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Guagliano M, Cristiani C, Dell’Anno M, Dotelli G, Finocchio E, Lacalamita M, Mesto E, Reggi S, Rossi L, Schingaro E. A Commercial Clay-Based Material as a Carrier for Targeted Lysozyme Delivery in Animal Feed. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2965. [PMID: 37999319 PMCID: PMC10674955 DOI: 10.3390/nano13222965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
The controlled supply of bioactive molecules is a subject of debate in animal nutrition. The release of bioactive molecules in the target organ, in this case the intestine, results in improved feed, as well as having a lower environmental impact. However, the degradation of bioactive molecules' in transit in the gastrointestinal passage is still an unresolved issue. This paper discusses the feasibility of a simple and cost-effective procedure to bypass the degradation problem. A solid/liquid adsorption procedure was applied, and the operating parameters (pH, reaction time, and LY initial concentration) were studied. Lysozyme is used in this work as a representative bioactive molecule, while Adsorbo®, a commercial mixture of clay minerals and zeolites which meets current feed regulations, is used as the carrier. A maximum LY loading of 32 mgLY/gAD (LY(32)-AD) was obtained, with fixing pH in the range 7.5-8, initial LY content at 37.5 mgLY/gAD, and reaction time at 30 min. A full characterisation of the hybrid organoclay highlighted that LY molecules were homogeneously spread on the carrier's surface, where the LY-carrier interaction was mainly due to charge interaction. Preliminary release tests performed on the LY(32)-AD synthesised sample showed a higher releasing capacity, raising the pH from 3 to 7. In addition, a preliminary Trolox equivalent antioxidant capacity (TEAC) assay showed an antioxidant capacity for the LY of 1.47 ± 0.18 µmol TroloxEq/g with an inhibition percentage of 33.20 ± 3.94%.
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Affiliation(s)
- Marianna Guagliano
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo Da Vinci 32, 20133 Milano, Italy;
| | - Cinzia Cristiani
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo Da Vinci 32, 20133 Milano, Italy;
| | - Matteo Dell’Anno
- Dipartimento di Medicina Veterinaria e Scienze Animali—DIVAS, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (M.D.); (S.R.); (L.R.)
| | - Giovanni Dotelli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo Da Vinci 32, 20133 Milano, Italy;
| | - Elisabetta Finocchio
- Dipartimento di Ingegneria Civile, Chimica e Ambientale, Università di Genova, Via Opera Pia 15, 16145 Genova, Italy;
| | - Maria Lacalamita
- Dipartimento di Scienze della Terra e Geoambientali, Università degli Studi di Bari Aldo Moro, Via Edoardo Orabona 4, 70125 Bari, Italy; (M.L.); (E.M.); (E.S.)
| | - Ernesto Mesto
- Dipartimento di Scienze della Terra e Geoambientali, Università degli Studi di Bari Aldo Moro, Via Edoardo Orabona 4, 70125 Bari, Italy; (M.L.); (E.M.); (E.S.)
| | - Serena Reggi
- Dipartimento di Medicina Veterinaria e Scienze Animali—DIVAS, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (M.D.); (S.R.); (L.R.)
| | - Luciana Rossi
- Dipartimento di Medicina Veterinaria e Scienze Animali—DIVAS, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (M.D.); (S.R.); (L.R.)
| | - Emanuela Schingaro
- Dipartimento di Scienze della Terra e Geoambientali, Università degli Studi di Bari Aldo Moro, Via Edoardo Orabona 4, 70125 Bari, Italy; (M.L.); (E.M.); (E.S.)
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2
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Bhattacharjee N, Alonso-Cotchico L, Lucas MF. Enzyme immobilization studied through molecular dynamic simulations. Front Bioeng Biotechnol 2023; 11:1200293. [PMID: 37362217 PMCID: PMC10285225 DOI: 10.3389/fbioe.2023.1200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.
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3
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Liu C, Steer DL, Song H, He L. Superior Binding of Proteins on a Silica Surface: Physical Insight into the Synergetic Contribution of Polyhistidine and a Silica-Binding Peptide. J Phys Chem Lett 2022; 13:1609-1616. [PMID: 35142521 DOI: 10.1021/acs.jpclett.1c03306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Controllable protein attachment onto solid interfaces is essential for the functionality of proteins with broad applications. Silica-binding peptides (SBPs) have emerged as an important tool enabling convenient binding of proteins onto a silica surface. Surprisingly, we found that removal of polyhistidines, a common tag for protein purification, dramatically decrease the binding affinity of a SBP-tagged nanobody onto a silica surface. We hypothesized that polyhistidines and SBPs can be combined to enhance affinity. Through a series of purposely designed SBPs, we identified that the relative orientation of amino acids is a key factor affecting the surface binding strength. One re-engineered SBP, SBP4, exhibits a 4000-fold improvement compared to the original sequence. Guided by physical insights, the work provides a simple strategy that can dramatically improve affinity between a SBP and a silica surface, promising a new way for controllable immobilization of proteins, as demonstrated using nanobodies.
