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Xiao Y, Zhou Z, Zuo Y, Wu X, Liu Y, Li Y, Gao Y, Zhang X, Wang Y, Hu L, Li C. Layer-by-layer fabrication of alginate/polyethyleneimine multilayer on magnetic interface with enhanced efficiency in immuno-capturing circulating tumor cells. Anal Chim Acta 2024; 1312:342778. [PMID: 38834257 DOI: 10.1016/j.aca.2024.342778] [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: 02/02/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND The technology of capturing circulating tumor cells (CTCs) plays a crucial role in the diagnosis, evaluation of therapeutic efficacy, and prediction of prognosis in lung cancer. However, the presence of complex blood environment often results in severe nonspecific protein adsorption and interferences from blood cells, which negatively impacts the specificity of CTCs capture. There is a great need for development of novel nanomaterials for CTCs capture with prominent anti-nonspecific adsorptions from proteins or blood cells. RESULTS We present a novel immune magnetic probe Fe3O4@(PEI/AA)4@Apt. The surface of Fe3O4 particles was modified with four layers of PEI/AA composite by layer-by-layer assembly. Furthermore, aptamers targeting epithelial marker EpCAM (SYL3C) and mesenchymal marker CSV (ZY5C) were simultaneously connected on Fe3O4@(PEI/AA)4 to improve the detection of different phenotypic CTCs and reduce false negatives. The results demonstrated that the (PEI/AA)4 coatings not only minimized non-specific protein adsorptions, but also significantly reduced the adsorption rate of red blood cells to a mere 1 %, as a result of which, the Fe3O4@(PEI/AA)4@Apt probe achieved a remarkably high capture efficiency toward CTCs (95.9 %). In the subsequent validation of clinical samples, the probe was also effective in capturing rare CTCs from lung cancer patients. SIGNIFICANCE AND NOVELTY A (PEI/AA) polymerized composite with controllable layers was fabricated by layer-by-layer self-assembly technique, which displayed remarkable anti-nonspecific adsorption capabilities toward proteins and cells. Importantly, Fe3O4@(PEI/AA)4@Apt probe significantly improved CTCs capture purity in lung cancer patients to 89.36 %. For the first time, this study combined controllable (PEI/AA) layers with magnetic separation to innovatively build a resistant interface that significantly improves the specific capture performances of CTCs, broadening the application of this polymerized composite.
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Affiliation(s)
- Yang Xiao
- School of Anesthesiology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Zhiyi Zhou
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Yifan Zuo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Xueyuan Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Yuping Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Yichen Li
- School of Anesthesiology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Yuetong Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Xiashu Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China
| | - Yu Wang
- Department of Pharmacy, Xuzhou Traditional Chinese Medicine Hospital, 169 Zhongshan South Road, Xuzhou, 221004, China
| | - Lili Hu
- Department of Pharmacy, Affiliated Hospital of Xuzhou Medical University, 99 Huaihai West Road, Xuzhou, 221004, China
| | - Chenglin Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China.
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Li Y, Ji R, Li Y, Li J, Chen H. Early-Stage Protein Adsorption Sequence on Blood-Contacting Surfaces: Answer to Vroman's Question. Anal Chem 2024; 96:10434-10442. [PMID: 38866710 DOI: 10.1021/acs.analchem.4c01697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Plasma protein adsorption on blood-contacting surfaces is the initiating significant event and modulates the subsequent coagulation response. Despite decades of research in this area, Vroman's questions in 1986 "Who gets there first?" and "When does the next protein arrive?" remain unanswered due to the lack of detection techniques with sufficient temporal resolution. In this work, we develop a droplet microfluidic technology to detect protein adsorption sequences on six typical blood-contacting surfaces in milliseconds. Apolipoproteins (Apo) are found to be the first proteins to adsorb onto the surfaces in a plasma droplet, and the specific type of apolipoprotein depends on the surface. Apo CI is the first protein adsorbed on gold, platinum, graphene, stainless steel, and polyvinyl chloride with the adsorption time varying from 0.01 to 1 s, while Apo CIII preferentially reaches the titanium alloy surface within 1 s. Subsequent to the initial adsorption, Apo AI, AII, and other proteins continue to adsorb until albumin arrives. Thus, the adsorption sequence is revealed, and Vroman's questions are answered. Moreover, this finding demonstrates the influence of the initial protein adsorption on subsequent coagulation at the surface, and it offers new insights into the development of anticoagulant surfaces.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Tribology, Mechanical Engineering Department, Tsinghua University, Beijing 100084, China
| | - Rui Ji
- State Key Laboratory of Tribology, Mechanical Engineering Department, Tsinghua University, Beijing 100084, China
| | - Yongjian Li
- State Key Laboratory of Tribology, Mechanical Engineering Department, Tsinghua University, Beijing 100084, China
| | - Jiang Li
- Department of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Haosheng Chen
- State Key Laboratory of Tribology, Mechanical Engineering Department, Tsinghua University, Beijing 100084, China
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3
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Alnaanah SA, Mendes SB. Investigating the influence of solvent type and pH on protein adsorption onto silica surface by evanescent-wave cavity ring-down spectroscopy. ANAL SCI 2024; 40:1089-1099. [PMID: 38512454 DOI: 10.1007/s44211-024-00529-3] [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: 11/22/2023] [Accepted: 01/31/2024] [Indexed: 03/23/2024]
Abstract
Several studies have explored the adsorption of various proteins onto solid-liquid interfaces, revealing the crucial role of buffer solutions in biological processes. However, a comprehensive evaluation of the buffer's influence on protein absorption onto fused silica is still lacking. This study employs evanescent-wave cavity ring-down spectroscopy (EW-CRDS) to assess the influence of buffer solutions and pH on the adsorption kinetics of three globular proteins: hemoglobin (Hb), myoglobin (Mb), and cytochrome c (Cyt-C) onto fused silica. The EW-CRDS tool, with a ring-down time of 1.4 μ s and a minimum detectable absorbance of 1 × 10 - 6 , enabled precise optical measurements at solid-liquid interfaces. The three heme proteins' adsorption behavior was investigated at pH 7 in three different solvents: deionized (DI) water, tris(hydroxymethyl)-aminomethane hydrochloride (Tris-HCl), and phosphate buffered saline (PBS). For each protein, the surface coverage, the adsorption and desorption constants, and the surface equilibrium constant were optically measured by our EW-CRDS tool. Depending on the nature of each solvent, the proteins showed a completely different adsorption trend on the silica surface. The adsorption of Mb on the silica surface was depressed in the presence of both Tris-HCl and PBS buffers compared with unbuffered (DI water) solutions. In contrast, Cyt-C adsorption appears to be relatively unaffected by the choice of buffer, as it involves strong electrostatic interactions with the surface. Notably, Hb exhibits an opposite trend, with enhanced protein adsorption in the presence of Tris-HCl and PBS buffer. The pH investigations demonstrated that the electrostatic interactions between the proteins and the surface had a major influence on protein adsorption on the silica surface, with adsorption being greatest when the pH values were around the protein's isoelectric point. This study demonstrated the ability of the highly sensitive EW-CRDS tool to study the adsorption events of the evanescent-field-confined protein species in real-time at low surface coverages with fast resolution, making it a valuable tool for studying biomolecule kinetics at solid-liquid interfaces.
