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Żeliszewska P, Wasilewska M, Batys P, Pogoda K, Deptuła P, Bucki R, Adamczyk Z. SARS-CoV-2 Spike Protein (RBD) Subunit Adsorption at Abiotic Surfaces and Corona Formation at Polymer Particles. Int J Mol Sci 2022; 23:ijms232012374. [PMID: 36293231 PMCID: PMC9604293 DOI: 10.3390/ijms232012374] [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: 08/31/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 12/29/2022] Open
Abstract
The adsorption kinetics of the SARS-CoV-2 spike protein subunit with the receptor binding domain at abiotic surfaces was investigated. A combination of sensitive methods was used such as atomic force microscopy yielding a molecular resolution, a quartz microbalance, and optical waveguide lightmode spectroscopy. The two latter methods yielded in situ information about the protein adsorption kinetics under flow conditions. It was established that at pH 3.5-4 the protein adsorbed on mica and silica surfaces in the form of compact quasi-spherical aggregates with an average size of 14 nm. The maximum coverage of the layers was equal to 3 and 1 mg m-2 at pH 4 and 7.4, respectively. The experimental data were successfully interpreted in terms of theoretical results derived from modeling. The experiments performed for flat substrates were complemented by investigations of the protein corona formation at polymer particles carried out using in situ laser Doppler velocimetry technique. In this way, the zeta potential of the protein layers was acquired as a function of the coverage. Applying the electrokinetic model, these primary data were converted to the dependence of the subunit zeta potential on pH. It was shown that a complete acid-base characteristic of the layer can be acquired only using nanomolar quantities of the protein.
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Affiliation(s)
- Paulina Żeliszewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
- Correspondence: (P.Ż.); (Z.A.)
| | - Monika Wasilewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
| | - Piotr Batys
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
| | - Katarzyna Pogoda
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Kraków, Poland
| | - Piotr Deptuła
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, 15-222 Białystok, Poland
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, 15-222 Białystok, Poland
| | - Zbigniew Adamczyk
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
- Correspondence: (P.Ż.); (Z.A.)
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Wei J, Wang J, Shao Z. Bioinspired cellulose nanofibrils and
NaCl
composited polyacrylamide hydrogels with improved toughness, resilience, and strain‐sensitive conductivity. J Appl Polym Sci 2022. [DOI: 10.1002/app.53188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jie Wei
- Beijing Engineering Research Center of Cellulose and Its Derivatives, School of Materials Science and Engineering Beijing Institute of Technology Beijing People's Republic of China
- Advanced Materials Research Center Petrochemical Research Institute, PetroChina Company Limited Beijing People's Republic of China
| | - Jianquan Wang
- Beijing Engineering Research Center of Cellulose and Its Derivatives, School of Materials Science and Engineering Beijing Institute of Technology Beijing People's Republic of China
| | - Ziqiang Shao
- Beijing Engineering Research Center of Cellulose and Its Derivatives, School of Materials Science and Engineering Beijing Institute of Technology Beijing People's Republic of China
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Yokoyama K, Lam T, Santariello J, Ichiki A. Nano-size dependent protein corona formation by SARS-CoV-2 Omicron spike protein over gold nano-colloid and reversible aggregation. Colloids Surf A Physicochem Eng Asp 2022; 647:128967. [PMID: 35466287 PMCID: PMC9012667 DOI: 10.1016/j.colsurfa.2022.128967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Accepted: 04/09/2022] [Indexed: 11/24/2022]
Abstract