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Affiliation(s)
- Chang Liu
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - David L Steer
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Haipeng Song
- Shenzhen Innova Nanobodi Company, 1301 Sightseeing Road, Shengzhen, Guangdong 518000, People's Republic of China
| | - Lizhong He
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
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4
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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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5
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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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6
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García-Álvarez R, Vallet-Regí M. Hard and Soft Protein Corona of Nanomaterials: Analysis and Relevance. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:888. [PMID: 33807228 PMCID: PMC8067325 DOI: 10.3390/nano11040888] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 12/15/2022]
Abstract
Upon contact with a biological milieu, nanomaterials tend to interact with biomolecules present in the media, especially proteins, leading to the formation of the so-called "protein corona". As a result of these nanomaterial-protein interactions, the bio-identity of the nanomaterial is altered, which is translated into modifications of its behavior, fate, and pharmacological profile. For biomedical applications, it is fundamental to understand the biological behavior of nanomaterials prior to any clinical translation. For these reasons, during the last decade, numerous publications have been focused on the investigation of the protein corona of many different types of nanomaterials. Interestingly, it has been demonstrated that the structure of the protein corona can be divided into hard and soft corona, depending on the affinity of the proteins for the nanoparticle surface. In the present document, we explore the differences between these two protein coronas, review the analysis techniques used for their assessment, and reflect on their relevance for medical purposes.
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Affiliation(s)
- Rafaela García-Álvarez
- Departamento Química en Ciencias Farmaceúticas, Unidad de Química Inorgánica y Bioinorgánica, Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - María Vallet-Regí
- Departamento Química en Ciencias Farmaceúticas, Unidad de Química Inorgánica y Bioinorgánica, Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, 28029 Madrid, Spain
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7
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Precupas A, Gheorghe D, Botea-Petcu A, Leonties AR, Sandu R, Popa VT, Mariussen E, Naouale EY, Rundén-Pran E, Dumit V, Xue Y, Cimpan MR, Dusinska M, Haase A, Tanasescu S. Thermodynamic Parameters at Bio-Nano Interface and Nanomaterial Toxicity: A Case Study on BSA Interaction with ZnO, SiO 2, and TiO 2. Chem Res Toxicol 2020; 33:2054-2071. [PMID: 32600046 DOI: 10.1021/acs.chemrestox.9b00468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding nanomaterial (NM)-protein interactions is a key issue in defining the bioreactivity of NMs with great impact for nanosafety. In the present work, the complex phenomena occurring at the bio/nano interface were evaluated in a simple case study focusing on NM-protein binding thermodynamics and protein stability for three representative metal oxide NMs, namely, zinc oxide (ZnO; NM-110), titanium dioxide (TiO2; NM-101), and silica (SiO2; NM-203). The thermodynamic signature associated with the NM interaction with an abundant protein occurring in most cell culture media, bovine serum albumin (BSA), has been investigated by isothermal titration and differential scanning calorimetry. Circular dichroism spectroscopy offers additional information concerning adsorption-induced protein conformational changes. The BSA adsorption onto NMs is enthalpy-controlled, with the enthalpic character (favorable interaction) decreasing as follows: ZnO (NM-110) > SiO2 (NM-203) > TiO2 (NM-101). The binding of BSA is spontaneous, as revealed by the negative free energy, ΔG, for all systems. The structural stability of the protein decreased as follows: TiO2 (NM-101) > SiO2 (NM-203) > ZnO (NM-110). As protein binding may alter NM reactivity and thus the toxicity, we furthermore assessed its putative influence on DNA damage, as well as on the expression of target genes for cell death (RIPK1, FAS) and oxidative stress (SOD1, SOD2, CAT, GSTK1) in the A549 human alveolar basal epithelial cell line. The enthalpic component of the BSA-NM interaction, corroborated with BSA structural stability, matched the ranking for the biological alterations, i.e., DNA strand breaks, oxidized DNA lesions, cell-death, and antioxidant gene expression in A549 cells. The relative and total content of BSA in the protein corona was determined using mass-spectrometry-based proteomics. For the present case study, the thermodynamic parameters at bio/nano interface emerge as key descriptors for the dominant contributions determining the adsorption processes and NMs toxicological effect.
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Affiliation(s)
- Aurica Precupas
- Institute of Physical Chemistry "Ilie Murgulescu" of the Romanian Academy, Bucharest 060021, Romania
| | - Daniela Gheorghe
- Institute of Physical Chemistry "Ilie Murgulescu" of the Romanian Academy, Bucharest 060021, Romania
| | - Alina Botea-Petcu
- Institute of Physical Chemistry "Ilie Murgulescu" of the Romanian Academy, Bucharest 060021, Romania
| | - Anca Ruxandra Leonties
- Institute of Physical Chemistry "Ilie Murgulescu" of the Romanian Academy, Bucharest 060021, Romania
| | - Romica Sandu
- Institute of Physical Chemistry "Ilie Murgulescu" of the Romanian Academy, Bucharest 060021, Romania
| | - Vlad Tudor Popa
- Institute of Physical Chemistry "Ilie Murgulescu" of the Romanian Academy, Bucharest 060021, Romania
| | - Espen Mariussen
- NILU-Norwegian Institute for Air Research, Kjeller 2027, Norway
| | | | | | - Veronica Dumit
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Ying Xue
- Department of Clinical Dentistry, Faculty of Medicine, University of Bergen, Bergen 5020, Norway
| | - Mihaela Roxana Cimpan
- Department of Clinical Dentistry, Faculty of Medicine, University of Bergen, Bergen 5020, Norway
| | - Maria Dusinska
- NILU-Norwegian Institute for Air Research, Kjeller 2027, Norway
| | - Andrea Haase
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Speranta Tanasescu
- Institute of Physical Chemistry "Ilie Murgulescu" of the Romanian Academy, Bucharest 060021, Romania
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8
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Penna M, Yarovsky I. Nanoscale in silico classification of ligand functionalised surfaces for protein adsorption resistance. NANOSCALE 2020; 12:7240-7255. [PMID: 32196038 DOI: 10.1039/c9nr10009a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-specific protein adsorption represents a significant challenge for the design of efficient and safe nanoparticles for biomedical applications since it may prevent functional ligands to target the desired specific receptors which can limit the efficacy of novel drug delivery systems and biosensors. The biofilm formation initiated by protein adsorption on surfaces limits the lifetime and safety of medical implants and tissue regenerative scaffolds. The development of biofouling resistant surfaces is therefore a major goal for the widespread uptake of nanomedicine. Here, we provide a relatively simple computational screening method based on the rational physically grounded criteria that may suffice in selection of surface grafted ligands for protein rejection, and test whether these criteria can be extrapolated from a specific protein to generic protein-resistant surfaces. Using all-atom molecular dynamics simulations we characterise four types of ligand functionalised surfaces at aqueous interfaces in terms of the surface hydrophobicity and ligand dynamics. We demonstrate how our hypothesised interfacial design based on the select physical characteristics of the ligated surfaces can enable the rejection of a protein from the surface. The ligand screening procedure and the detailed atomistic characterisation of the protein rejection process presented suggest that minimizing the adsorption of surface active proteins requires specific surface topographies and ligand chemistries that are able to maximise the entropic penalty associated with the restriction of the ligand dynamics and trapping interfacial water by adsorbed proteins.
