1
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Singh NK, Pushpavanam K, Radhakrishna M. Tuning Electrostatic Interactions To Control Orientation of GFP Protein Adsorption on Silica Surface. ACS APPLIED BIO MATERIALS 2024; 7:596-608. [PMID: 37347172 DOI: 10.1021/acsabm.3c00125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
The adsorption of green fluorescent protein (GFP) on silica surfaces has been the subject of growing interest due to its potential applications in various fields, including biotechnology and biomedicine. In this study, we used all-atom molecular dynamics simulations to investigate the charge-driven adsorption of wild type GFP and its supercharged variants on silica surfaces. The results showed that the positively charged variant of GFP adsorbed on the negatively charged silica surface with minimal loss in its secondary structure. Further studies were conducted to understand the role of surface charge distribution on two other positively charged variants of GFP, and the results showed that the orientation of GFP on silica can be easily tuned by careful mutations of the charged amino acid residues on the GFP. This study provides valuable molecular insights into the role of electrostatic-driven adsorption of GFP and highlights the importance of charge interactions in the adsorption process.
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Affiliation(s)
- Nitin Kumar Singh
- Discipline of Chemical Engineering Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Karthik Pushpavanam
- Discipline of Chemical Engineering Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Mithun Radhakrishna
- Discipline of Chemical Engineering Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
- Center for Biomedical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
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2
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Maheshwari A, Kishore N. pH-dependent interactions of biologically important metal ions with hen egg white lysozyme based on its hydration properties: Thermodynamic and mechanistic insights. Int J Biol Macromol 2024; 259:129297. [PMID: 38211927 DOI: 10.1016/j.ijbiomac.2024.129297] [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: 10/20/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Importance of metal ion selectivity in biomolecules and their key role in proteins are widely explored. However, understanding the thermodynamics of how hydrated metal ions alter the protein hydration and their conformation is also important. In this study, the interaction of some biologically important Ca2+, Mn2+, Co2+, Cu2+, and Zn2+ ions with hen egg white lysozyme at pH 2.1, 3.0, 4.5 and 7.4 has been investigated. Intrinsic fluorescence studies have been employed for metal ion-induced protein conformational changes analysis. Thermostability based on protein hydration has been investigated using differential scanning calorimetry (DSC). Thermodynamic parameters emphasizing on metal ion-protein binding mechanistic insights have been well discussed using isothermal titration calorimetry (ITC). Overall, these experiments have reported that their interactions are pH-dependent and entropically driven. This research also reports the strongly hydrated metal ions as water structure breaker unlike osmolytes based on DSC studies. These experimental results have highlighted higher concentrations of different metal ions effect on the protein hydration and thermostability which might be helpful in understanding their interactions in aqueous solutions.
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Affiliation(s)
- Anjali Maheshwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India.
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3
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Atabay M, Sardroodi JJ, Ebrahimzadeh AR, Avestan MS. Modeling the Interaction of Anticancer Protein Azurin with the Nanosheets for Medical Applications. ChemistrySelect 2022. [DOI: 10.1002/slct.202202633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Chemistry Azarbaijan Shahid Madani University Tabriz Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Chemistry Azarbaijan Shahid Madani University Tabriz Iran
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Physics Azarbaijan Shahid Madani University Tabriz Iran
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4
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Gan N, Lin Y, Zhang Y, Gitis V, Lin Q, Matsuyama H. Surface Mineralization of the TiO 2-SiO 2/PES Composite Membrane with Outstanding Separation Property via Facile Vapor-Ventilated In Situ Chemical Deposition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12951-12960. [PMID: 36242562 DOI: 10.1021/acs.langmuir.2c02178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Conventional polymeric membranes are broadly employed in water treatment processes; however, most of them suffer from relatively low water permeance and severe membrane fouling phenomena owing to their relatively hydrophobic nature. In this work, a novel class of inorganic-organic composite membranes was developed through a newly developed vapor-ventilated in situ chemical deposition method, where the Ti and Si precursors were first hydrolyzed and then conferred into metal oxides to form a continuous TiO2-SiO2 modification layer. Owing to the distinct physicochemical properties, the Ti and Si precursors were leveraged as quasi-molecular regulators to tune the membrane surface chemistry and pore aperture (within the nanoscale) to benefit highly efficient water purification by underpinning the rapid transport of water molecules and featuring an excellent fouling-resistant and fouling-releasing property against typical pollutants. The as-developed TiO2-SiO2/PES composite membrane showed a high water permeance of 187.4 L·m-2·h-1·bar-1, together with a relatively small mean pore aperture of 4.2 nm, showing an outstanding permeating efficiency among state-of-the-art membranes with a similar separation accuracy. This study provides a paradigm shift in membrane materials that could open avenues for developing high-performance inorganic-organic composite membranes for complex wastewater treatment.
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Affiliation(s)
- Ning Gan
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang550025, Guizhou, China
- School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai200237, China
| | - Yuqing Lin
- School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai200237, China
| | - Yiren Zhang
- School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai200237, China
| | - Vitaly Gitis
- Unit of Environmental Engineering, The Faculty of Engineering Science, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva84105, Israel
| | - Qian Lin
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang550025, Guizhou, China
- School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai200237, China
| | - Hideto Matsuyama
- Research Center for Membrane and Film Technology, Department of Chemical Science and Engineering, Kobe University, Kobe657-8501, Japan
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5
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Dey D, Nunes-Alves A, Wade RC, Schreiber G. Diffusion of small molecule drugs is affected by surface interactions and crowder proteins. iScience 2022; 25:105088. [PMID: 36157590 PMCID: PMC9490042 DOI: 10.1016/j.isci.2022.105088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/04/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Crowded environments are known to affect the diffusion of macromolecules, but their effects on the diffusion of small molecules are largely uncharacterized. We investigate how three protein crowders, bovine serum albumin (BSA), hen egg-white lysozyme, and myoglobin, influence the diffusion rates and interactions of four small molecules: fluorescein, and three drugs, doxorubicin, glycogen synthase kinase-3 inhibitor SB216763, and quinacrine. Using Line-FRAP measurements, Brownian dynamics simulations, and molecular docking, we find that the diffusion rates of the small molecules are highly affected by self-aggregation, interactions with the proteins, and surface adsorption. The diffusion of fluorescein is decreased because of its interactions with the protein crowders and their surface adsorption. Protein crowders increase the diffusion rates of doxorubicin and SB216763 by reducing surface interactions and self-aggregation, respectively. Quinacrine diffusion was not affected by protein crowders. The mechanistic insights gained here may assist in optimization of compounds for higher mobility in complex macromolecular environments.
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Affiliation(s)
- Debabrata Dey
- Department of Biomolecular Sciences, Weizmann Institute of Science, Israel
| | - Ariane Nunes-Alves
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg, Germany
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Israel
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6
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Biswas S, Melton LD, Nelson ARJ, Le Brun AP, Heinrich F, McGillivray DJ, Xu AY. The Assembly Mechanism and Mesoscale Architecture of Protein-Polysaccharide Complexes Formed at the Solid-liquid Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12551-12561. [PMID: 36194692 DOI: 10.1021/acs.langmuir.2c02003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein-polysaccharide composite materials have generated much interest due to their potential use in medical science and biotechnology. A comprehensive understanding of the assembly mechanism and the mesoscale architecture is needed for fabricating protein-polysaccharide composite materials with desired properties. In this study, complex assemblies were built on silica surfaces through a layer-by-layer (LbL) approach using bovine beta-lactoglobulin variant A (βLgA) and pectin as model protein and polysaccharide, respectively. We demonstrated the combined use of quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR) for elucidating the assembly mechanism as well as the internal architecture of the protein-polysaccharide complexes formed at the solid-liquid interface. Our results show that βLgA and pectin interacted with each other and formed a cohesive matrix structure at the interface consisting of intertwined pectin chains that were cross-linked by βLgA-rich domains. Although the complexes were fabricated in an LbL fashion, the complexes appeared to be relatively homogeneous with βLgA and pectin molecules spatially distributed within the matrix structure. Our results also demonstrate that the density of βLgA-pectin complex assemblies increased with both the overall and local charge density of pectin molecules. Therefore, the physical properties of the protein-polysaccharide matrix structure, including density and level of hydration, can be tuned by using polysaccharides with varying charge patterns, thus promoting the development of composite materials with desired properties.