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Affiliation(s)
- Shadi A Alnaanah
- Department of Physics and Astronomy, University of Louisville, Louisville, KY, 40208, USA.
- Department of Applied Physics, Tafila Technical University, Al-Eis, Tafila, 66110, Jordan.
| | - Sergio B Mendes
- Department of Physics and Astronomy, University of Louisville, Louisville, KY, 40208, USA
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Gong M, Dong Y, Zhu M, Qin F, Wang T, Shah FU, An R. Cation Chain Length of Nonhalogenated Ionic Liquids Matters in Enhancing SERS of Cytochrome c on Zr-Al-Co-O Nanotube Arrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8886-8896. [PMID: 38622867 DOI: 10.1021/acs.langmuir.4c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Surface-enhanced Raman scattering (SERS) is a remarkably powerful analytical technique enabling trace-level detection of biological molecules. The interaction of a probe molecule with the SERS substrate shows important distinctions in the SERS spectra, providing inherent fingerprint information on the probe molecule. Herein, nonhalogenated phosphonium-based ionic liquids (ILs) containing cations with varying chain lengths were used as trace additives to amplify the interaction between the cytochrome c (Cyt c) and Zr-Al-Co-O (ZACO) nanotube arrays, strengthening the SERS signals. An increased enhancement factor (EF) by 2.5-41.2 times compared with the system without ILs was achieved. The improvement of the SERS sensitivity with the introduction of these ILs is strongly dependent on the cation chain length, in which the increasing magnitude of EF is more pronounced in the system with a longer alkyl chain length on the cation. Comparing the interaction forces measured by Cyt c-grafted atomic force microscopy (AFM) probes on ZACO substrates with those predicted by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, the van der Waals forces became increasingly dominant as the chain length of the cations increased, associated with stronger Cyt c-ZACO XDLVO interaction forces. The major contributing component, van der Waals force, stems from the longer cation chains of the IL, which act as a bridge to connect Cyt c and the ZACO substrate, promoting the anchoring of the Cyt c molecules onto the substrate, thereby benefiting SERS enhancement.
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Affiliation(s)
- Mian Gong
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yihui Dong
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Minghai Zhu
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Fengxiang Qin
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Tianchi Wang
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Faiz Ullah Shah
- Chemistry of Interfaces, Luleå University of Technology, 97187 Luleå, Sweden
| | - Rong An
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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5
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Mukhopadhyay T, Ghosh A, Datta A. Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook. ACS PHYSICAL CHEMISTRY AU 2024; 4:97-121. [PMID: 38560753 PMCID: PMC10979489 DOI: 10.1021/acsphyschemau.3c00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 04/04/2024]
Abstract
Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.
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Affiliation(s)
- Titas
Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Anupam Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
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Xue J, Ji M, Lu Y, Pan D, Yang X, Yang X, Xu Z. The impact of chemical properties of the solid-liquid-adsorbate interfaces on the entropy-enthalpy compensation involved in adsorption. Phys Chem Chem Phys 2024; 26:8704-8715. [PMID: 38415756 DOI: 10.1039/d3cp05669d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Despite extensive studies on the thermodynamic mechanism governing molecular adsorption at the solid-water interface, a comprehensive understanding of the crucial role of interface properties in mediating the entropy-enthalpy compensation during adsorption is lacking, particularly at a quantitative level. Herein, we employed two types of surface models (hydroxyapatite and graphene) along with a series of amino acids to successfully elucidate how distinct interfacial features dictate the delicate balance between entropy and enthalpy variations. The adsorption of all amino acids on the hydroxyapatite surface is an enthalpy-dominated process, where the water-induced enthalpic component of the free energy and the surface-adsorbate electrostatic interaction term alternatively act as the driving force for adsorption in different regions of the surface. Although favorable interactions are observed between amino acids and the graphene surface, the entropy-enthalpy compensation exhibits dependence on the molecular size of the adsorbates. For small amino acids, favorable enthalpy changes predominantly determine their adsorption behavior; however, larger amino acids tend to bind more tightly with the graphene surface, which is thermodynamically dominated by the entropy variations despite the structural characteristics of amino acids. This study reveals specific entropy-enthalpy mechanisms underlying amino acid adsorption at the solid-liquid interface, providing guidance for surface design and synthesis of new biomolecules.