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Affiliation(s)
- Matthew Penna
- School of Engineering, RMIT University, Melbourne, VIC 3000, Australia.
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9
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Grasso G, Mercuri S, Danani A, Deriu MA. Biofunctionalization of Silica Nanoparticles with Cell-Penetrating Peptides: Adsorption Mechanism and Binding Energy Estimation. J Phys Chem B 2019; 123:10622-10630. [DOI: 10.1021/acs.jpcb.9b08106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Stefano Mercuri
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Marco A. Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
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10
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Atacan K, Güy N, Çakar S, Özacar M. Efficiency of glucose oxidase immobilized on tannin modified NiFe2O4 nanoparticles on decolorization of dye in the Fenton and photo-biocatalytic processes. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.111935] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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11
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Coglitore D, Janot JM, Balme S. Protein at liquid solid interfaces: Toward a new paradigm to change the approach to design hybrid protein/solid-state materials. Adv Colloid Interface Sci 2019; 270:278-292. [PMID: 31306853 DOI: 10.1016/j.cis.2019.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
This review gives an overview of protein adsorption at solid/liquid interface. Compared to the other ones, we have focus on three main questions with the point of view of the protein. The first question is related to the kinetic and especially the using of Langmuir model to describe the protein adsorption. The second question is about the concept of hard and soft protein. In this part, we report the protein structural modification induced by adsorption regarding their intrinsic structure. This allows formulating of a new concept to classify the protein to predict their behavior at solid/liquid interface. The last question is related to the protein corona. We give an overview about the soft/hard corona and attempt to make correlation with the concept of hard/soft protein.
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12
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13
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Stawski TM, van den Heuvel DB, Besselink R, Tobler DJ, Benning LG. Mechanism of silica-lysozyme composite formation unravelled by in situ fast SAXS. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2019; 10:182-197. [PMID: 30746312 PMCID: PMC6350881 DOI: 10.3762/bjnano.10.17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/11/2018] [Indexed: 05/31/2023]
Abstract
A quantitative understanding of aggregation mechanisms leading to the formation of composites of inorganic nanoparticles (NPs) and proteins in aqueous media is of paramount interest for colloid chemistry. In particular, the interactions between silica (SiO2) NPs and lysozyme (LZM) have attracted attention, because LZM is well-known to adsorb strongly to silica NPs, while at the same time preserving its enzymatic activity. The inherent nature of the aggregation processes leading to NP-LZM composites involves structural changes at length scales from few to at least hundreds of nanometres but also time scales much smaller than one second. To unravel these we used in situ synchrotron-based small-angle X-ray scattering (SAXS) and followed the subtle interparticle interactions in solution at a time resolution of 50 ms/frame (20 fps). We show that if the size of silica NPs (ca. 5 nm diameter) is matched by the dimensions of LZM, the evolving scattering patterns contain a unique structure-factor contribution originating from the presence of LZM. We developed a scattering model and applied it to analyse this structure function, which allowed us to extract structural information on the deformation of lysozyme molecules during aggregation, as well as to derive the mechanisms of composite formation.