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Affiliation(s)
- Shanta Biswas
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
| | - Laurence D Melton
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland1142, New Zealand
| | - Andrew R J Nelson
- Australian Centre for Neutron Scattering, ANSTO, Locked Bag 2001, Kirrawee DC, New South Wales2232, Australia
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, ANSTO, Locked Bag 2001, Kirrawee DC, New South Wales2232, Australia
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania15213, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland20899, United States
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland1142, New Zealand
| | - Amy Y Xu
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
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7
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Chen J, Xu E, Wei Y, Chen M, Wei T, Zheng S. Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10817-10825. [PMID: 36001808 DOI: 10.1021/acs.langmuir.2c01331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding the interfacial behaviors of biomolecules is crucial to applications in biomaterials and nanoparticle-based biosensing technologies. In this work, we utilized autoencoder-based graph clustering to analyze discontinuous molecular dynamics (DMD) simulations of lysozyme adsorption on a graphene surface. Our high-throughput DMD simulations integrated with a Go̅-like protein-surface interaction model makes it possible to explore protein adsorption at a large temporal scale with sufficient accuracy. The graph autoencoder extracts a low-dimensional feature vector from a contact map. The sequence of the extracted feature vectors is then clustered, and thus the evolution of the protein molecule structure in the absorption process is segmented into stages. Our study demonstrated that the residue-surface hydrophobic interactions and the π-π stacking interactions play key roles in the five-stage adsorption. Upon adsorption, the tertiary structure of lysozyme collapsed, and the secondary structure was also affected. The folding stages obtained by autoencoder-based graph clustering were consistent with detailed analyses of the protein structure. The combination of machine learning analysis and efficient DMD simulations developed in this work could be an important tool to study biomolecules' interfacial behaviors.
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Affiliation(s)
- Jing Chen
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
| | | | - Yong Wei
- Department of Computer Science, High Point University, High Point, North Carolina 27268, United States
| | | | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Size Zheng
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
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8
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Tiwari S, Adupa V, Das DS, Anki Reddy K, Bharat TV. Structural and Dynamic Insights into SARS-CoV-2 Spike-Protein-Montmorillonite Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9186-9194. [PMID: 35855632 PMCID: PMC9344787 DOI: 10.1021/acs.langmuir.2c00837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/21/2022] [Indexed: 06/01/2023]
Abstract
The spike (S) protein of SARS-CoV-2 has been found to play a decisive role in the cell entry mechanism of the virus and has been the prime target of most vaccine development efforts. Although numerous vaccines are already in use and more than half of the world population has been fully vaccinated, the emergence of new variants of the virus poses a challenge to the existing vaccines. Hence, developing an effective drug therapy is a crucial step in ending the pandemic. Nanoparticles can play a crucial role as a drug or a drug carrier and help tackle the pandemic effectively. Here, we performed explicit all-atom molecular dynamics simulations to probe interactions between S protein and Montmorillonite (MMT) nano clay surface. We built two systems with different counterions (Na+ and Ca2+), namely Na-MMT and Ca-MMT, to investigate the effect of different ions on S protein-MMT interaction. Structural modification of S protein was observed in the presence of MMT surface, particularly the loss of helical content of S protein. We revealed that electrostatic and hydrophobic interactions synergistically govern the S protein-MMT interactions. However, hydrophobic interactions were more pronounced in the Na-MMT system than in Ca-MMT. We also revealed residues and glycans of S protein closely interacting with the MMT surface. Interestingly, N165 and N343, which we found to be closely interacting with MMT in our simulations, also have a critical role in cell entry and in thwarting the cell's immune response in recent studies. Overall, our work provides atomistic insights into S protein-MMT interaction and enriches our understanding of the nanoparticle-S protein interaction mechanism, which will help develop advanced therapeutic techniques in the future.
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Affiliation(s)
- Shivam Tiwari
- Department
of Chemical Engineering, Indian Institute
of Technology, Guwahati, Assam 781039, India
| | - Vasista Adupa
- Department
of Chemical Engineering, Indian Institute
of Technology, Guwahati, Assam 781039, India
| | - Dhanesh Sing Das
- Department
of Civil Engineering, Indian Institute of
Technology, Guwahati, Assam 781039, India
| | - K. Anki Reddy
- Department
of Chemical Engineering, Indian Institute
of Technology, Tirupati, Andhra Pradesh 517506, India
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9
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Cathcarth M, Picco AS, Mondo GB, Cardoso MB, Longo GS. Competitive protein adsorption on charge regulating silica-like surfaces: the role of protonation equilibrium. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:364001. [PMID: 35366656 DOI: 10.1088/1361-648x/ac6388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
We develop a molecular thermodynamic theory to study the interaction of some proteins with a charge regulating silica-like surface under a wide range of conditions, including pH, salt concentration and protein concentration. Proteins are modeled using their three dimensional structure from crystallographic data and the average experimental pKa of amino acid residues. As model systems, we study single-protein and binary solutions of cytochrome c, green fluorescent protein, lysozyme and myoglobin. Our results show that protonation equilibrium plays a critical role in the interactions of proteins with these type of surfaces. The terminal hydroxyl groups on the surface display considerable extent of charge regulation; protein residues with titratable side chains increase protonation according to changes in the local environment and the drop in pH near the surface. This behavior defines protein-surface interactions and leads to the emergence of several phenomena: (i) a complex non-ideal surface charge behavior; (ii) a non-monotonic adsorption of proteins as a function of pH; and (iii) the presence of two spatial regions, a protein-rich and a protein-depleted layer, that occur simultaneously at different distances from the surface when pH is slightly above the isoelectric point of the protein. In binary mixtures, protein adsorption and surface-protein interactions cannot be predicted from single-protein solution considerations.
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Affiliation(s)
- Marilina Cathcarth
- Instituto de Investigaciones Fisicoquímicas, Teóricas y Aplicadas (INIFTA), UNLP-CONICET, La Plata, Argentina
| | - Agustin S Picco
- Instituto de Investigaciones Fisicoquímicas, Teóricas y Aplicadas (INIFTA), UNLP-CONICET, La Plata, Argentina
| | - Gabriela B Mondo
- Brazilian Synchrotron (LNLS) and Brazilian Nanotechnology Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), Campinas, Brazil
| | - Mateus B Cardoso
- Brazilian Synchrotron (LNLS) and Brazilian Nanotechnology Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), Campinas, Brazil
| | - Gabriel S Longo
- Instituto de Investigaciones Fisicoquímicas, Teóricas y Aplicadas (INIFTA), UNLP-CONICET, La Plata, Argentina
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10
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Capocefalo A, Bizien T, Sennato S, Ghofraniha N, Bordi F, Brasili F. Responsivity of Fractal Nanoparticle Assemblies to Multiple Stimuli: Structural Insights on the Modulation of the Optical Properties. NANOMATERIALS 2022; 12:nano12091529. [PMID: 35564238 PMCID: PMC9099587 DOI: 10.3390/nano12091529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
Multi-responsive nanomaterials based on the self-limited assembly of plasmonic nanoparticles are of great interest due to their widespread employment in sensing applications. We present a thorough investigation of a hybrid nanomaterial based on the protein-mediated aggregation of gold nanoparticles at varying protein concentration, pH and temperature. By combining Small Angle X-ray Scattering with extinction spectroscopy, we are able to frame the morphological features of the formed fractal aggregates in a theoretical model based on patchy interactions. Based on this, we established the main factors that determine the assembly process and their strong correlation with the optical properties of the assemblies. Moreover, the calibration curves that we obtained for each parameter investigated based on the extinction spectra point out to the notable flexibility of this nanomaterial, enabling the selection of different working ranges with high sensitivity. Our study opens for the rational tuning of the morphology and the optical properties of plasmonic assemblies to design colorimetric sensors with improved performances.