The adsorption process of SARS-CoV-2 Omicron spike protein to the nano-gold colloid surfaces was examined by monitoring the surface plasmon resonance (SPR) band shift of gold-nano particles ranging between diameters of d = 10–100 nm. The externally changed pH between 3 and 11 at 24.5 ± 0.4 °C initiated a reversible formation of the gold colloid aggregates, where formation/deformation of the aggregates were monitored by red/blue shift of the peak of the SPR band. There was no sign of reversible aggregation for d = 10, 15, and 20 nm gold colloids. A clear undulation of the peak shift corresponding to pH hopping between pH ~3 and ~11 was confirmed for colloidal d > 30 nm. This degree of the reversibility was compared to previously reported SARS-CoV-2 Alpha spike protein coated gold colloids. It was concluded that Omicron spike protein possesses a similar low affinity for gold nano particle d < 20 nm and possesses the higher affinity to the gold nanoparticles of d > 30 nm. However, the Omicron spike protein conformation was presumed to be more denatured compared to the SARS-CoV-2 Alpha spike protein. Our finding suggested Omicron spike protein was more acid labile/flexible.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Theresa Lam
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Jack Santariello
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Akane Ichiki
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
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Adamczyk Z, Batys P, Barbasz J. SARS-CoV-2 virion physicochemical characteristics pertinent to abiotic substrate attachment. Curr Opin Colloid Interface Sci 2021; 55:101466. [PMID: 34093061 PMCID: PMC8169569 DOI: 10.1016/j.cocis.2021.101466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The structure, size, and main physicochemical characteristics of the SARS-CoV-2 virion with the spike transmembrane protein corona were discussed. Using these data, diffusion coefficients of the virion in aqueous media and in air were calculated. The structure and dimensions of the spike protein derived from molecular dynamic modeling and thorough cryo-electron microscopy measurements were also analyzed. The charge distribution over the molecule was calculated and shown to be largely heterogeneous. Although the stalk part is negatively charged, the top part of the spike molecule, especially the receptor binding domain, remains positively charged for a broad range of pH. It is underlined that such a charge distribution promotes the spike corona stability and enhances the virion attachment to receptors and surfaces, mostly negatively charged. The review is completed by the analysis of experimental data pertinent to the spike protein adsorption at abiotic surfaces comprising nanoparticle carrier particles. It is argued that these theoretical and experimental data can be used for developing quantitative models of virus attachment to surfaces, facilitating adequate analysis of future experimental results.
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Kulkarni SA, Krishnan SBB, Chandrasekhar B, Banerjee K, Sohn H, Madhavan T. Characterization of Phytochemicals in Ulva intestinalis L. and Their Action Against SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain. Front Chem 2021; 9:735768. [PMID: 34650958 PMCID: PMC8506597 DOI: 10.3389/fchem.2021.735768] [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: 07/03/2021] [Accepted: 09/10/2021] [Indexed: 12/24/2022] Open
Abstract
Coronavirus disease-2019 (COVID-19) has caused a severe impact on almost all aspects of human life and economic development. Numerous studies are being conducted to find novel therapeutic strategies to overcome COVID-19 pandemic in a much effective way. Ulva intestinalis L. (Ui), a marine microalga, known for its antiviral property, was considered for this study to determine the antiviral efficacy against severe acute respiratory syndrome-associated Coronavirus-2 (SARS-CoV-2). The algal sample was dried and subjected to ethanolic extraction, followed by purification and analysis using gas chromatography-coupled mass spectrometry (GC-MS). Forty-three known compounds were identified and docked against the S1 receptor binding domain (RBD) of the spike (S) glycoprotein. The compounds that exhibited high binding affinity to the RBD of S1 protein were further analyzed for their chemical behaviour using conceptual density-functional theory (C-DFT). Finally, pharmacokinetic properties and drug-likeliness studies were carried out to test if the compounds qualified as potential leads. The results indicated that mainly phenols, polyenes, phytosteroids, and aliphatic compounds from the extract, such as 2,4-di-tert-butylphenol (2,4-DtBP), doconexent, 4,8,13-duvatriene-1,3-diol (DTD), retinoyl-β-glucuronide 6',3'-lactone (RBGUL), and retinal, showed better binding affinity to the target. Pharmacokinetic validation narrowed the list to 2,4-DtBP, retinal and RBGUL as the possible antiviral candidates that could inhibit the viral spike protein effectively.