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Affiliation(s)
- Tomasz M Stawski
- German Research Centre for Geosciences, GFZ, Interface Geochemistry, Telegrafenberg, 14473, Potsdam, Germany
| | - Daniela B van den Heuvel
- School of Earth and Environment, University of Leeds, Woodhouse Lane, LS2 9 JT, Leeds, UK
- Rock-Water Interaction Group, Institute of Geological Sciences, University of Bern, Baltzerstrasse 3, 3012, Bern, Switzerland
| | - Rogier Besselink
- German Research Centre for Geosciences, GFZ, Interface Geochemistry, Telegrafenberg, 14473, Potsdam, Germany
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, IFSTTAR, ISTerre, 38000 Grenoble, France
| | - Dominique J Tobler
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Liane G Benning
- German Research Centre for Geosciences, GFZ, Interface Geochemistry, Telegrafenberg, 14473, Potsdam, Germany
- School of Earth and Environment, University of Leeds, Woodhouse Lane, LS2 9 JT, Leeds, UK
- Department of Earth Sciences, Free University of Berlin, Malteserstr. 74–100 / Building A, 12249, Berlin, Germany
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14
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Atacan K, Kursunlu AN, Ozmen M. Preparation of pillar[5]arene immobilized trypsin and its application in microwave-assisted digestion of Cytochrome c. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 94:886-893. [DOI: 10.1016/j.msec.2018.10.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 09/06/2018] [Accepted: 10/09/2018] [Indexed: 11/17/2022]
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15
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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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16
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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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18
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Givens BE, Xu Z, Fiegel J, Grassian VH. Bovine serum albumin adsorption on SiO2 and TiO2 nanoparticle surfaces at circumneutral and acidic pH: A tale of two nano-bio surface interactions. J Colloid Interface Sci 2017; 493:334-341. [DOI: 10.1016/j.jcis.2017.01.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/29/2022]
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19
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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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20
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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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21
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Improvement of the stability and activity of immobilized trypsin on modified Fe3O4 magnetic nanoparticles for hydrolysis of bovine serum albumin and its application in the bovine milk. Food Chem 2016; 212:460-8. [DOI: 10.1016/j.foodchem.2016.06.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/26/2016] [Accepted: 06/05/2016] [Indexed: 01/05/2023]
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22
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Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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23
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Rubinstein AI, Sabirianov RF, Namavar F. Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach. NANOTECHNOLOGY 2016; 27:415703. [PMID: 27585807 DOI: 10.1088/0957-4484/27/41/415703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.
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Affiliation(s)
- Alexander I Rubinstein
- Department of Physics, Laboratory of Applied Spectroscopy, Ariel University, Ariel 40700, West Bank. Department of Physics, University of Nebraska at Omaha, Omaha, NE 68182, USA
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24
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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: 69] [Impact Index Per Article: 8.6] [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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25
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Andersen A, Reardon PN, Chacon SS, Qafoku NP, Washton NM, Kleber M. Protein-Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6194-6209. [PMID: 27243116 DOI: 10.1021/acs.langmuir.6b01198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na(+)-montmorillonite (001), Ca(2+)-montmorillonite (001), goethite (100), and Na(+)-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na(+)-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.
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Affiliation(s)
| | | | - Stephany S Chacon
- Department of Crop and Soil Science, Oregon State University , Corvallis, Oregon 97331, United States
| | | | | | - Markus Kleber
- Department of Crop and Soil Science, Oregon State University , Corvallis, Oregon 97331, United States
- Institut für Bodenlandschaftsforschung, Leibniz Zentrum für Agrarlandschaftsforschung (ZALF) , Eberswalder Straβe 84, 15374 Müncheberg, Germany
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26
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Mulheran PA, Connell DJ, Kubiak-Ossowska K. Steering protein adsorption at charged surfaces: electric fields and ionic screening. RSC Adv 2016. [DOI: 10.1039/c6ra16391b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Protein adsorption at charged surfaces is a common process in the development of functional technological devices.
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Affiliation(s)
- Paul A. Mulheran
- Department of Chemical and Process Engineering
- University of Strathclyde
- Glasgow G1 1XJ
- UK
| | - David J. Connell
- Department of Chemical and Process Engineering
- University of Strathclyde
- Glasgow G1 1XJ
- UK
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27
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Yu L, Zhang L, Sun Y. Protein behavior at surfaces: Orientation, conformational transitions and transport. J Chromatogr A 2015; 1382:118-34. [DOI: 10.1016/j.chroma.2014.12.087] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/26/2014] [Accepted: 12/31/2014] [Indexed: 12/18/2022]
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28
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Kubiak-Ossowska K, Mulheran PA, Nowak W. Fibronectin Module FNIII9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics. J Phys Chem B 2014; 118:9900-8. [DOI: 10.1021/jp5020077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudziadzka 5/7, 87-100 Torun, Poland
| | - Paul A. Mulheran
- Department
of Chemical and Process Engineering, University of Strathclyde, James
Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Wieslaw Nowak
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudziadzka 5/7, 87-100 Torun, Poland
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29
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Yu G, Liu J, Zhou J. Mesoscopic coarse-grained simulations of lysozyme adsorption. J Phys Chem B 2014; 118:4451-60. [PMID: 24785197 DOI: 10.1021/jp409326f] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a "top end-on" orientation, while they are exposed to the liquid phase on the hydrophilic surface with a "back-on" orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale.
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Affiliation(s)
- Gaobo Yu
- School of Chemistry and Chemical Engineering, South China University of Technology , Guangzhou, Guangdong 510640, China
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30
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Mu Y, Tang B, Yu M. Length-dependent β-sheet growth mechanisms of polyalanine peptides in water and on hydrophobic surfaces. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:032711. [PMID: 24730878 DOI: 10.1103/physreve.89.032711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 06/03/2023]
Abstract
Fibrillar assemblies by peptides are becoming one of the most promising nanomaterials due to their exceptional properties. The self-assembly of peptides into β sheets is a critical step in the fibrillization pathway. We investigated the length-dependent β-sheet growth mechanisms of polyalanine [poly(A)] peptides consisting of 6 to 24 alanines (A6 to A24) in water and on the hydrophobic surface, respectively, by molecular dynamics simulations. β-sheet growth behavior in water fits negative exponential growth model, showing that β-sheet growth rate decays exponentially with time. Meanwhile, increasing chain length leads to an accelerated decay of the β-sheet growth rate. By contrast, β-sheet growth on the surface from A6 to A18 occurs in two consecutive stages, both of which fit linear growth models. β-sheet growth rate in the first stage increases as chain length is increased, while the intermediate length peptide A12 has the highest β-sheet growth rate in the second stage. β-sheet growth behavior of A24 on the surface still fits negative exponential model. Overall, the hydrophobic surface accelerates β-sheet growth by enhancing local concentration and reducing conformational entropy of poly(A) peptide, and the β-sheet growth of the intermediate length peptide A12 is the fastest on the surface. Our simulation results shed light on understanding the accelerated peptide fibrillization on the hydrophobic surface.