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Affiliation(s)
- Angela Capocefalo
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (A.C.); (F.B.)
| | - Thomas Bizien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, CEDEX, 91192 Gif-sur-Yvette, France;
| | - Simona Sennato
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
| | - Neda Ghofraniha
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
| | - Federico Bordi
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Brasili
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (A.C.); (F.B.)
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11
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Erwardt P, Roszek K, Wiśniewski M. Determination of Graphene Oxide Adsorption Space by Lysozyme Uptake─Mechanistic Studies. J Phys Chem B 2022; 126:928-933. [PMID: 35077166 PMCID: PMC8819649 DOI: 10.1021/acs.jpcb.1c08294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Paulina Erwardt
- Faculty of Chemistry, Physicochemistry of Carbon Materials Research Group, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
| | - Katarzyna Roszek
- Department of Biochemistry, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Marek Wiśniewski
- Faculty of Chemistry, Physicochemistry of Carbon Materials Research Group, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
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12
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Li B, Hao C, Liu H, Yang H, Zhong K, Zhang M, Sun R. Interaction of graphene oxide with lysozyme:Insights from conformational structure and surface charge investigations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120207. [PMID: 34419829 DOI: 10.1016/j.saa.2021.120207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/26/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Lysozyme (Lyz) is an important antibacterial protein that exists widely in nature. In recent years, the application of graphene oxide (GO) in the field of biotechnology electronics, optics, chemistry and energy storage has been extensively studied. However, due to the unique properties of GO, the mechanism of its interaction with biomacromolecule proteins is very complex. To further explore the interaction between GO and proteins we explore the influence of different pH and heat treatment conditions on the interaction between GO and Lyz, the GO (0-20 μg/mL) was added at a fixed Lyz concentration (0.143 mg/mL) under different pHs. The structure and surface charge changes of Lyz were measured by spectroscopic analysis and zeta potential. The results showed that the interaction between GO and Lyz depends on temperature and pH, significant changes have taken place in its tertiary and secondary structures. By analyzing the UV absorption spectrum, it was found that lysozyme and GO formed a stable complex, and the conformation of the enzyme was changed. In acidic pH conditions (i.e., pH < pI), a high density of Lyz were found to adsorb on the GO surface, whereas an increase in pH resulted in a progressive decrease in the density of the adsorbed Lyz. This pH-dependent adsorption is ascribed to the electrostatic interactions between the negatively charged GO surface and the tunable ionization of the Lyz molecules. The secondary structure of Lyz adsorbed on GO was also found to be highly dependent on the pH. In this paper, we investigated the exact mechanism of pH-influenced GO binding to lysozyme, which has important guidance significance for the potential toxicity of GO biology and its applications in biomedical fields such as structure-based drug design.
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Affiliation(s)
- Binbin Li
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Changchun Hao
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China.
| | - Hengyu Liu
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Haiyan Yang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Kunfeng Zhong
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Mingduo Zhang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China.
| | - Runguang Sun
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
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13
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Caetano DLZ, Metzler R, Cherstvy AG, de Carvalho SJ. Adsorption of lysozyme into a charged confining pore. Phys Chem Chem Phys 2021; 23:27195-27206. [PMID: 34821240 DOI: 10.1039/d1cp03185f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Several applications arise from the confinement of proteins on surfaces because their stability and biological activity are enhanced. It is also known that the way in which a protein adsorbs on the surface is important for its biological function since its active sites should not be obstructed. In this study, the adsorption properties of hen egg-white lysozyme, HEWL, into a negatively charged silica pore is examined by employing a coarse-grained model and constant-pH Monte Carlo simulations. The role of electrostatic interactions is taken into account via including the Debye-Hückel potentials into the Cα structure-based model. We evaluate the effects of pH, salt concentration, and pore radius on the protein preferential orientation and spatial distribution of its residues regarding the pore surface. By mapping the residues that stay closer to the pore surface, we find that the increase of pH leads to orientational changes of the adsorbed protein when the solution pH gets closer to the HEWL isoelectric point. Under these conditions, the pKa shift of these important residues caused by the adsorption into the charged confining surface results in a HEWL charge distribution that stabilizes the adsorption in the observed protein orientation. We compare our observations to the results of the pKa shift for HEWL available in the literature and to some experimental data.
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Affiliation(s)
- Daniel L Z Caetano
- Institute of Chemistry, State University of Campinas (UNICAMP), Campinas, Brazil.,Center for Computational Engineering and Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.,Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Sidney J de Carvalho
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, Brazil.
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14
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Komorek P, Jachimska B, Brand I. Adsorption of lysozyme on gold surfaces in the presence of an external electric potential. Bioelectrochemistry 2021; 142:107946. [PMID: 34507162 DOI: 10.1016/j.bioelechem.2021.107946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/30/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Adsorbed protein films consist of essential building blocks of many biotechnological and biomedical devices. The electrostatic potential may significantly modulate the protein behaviour on surfaces, affecting their structure and biological activity. In this study, lysozyme was used to investigate the effects of applied electric potentials on adsorption and the protein structure. The pH and the surface charge determine the amount and secondary structure of adsorbed lysozyme on a gold surface. In-situ measurements using polarization modulation infrared reflection absorption spectroscopy indicated that the concentration of both the adsorbed anions and the lysozyme led to conformational changes in the protein film, which was demonstrated by a greater amount of aggregated β-sheets in films fabricated at net positive charges of the Au electrode (Eads > Epzc). The changes in secondary structure involved two parallel processes. One comprised changes in the hydration/hydrogen-bond network at helices, leading to diverse helical structures: α-, 310- and/or π-helices. In the second process β-turns, β-sheets, and random coils displayed an ability to form aggregated β-sheet structures. The study illuminates the understanding of electrical potential-dependent changes involved in the protein misfolding process.
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Affiliation(s)
- Paulina Komorek
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland.
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg, 26111 Oldenburg, Germany.
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15
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Yoon BK, Ma GJ, Park H, Ferhan AR, Cho NJ, Jackman JA. Solvent-induced conformational tuning of lysozyme protein adlayers on silica surfaces: A QCM-D and LSPR study. Int J Biol Macromol 2021; 182:1906-1914. [PMID: 34022315 DOI: 10.1016/j.ijbiomac.2021.05.113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 10/24/2022]
Abstract
There is broad interest in functionalizing solid surfaces with lysozyme, which is a widely studied antimicrobial protein. To date, most efforts have focused on developing more effective immobilization schemes to promote lysozyme attachment in fully aqueous conditions, while there remains an outstanding need to understand how tuning the solution-phase conformational stability of lysozyme proteins can modulate adsorption behavior and resulting adlayer properties. Inspired by the unique conformational behavior of lysozyme proteins in water-ethanol mixtures, we conducted quartz crystal microbalance-dissipation (QCM-D) and localized surface plasmon resonance (LSPR) measurements to systematically investigate the adsorption behavior of lysozyme proteins onto silica surfaces across a wide range of water-ethanol mixtures. Our findings revealed that lysozyme adsorption behavior strongly depended on the ethanol fraction in a non-monotonic fashion and this trend could be rationalized by taking into account how competing effects of water and ethanol solvation influence solution-phase protein size and conformational stability. Integrated analysis of the QCM-D and LSPR measurement trends enabled quantitative determination of the solvent mass within lysozyme adlayers, which tended to decrease at higher ethanol fractions and supported that the hydrodynamic properties of lysozyme adlayers are mainly influenced by the degree of protein conformational flexibility as opposed to solvation effects alone.