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Affiliation(s)
- Seema A Kulkarni
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Sabari B B Krishnan
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Bavya Chandrasekhar
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Kaushani Banerjee
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
| | - Honglae Sohn
- Department of Chemistry and Department of Carbon Materials, Chosun University, Gwangju, South Korea
| | - Thirumurthy Madhavan
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chengalpattu, India
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Yang CH, Wu TH, Chang CC, Lo HY, Liu HW, Huang NT, Lin CW. Biosensing Amplification by Hybridization Chain Reaction on Phase-Sensitive Surface Plasmon Resonance. BIOSENSORS-BASEL 2021; 11:bios11030075. [PMID: 33800935 PMCID: PMC7998988 DOI: 10.3390/bios11030075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023]
Abstract
Surface Plasmon Resonance (SPR) is widely used in biological and chemical sensing with fascinating properties. However, the application of SPR to detect trace targets is hampered by non-specific binding and poor signal. A variety of approaches for amplification have been explored to overcome this deficiency including DNA aptamers as versatile target detection tools. Hybridization chain reaction (HCR) is a high-efficiency enzyme-free DNA amplification method operated at room temperature, in which two stable species of DNA hairpins coexist in solution until the introduction of the initiator strand triggers a cascade of hybridization events. At an optimal salt condition, as the concentrations of H1 and H2 increased, the HCR signals were enhanced, leading to signal amplification reaching up to 6.5-fold of the detection measure at 30 min. This feature enables DNA to act as an amplifying transducer for biosensing applications to provide an enzyme-free alternative that can easily detect complex DNA sequences. Improvement of more diverse recognition events can be achieved by integrating HCR with a phase-sensitive SPR (pSPR)-tested aptamer stimulus. This work seeks to establish pSPR aptamer system for highly informative sensing by means of an amplification HCR. Thus, combining pSPR and HCR technologies provide an expandable platform for sensitive biosensing.
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Affiliation(s)
- Ching-Hsu Yang
- Graduate Institute of Bioelectronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan; (C.-H.Y.); (T.-H.W.)
| | - Tzu-Heng Wu
- Graduate Institute of Bioelectronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan; (C.-H.Y.); (T.-H.W.)
| | - Chia-Chen Chang
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Hui-Yun Lo
- Department of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan; (H.-Y.L.); (H.-W.L.)
| | - Hui-Wen Liu
- Department of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan; (H.-Y.L.); (H.-W.L.)
| | - Nien-Tsu Huang
- Graduate Institute of Bioelectronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan; (C.-H.Y.); (T.-H.W.)
- Department of Electrical Engineering, National Taiwan University, Taipei 106, Taiwan
- Correspondence: (N.-T.H.); (C.-W.L.)
| | - Chii-Wann Lin
- Department of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan; (H.-Y.L.); (H.-W.L.)
- Department of Electrical Engineering, National Taiwan University, Taipei 106, Taiwan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu 310, Taiwan
- Correspondence: (N.-T.H.); (C.-W.L.)
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Yokoyama K, Ichiki A. Spectroscopic investigation on the affinity of SARS-CoV-2 spike protein to gold nano-particles. COLLOID AND INTERFACE SCIENCE COMMUNICATIONS 2021; 40:100356. [PMID: 33520676 PMCID: PMC7833638 DOI: 10.1016/j.colcom.2020.100356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/15/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
The affinity of the SARS-CoV-2 spike protein (S protein) to gold nano-particles was examined through spectral shifts of SPR (Surface Plasmon Resonance) band. Gold nano-colloidal particles are sensitive to the conformational change of the protein adsorbed over the particles' surface. As the pH value was gradually lowered from approximately neutral pH to an acidic pH (ca. pH 2), all mixtures of S protein with the gold colloids ≥30 nm in diameter exhibited a drastic red-shift of the average SPR band peak at one pH value more than that observed for bare gold colloids. The surface coverage fraction (Θ) of S protein over the nano-particle's surface was extracted and all showed relatively small coverage values (i.e., Θ ~ 0.30). The SPR band peak shift was also examined as the pH values were hopped between pH ~ 3 and pH ~ 10 (pH hopping). As the pH values hopped, an alternation of the average SPR band peaks were observed. A significant amplitude of an alternation was especially observed for the mixture of S protein with gold ≥30 nm of gold size implying the reproduction of pH induced reversible protein folding. We hypothesize that the pH hopping scheme captured a reversible transition between folded or Down conformation (pH ≥ ~7) and unfolded or Up (pH ~ 3) conformation of RBD (receptor binding domain). The acidic condition may also dimerize the S protein through RBD. The Up conformation or dimerization of S protein are considered to be connected to the other gold nano particles forming gold nano-particle aggregates.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, 1 College Cir., Geneseo, NY 14454, USA
| | - Akane Ichiki
- Department of Chemistry, The State University of New York Geneseo College, 1 College Cir., Geneseo, NY 14454, USA
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