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Affiliation(s)
- Jinling Xue
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Mingyu Ji
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Yuanyuan Lu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Dan Pan
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Xiao Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Xiaoning Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Zhijun Xu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
- Zhangjiagang Institute of Nanjing Tech University, Zhangjiagang 215699, China
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7
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Kato T, Uchida J, Ishii Y, Watanabe G. Aquatic Functional Liquid Crystals: Design, Functionalization, and Molecular Simulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306529. [PMID: 38126650 PMCID: PMC10885670 DOI: 10.1002/advs.202306529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Aquatic functional liquid crystals, which are ordered molecular assemblies that work in water environment, are described in this review. Aquatic functional liquid crystals are liquid-crystalline (LC) materials interacting water molecules or aquatic environment. They include aquatic lyotropic liquid crystals and LC based materials that have aquatic interfaces, for example, nanoporous water treatment membranes that are solids preserving LC order. They can remove ions and viruses with nano- and subnano-porous structures. Columnar, smectic, bicontinuous LC structures are used for fabrication of these 1D, 2D, 3D materials. Design and functionalization of aquatic LC sensors based on aqueous/LC interfaces are also described. The ordering transitions of liquid crystals induced by molecular recognition at the aqueous interfaces provide distinct optical responses. Molecular orientation and dynamic behavior of these aquatic functional LC materials are studied by molecular dynamics simulations. The molecular interactions of LC materials and water are key of these investigations. New insights into aquatic functional LC materials contribute to the fields of environment, healthcare, and biotechnology.
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Affiliation(s)
- Takashi Kato
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Research Initiative for Supra-Materials, Shinshu University, Nagano, 380-8553, Japan
| | - Junya Uchida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshiki Ishii
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, 252-0373, Japan
| | - Go Watanabe
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, 252-0373, Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC), Ebina, 243-0435, Japan
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8
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Li Y, Yang J, He X. Characterizing polyproline II conformational change of collagen superhelix unit on adsorption on gold surface. NANOSCALE ADVANCES 2023; 5:5322-5331. [PMID: 37767030 PMCID: PMC10521299 DOI: 10.1039/d3na00185g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023]
Abstract
The dynamic process of protein binding onto a metal surface is a frequent occurrence as gold nanoparticles are increasingly being used in biomedical applications, including wound treatment and drug transport. Collagen, as a major component of the extracellular matrix, has potentially advantageous biomedical applications, due to its excellent biocompatibility and elasticity properties. Therefore, a mechanistic comprehension of how and which species in collagen interact with gold nanoparticles is a prerequisite for collagen-gold complexes in clinical application. However, the dynamic behavior of collagen with the polyproline II (PPII) conformation on gold sheets at the molecular level is too complex to capture under current experimental conditions. Here, using molecular dynamics simulations, we investigate the adsorption process and conformational behavior of the tripeptide Gly-Pro-Hyp with the repetitive unit of the collagen superhelix on the gold surface as a function of number of repeating units from 1 to 10. The different numbers of repeating units all prefer to approach the gold surface and adsorb via charged residues at the C-terminal or N-terminal ends, tending to form arch structures on the gold surface. Compared with the various tripeptide units in solution still retaining the native PPII conformation, the presence of the gold surface affects the formation of hydrogen bonds between the protein and water molecules, thus disrupting the PPII conformation of collagen. Specifically, the interaction between the gold surface and HYP limits the rotation of the dihedral angle of collagen, resulting in a tendency for the PPII conformation of the gold surface to transform to the β-sheet conformation. The results provide an indication of how to improve the interaction between the terminal groups and the gold surface for the design of a bioavailable protein-gold material for medicinal purposes.
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Affiliation(s)
- Yuntao Li
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Jinrong Yang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai Shanghai 200062 China
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9
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Yagasaki T, Matubayasi N. Molecular Dynamics Study of the Antifouling Mechanism of Hydrophilic Polymer Brushes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:13158-13168. [PMID: 37672759 DOI: 10.1021/acs.langmuir.3c01552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
We perform all-atom molecular dynamics simulations of the adsorption of amino acid side-chain analogues on polymer brushes. The analogues examined are nonpolar isobutane, polar propionamide, negatively charged propionate ion, and positively charged butylammonium ion. The polymer brushes consist of a sheet of graphene and strongly hydrophilic poly(carboxybetaine methacrylate) (PCBMA) or weakly hydrophilic poly(2-hydroxyethyl methacrylate) (PHEMA). The effective interactions between isobutane and polymer chains are repulsive for PCBMA and attractive for PHEMA. Gibbs energy decomposition analysis shows that this is due to the abundance of water in the PCBMA brush, which increases the steric repulsion and decreases the Lennard-Jones attraction. The affinity of the hydrophilic analogues is low for both PCBMA and PHEMA chains, but the balance between the components of the Gibbs energy is different for the two polymers. The simulations are performed at several θ, where θ is the degree of overlap of polymer chains. The antifouling performance against the neutral analogues is better for PCBMA than for PHEMA in the low and high θ regimes. However, in the middle θ regime, the antifouling performance of PHEMA is close to or better than that of PCBMA. This is attributed to the formation of a dense layer of PHEMA on the graphene surface that inhibits direct adsorption of analogue molecules on graphene. The charged analogues do not bind to either the PHEMA or PCBMA brush irrespective of θ.
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Affiliation(s)
- Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan
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10
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DelRe C, Hong H, Wenny MB, Erdosy DP, Cho J, Lee B, Mason JA. Design Principles for Using Amphiphilic Polymers To Create Microporous Water. J Am Chem Soc 2023; 145:19982-19988. [PMID: 37655897 DOI: 10.1021/jacs.3c06627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Aqueous dispersions of microporous nanocrystals with dry, gas-accessible pores─referred to as "microporous water"─enable high densities of gas molecules to be transported through water. For many applications of microporous water, generalizable strategies are required to functionalize the external surface of microporous particles to control their dispersibility, stability, and interactions with other solution-phase components─including catalysts, proteins, and cells─while retaining as much of their internal pore volume as possible. Here, we establish design principles for the noncovalent surface functionalization of hydrophobic metal-organic frameworks with amphiphilic polymers that render the particles dispersible in water and enhance their hydrolytic stability. Specifically, we show that block co-polymers with persistence lengths that exceed the micropore aperture size of zeolitic imidazolate frameworks (ZIFs) can dramatically enhance ZIF particle dispersibility and stability while preserving porosity and >80% of the theoretical O2 carrying capacity. Moreover, enhancements in hydrolytic stability are greatest when the polymer can form strong bonds to exposed metal sites on the external particle surface. More broadly, our insights provide guidelines for controlling the interface between polymers and metal-organic framework particles in aqueous environments to augment the properties of microporous water.
