DOI: 10.1021/ja2054572] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jianhui Tian
- Department of Physics, Applied Physics and Astronomy and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Angel E. Garcia
- Department of Physics, Applied Physics and Astronomy and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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