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Affiliation(s)
- Bo Kyeong Yoon
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gamaliel Junren Ma
- School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore
| | - Hyeonjin Park
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea; School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore
| | - Abdul Rahim Ferhan
- School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore.
| | - Joshua A Jackman
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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16
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Arruebo-Rivera PL, Castillo-Alfonso F, Troya A, Cárdenas-Moreno Y, Pérez-Ramos P, González-Bacerio J, Seijas JMG, Del Monte-Martínez A. Modeling and Experimental Validation of Algorithms for Maximum Quantity of Protein to be Immobilized on Solid Supports by Electrostatic Adsorption in the Strategy of Rational Design of Immobilized Derivatives. Protein J 2021; 40:576-588. [PMID: 33973097 DOI: 10.1007/s10930-021-09992-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 11/29/2022]
Abstract
Protein immobilization by electrostatic adsorption to a support could represent a good option. On the other hand, lysozyme (EC 3.2.1.17) is a little and basic protein. The objective of this work was to test the functionality of the strategy of Rational Design of Immobilized Derivatives for the immobilization by electrostatic adsorption of egg white lysozyme on SP-Sepharose FastFlow support. The RDID1.0 software was used to predict the superficial lysozyme clusters, the electrostatic configuration probability for each cluster, and the theoretical and estimated maximum quantity of protein to be immobilized. In addition, immobilization was performed and the experimental parameter practical maximum quantity of protein to be immobilized and the enzymatic activity of the immobilized derivative were assessed. The estimated maximum quantity of protein to be immobilized (9.49 protein mg/support g) was close to the experimental practical maximum quantity of protein to be immobilized (14.73 ± 0.09 protein mg/support g). The enzymatic activity assay with the chitosan substrate showed the catalytic functionality of the lysozyme-SP-Sepharose immobilized derivative (35.85 ± 3.07 U/support g), which preserved 78% functional activity. The used algorithm to calculate the estimated maximum quantity of protein to be immobilized works for other proteins, porous solid supports and immobilization methods, and this parameter has a high predictive value, useful for obtaining optimum immobilized derivatives. The applied methodology is valid to predict the most probable protein-support configurations and their catalytic competences, which concur with the experimental results. The produced biocatalyst had a high retention of functional activity. This indicates its functionality in enzymatic bioconversion processes.
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Affiliation(s)
- Pedro L Arruebo-Rivera
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba
| | - Freddy Castillo-Alfonso
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Posgrado en Ciencias Naturales E Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, 05348, Mexico City, Mexico
| | - Amanda Troya
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Instituto de Farmacia y Alimentos, Universidad de La Habana, San Lázaro y L, Vedado, 10400, Havana, Cuba
| | - Yosberto Cárdenas-Moreno
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Departamento de Microbiología y Virología, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba
| | - Patricia Pérez-Ramos
- Instituto de Farmacia y Alimentos, Universidad de La Habana, San Lázaro y L, Vedado, 10400, Havana, Cuba
| | - Jorge González-Bacerio
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.
| | - José M Guisán Seijas
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, Consejo Superior de Investigaciones Científicas (CSIC), Campus Cantoblanco, 28049, Madrid, Spain
| | - Alberto Del Monte-Martínez
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.
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17
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Barberi J, Spriano S. Titanium and Protein Adsorption: An Overview of Mechanisms and Effects of Surface Features. MATERIALS (BASEL, SWITZERLAND) 2021; 14:1590. [PMID: 33805137 PMCID: PMC8037091 DOI: 10.3390/ma14071590] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 12/14/2022]
Abstract
Titanium and its alloys, specially Ti6Al4V, are among the most employed materials in orthopedic and dental implants. Cells response and osseointegration of implant devices are strongly dependent on the body-biomaterial interface zone. This interface is mainly defined by proteins: They adsorb immediately after implantation from blood and biological fluids, forming a layer on implant surfaces. Therefore, it is of utmost importance to understand which features of biomaterials surfaces influence formation of the protein layer and how to guide it. In this paper, relevant literature of the last 15 years about protein adsorption on titanium-based materials is reviewed. How the surface characteristics affect protein adsorption is investigated, aiming to provide an as comprehensive a picture as possible of adsorption mechanisms and type of chemical bonding with the surface, as well as of the characterization techniques effectively applied to model and real implant surfaces. Surface free energy, charge, microroughness, and hydroxylation degree have been found to be the main surface parameters to affect the amount of adsorbed proteins. On the other hand, the conformation of adsorbed proteins is mainly dictated by the protein structure, surface topography at the nano-scale, and exposed functional groups. Protein adsorption on titanium surfaces still needs further clarification, in particular concerning adsorption from complex protein solutions. In addition, characterization techniques to investigate and compare the different aspects of protein adsorption on different surfaces (in terms of roughness and chemistry) shall be developed.
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Affiliation(s)
- Jacopo Barberi
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Turin, Italy;
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18
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Affiliation(s)
- Yunqiao Ma
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
| | - Andrew L. Zydney
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania USA
| | - Jia Wei Chew
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
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19
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Adsorption and Conformation Behavior of Lysozyme on a Gold Surface Determined by QCM-D, MP-SPR, and FTIR. Int J Mol Sci 2021; 22:ijms22031322. [PMID: 33525751 PMCID: PMC7865459 DOI: 10.3390/ijms22031322] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
The physicochemical properties of protein layers at the solid–liquid interface are essential in many biological processes. This study aimed to link the structural analysis of adsorbed lysozyme at the water/gold surface at pH 7.5 in a wide range of concentrations. Particular attention was paid to the protein’s structural stability and the hydration of the protein layers formed at the interface. Complementary methods such as multi-parameter surface plasmon resonance (MP-SPR), quartz crystal microbalance with energy dissipation (QCM-D), and infrared spectroscopy (FTIR) were used for this purpose. The MP-SPR and QCM-D studies showed that, during the formation of a monolayer on the gold surface, the molecules’ orientation changes from side-on to end-on. In addition, bilayer formation is observed when adsorbing in the high-volume concentration range >500 ppm. The degree of hydration of the monolayer and bilayer varies depending on the degree of surface coverage. The hydration of the system decreases with filling the layer in both the monolayer and the bilayer. Hydration for the monolayer varies in the range of 50–70%, because the bilayer is much higher than 80%. The degree of hydration of the adsorption layer has a crucial influence on the protein layers’ viscoelastic properties. In general, an increase in the filling of a layer is characterized by a rise in its rigidity. The use of infrared spectroscopy allowed us to determine the changes taking place in the secondary structure of lysozyme due to its interaction with the gold surface. Upon adsorption, the content of II-structures corresponding to β-turn and random lysozyme structures increases, with a simultaneous decrease in the content of the β-sheet. The increase in the range of β-turn in the structure determines the lysozyme structure’s stability and prevents its aggregation.
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20
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Revisiting the Rate-Limiting Step of the ANS-Protein Binding at the Protein Surface and Inside the Hydrophobic Cavity. Molecules 2021; 26:molecules26020420. [PMID: 33466888 PMCID: PMC7830758 DOI: 10.3390/molecules26020420] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 11/17/2022] Open
Abstract
8-Anilino-1-naphthalenesulfonic acid (ANS) is used as a hydrophobic fluorescence probe due to its high intensity in hydrophobic environments, and also as a microenvironment probe because of its unique ability to exhibit peak shift and intensity change depending on the surrounding solvent environment. The difference in fluorescence can not only be caused by the microenvironment but can also be affected by the binding affinity, which is represented by the binding constant (K). However, the overall binding process considering the binding constant is not fully understood, which requires the ANS fluorescence binding mechanism to be examined. In this study, to reveal the rate-limiting step of the ANS-protein binding process, protein concentration-dependent measurements of the ANS fluorescence of lysozyme and bovine serum albumin were performed, and the binding constants were analyzed. The results suggest that the main factor of the binding process is the microenvironment at the binding site, which restricts the attached ANS molecule, rather than the attractive diffusion-limited association. The molecular mechanism of ANS-protein binding will help us to interpret the molecular motions of ANS molecules at the binding site in detail, especially with respect to an equilibrium perspective.
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21
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Erol K, Tatar D, Veyisoğlu A, Tokatlı A. Antimicrobial magnetic poly(GMA) microparticles: synthesis, characterization and lysozyme immobilization. JOURNAL OF POLYMER ENGINEERING 2020. [DOI: 10.1515/polyeng-2020-0191] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract
Micron-sized magnetic particles currently find a wide range of applications in many areas including biotechnology, biochemistry, colloid sciences and medicine. In this study, magnetic poly(glycidyl methacrylate) microparticles were synthesized by providing a polymerization around Fe(II)-Ni(II) magnetic double salt. Adsorption of lysozyme protein from aqueous systems was studied with these particles. Adsorption studies were performed with changing pH values, variable amount of adsorbent, different interaction times and lysozyme amounts. The adsorption capacity of the particles was investigated, and a value of about 95.6 mg lysozyme/g microparticle was obtained. The enzyme activity of the immobilized lysozyme was examined and found to be more stable and reusable compared to the free enzyme. The immobilized enzyme still showed 80% activity after five runs and managed to maintain 78% of its initial activity at the end of 60 days. Besides, in the antimicrobial analysis study for six different microorganisms, the minimum inhibitory concentration value of lysozyme immobilized particles was calculated as 125 μg/mL like free lysozyme. Finally, the adsorption interaction was found to be compatible with the Langmuir isotherm model. Accordingly, it can be said that magnetic poly(GMA) microparticles are suitable materials for lysozyme immobilization and immobilized lysozyme can be used in biotechnological studies.