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Affiliation(s)
- Christopher DelRe
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Hyukhun Hong
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Malia B Wenny
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel P Erdosy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Joy Cho
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, Illinois 60439, United States
| | - Jarad A Mason
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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11
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Maurer J, Grouzmann E, Eugster PJ. Tutorial review for peptide assays: An ounce of pre-analytics is worth a pound of cure. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1229:123904. [PMID: 37832388 DOI: 10.1016/j.jchromb.2023.123904] [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: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
The recent increase in peptidomimetic-based medications and the growing interest in peptide hormones has brought new attention to the quantification of peptides for diagnostic purposes. Indeed, the circulating concentrations of peptide hormones in the blood provide a snapshot of the state of the body and could eventually lead to detecting a particular health condition. Although extremely useful, the quantification of such molecules, preferably by liquid chromatography coupled to mass spectrometry, might be quite tricky. First, peptides are subjected to hydrolysis, oxidation, and other post-translational modifications, and, most importantly, they are substrates of specific and nonspecific proteases in biological matrixes. All these events might continue after sampling, changing the peptide hormone concentrations. Second, because they include positively and negatively charged groups and hydrophilic and hydrophobic residues, they interact with their environment; these interactions might lead to a local change in the measured concentrations. A phenomenon such as nonspecific adsorption to lab glassware or materials has often a tremendous effect on the concentration and needs to be controlled with particular care. Finally, the circulating levels of peptides might be low (pico- or femtomolar range), increasing the impact of the aforementioned effects and inducing the need for highly sensitive instruments and well-optimized methods. Thus, despite the extreme diversity of these peptides and their matrixes, there is a common challenge for all the assays: the need to keep concentrations unchanged from sampling to analysis. While significant efforts are often placed on optimizing the analysis, few studies consider in depth the impact of pre-analytical steps on the results. By working through practical examples, this solution-oriented tutorial review addresses typical pre-analytical challenges encountered during the development of a peptide assay from the standpoint of a clinical laboratory. We provide tips and tricks to avoid pitfalls as well as strategies to guide all new developments. Our ultimate goal is to increase pre-analytical awareness to ensure that newly developed peptide assays produce robust and accurate results.
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Affiliation(s)
- Jonathan Maurer
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eric Grouzmann
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe J Eugster
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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12
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Zhang Y, Liu Y, Liu Y, Zuo P, Miao S, Hu B, Kang Y, Liu W, Yang Q, Ren H, Yang P. α-Helix-Mediated Protein Adhesion. J Am Chem Soc 2023; 145:17125-17135. [PMID: 37505921 DOI: 10.1021/jacs.3c03581] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Proteins have been adopted by natural living organisms to create robust bioadhesive materials, such as biofilms and amyloid plaques formed in microbes and barnacles. In these cases, β-sheet stacking is recognized as a key feature that is closely related to the interfacial adhesion of proteins. Herein, we challenge this well-known recognition by proposing an α-helix-mediated interfacial adhesion model for proteins. By using bovine serum albumin (BSA) as a model protein, it was discovered that the reduction of disulfide bonds in BSA results in random coils from unfolded BSA dragging α-helices to gather at the solid/liquid interface (SLI). The hydrophobic residues in the α-helix then expose and break through the hydration layer of the SLI, followed by the random deposition of hydrophilic and hydrophobic residues to achieve interfacial adhesion. As a result, the first assembled layer is enriched in the α-helix secondary structure, which is then strengthened by intermolecular disulfide bonds and further initiates stepwise layering protein assembly. In this process, β-sheet stacking is transformed from the α-helix in a gradually evolving manner. This finding thus indicates a valuable clue that β-sheet-featuring amyloid may form after the interfacial adhesion of proteins. Furthermore, the finding of the α-helix-mediated interfacial adhesion model of proteins affords a unique strategy to prepare protein nanofilms with a well-defined layer number, presenting robust and modulable adhesion on various substrates and exhibiting good resistance to acid, alkali, organic solvent, ultrasonic, and adhesive tape peeling.
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Affiliation(s)
- Yingying Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yongchun Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yonggang Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Ping Zuo
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Shuting Miao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bowen Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yu Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Wei Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Qingmin Yang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, China
| | - Hao Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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13
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Galata AA, Kröger M. Globular Proteins and Where to Find Them within a Polymer Brush-A Case Study. Polymers (Basel) 2023; 15:polym15102407. [PMID: 37242983 DOI: 10.3390/polym15102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Protein adsorption by polymerized surfaces is an interdisciplinary topic that has been approached in many ways, leading to a plethora of theoretical, numerical and experimental insight. There is a wide variety of models trying to accurately capture the essence of adsorption and its effect on the conformations of proteins and polymers. However, atomistic simulations are case-specific and computationally demanding. Here, we explore universal aspects of the dynamics of protein adsorption through a coarse-grained (CG) model, that allows us to explore the effects of various design parameters. To this end, we adopt the hydrophobic-polar (HP) model for proteins, place them uniformly at the upper bound of a CG polymer brush whose multibead-spring chains are tethered to a solid implicit wall. We find that the most crucial factor affecting the adsorption efficiency appears to be the polymer grafting density, while the size of the protein and its hydrophobicity ratio come also into play. We discuss the roles of ligands and attractive tethering surfaces to the primary adsorption as well as secondary and ternary adsorption in the presence of attractive (towards the hydrophilic part of the protein) beads along varying spots of the backbone of the polymer chains. The percentage and rate of adsorption, density profiles and the shapes of the proteins, alongside with the respective potential of mean force are recorded to compare the various scenarios during protein adsorption.