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Affiliation(s)
- Yan Mu
- College of Materials Science and Engineering, South China University of Technology, Guangzhou Guangdong, 510641, China
| | - Binqing Tang
- College of Materials Science and Engineering, South China University of Technology, Guangzhou Guangdong, 510641, China
| | - Meng Yu
- College of Materials Science and Engineering, South China University of Technology, Guangzhou Guangdong, 510641, China
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31
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Bharti B, Meissner J, Klapp SHL, Findenegg GH. Bridging interactions of proteins with silica nanoparticles: the influence of pH, ionic strength and protein concentration. SOFT MATTER 2014; 10:718-28. [PMID: 24835283 DOI: 10.1039/c3sm52401a] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Charge-driven bridging of nanoparticles by macromolecules represents a promising route for engineering functional structures, but the strong electrostatic interactions involved when using conventional polyelectrolytes impart irreversible complexation and ill-defined structures. Recently it was found that the electrostatic interaction of silica nanoparticles with small globular proteins leads to aggregate structures that can be controlled by pH. Here we study the combined influence of pH and electrolyte concentration on the bridging aggregation of silica nanoparticles with lysozyme in dilute aqueous dispersions. We find that protein binding to the silica particles is determined by pH irrespective of the ionic strength. The hetero-aggregate structures formed by the silica particles with the protein were studied by small-angle X-ray scattering (SAXS) and the structure factor data were analyzed on the basis of a short-range square-well attractive pair potential (close to the sticky-hard-sphere limit). It is found that the electrolyte concentration has a strong influence on the stickiness near pH 5, where the weakly charged silica particles are bridged by the strongly charged protein. An even stronger influence of the electrolyte is found in the vicinity of the isoelectric point of the protein (pI = 10.7) and is attributed to shielding of the repulsion between the highly charged silica particles and hydrophobic interactions between the bridging protein molecules.
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Affiliation(s)
- Bhuvnesh Bharti
- Institut für Chemie, Stranski Laboratorium, TC 7, Technische Universität Berlin, Strasse des 17. Juni 124, D-10623 Berlin, Germany.
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32
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Kubiak-Ossowska K, Burley G, Patwardhan SV, Mulheran PA. Spontaneous membrane-translocating peptide adsorption at silica surfaces: a molecular dynamics study. J Phys Chem B 2013; 117:14666-75. [PMID: 24176015 PMCID: PMC3871889 DOI: 10.1021/jp409130s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Spontaneous membrane-translocating
peptides (SMTPs) have recently
been shown to directly penetrate cell membranes. Adsorption of a SMTP,
and some engineered extensions, at model silica surfaces is studied
herein using fully atomistic molecular dynamics simulations in order
to assess their potential to construct novel drug delivery systems.
The simulations are designed to reproduce the electric fields above
single, siloxide-rich charged surfaces, and the trajectories indicate
that the main driving force for adsorption is electrostatic. An increase
in the salt concentration slows down but does not prevent adsorption
of the SMTP to the surface; it also does not result in peptide desorption,
suggesting additional binding via hydrophobic forces. The results
are used to design extensions to the peptide sequence which we find
enhance adsorption but do not affect the adsorbed conformation. We
also investigate the effect of surface hydroxylation on the peptide
adsorption. In all cases, the final adsorbed conformations are with
the peptide flattened to the surface with arginine residues, which
are key to the peptide’s function, anchoring it to the surface
so that they are not exposed to solution. This conformation could
impact their role in membrane translocation and thus has important
implications for the design of future drug delivery vehicles.
