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Zhang Y, Zhang L, Cai C, Zhang J, Lu P, Shi N, Zhu W, He N, Pan X, Wang T, Feng Z. In situ study of structural changes: Exploring the mechanism of protein corona transition from soft to hard. J Colloid Interface Sci 2024; 654:935-944. [PMID: 37898077 DOI: 10.1016/j.jcis.2023.10.095] [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: 06/17/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023]
Abstract
HYPOTHESIS The process of protein corona changes has been widely believed to follow the Vroman effect, while protein structural change during the process is rarely reported, due to the lack of analytical methods. In-situ interpretation for protein structural change is critical to processes such as the recognition and transport of nanomaterials. EXPERIMENTS Molecular dynamics (MD) simulation was used to predict the deflection and twist of the protein tertiary structure. The structural changes of the surface protein corona during the interaction of nanoparticles (NPs) with lipid bilayer were probed in situ and real-time by sum frequency generation (SFG) spectroscopy. FINDINGS The ring tertiary structure of the protein corona is altered from vertical to horizontal on particle surface, a process of the soft-to-hard structural transition, which is contributed by the hydrogen bonding force between the protein and water molecules. The negatively charged protein corona can induce the redistribution of interfacial charge, leading to a more stable hydrogen bond network of the interfacial water. Our findings suggest that the structural change from flexible to rigid is a crucial process in the soft-to-hard transition of the protein corona, which will be a beneficial supplement to the Vroman effect of protein adsorption.
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Affiliation(s)
- Yixin Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liqiang Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Chenglong Cai
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jixiang Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Pengyu Lu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Neng Shi
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Weiran Zhu
- SceneRay Co., Ltd., Suzhou 215123, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuchao Pan
- Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Ting Wang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zhangqi Feng
- Nanjing University of Science and Technology, Nanjing 210094, China
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Bañuelos JL, Borguet E, Brown GE, Cygan RT, DeYoreo JJ, Dove PM, Gaigeot MP, Geiger FM, Gibbs JM, Grassian VH, Ilgen AG, Jun YS, Kabengi N, Katz L, Kubicki JD, Lützenkirchen J, Putnis CV, Remsing RC, Rosso KM, Rother G, Sulpizi M, Villalobos M, Zhang H. Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment. Chem Rev 2023; 123:6413-6544. [PMID: 37186959 DOI: 10.1021/acs.chemrev.2c00130] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.
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Affiliation(s)
- José Leobardo Bañuelos
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Eric Borguet
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Gordon E Brown
- Department of Earth and Planetary Sciences, The Stanford Doerr School of Sustainability, Stanford University, Stanford, California 94305, United States
| | - Randall T Cygan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - James J DeYoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Patricia M Dove
- Department of Geosciences, Department of Chemistry, Department of Materials Science and Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France
| | - Franz M Geiger
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2Canada
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - Anastasia G Ilgen
- Geochemistry Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Young-Shin Jun
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Nadine Kabengi
- Department of Geosciences, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lynn Katz
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Kubicki
- Department of Earth, Environmental & Resource Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Johannes Lützenkirchen
- Karlsruher Institut für Technologie (KIT), Institut für Nukleare Entsorgung─INE, Eggenstein-Leopoldshafen 76344, Germany
| | - Christine V Putnis
- Institute for Mineralogy, University of Münster, Münster D-48149, Germany
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Kevin M Rosso
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Gernot Rother
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Marialore Sulpizi
- Department of Physics, Ruhr Universität Bochum, NB6, 65, 44780, Bochum, Germany
| | - Mario Villalobos
- Departamento de Ciencias Ambientales y del Suelo, LANGEM, Instituto De Geología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Huichun Zhang
- Department of Civil and Environmental Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
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Interaction of Aluminum-adjuvanted Recombinant P[4] Protein Antigen With Preservatives: Storage Stability and Backbone Flexibility Studies. J Pharm Sci 2021; 111:970-981. [PMID: 34758340 DOI: 10.1016/j.xphs.2021.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 11/24/2022]
Abstract
Eight antimicrobial preservatives used in parenteral multidose formulations (thimerosal, 2-phenoxy ethanol, phenol, benzyl alcohol, m-cresol, chlorobutanol, methyl paraben, propyl paraben) were examined for their effects on the storage stability (4 °C, 25 °C) of an Alhydrogel® (AH) adjuvanted formulation of the non-replicating rotavirus vaccine (NRRV) recombinant P[4] protein antigen. The stability of AH-adsorbed P[4] was monitored for antigen-antibody binding, conformational stability, and antigen-adjuvant interaction via competitive ELISA, DSC, and SDS-PAGE, respectively. There was an unexpected correlation between increasing storage stability of the AH-adsorbed P[4] and preservative hydrophobicity (log P) (e.g., the parabens and chlorobutanol were least destabilizing). We used hydrogen exchange-mass spectrometry (HX-MS) to better understand the destabilizing effects of temperature and preservative on backbone flexibility of AH-adsorbed P[4]. Thimerosal addition immediately increased the backbone flexibility across much of the AH-adsorbed P[4] protein backbone (except the N-terminal P2 region and residues G17-Y38), and further increase in P[4] backbone flexibility was observed after storage (4 °C, 4 weeks). HX-MS analysis of AH-adsorbed P[4] stored for 4 weeks at 25 °C revealed structural alterations in some regions of the epitope involved in P[4] specific mAb binding. These combined results are discussed in terms of a generalized workflow for multi-dose vaccine formulation development for recombinant protein antigens.