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Affiliation(s)
- Aikaterini A Galata
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Kröger
- Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
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14
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Coating peanut shell lignin nanospheres with gelatin via non-covalent adsorption: Key parameters, consequences, and underlying interactions. Int J Biol Macromol 2023; 233:123607. [PMID: 36773874 DOI: 10.1016/j.ijbiomac.2023.123607] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/24/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
In the present work, lignin nanospheres (LNS, average diameter 166.43 nm) were prepared and the affecting parameters, the absorbed types, and mechanisms of their interactions with type-A gelatin (AG) were explored. The findings demonstrated that upon AG coating, the ζ-potential of LNS sharply decreased and concluded a negative-to-positive shift, while the average diameter and polydispersity index increased significantly. AG presented the highest coating capacity (0.32 mg/mg, db) onto LNS (0.5 mg/mL) at an optimum pH of 4.0 and an AG concentration of 1.0 mg/mL. The adsorption of AG onto LNS could be well described by the Hill model (R2 = 0.9895), which was characterized as positive synergistic adsorption by the Hill coefficient (1.32) and physical adsorption by the free energy (3.70 kJ/mg). The spectral analysis revealed that the interactions between AG and LNS were mainly driven by electrostatic forces (ΔG < 0, ΔH < 0, and ΔS > 0) together with the assistance of hydrogen bonds and hydrophobic interactions, which companied a decrease of α-helix (4.04 %) and β-turn (0.60 %) and an increase of β-sheet (3.10 %) and random coil (1.53 %) of the secondary structure of AG. The results herein certainly favored the hydrophilic/hydrophobic change of LNS/AG and the quality control of a binary system consisting of lignin and gelatin.
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15
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Serizawa T, Yamaguchi S, Amitani M, Ishii S, Tsuyuki H, Tanaka Y, Sawada T, Kawamura I, Watanabe G, Tanaka M. Alkyl chain length-dependent protein nonadsorption and adsorption properties of crystalline alkyl β-celluloside assemblies. Colloids Surf B Biointerfaces 2022; 220:112898. [DOI: 10.1016/j.colsurfb.2022.112898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 11/27/2022]
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16
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Hydration and antibiofouling of TMAO-derived zwitterionic polymers surfaces studied with atomistic molecular dynamics simulations. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Lyu K, Chen H, Gao J, Jin J, Shi H, Schwartz DK, Wang D. Protein Desorption Kinetics Depends on the Timescale of Observation. Biomacromolecules 2022; 23:4709-4717. [PMID: 36205402 DOI: 10.1021/acs.biomac.2c00917] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The presence of so-called reversible and irreversible protein adsorption on solid surfaces is well documented in the literature and represents the basis for the development of nanoparticles and implant materials to control interactions in physiological environments. Here, using a series of complementary single-molecule tracking approaches appropriate for different timescales, we show that protein desorption kinetics is much more complex than the traditional reversible-irreversible binary picture. Instead, we find that the surface residence time distribution of adsorbed proteins transitions from power law to exponential behavior when measured over a large range of timescales (10-2-106 s). A comparison with macroscopic results obtained using a quartz crystal microbalance suggested that macroscopic measurements have generally failed to observe such nonequilibrium phenomena because they are obscured by ensemble-averaging effects. These findings provide new insights into the complex phenomena associated with protein adsorption and desorption.
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Affiliation(s)
- Kaixuan Lyu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.,University of Science and Technology of China, Hefei 230026, P. R. China
| | - Hongbo Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Jing Jin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Hengchong Shi
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Dapeng Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.,University of Science and Technology of China, Hefei 230026, P. R. China
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18
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Yagasaki T, Matubayasi N. Molecular dynamics study of the interactions between a hydrophilic polymer brush on graphene and amino acid side chain analogues in water. Phys Chem Chem Phys 2022; 24:22877-22888. [PMID: 36124732 DOI: 10.1039/d2cp03112d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We perform all-atom molecular dynamics simulations of poly(2-hydroxyethyl methacrylate) (PHEMA) brushes in aqueous solutions of isobutane, propionamide, and sodium propionate. These solutes are side chain analogues to leucine, glutamine, and glutamic acid, respectively. We compute the Gibbs energy profile of the solute's adsorption to the polymer brush and decompose it into the contributions from the steric repulsion, van der Waals interaction, and Coulomb interaction to reveal the energetic origin of repulsion or attraction of the solute by the polymer brush. The Henry adsorption constant is the amount of adsorption normalized by the concentration in aqueous solution. We examine the dependence of this quantity on the grafting density and chain length. Our results suggest that the concurrent primary and ternary adsorption mechanism may be more important than previously expected when the solute is hydrophobic.
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Affiliation(s)
- Takuma Yagasaki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan.
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Japan.
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19
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Zhang J, Wang Z, Zhuang W, Rabiee H, Zhu C, Deng J, Ge L, Ying H. Amphiphilic Nanointerface: Inducing the Interfacial Activation for Lipase. ACS APPLIED MATERIALS & INTERFACES 2022; 14:39622-39636. [PMID: 35980131 DOI: 10.1021/acsami.2c11500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Graphene-based materials are widely used in the field of immobilized enzymes due to their easily tunable interfacial properties. We designed amphiphilic nanobiological interfaces between graphene oxide (GO) and lipase TL (Thermomyces lanuginosus) with tunable reduction degrees through molecular dynamics simulations and a facile chemical modulation, thus revealing the optimal interface for the interfacial activation of lipase TL and addressing the weakness of lipase TL, which exhibits weak catalytic activity due to an inconspicuous active site lid. It was demonstrated that the reduced graphene oxide (rGO) after 4 h of ascorbic acid reduction could boost the relative enzyme activity of lipase TL to reach 208%, which was 48% higher than the pristine GO and 120% higher than the rGO after 48 h of reduction. Moreover, TL-GO-4 h's tolerance against heat, organic solvent, and long-term storage environment was higher than that of free TL. The drawbacks of strong hydrophobic nanomaterials on lipase production were explored in depth with the help of molecular dynamics simulations, which explained the mechanism of enzyme activity enhancement. We demonstrated that nanomaterials with certain hydrophilicity could facilitate the lipase to undergo interfacial activation and improve its stability and protein loading rate, displaying the potential of the extensive application.