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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
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33
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Effects of external electric fields on lysozyme adsorption by molecular dynamics simulations. Biophys Chem 2013; 179:26-34. [DOI: 10.1016/j.bpc.2013.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 04/28/2013] [Accepted: 05/01/2013] [Indexed: 11/23/2022]
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34
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Tong C. The numerical study of the adsorption of flexible polyelectrolytes with the annealed charge distribution onto an oppositely charged sphere by the self-consistent field theory. J Chem Phys 2013; 139:084903. [DOI: 10.1063/1.4819037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Cao F, Wang L, Jiang X, Guo LP. Investigation of the effects of surface chemistry on adsorption of albumin by surface-enhanced FTIR spectroscopy. RSC Adv 2013. [DOI: 10.1039/c3ra40665b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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36
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Kubiak-Ossowska K, Mulheran PA. Protein diffusion and long-term adsorption states at charged solid surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15577-15585. [PMID: 23062108 DOI: 10.1021/la303323r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The diffusion pathways of lysozyme adsorbed to a model charged ionic surface are studied using fully atomistic steered molecular dynamics simulation. The simulations start from existing protein adsorption trajectories, where it has been found that one particular residue, Arg128 at the N,C-terminal face, plays a crucial role in anchoring the lysozyme to the surface [Langmuir 2010 , 26 , 15954 - 15965]. We first investigate the desorption pathway for the protein by pulling the Arg128 side chain away from the surface in the normal direction, and its subsequent readsorption, before studying diffusion pathways by pulling the Arg128 side chain parallel to the surface. We find that the orientation of this side chain plays a decisive role in the diffusion process. Initially, it is oriented normal to the surface, aligning in the electrostatic field of the surface during the adsorption process, but after resorption it lies parallel to the surface, being unable to return to its original orientation due to geometric constraints arising from structured water layers at the surface. Diffusion from this alternative adsorption state has a lower energy barrier of ∼0.9 eV, associated with breaking hydrogen bonds along the pathway, in reasonable agreement with the barrier inferred from previous experimental observation of lysozyme surface clustering. These results show the importance of studying protein diffusion alongside adsorption to gain full insight into the formation of protein clusters and films, essential steps in the future development of functionalized surfaces.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow, United Kingdom
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Wei T, Carignano MA, Szleifer I. Molecular dynamics simulation of lysozyme adsorption/desorption on hydrophobic surfaces. J Phys Chem B 2012; 116:10189-94. [PMID: 22882159 DOI: 10.1021/jp304057e] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we present a series of fully atomistic molecular dynamics (MD) simulations to study lysozyme's orientation-dependent adsorption on polyethylene (PE) surface in explicit water. The simulations show that depending on the orientation of the initial approach to the surface the protein may adsorb or bounce from the surface. The protein may completely leave the surface or reorient and approach the surface resulting in adsorption. The success of the trajectory to adsorb on the surface is the result of different competing interactions, including protein-surface interactions and the hydration of the protein and the hydrophobic PE surface. The difference in the hydration of various protein sites affects the protein's orientation-dependent behavior. Side-on orientation is most likely to result in adsorption as the protein-surface exhibits the strongest attraction. However, adsorption can also happen when lysozyme's longest axis is tilted on the surface if the protein-surface interaction is large enough to overcome the energy barrier that results from dehydrating both the protein and the surface. Our study demonstrates the significant role of dehydration process on hydrophobic surface during protein adsorption.
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Affiliation(s)
- Tao Wei
- Department of Biomedical Engineering, Department of Chemistry and Chemistry of Life Processes Institute, Northwestern University , Evanston, Illinois 60208, United States
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Namavar F, Rubinstein A, Sabirianov RF, Thiele GM, Sharp JG, Pokharel U, Namavar RM, Garvin KL. Engineered Nanostructured Coatings for Enhanced Protein Adsorption and Cell Growth. ACTA ACUST UNITED AC 2012. [DOI: 10.1557/opl.2012.394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTWe designed and produced pure cubic zirconia (ZrO2) ceramic1 coatings by an ion beam assisted deposition (IBAD) with nanostructures comparable to the size of proteins. Our ceramic coatings exhibit high hardness and a zero contact angle with serum. In contrast to hydroxyapatite (HA), nano-engineered zirconia films possess excellent adhesion to all orthopaedic materials. Cell adhesion and proliferation experiments were performed with a bona fide mesenchymal stromal cell line (OMA-AD). Our experimental results indicate that the nano-engineered cubic zirconia is superior in supporting growth, adhesion, and proliferation. Since cell attachment is mediated by adhesive proteins such as fibronectin (FN), to elucidate why cells attach more effectively to our nanostructures, we performed a comparative analysis of adsorption energies of FN fragment using quantum mechanical calculations and Monte Carlo (MC) simulation both on smooth and nanostructured surfaces. We have found that a FN fragment adsorbs significantly stronger on the nanostructured surface than on the smooth surface2.
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Modelling of lysozyme binding to a cation exchange surface at atomic detail: the role of flexibility. Biophys J 2011; 100:3016-24. [PMID: 21689536 DOI: 10.1016/j.bpj.2011.05.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 05/03/2011] [Accepted: 05/09/2011] [Indexed: 11/21/2022] Open
Abstract
Different approaches were made to predict the adsorbed orientation based on rigid, flexible, or a mixture of both models. To determine the role of flexibility during adsorption, the orientation of lysozyme adsorbed to a negatively charged ligand surface was predicted by a rigid and a flexible model based on two differing protein structures at atomic resolution. For the rigid model, the protein structures were placed at different distances from the ligand surface and the electrostatic interaction energy was calculated for all possible orientations. The results were compared to a flexible model where the binding to the ligand surface was modeled by multiple molecular dynamics simulations starting with 14 initial orientations. Different aspects of the adsorption process were not covered by the rigid model and only detectable by the flexible model. Whereas the results of the rigid model depended sensitively on the protein-surface distance and the protein structure, the preferred orientation obtained by the flexible model was closer to a previous experimental determined orientation, robust toward the initial orientation and independent of the initial protein structure. Additionally, it was possible to obtain insights into the preferred binding process of lysozyme on a negatively charged surface by the flexible model.