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Affiliation(s)
- Kadir Erol
- Department of Medical Services and Techniques , Vocational School of Health Services, Hitit University , Çorum , Turkey
| | - Demet Tatar
- Department of Medical Services and Techniques , Osmancık Ömer Derindere Vocational School, Hitit University , Çorum , Turkey
| | - Aysel Veyisoğlu
- Department of Medical Services and Techniques , Vocational School of Health Services, Sinop University , Sinop , Turkey
| | - Ali Tokatlı
- Department of Biology , Faculty of Art and Science, Ondokuz Mayıs University , Samsun , Turkey
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22
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Antosiewicz JM, Długosz M. Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface. ACS OMEGA 2020; 5:30282-30298. [PMID: 33251463 PMCID: PMC7689933 DOI: 10.1021/acsomega.0c04817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/04/2020] [Indexed: 05/04/2023]
Abstract
We have developed a rigid-body Brownian dynamics algorithm that allows for simulations of a globular protein suspended in an ionic solution confined by a charged planar boundary, with an explicit treatment of pH-dependent protein protonation equilibria and their couplings to the electrostatic potential of the plane. Electrostatic interactions are described within a framework of the continuum Poisson-Boltzmann model, whereas protein-plane hydrodynamic interactions are evaluated based on analytical expressions for the position- and orientation-dependent near-wall friction tensor of a spheroid. The algorithm was applied to simulate near-surface diffusion of lysozyme in solutions having pH in the range 4-10 and ionic strengths of 10 and 150 mM. As a reference, we performed Brownian dynamics simulations in which the protein is assigned a fixed, most probable protonation state, appropriate for given solution conditions and unaffected by the presence of the charged plane, and Brownian dynamics simulations in which the protein probes possible protonation states with the pH-dependent probability, but these variations are not coupled to the electric field generated by the boundary. We show that electrostatic interactions with the negatively charged plane substantially modify probabilities of different protonation states of lysozyme and shift protonation equilibria of both acidic and basic amino acid side chains toward higher pH values. Consequently, equilibrium energy distributions, equilibrium position-orientation distributions, and functions that characterize rotational dynamics, which for a protein with multiple ionization sites, such as lysozyme, in the presence of a charged obstacle are pH-dependent, are significantly affected by the approach taken to incorporate the solution pH into simulations.
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23
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Li Y, Wang M, Zhang Y, Koopal LK, Tan W. Goethite effects on transport and activity of lysozyme with humic acid in quartz sand. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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24
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Chrzanowska A, Derylo-Marczewska A, Wasilewska M. Mesocellular Silica Foams (MCFs) with Tunable Pore Size as a Support for Lysozyme Immobilization: Adsorption Equilibrium and Kinetics, Biocomposite Properties. Int J Mol Sci 2020; 21:E5479. [PMID: 32751874 PMCID: PMC7432670 DOI: 10.3390/ijms21155479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
The effect of the porous structure of mesocellular silica foams (MCFs) on the lysozyme (LYS) adsorption capacity, as well as the rate, was studied to design the effective sorbent for potential applications as the carriers of biomolecules. The structural (N2 adsorption/desorption isotherms), textural (SEM, TEM), acid-base (potentiometric titration), adsorption properties, and thermal characteristics of the obtained lysozyme/silica composites were studied. The protein adsorption equilibrium and kinetics showed significant dependence on silica pore size. For instance, LYS adsorption uptake on MCF-6.4 support (pore diameter 6.4 nm) was about 0.29 g/g. The equilibrium loading amount of LYS on MCF-14.5 material (pore size 14.5 nm) increased to 0.55 g/g. However, when the pore diameter was larger than 14.5 nm, the LYS adsorption value systematically decreased with increasing pore size (e.g., for MCF-30.1 was only 0.27 g/g). The electrostatic attractive interactions between the positively charged lysozyme (at pH = 7.4) and the negatively charged silica played a significant role in the immobilization process. The differences in protein adsorption and surface morphology for the biocomposites of various pore sizes were found. The thermal behavior of the studied bio/systems was conducted by TG/DSC/FTIR/MS coupled method. It was found that the thermal degradation of lysozyme/silica composites was a double-stage process in the temperature range 165-420-830 °C.
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Affiliation(s)
- Agnieszka Chrzanowska
- Department of Physical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin, M. Curie-Sklodowska Sq. 3, 20-031 Lublin, Poland; (A.D.-M.); (M.W.)
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25
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Hornos F, Esquembre R, Gómez J. Competitive inhibition of protein adsorption to silica surfaces by their coating with high density charge polyelectrolytes. Colloids Surf B Biointerfaces 2020; 191:110993. [DOI: 10.1016/j.colsurfb.2020.110993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/04/2020] [Accepted: 03/23/2020] [Indexed: 12/23/2022]
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26
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Komorek P, Wałek M, Jachimska B. Mechanism of lysozyme adsorption onto gold surface determined by quartz crystal microbalance and surface plasmon resonance. Bioelectrochemistry 2020; 135:107582. [PMID: 32535493 DOI: 10.1016/j.bioelechem.2020.107582] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 01/23/2023]
Abstract
In this study, the physicochemical characterization of lysozyme adsorbed on gold was investigated. Through the use of MP-SPR it was possible to establish that the orientation of molecules changes from side-on to between or end-on with increasing surface coverage. The data confirms that the process of adsorption is driven primarily by electrostatic interactions but also by hydrophobic forces. MP-SPR data was compared with the Random Sequential Adsorption model for a molecule with an ellipsoidal shape. Contact angle measurements showed that higher surface coverage also translates in more hydrophilic properties of obtained lysozyme layer. Comparison of CD and PM-IRRAS spectra in solution and adsorbed state respectively showed changes in the secondary structures of lysozyme. These changes are dependent on pH, but fundamentally they go in the direction of the increase of β-turn/random content with a simultaneous decrease in β-sheet fraction, which suggests that aggregation is not occurring. The combination of MP-SPR and QCM-D measurements allowed the estimation of the number of water molecules associated with the lysozymes films. It has been observed that hydration decreases from 70% in pH = 4 to 30% in pH = 11. This data indicates that hydration is driven mainly by the degree of protonation of lysozyme molecules.
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Affiliation(s)
- P Komorek
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - M Wałek
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - B Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland.
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27
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Yamaguchi A, Kobayashi M, Adachi Y. Yield stress of mixed suspension of silica particles and lysozymes: The effect of zeta potential and adsorbed amount. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.123575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Arooj M, Arrigan DWM, Mancera RL. Characterization of Protein-Facilitated Ion-Transfer Mechanism at a Polarized Aqueous/Organic Interface. J Phys Chem B 2019; 123:7436-7444. [PMID: 31379167 DOI: 10.1021/acs.jpcb.9b04746] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein electrochemistry studies at a polarized interface between two immiscible electrolyte solutions (ITIES) indicate that the detection mechanism of a protein at the interface involves a combination of protein-anion complexation and interfacial adsorption processes. A detailed characterization of the protein-facilitated mechanism of ion transfer at the ITIES will allow the development of new label-free biomolecular detection tools. Molecular dynamics simulations were performed to describe the mechanism of transfer of the hydrophobic anion tetraphenylborate (TPB-) from a 1,2-dichloroethane (organic) phase to an aqueous phase mediated by lysozyme as a model protein under the action of an external electric field. The anion migrated to the protein at the interface and formed multiple contacts. The side chains of positively charged Lys and Arg residues formed electrostatic interactions with the anion. Nonpolar residues like Trp, Met, and Val formed hydrophobic contacts with the anion as it moved along the protein surface. During this process, lysozyme adopted multiple, partially unfolded conformations at the interface, all involving various anion-protein complexes with small free-energy barriers between them. The general mechanism of protein-facilitated ion transfer at a polarized liquid-liquid interface thus likely involves the movement of a hydrophobic anion along the protein surface through a combination of electrostatic and hydrophobic interactions.