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Affiliation(s)
- Jihang Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Zhaoxin Wang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Hesamoddin Rabiee
- Centre for Future Materials, University of Southern Queensland, Springfield, QLD 4300, Australia
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chenjie Zhu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Jiawei Deng
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Lei Ge
- Centre for Future Materials, University of Southern Queensland, Springfield, QLD 4300, Australia
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
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20
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Yang X, Ji M, Zhang C, Yang X, Xu Z. Physical insight into the entropy-driven ion association. J Comput Chem 2022; 43:1621-1632. [PMID: 35801676 DOI: 10.1002/jcc.26963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
The ion association is widely believed to be dominated by the favorable entropy change arising from the release of water molecules from ion hydration shells. However, no direct thermodynamic evidence exists to validate the reliability and suitability of this view. Herein, we employ complicated free energy calculations to rigorously split the free energy including its entropic and enthalpic components into the water-induced contributions and ion-ion interaction terms for several ion pairs from monatomic to polyatomic ions, spanning the size range from small kosmotropes to large chaotropes (Na+ , Cs+ , Ca2+ , F- , I- , CO3 2- , and HPO4 2- ). Our results successfully reveal that though ion associations are indeed determined by a delicate balance between the favorable entropy variation and the repulsive enthalpy change, the entropy gain dominated by the solvent occurs only for the monatomic ion pairing. The water-induced entropic contribution significantly goes against the ion pairing between polyatomic anion and cation, which is, alternatively, dominated by the favorable entropy from the ion-ion interaction term, due to the configurational arrangement of polyatomic anions involved in ion association. The structural and dynamic analysis demonstrates that the entropy penalty from the water phase is primarily ascribed to the enhanced stability of water molecules around the cation imposed by the incoming anion. Our study successfully provides a fundamental understanding of water-mediated ion associations and highlights disparate lengthscale dependencies of the dehydration thermodynamics on the specific types of ions.
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Affiliation(s)
- Xiao Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, China
| | - Mingyu Ji
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, China
| | - Cong Zhang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, China
| | - Xiaoning Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, China
| | - Zhijun Xu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, China.,Zhangjiagang Institute of Nanjing Tech University, Zhangjiagang, China
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21
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Chen SH, Bell DR, Luan B. Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes. Adv Drug Deliv Rev 2022; 186:114336. [PMID: 35597306 PMCID: PMC9212071 DOI: 10.1016/j.addr.2022.114336] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 12/28/2022]
Abstract
Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.
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Affiliation(s)
- Serena H Chen
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - David R Bell
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Binquan Luan
- IBM Thomas J. Watson Research, Yorktown Heights, New York 10598, USA.
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22
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Farouq MAH, Kubiak-Ossowska K, Al Qaraghuli MM, Ferro VA, Mulheran PA. Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study. Int J Mol Sci 2022; 23:ijms23094832. [PMID: 35563221 PMCID: PMC9103475 DOI: 10.3390/ijms23094832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/07/2022] Open
Abstract
Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.
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Affiliation(s)
- Mohammed A. H. Farouq
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
- Correspondence: ; Tel.: +44-01-4155-24400
| | - Karina Kubiak-Ossowska
- Department of Physics/Archie-West HPC, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK;
| | - Mohammed M. Al Qaraghuli
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
- EPSRC Future Manufacturing Research Hub for Continuous Manufacturing and Advanced Crystallisation (CMAC), University of Strathclyde, 99 George Street, Glasgow G1 1RD, 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; (M.M.A.Q.); (P.A.M.)
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23
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Lugasi L, Otis G, Oliel M, Margel S, Mastai Y. Chirality of proteinoid nanoparticles made of lysine and phenylalanine. POLYM ADVAN TECHNOL 2022. [DOI: 10.1002/pat.5667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Liroy Lugasi
- Department of Chemistry Institute of Nanotechnology—Bar‐Ilan University Ramat‐Gan Israel
| | - Gil Otis
- Department of Chemistry Institute of Nanotechnology—Bar‐Ilan University Ramat‐Gan Israel
| | - Matan Oliel
- Department of Chemistry Institute of Nanotechnology—Bar‐Ilan University Ramat‐Gan Israel
| | - Shlomo Margel
- Department of Chemistry Institute of Nanotechnology—Bar‐Ilan University Ramat‐Gan Israel
| | - Yitzhak Mastai
- Department of Chemistry Institute of Nanotechnology—Bar‐Ilan University Ramat‐Gan Israel
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24
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Kyriakides TR, Kim HJ, Zheng C, Harkins L, Tao W, Deschenes E. Foreign body response to synthetic polymer biomaterials and the role of adaptive immunity. Biomed Mater 2022; 17:10.1088/1748-605X/ac5574. [PMID: 35168213 PMCID: PMC9159526 DOI: 10.1088/1748-605x/ac5574] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/15/2022] [Indexed: 02/06/2023]
Abstract
Implanted biomaterials elicit a series of distinct immune and repair-like responses that are collectively known as the foreign body reaction (FBR). These include processes involving innate immune inflammatory cells and wound repair cells that contribute to the encapsulation of biomaterials with a dense collagenous and largely avascular capsule. Numerous studies have shown that the early phase is dominated by macrophages that fuse to form foreign body giant cells that are considered a hallmark of the FBR. With the advent of more precise cell characterization techniques, specific macrophage subsets have been identified and linked to more or less favorable outcomes. Moreover, studies comparing synthetic- and natural-based polymer biomaterials have allowed the identification of macrophage subtypes that distinguish between fibrotic and regenerative responses. More recently, cells associated with adaptive immunity have been shown to participate in the FBR to synthetic polymers. This suggests the existence of cross-talk between innate and adaptive immune cells that depends on the nature of the implants. However, the exact participation of adaptive immune cells, such as T and B cells, remains unclear. In fact, contradictory studies suggest either the independence or dependence of the FBR on these cells. Here, we review the evidence for the involvement of adaptive immunity in the FBR to synthetic polymers with a focus on cellular and molecular components. In addition, we examine the possibility that such biomaterials induce specific antibody responses resulting in the engagement of adaptive immune cells.