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Sit I, Wu H, Grassian VH. Environmental Aspects of Oxide Nanoparticles: Probing Oxide Nanoparticle Surface Processes Under Different Environmental Conditions. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:489-514. [PMID: 33940931 DOI: 10.1146/annurev-anchem-091420-092928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Surface chemistry affects the physiochemical properties of nanoparticles in a variety of ways. Therefore, there is great interest in understanding how nanoparticle surfaces evolve under different environmental conditions of pH and temperature. Here, we discuss the use of vibrational spectroscopy as a tool that allows for in situ observations of oxide nanoparticle surfaces and their evolution due to different surface processes. We highlight oxide nanoparticle surface chemistry, either engineered anthropogenic or naturally occurring geochemical nanoparticles, in complex media, with a focus on the impact of (a) pH on adsorption, intermolecular interactions, and conformational changes; (b) surface coatings and coadsorbates on protein adsorption kinetics and protein conformation; (c) surface adsorption on the temperature dependence of protein structure phase changes; and (d) the use of two-dimensional correlation spectroscopy to analyze spectroscopic results for complex systems. An outlook of the field and remaining challenges is also presented.
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Affiliation(s)
- Izaac Sit
- Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, USA; ,
| | - Haibin Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA;
| | - Vicki H Grassian
- Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, USA; ,
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA;
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, USA
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5
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Duan Y, Liu Y, Coreas R, Zhong W. Mapping Molecular Structure of Protein Locating on Nanoparticles with Limited Proteolysis. Anal Chem 2019; 91:4204-4212. [PMID: 30798594 PMCID: PMC6613589 DOI: 10.1021/acs.analchem.9b00482] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The molecular structure of a protein could be altered when it is attached to nanoparticles (NPs), affecting the performance of NPs present in biological systems. Limited proteolysis coupled with LC-MS/MS could reveal the changes in protein structure when it binds to a variety of entities, including macro-molecules and small drugs, but it has not yet been applied to study protein-NP interaction. Herein, adsorption of proteins, transferrin, and catalase on the polystyrene (PS) or iron oxide (IO) NPs was analyzed with this method. Both increased and decreased proteolytic efficiency in certain regions on the proteins were observed. Identification of the peptides affected by protein-NP interaction led to proper prediction of alterations to protein function as well as to colloidal stability of NPs. Overall, the present work has demonstrated the utility of limited proteolysis in helping to elucidate the potential biological outcomes of the protein-NP conjugate, obtaining knowledge to guide improvement of the rational design of the protein-conjugated NPs for biomedical applications and to understand the biological behaviors of the engineered NPs.
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Affiliation(s)
- Yaokai Duan
- Department of Chemistry, University of California, Riverside, California 92507, United States
| | - Yang Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92507, United States
| | - Roxana Coreas
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92507, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, California 92507, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92507, United States
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6
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Sannigrahi A, Chall S, Jawed JJ, Kundu A, Majumdar S, Chattopadhyay K. Nanoparticle Induced Conformational Switch Between α-Helix and β-Sheet Attenuates Immunogenic Response of MPT63. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8807-8817. [PMID: 29986589 DOI: 10.1021/acs.langmuir.8b00354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although significant efforts have been devoted to develop nanoparticle-based biopharmaceuticals, it is not understood how protein conformation and nanoparticle surface modulate each other in optimizing the activity and/or toxicity of the biological molecules. This is particularly important for a protein, which can adopt different conformational states separated by a relatively small energy barrier. In this paper, we have studied nanoparticle binding-induced conformational switch from β-sheet to α-helix of MPT63, a small major secreted protein from Mycobacterium tuberculosis and a drug target against Tuberculosis. The binding of magnetite nanoparticles to MPT63 results in a β-sheet to α-helix switch near the sequence stretch between the 19th and 30th amino acids. As a consequence, the immunogenic response of the protein becomes compromised, which could be restored by protein engineering. This study emphasizes that conformational stability toward NP surface binding may require optimization involving genetic engineering for development of a nanoparticle conjugated pharmaceutical.
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Affiliation(s)
- Achinta Sannigrahi
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
| | - Sayantani Chall
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
| | | | - Amrita Kundu
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
| | - Subrata Majumdar
- Department of Molecular Medicine , Bose Institute , Kolkata 700054 , India
| | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
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7
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Mirzaei S, Hadadi Z, Attar F, Mousavi SE, Zargar SS, Tajik A, Saboury AA, Rezayat SM, Falahati M. ROS-mediated heme degradation and cytotoxicity induced by iron nanoparticles: hemoglobin and lymphocyte cells as targets. J Biomol Struct Dyn 2017; 36:4235-4245. [DOI: 10.1080/07391102.2017.1411832] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sepideh Mirzaei
- Department of Cellular and Molecular Biology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Zari Hadadi
- Department of Cellular and Molecular Biology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry & Agriculture, Standard Research Institute (SRI), Karaj, Iran
| | - Seyyedeh Elaheh Mousavi
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Shahaboddin Zargar
- Department of Toxicology–Pharmacology, Faculty of Pharmacy, Pharmaceutical Science Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Aida Tajik
- Department of Toxicology–Pharmacology, Faculty of Pharmacy, Pharmaceutical Science Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Ali Akbar Saboury
- Department of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Seyed Mahdi Rezayat
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran
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