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Affiliation(s)
- Mahreen Arooj
- Department of Chemistry, College of Sciences , University of Sharjah , Sharjah 27272 , United Arab Emirates
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29
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30
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Molecular simulation of protein adsorption and conformation at gas-liquid, liquid–liquid and solid–liquid interfaces. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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32
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Swiatek S, Komorek P, Jachimska B. Adsorption of β-lactoglobulin A on gold surface determined in situ by QCM-D measurements. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2019.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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33
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Insight into the mechanism and factors on encapsulating basic model protein, lysozyme, into heparin doped CaCO3. Colloids Surf B Biointerfaces 2019; 175:184-194. [DOI: 10.1016/j.colsurfb.2018.11.079] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/25/2018] [Accepted: 11/28/2018] [Indexed: 11/17/2022]
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34
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Tiwari S, Gogoi A, Reddy KA. What governs the nature of fouling in forward osmosis (FO) and reverse osmosis (RO)? A molecular dynamics study. Phys Chem Chem Phys 2019; 21:24165-24176. [DOI: 10.1039/c9cp04393d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Difference in the distribution of water molecules around the protein leads to different fouling structures in FO and RO.
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Affiliation(s)
- Shivam Tiwari
- Department of Chemical Engineering
- Indian Institute of Technology Guwahati
- India
| | - Abhijit Gogoi
- Department of Mechanical Engineering
- Indian Institute of Technology Guwahati
- India
| | - K. Anki Reddy
- Department of Chemical Engineering
- Indian Institute of Technology Guwahati
- India
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35
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Boubeta FM, Soler-Illia GJAA, Tagliazucchi M. Electrostatically Driven Protein Adsorption: Charge Patches versus Charge Regulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15727-15738. [PMID: 30451508 DOI: 10.1021/acs.langmuir.8b03411] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The mechanisms of electrostatically driven adsorption of proteins on charged surfaces are studied with a new theoretical framework. The acid-base behavior, charge distribution, and electrostatic contributions to the thermodynamic properties of the proteins are modeled in the presence of a charged surface. The method is validated against experimental titration curves and apparent p Kas. The theory predicts that electrostatic interactions favor the adsorption of proteins at their isoelectric points on charged surfaces despite the fact that the protein has no net charge in solution. Two known mechanisms explain adsorption under these conditions: (i) charge regulation (the charge of the protein changes due to the presence of the surface) and (ii) charge patches (the protein orients to place charged amino acids near opposite surface charges). This work shows that both mechanisms contribute to adsorption at low ionic strengths, whereas only the charge-patch mechanism operates at high ionic strength. Interestingly, the contribution of charge regulation is insensitive to protein orientation under all conditions, which validates the use of constant-charge simulations to determine the most stable orientation of adsorbed proteins. The present study also shows that the charged surface can induce large shifts in the apparent p Kas of individual amino acids in adsorbed proteins. Our conclusions are valid for all proteins studied in this work (lysozyme, α-amylase, ribonuclease A, and β-lactoglobulin), as well as for proteins that are not isoelectric but have instead a net charge in solution of the same sign as the surface charge, i.e. the problem of protein adsorption on the "wrong side" of the isoelectric point.
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Affiliation(s)
| | - G J A A Soler-Illia
- Instituto de Nanosistemas , Universidad Nacional de General San Martín , Avenida 25 de Mayo y Francia , 1650 San Martín , Argentina
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36
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Świątek S, Komorek P, Turner G, Jachimska B. β-Lactoglobulin as a potential carrier for bioactive molecules. Bioelectrochemistry 2018; 126:137-145. [PMID: 30590224 DOI: 10.1016/j.bioelechem.2018.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022]
Abstract
In this study, the interaction and binding behavior of anesthetic tetracaine (TET) with bovine β-lactoglobulin (LGB) isoform A and a mixture of isoforms A and B were investigated under varying environmental conditions (pH, ionic strength, concentration, LGB-TET complex molar ratio). A wide range of analytical techniques (dynamic light scattering (DLS), electrophoretic mobility, UV-Vis spectroscopy, circular dichroism (CD), quartz crystal microbalance (QCM-D) were used to analyze the physicochemical properties of the complexes in bulk solution and on the surface of gold. The experiments revealed that TET, which is amphiphilic, could bind with LGB not only in the β-barrel but also onto the surface. The zeta potential of the LGB becomes more positively charged upon interaction with TET due to electrostatic interaction of the amino group present in the TET structure. Changes in the zeta potential values are mostly visible above pH 6 for all tested systems. CD spectra show that interaction with the ligand does not change the secondary structure of the protein. The physicochemical properties of LGB-TET complex were examined in an adsorbed state on a gold surface using the QCM-D method. Additionally, molecular docking was used to evaluate the most likely binding site for TET with LGB.
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Affiliation(s)
- S Świątek
- Polish Academy of Sciences, Jerzy Haber Institute of Catalysis and Surface Chemistry, Niezapominajek 8, Cracow 30-239, Poland
| | - P Komorek
- Polish Academy of Sciences, Jerzy Haber Institute of Catalysis and Surface Chemistry, Niezapominajek 8, Cracow 30-239, Poland
| | - G Turner
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, UK
| | - B Jachimska
- Polish Academy of Sciences, Jerzy Haber Institute of Catalysis and Surface Chemistry, Niezapominajek 8, Cracow 30-239, Poland.
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37
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Connell DJ, Gebril A, Khan MAH, Patwardhan SV, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Rationalising drug delivery using nanoparticles: a combined simulation and immunology study of GnRH adsorbed to silica nanoparticles. Sci Rep 2018; 8:17115. [PMID: 30459397 PMCID: PMC6244087 DOI: 10.1038/s41598-018-35143-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/26/2018] [Indexed: 11/30/2022] Open
Abstract
Silica nanoparticles (SiNPs) have been shown to have significant potential for drug delivery and as adjuvants for vaccines. We have simulated the adsorption of GnRH-I (gonadotrophin releasing hormone I) and a cysteine-tagged modification (cys-GnRH-I) to model silica surfaces, as well as its conjugation to the widely-used carrier protein bovine serum albumin (BSA). Our subsequent immunological studies revealed no significant antibody production was caused by the peptide-SiNP systems, indicating that the treatment was not effective. However, the testosterone response with the native peptide-SiNPs indicated a drug effect not found with cys-GnRH-I-SiNPs; this behaviour is explained by the specific orientation of the peptides at the silica surface found in the simulations. With the BSA systems, we found significant testosterone reduction, particularly for the BSA-native conjugates, and an antibody response that was notably higher with the SiNPs acting as an adjuvant; this behaviour again correlates well with the epitope presentation predicted by the simulations. The range of immunological and hormone response can therefore be interpreted and understood by the simulation results and the presentation of the peptides to solution, paving the way for the future rational design of drug delivery and vaccine systems guided by biomolecular simulation.
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Affiliation(s)
- David J Connell
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| | - Ayman Gebril
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Mohammad A H Khan
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Siddharth V Patwardhan
- Department of Chemical and Biological Engineering, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| | - Valerie A Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul A Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK.