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Affiliation(s)
- Themis R. Kyriakides
- Department of Biomedical Engineering, Yale University. New Haven CT 06405,Department of Pathology, Yale University. New Haven CT 06405,Vascular Biology and Therapeutics Program. Yale University. New Haven CT 06405
| | - Hyun-Je Kim
- Department of Biomedical Engineering, Yale University. New Haven CT 06405
| | - Christy Zheng
- Department of Biomedical Engineering, Yale University. New Haven CT 06405
| | - Lauren Harkins
- Department of Biomedical Engineering, Yale University. New Haven CT 06405
| | - Wanyun Tao
- Department of Biomedical Engineering, Yale University. New Haven CT 06405
| | - Emily Deschenes
- Department of Biomedical Engineering, Yale University. New Haven CT 06405
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25
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Subbotina J, Lobaskin V. Multiscale Modeling of Bio-Nano Interactions of Zero-Valent Silver Nanoparticles. J Phys Chem B 2022; 126:1301-1314. [PMID: 35132861 PMCID: PMC8859825 DOI: 10.1021/acs.jpcb.1c09525] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Understanding the
specifics of interaction between the protein
and nanomaterial is crucial for designing efficient, safe, and selective
nanoplatforms, such as biosensor or nanocarrier systems. Routing experimental
screening for the most suitable complementary pair of biomolecule
and nanomaterial used in such nanoplatforms might be a resource-intensive
task. While a range of computational tools are available for prescreening
libraries of proteins for their interactions with small molecular
ligands, choices for high-throughput screening of protein libraries
for binding affinities to new and existing nanomaterials are very
limited. In the current work, we present the results of the systematic
computational study of interaction of various biomolecules with pristine
zero-valent noble metal nanoparticles, namely, AgNPs, by using the UnitedAtom multiscale approach. A set of blood plasma and
dietary proteins for which the interaction with AgNPs was described
experimentally were examined computationally to evaluate the performance
of the UnitedAtom method. A set of interfacial descriptors
(log PNM, adsorption affinities, and adsorption
affinity ranking), which can characterize the relative hydrophobicity/hydrophilicity/lipophilicity
of the nanosized silver and its ability to form bio(eco)corona, was
evaluated for future use in nano-QSAR/QSPR studies.
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Affiliation(s)
- Julia Subbotina
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
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26
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Cho DH, Xie T, Mulcahey PJ, Kelleher NP, Hahm JI. Distinctive Adsorption Mechanism and Kinetics of Immunoglobulin G on a Nanoscale Polymer Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1458-1470. [PMID: 35037456 DOI: 10.1021/acs.langmuir.1c02710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Elucidation of protein adsorption beyond simple polymer surfaces to those presenting greater chemical complexity and nanoscopic features is critical to developing well-controlled nanobiomaterials and nanobiosensors. In this study, we repeatedly and faithfully track individual proteins on the same nanodomain areas of a block copolymer (BCP) surface and monitor the adsorption and assembly behavior of a model protein, immunoglobulin G (IgG), over time into a tight surface-packed structure. With discrete protein adsorption events unambiguously visualized at the biomolecular level, the detailed assembly and packing states of IgG on the BCP nanodomain surface are subsequently correlated to various regimes of IgG adsorption kinetic plots. Intriguing features, entirely different from those observed from macroscopic homopolymer templates, are identified from the IgG adsorption isotherms on the nanoscale, chemically varying BCP surface. They include the presence of two Langmuir-like adsorption segments and a nonmonotonic regime in the adsorption plot. Via correlation to time-corresponding topographic data, the unique isotherm features are explained with single biomolecule level details of the IgG adsorption pathway on the BCP. This work not only provides much needed, direct experimental evidence for time-resolved, single protein level, adsorption events on nanoscale polymer surfaces but also signifies mutual linking between specific topographic states of protein adsorption and assembly to particular segments of adsorption isotherms. From the fundamental research viewpoint, the correlative ability to examine the nanoscopic surface organizations of individual proteins and their local as well as global adsorption kinetic profiles will be highly valuable for accurately determining protein assembly mechanisms and interpreting protein adsorption kinetics on nanoscale surfaces. Application-wise, such knowledge will also be important for fundamentally guiding the design and development of biomaterials and biomedical devices that exploit nanoscale polymer architectures.
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Affiliation(s)
- David H Cho
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Tian Xie
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Patrick J Mulcahey
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Noah P Kelleher
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Jong-In Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
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Sarker P, Sajib MSJ, Tao X, Wei T. Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption. J Phys Chem B 2022; 126:601-608. [PMID: 35026946 DOI: 10.1021/acs.jpcb.1c08267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs' chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs' size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP's size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface.