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Madden C, Vaughn MD, Díez-Pérez I, Brown KA, King PW, Gust D, Moore AL, Moore TA. Catalytic Turnover of [FeFe]-Hydrogenase Based on Single-Molecule Imaging. J Am Chem Soc 2011; 134:1577-82. [DOI: 10.1021/ja207461t] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher Madden
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Michael D. Vaughn
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Ismael Díez-Pérez
- Center for Bioelectronics and Biosensors, Biodesign Institute and Department of Electrical Engineering, Arizona State University, Tempe, Arizona 85287, United States
- Department of Physical Chemistry, University of Barcelona, Barcelona, Spain 08028
| | - Katherine A. Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Paul W. King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Devens Gust
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Ana L. Moore
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas A. Moore
- Center for Bioenergy and Photosynthesis, Center for Bio-Inspired Solar Fuel Production and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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Dimov N, Muñoz L, Carot-Sans G, Verhoeven MLPM, Bula WP, Kocer G, Guerrero A, Gardeniers HJGE. Pheromone synthesis in a biomicroreactor coated with anti-adsorption polyelectrolyte multilayer. BIOMICROFLUIDICS 2011; 5:34102-3410212. [PMID: 22662033 PMCID: PMC3364821 DOI: 10.1063/1.3608138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 06/13/2011] [Indexed: 06/01/2023]
Abstract
To prepare a biosynthetic module in an infochemical communication project, we designed a silicon/glass microreactor with anti-adsorption polyelectrolyte multilayer coating and immobilized alcohol acetyl transferase (atf), one of the key biosynthetic enzymes of the pheromone of Spodoptera littoralis, on agarose beads inside. The system reproduces the last step of the biosynthesis in which the precursor diene alcohol (Z,E)-9,11-tetradecadienol is transformed into the major component (Z,E)-9,11-tetradecadienyl acetate. The scope of this study was to analyze and implement a multilayer, anti-adsorption coating based on layer-by-layer deposition of polyethylenimine/dextransulfate sodium salt (PEI/DSS). The multilayers were composed of two PEI with molecular weights 750 and 1.2 kDa at pH 9.2 or 6.0. Growth, morphology, and stability of the layers were analyzed by ellipsometry and atomic force microscopy (AFM). The anti-adsorption functionality of the multilayer inside the microreactor was validated. The activity of His(6)-(atf) was measured by gas chromatography coupled to mass spectrometer (GC-MS).
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Mu Y. Effects of surface hydrophobicity on the conformational changes of polypeptides of different length. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031906. [PMID: 22060402 DOI: 10.1103/physreve.84.031906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Indexed: 05/31/2023]
Abstract
We studied the effects of surface hydrophobicity on the conformational changes of different length polypeptides by calculating the free energy difference between peptide structures using the bias-potential Monte Carlo technique and the probability ratio method. It was found that the hydrophobic surface plays an important role in the stability of secondary structures of the polypeptides with hydrophobic side chains. For short GAAAAG peptides, the hydrophobic surface destabilizes the α helix but stabilizes the β hairpin in the entire temperature region considered in our study. Interestingly, when the surface hydrophobic strength ε(hpsf)≥ε(hp), the most stable structure in the low temperature region changes from α helix to β hairpin, and the corresponding phase transition temperature increases slightly. For longer GAAAAAAAAAAG peptides, the effects of the relatively weak hydrophobic surface (ε(hpsf) < ε(hp)) on α-helical structures may be neglected, while the relatively strongly hydrophobic surface (ε(hpsf)≥ε(hp)) leads to the obvious partial helicity loss. In contrast, the stability of β structures can be enhanced significantly by the hydrophobic surface, especially by the strongly hydrophobic surface, at low and intermediate temperatures. At high temperatures, in addition to thermal fluctuations, the strongly hydrophobic surface (ε(hpsf)>ε(hp)) may further disturb the formation of both α-helical and β structures. Moreover, the phase transition temperature between α-helical structures and random coils significantly decreases due to the helicity loss when ε(hpsf)>ε(hp). Our findings provide a basic and quantitative picture for understanding the effects of a hydrophobic surface on the conformational changes of the polypeptides with hydrophobic side chains. From an application viewpoint, the present study is helpful in developing alternative strategies of producing high-quality biological fibrillar materials and functional nanoscale devices by the self-assembly of the polypeptides on hydrophobic surfaces.
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Affiliation(s)
- Yan Mu
- College of Materials Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China
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Kubiak-Ossowska K, Mulheran PA. Multiprotein interactions during surface adsorption: a molecular dynamics study of lysozyme aggregation at a charged solid surface. J Phys Chem B 2011; 115:8891-900. [PMID: 21671567 PMCID: PMC3662390 DOI: 10.1021/jp1121239] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 05/28/2011] [Indexed: 11/30/2022]
Abstract
Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein-protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein-protein and protein-surface), and gives an insight into processes to be considered in the development of new functionalized material systems.
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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
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudziadzka 5/7, 87-100 Torun, 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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Hoefling M, Monti S, Corni S, Gottschalk KE. Interaction of β-sheet folds with a gold surface. PLoS One 2011; 6:e20925. [PMID: 21687744 PMCID: PMC3110247 DOI: 10.1371/journal.pone.0020925] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 05/15/2011] [Indexed: 12/04/2022] Open
Abstract
The adsorption of proteins on inorganic surfaces is of fundamental biological importance. Further, biomedical and nanotechnological applications increasingly use interfaces between inorganic material and polypeptides. Yet, the underlying adsorption mechanism of polypeptides on surfaces is not well understood and experimentally difficult to analyze. Therefore, we investigate here the interactions of polypeptides with a gold(111) surface using computational molecular dynamics (MD) simulations with a polarizable gold model in explicit water. Our focus in this paper is the investigation of the interaction of polypeptides with β-sheet folds. First, we concentrate on a β-sheet forming model peptide. Second, we investigate the interactions of two domains with high β-sheet content of the biologically important extracellular matrix protein fibronectin (FN). We find that adsorption occurs in a stepwise mechanism both for the model peptide and the protein. The positively charged amino acid Arg facilitates the initial contact formation between protein and gold surface. Our results suggest that an effective gold-binding surface patch is overall uncharged, but contains Arg for contact initiation. The polypeptides do not unfold on the gold surface within the simulation time. However, for the two FN domains, the relative domain-domain orientation changes. The observation of a very fast and strong adsorption indicates that in a biological matrix, no bare gold surfaces will be present. Hence, the bioactivity of gold surfaces (like bare gold nanoparticles) will critically depend on the history of particle administration and the proteins present during initial contact between gold and biological material. Further, gold particles may act as seeds for protein aggregation. Structural re-organization and protein aggregation are potentially of immunological importance.