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Li Y, Koopal LK, Xiong J, Wang M, Yang C, Tan W. Influence of humic acid on transport, deposition and activity of lysozyme in quartz sand. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:298-306. [PMID: 29990937 DOI: 10.1016/j.envpol.2018.06.096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/24/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
Interaction with natural organic matter (NOM) is hypothesized to impact the fate and bioavailability of enzymes and some hazardous proteins in terrestrial and aquatic environments. By using saturated column transport experiments the transport and deposition of the model enzyme lysozyme (LSZ), in the absence and presence of purified Aldrich humic acid (PAHA), was investigated at a series of mass ratios PAHA/LSZ at pH 5 and 8 and two ionic strength values (0.5 mM and 50 mM KCl solution). PAHA decreased LSZ transport under all conditions. The shapes of breakthrough curves (BTCs) and retention profiles (RPs) during cotransport of both colloids evolved from symmetrical to blocking with time and from flat to hyper-exponential with depth, respectively, in response to increases in mass ratio PAHA/LSZ. The results indicated that the "size-selective retention" and concurrent homo- and hetero-aggregation induced straining, which resulted in preferential retention of relatively large PAHA-LSZ aggregates in the column and elution of relatively small ones. Due to differences in aggregate size, in general, the enzyme activity of LSZ in the effluent was larger and that of the retained LSZ was smaller than that of the influent. Therefore, protein transport process could partially increase the enzyme activity and bring potential environmental hazards.
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Affiliation(s)
- Yan Li
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Luuk K Koopal
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China; Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Juan Xiong
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingxia Wang
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Chenfeng Yang
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wenfeng Tan
- Key Laboratory of Horticultural Plant Biology, The Ministry of Education, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China.
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39
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Adsorption of Fibronectin Fragment on Surfaces Using Fully Atomistic Molecular Dynamics Simulations. Int J Mol Sci 2018; 19:ijms19113321. [PMID: 30366398 PMCID: PMC6275015 DOI: 10.3390/ijms19113321] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023] Open
Abstract
The effect of surface chemistry on the adsorption characteristics of a fibronectin fragment (FNIII8⁻10) was investigated using fully atomistic molecular dynamics simulations. Model surfaces were constructed to replicate self-assembled monolayers terminated with methyl, hydroxyl, amine, and carboxyl moieties. It was found that adsorption of FNIII8⁻10 on charged surfaces is rapid, specific, and driven by electrostatic interactions, and that the anchoring residues are either polar uncharged or of opposing charge to that of the targeted surfaces. On charged surfaces the presence of a strongly bound layer of water molecules and ions hinders FNIII8⁻10 adsorption. In contrast, adsorption kinetics on uncharged surfaces are slow and non-specific, as they are driven by van der Waals interactions, and the anchoring residues are polar uncharged. Due to existence of a positively charged area around its cell-binding region, FNIII8⁻10 is available for subsequent cell binding when adsorbed on a positively charged surface, but not when adsorbed on a negatively charged surface. On uncharged surfaces, the availability of the fibronectin fragment's cell-binding region is not clearly distinguished because adsorption is much less specific.
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Abstract
We study the influence of surface functionalization of a silica surface on insulin adsorption using accelerated molecular dynamics simulation. Three different functional groups are studied, CH3, OH, and COOH. Due to the partial charges of these groups, the surface polarity of silica is strongly altered. We find that the adsorption energies of insulin change in agreement with the decreasing surface polarity. Conformational changes in the adsorbed protein and the magnitude of the molecular dipole moment in the adsorbed state are consistent with this result. We conclude that protein adsorption on functionalized polar surfaces is governed by the induced changes in surface polarity.
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41
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Russell BA, Jachimska B, Komorek P, Mulheran PA, Chen Y. Lysozyme encapsulated gold nanoclusters: effects of cluster synthesis on natural protein characteristics. Phys Chem Chem Phys 2018; 19:7228-7235. [PMID: 28234394 DOI: 10.1039/c7cp00540g] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The study of gold nanoclusters (AuNCs) has seen much interest in recent history due to their unique fluorescence properties and environmentally friendly synthesis method using proteins as a growth scaffold. The differences in the physicochemical properties of lysozyme encapsulated AuNCs in comparison to natural lysozyme are characterised in order to determine the effects AuNCs have on natural protein behaviour. The hydrodynamic radius (dynamic light scattering), light absorbance (UV-Vis), electrophoretic mobility, relative density, dynamic viscosity, adsorption (quartz crystal microbalance) and circular dichroism (CD) characteristics of the molecules were studied. It was found that lysozyme forms small dimer/trimer aggregates upon the synthesis of AuNCs within the protein. The diameter of Ly-AuNCs was found to be 8.0 nm across a pH range of 2-11 indicating dimer formation, but larger aggregates with diameters >20 nm were formed between pH 3 and 6. The formation of larger aggregates limits the use of Ly-AuNCs as a fluorescent probe in this pH range. A large shift in the protein's isoelectric point was also observed, shifting from 11.0 to 4.0 upon AuNC synthesis. This resulted in major changes to the adsorption characteristics of lysozyme, observed using a QCM. A monolayer of 8 nm was seen for Ly-AuNCs at pH 4, offering further evidence that the proteins form small aggregates, unlike the natural monomer form of lysozyme. The adsorption of Ly-AuNCs was seen to decrease as pH was increased; this is in major contrast to the lysozyme adsorption behaviour. A decrease in the α-helix content was observed from 25% in natural lysozyme to 1% in Ly-AuNCs. This coincided with an increase in the β-sheet content after AuNC synthesis indicating that the natural structure of lysozyme was lost. The formation of protein dimers, the change in the protein surface charge from positive to negative, and secondary structure alteration caused by the AuNC synthesis must be considered before attempting to utilise Ly-AuNCs as in vivo probes.
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Affiliation(s)
- B A Russell
- Department of Physics, Strathclyde University, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, UK.
| | - B Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - P Komorek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland and Faculty of Physics, Astronomy and Applied Computer Science, Jagellonian University, Stanislawa Lojasiewicza, 30-348 Cracow, Poland
| | - P A Mulheran
- Department of Chemical and Process Engineering, Strathclyde University, Glasgow G1 1XJ, UK
| | - Y Chen
- Department of Physics, Strathclyde University, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, UK.
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42
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Huang Y, Yamaguchi A, Pham TD, Kobayashi M. Charging and aggregation behavior of silica particles in the presence of lysozymes. Colloid Polym Sci 2017. [DOI: 10.1007/s00396-017-4226-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Hilt S, Rojalin T, Viitala T, Koivuniemi A, Bunker A, Hogiu SW, Kálai T, Hideg K, Yliperttula M, Voss JC. Oligomerization Alters Binding Affinity Between Amyloid Beta and a Modulator of Peptide Aggregation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2017; 121:23974-23987. [PMID: 30214656 PMCID: PMC6130836 DOI: 10.1021/acs.jpcc.7b06164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The soluble oligomeric form of the amyloid beta (Aβ) peptide is the major causative agent in the molecular pathogenesis of Alzheimer's disease (AD). We have previously developed a pyrroline-nitroxyl fluorene compound (SLF) that blocks the toxicity of Aβ. Here we introduce the multi-parametric surface plasmon resonance (MP-SPR) approach to quantify SLF binding and effect on the self-association of the peptide via a label-free, real-time approach. Kinetic analysis of SLF binding to Aβ and measurements of layer thickness alterations inform on the mechanism underlying the ability of SLF to inhibit Aβ toxicity and its progression towards larger oligomeric assemblies. Depending on the oligomeric state of Aβ, distinct binding affinities for SLF are revealed. The Aβ monomer and dimer uniquely possess sub-nanomolar affinity for SLF via a non-specific mode of binding. SLF binding is weaker in oligomeric Aβ, which displays an affinity for SLF on the order of 100 μM. To complement these experiments we carried out molecular docking and molecular dynamics simulations to explore how SLF interacts with the Aβ peptide. The MP-SPR results together with in silico modeling provide affinity data for the SLF-Aβ interaction and allow us to develop a new general method for examining protein aggregation.