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Affiliation(s)
- Martin Hoefling
- Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Susanna Monti
- CNR Istituto di Chimica dei Composti OrganoMetallici (ICCOM), Pisa, Italy
| | | | - Kay Eberhard Gottschalk
- ZIK HIKE Centre for Humoral Immune Reactions in Cardiovascular Disease, Universität Greifswald, Greifswald, Germany
- * E-mail:
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Zhang L, Bai S, Sun Y. Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme. J Mol Graph Model 2011; 29:906-14. [DOI: 10.1016/j.jmgm.2011.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 02/21/2011] [Accepted: 02/24/2011] [Indexed: 10/18/2022]
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Leão-Silva AC, Naves AF, Pereira EMA, Petri DFS, Carmona-Ribeiro AM. Assembly of horseradish peroxidase within supported cationic bilayers. Biotechnol Prog 2011; 27:1433-41. [PMID: 21618457 DOI: 10.1002/btpr.640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 04/19/2011] [Indexed: 11/11/2022]
Abstract
The interaction between horseradish peroxidase (HRP) and dioctadecyldimethylammonium bromide (DODAB) bilayers supported on polystyrene microspheres (PSS) or on flat silicon wafers was evaluated from the following techniques: (1) dynamic light-scattering for determining size distributions, zeta-potentials and polydispersities for dispersions; (2) spectrophotometric determination of HRP concentration in supernatants of centrifuged mixtures; (3) in situ ellipsometry for mean thickness of deposited layers on wafers; (4) kinetics of product appearance for oxidation of 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid by H(2) O(2) in presence of free or immobilized enzyme. HRP incorporation (3.0 mg/m(2)) did not alter mean diameter and zeta-potential of PSS/DODAB particles but reduced enzyme activity by 50%, though activity persisted after several rinsing steps. In situ ellipsometry could not detect any HRP layer on top of the DODAB bilayer. HRP insertion in the bilayer core explained all results for both systems. Useful biotechnological applications are anticipated for such assemblies.
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Affiliation(s)
- Ana Carolina Leão-Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05513-970, São Paulo SP, Brazil
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Sabirianov RF, Rubinstein A, Namavar F. Enhanced initial protein adsorption on engineered nanostructured cubic zirconia. Phys Chem Chem Phys 2011; 13:6597-609. [DOI: 10.1039/c0cp02389b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Kubiak-Ossowska K, Mulheran PA. Mechanism of hen egg white lysozyme adsorption on a charged solid surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:15954-65. [PMID: 20873744 DOI: 10.1021/la102960m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mechanism of hen egg white lysozyme (HEWL) adsorption on a negatively charged, hydrophilic surface has been studied using atomistic molecular dynamics (MD) simulation. Sixteen 90 ns trajectories provide adequate data to allow a detailed description of the adsorption process to be formulated. Two distinct adsorption sites have been identified. The main one is located on the N,C-terminal protein face and comprises Arg128 (the crucial one), supplemented by Arg125, Arg5, and Lys1; the minor one is used accidentally and contains only Arg68. Adsorption of this protein is driven by electrostatics, where the orientation of the protein dipole moment defines the direction of protein movement. The diffusion range on the surface depends on protein side-chain penetration through the surface water layers. This is facilitated by the long-range electric field of the charged surface, which can align polar side chains to be perpendicular to the surface. A simulation of adsorption onto a neutral ionic surface shows no such surface water layer penetration. Therefore, protein flexibility is seen to be an important factor, and to adsorb the HEWL has to adjust its structure. Nevertheless, at a flat surface only a slight loss of α-helical content is required. The adsorbed HEWL molecule is oriented between side-on and end-on ways, where the angle between the protein long axis (which mostly approximates the dipole moment) and the surface varies between 45° and 90°. Simulations with targeted mutations confirm the picture that emerges from these studies. The active site is located on the opposite face to the main adsorption site; hence, the activity of the immobilized HEWL should not be affected by the surface interactions. Our results provide a detailed insight into the adsorption mechanism and protein mobility at the surface. This knowledge will aid the proper interpretation of experimental results and the design of new experiments and functional systems.
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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
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Lin Y, Su Z, Balizan E, Niu Z, Wang Q. Controlled assembly of protein in glass capillary. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:12803-12809. [PMID: 20608692 DOI: 10.1021/la1017888] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
By means of a slow drying process and the control of surface charge characteristics, protein stripe patterns were readily prepared on the luminal surface of a capillary. We systematically studied the effects of surface properties, pH, and protein concentration on pattern formation using optical microscopy, atomic force microscopy, and quartz crystal microbalance measurement. By balancing these parameters, a broad selection of proteins could be assembled within a capillary with well-defined stripe patterns. Neutravidin, one of the model proteins, was specifically chosen to demonstrate the bioactivity retained through the assembly process by interaction with fluorescently labeled biotin motifs. This technique therefore offers a facile approach for patterning proteins and other biomacromolecules in capillary tubes.
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Affiliation(s)
- Yuan Lin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China
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