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Affiliation(s)
- Silvia Hilt
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Tatu Rojalin
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Tapani Viitala
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Artturi Koivuniemi
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Alex Bunker
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Sebastian Wachsmann Hogiu
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Intellectual Ventures/Global Good, Bellevue, WA, USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Marjo Yliperttula
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
- Department of Pharmaceutical Sciences, University of Padova, Italy
| | - John C. Voss
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
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Tokarczyk K, Jachimska B. Quantitative interpretation of PAMAM dendrimers adsorption on silica surface. J Colloid Interface Sci 2017; 503:86-94. [PMID: 28500943 DOI: 10.1016/j.jcis.2017.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/16/2017] [Accepted: 05/01/2017] [Indexed: 01/30/2023]
Abstract
Understanding the dendrimer-solid support interaction is of great importance for dendrimer-based drug delivery system design. The maximum surface coverage on a hydrophilic silica surface was determined using the quartz crystal microbalance with dissipation monitoring (QCM-D) and multi-parametric surface plasmon resonance (MP-SPR) methods: the adsorption process depends on ionic strength and pH of solutions. The effectiveness of G6 adsorption is mainly determined by the range of electrostatic inter-dendrimer interactions and dendrimer-silica surface interactions. Changes in ionic strength have a strong effect on the binding affinity of dendrimers to the surface. The trends in the binding affinity and the surface saturation amount correspond well with the degree of change of protonation of the adsorbed molecules. The development of new research techniques makes it possible to attain a more profound understanding of the self-assembling behaviour of dendrimers. The comparison of QCM-D and MP-SPR allowed the estimation that the dendrimer film contains approximately 70% water. These results indicate that 6th generation PAMAM dendrimers form very hydrated films on silica surfaces. In this case the number of water molecules associated per dendrimer molecule varied from 10,450 to 9,200. The hydration of dendrimer films seems to be a crucial aspect of their implementation. This data confirmed that dendrimers are very promising candidates for many biological applications.
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Affiliation(s)
- Karolina Tokarczyk
- J. Haber Institute of Catalysis and Surface Chemistry, PAS, Niezapominajek 8, 30-239 Cracow, Poland
| | - Barbara Jachimska
- J. Haber Institute of Catalysis and Surface Chemistry, PAS, Niezapominajek 8, 30-239 Cracow, Poland.
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45
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Kubiak-Ossowska K, Tokarczyk K, Jachimska B, Mulheran PA. Bovine Serum Albumin Adsorption at a Silica Surface Explored by Simulation and Experiment. J Phys Chem B 2017; 121:3975-3986. [PMID: 28350173 DOI: 10.1021/acs.jpcb.7b01637] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molecular details of BSA adsorption on a silica surface are revealed by fully atomistic molecular dynamics (MD) simulations (with a 0.5 μs trajectory), supported by dynamic light scattering (DLS), zeta potential, multiparametric surface plasmon resonance (MP-SPR), and contact angle experiments. The experimental and theoretical methods complement one another and lead to a wider understanding of the mechanism of BSA adsorption across a range of pH 3-9. The MD results show how the negatively charged BSA at pH7 adsorbs to the negatively charged silica surface, and reveal a unique orientation with preserved secondary and tertiary structure. The experiments then show that the protein forms complete monolayers at ∼ pH6, just above the protein's isoelectric point (pH5.1). The surface contact angle is maximum when it is completely coated with protein, and the hydrophobicity of the surface is understood in terms of the simulated protein conformation. The adsorption behavior at higher pH > 6 is also consistently interpreted using the MD picture; both the contact angle and the adsorbed protein mass density decrease with increasing pH, in line with the increasing magnitude of negative charge on both the protein and the surface. At lower pH < 5 the protein starts to unfold, and the adsorbed mass dramatically decreases. The comprehensive picture that emerges for the formation of oriented protein films with preserved native conformation will help guide efforts to create functional films for new technologies.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, U.K
| | - Karolina Tokarczyk
- J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science (PAS) , Niezapominajek 8, 30-239 Cracow, Poland
| | - Barbara Jachimska
- J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science (PAS) , Niezapominajek 8, 30-239 Cracow, Poland
| | - Paul A Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, U.K
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46
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Dyawanapelly S, Jagtap DD, Dandekar P, Ghosh G, Jain R. Assessing safety and protein interactions of surface-modified iron oxide nanoparticles for potential use in biomedical areas. Colloids Surf B Biointerfaces 2017; 154:408-420. [PMID: 28388527 DOI: 10.1016/j.colsurfb.2017.03.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 01/01/2023]
Abstract
We have investigated the electrostatic interaction between bare iron oxide nanoparticles (IONPs) or low molecular weight chitosan coated iron oxide nanoparticles (LMWC-IONPs) and hen egg white lysozyme (HEWL) at different pH values using protein-nanoparticle reverse charge parity model. Physicochemical characterization of both IONPs and LMWC-IONPs were carried out using DLS, TEM, FE-SEM, XRD, TGA, XPS and VSM analysis. DLS, TEM and FE-SEM results indicated that both IONPs were monodispersed, with size ranging from 8 to 20nm. The coating of LMWC on IONPs was confirmed using zeta potential, TGA, XRD and XPS measurements. The cytotoxicity of both IONPs and LMWC-IONPs was studied in vitro in A549 human lung alveolar epithelial cells to assess their use in biomedical applications. Furthermore, the interactions between protein-nanoparticles were investigated by UV-visible, fluorescence and circular dichroism spectroscopic techniques. The present study suggests that water soluble LMWC surface modified IONPs are the promising nanomaterials. The safety and biocompatibility of these nanoparticles render them suitable for biomedical applications.
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Affiliation(s)
- Sathish Dyawanapelly
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India; Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, NP Marg, Matunga, Mumbai 400019, India
| | - Dhanashree D Jagtap
- Division of Structural Biology, National Institute for Research in Reproductive Health (Indian Council of Medical Research), Jehangir Merwanji Street, Parel, Mumbai 400012, India
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, NP Marg, Matunga, Mumbai 400019, India
| | - Goutam Ghosh
- UGC-DAE Consortium for Scientific Research, Trombay, Mumbai 400085, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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47
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Nejad MA, Mücksch C, Urbassek HM. Insulin adsorption on crystalline SiO2: Comparison between polar and nonpolar surfaces using accelerated molecular-dynamics simulations. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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48
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Atabay M, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A. Adsorption and immobilisation of human insulin on graphene monoxide, silicon carbide and boron nitride nanosheets investigated by molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1270452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Rastkar Ebrahimzadeh
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Physics, Azarbaijan Shahid Madani University, Tabriz, Iran
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49
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Borzooeian Z, Taslim ME, Borzooeian G, Ghasemi O, Aminlari M. Activity and stability analysis of covalent conjugated lysozyme-single walled carbon nanotubes: potential biomedical and industrial applications. RSC Adv 2017. [DOI: 10.1039/c7ra07189b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Analysis of covalent conjugated lysozyme-single walled carbon nanotubes.
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Affiliation(s)
- Z. Borzooeian
- Department of Mechanical and Industrial Engineering
- College of Engineering
- Northeastern University
- Boston
- USA
| | - M. E. Taslim
- Department of Mechanical and Industrial Engineering
- College of Engineering
- Northeastern University
- Boston
- USA
| | - G. Borzooeian
- Department of Biology
- Payame Noor University of Isfahan
- Iran
| | - O. Ghasemi
- Takeda Pharmaceuticals USA Inc
- Cambridge
- USA
| | - M. Aminlari
- Department of Biochemistry
- School of Veterinary Medicine
- Shiraz University
- Shiraz
- Iran
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Kubiak-Ossowska K, Jachimska B, Mulheran PA. How Negatively Charged Proteins Adsorb to Negatively Charged Surfaces: A Molecular Dynamics Study of BSA Adsorption on Silica. J Phys Chem B 2016; 120:10463-10468. [PMID: 27657173 DOI: 10.1021/acs.jpcb.6b07646] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How proteins adsorb to inorganic material surfaces is critically important for the development of new biotechnologies, since the orientation and structure of the adsorbed proteins impacts their functionality. While it is known that many negatively charged proteins readily adsorb to negatively charged oxide surfaces, a detailed understanding of how this process occurs is lacking. In this work we study the adsorption of BSA, an important transport protein that is negatively charged at physiological conditions, to a model silica surface that is also negatively charged. We use fully atomistic molecular dynamics to provide detailed understanding of the noncovalent interactions that bind the BSA to the silica surface. Our results provide new insight into the competing roles of long-range electrostatics and short-range forces, and the consequences this has for the orientation and structure of the adsorbed proteins.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Barbara Jachimska
- J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science (PAS) , Niezapominajek 8, 30-239 Cracow, Poland
| | - Paul A Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
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