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Affiliation(s)
- Pranab Sarker
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Md Symon Jahan Sajib
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Xiuping Tao
- Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, United States
| | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
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Tarjányi T, Bogár F, Minarovits J, Gajdács M, Tóth Z. Interaction of KRSR Peptide with Titanium Dioxide Anatase (100) Surface: A Molecular Dynamics Simulation Study. Int J Mol Sci 2021; 22:ijms222413251. [PMID: 34948048 PMCID: PMC8707641 DOI: 10.3390/ijms222413251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/04/2021] [Accepted: 12/05/2021] [Indexed: 11/19/2022] Open
Abstract
Due to its tensile strength and excellent biocompatibility, titanium (Ti) is commonly used as an implant material in medicine and dentistry. The success of dental implants depends on the formation of a contact between the oxidized surface of Ti implant and the surrounding bone tissue. The adsorption of proteins and peptides to the implant surface allows the bone-forming osteoblast cells to adhere to such modified surfaces. Recently, it has been observed that tetrapeptide KRSR (Lys-Arg-Ser-Arg) functionalization could promote osteoblast adhesion to implant surfaces. This may facilitate the establishment of an efficient bone-to implant contact and improve implant stability during the healing process. GROMACS, a molecular dynamics software package was used to perform a 200 ns simulation of adsorption of the KRSR peptide to the TiO2 (anatase) surface in an aqueous environment. The molecule conformations were mapped with Replica Exchange Molecular Dynamics (REMD) simulations to assess the possible peptide conformations on the anatase surface, and the umbrella sampling method was used to calculate the binding energy of the most common conformation. The simulations have shown that the KRSR peptide migrates and attaches to the surface in a stable position. The dominant amino acid residue interacting with the TiO2 surface was the N-terminal charged lysine (K) residue. REMD indicated that there is a distinct conformation that is taken by the KRSR peptide. In this conformation the surface interacts only with the lysine residue while the ser (S) and arg (R) residues interact with water molecules farther from the surface. The binding free energy of the most common conformation of KRSR peptide to the anatase (100) surface was ΔG = −8.817 kcal/mol. Our result suggests that the N-terminal lysine residue plays an important role in the adhesion of KRSR to the TiO2 surface and may influence the osseointegration of dental implants.
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Affiliation(s)
- Tamás Tarjányi
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, Tisza Lajos Körút 64-66, H-6720 Szeged, Hungary; (J.M.); (M.G.)
- Correspondence:
| | - Ferenc Bogár
- MTA-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), Dóm tér 8, H-6720 Szeged, Hungary;
| | - Janos Minarovits
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, Tisza Lajos Körút 64-66, H-6720 Szeged, Hungary; (J.M.); (M.G.)
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, Tisza Lajos Körút 64-66, H-6720 Szeged, Hungary; (J.M.); (M.G.)
| | - Zsolt Tóth
- Department of Experimental Physics, Faculty of Science and Informatics, University of Szeged, Dóm tér 9, H-6720 Szeged, Hungary;
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Protein Adsorption and Conformational Changes. Molecules 2021; 26:molecules26237079. [PMID: 34885661 PMCID: PMC8659092 DOI: 10.3390/molecules26237079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 12/04/2022] Open
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Touzeau J, Seydou M, Maurel F, Tallet L, Mutschler A, Lavalle P, Barbault F. Theoretical and Experimental Elucidation of the Adsorption Process of a Bioinspired Peptide on Mineral Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11374-11385. [PMID: 34516122 DOI: 10.1021/acs.langmuir.1c01994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Inorganic materials used for biomedical applications such as implants generally induce the adsorption of proteins on their surface. To control this phenomenon, the bioinspired peptidomimetic polymer 1 (PMP1), which aims to reproduce the adhesion of mussel foot proteins, is commonly used to graft specific proteins on various surfaces and to regulate the interfacial mechanism. To date and despite its wide application, the elucidation at the atomic scale of the PMP1 mechanism of adsorption on surfaces is still unknown. The purpose of the present work was thus to unravel this process through experimental and computational investigations of adsorption of PMP1 on gold, TiO2, and SiO2 surfaces. A common mechanism of adsorption is identified for the adsorption of PMP1 which emphasizes the role of electrostatics to approach the peptide onto the surface followed by a full adhesion process where the entropic desolvation step plays a key role. Besides, according to the fact that mussel naturally controls the oxidation states of its proteins, further investigations were performed for two distinct redox states of PMP1, and we conclude that even if both states are able to allow interaction of PMP1 with the surfaces, the oxidation of PMP1 leads to a stronger interaction.
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Affiliation(s)
- J Touzeau
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
| | - M Seydou
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
| | - F Maurel
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
| | - L Tallet
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR_S 1121 Biomaterials and Bioengineering, 11 rue Humann, 67000 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 67000 Strasbourg, France
| | - A Mutschler
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR_S 1121 Biomaterials and Bioengineering, 11 rue Humann, 67000 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 67000 Strasbourg, France
| | - P Lavalle
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR_S 1121 Biomaterials and Bioengineering, 11 rue Humann, 67000 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 67000 Strasbourg, France
| | - F Barbault
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
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Wang H, Yuan H, Wang J, Zhang E, Bai M, Sun Y, Wang J, Zhu S, Zheng Y, Guan S. Influence of the second phase on protein adsorption on biodegradable Mg alloys' surfaces: Comparative experimental and molecular dynamics simulation studies. Acta Biomater 2021; 129:323-332. [PMID: 33831575 DOI: 10.1016/j.actbio.2021.03.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 01/19/2023]
Abstract
The effect of the second phase on the mechanical properties and corrosion resistance of Mg alloys has been systematically studied. However, there is limited information on the effect of the second phase on protein adsorption behavior. In the present study, the effect of the second phase on protein adsorption on the surfaces of biodegradable Mg alloys was investigated using experimental methods and molecular dynamics (MD) simulations. The experimental results showed that the effect of the second phase on fibrinogen adsorption was type-dependent. Fibrinogen preferentially adsorbed on Y-, Ce-, or Nd-involved second phases, while the second phase containing Zn inhibited its adsorption. MD simulations revealed the mechanism of the second phase that influenced protein adsorption in terms of charge distribution, surface-protein interaction energy, and water molecule distribution. Our studies proposed a deep understanding of the design of Mg-based biomaterials with superior biocompatibility. STATEMENT OF SIGNIFICANCE: Mechanical properties, uniform degradation, and biocompatibility must be considered while designing biomedical Mg alloys. To improve the mechanical properties and corrosion resistance of Mg alloys, the second phase is usually required. However, the effects of the second phase on biocompatibility of Mg alloys have been rarely reported. Here, the influence of the second phase on protein adsorption was experimentally studied by designing Mg alloys with different types of second phase. The first principle calculation and MD simulation were used to reveal the mechanism by which the second phase influences protein adsorption. This work could be used to better elucidate the protein adsorption mechanisms and design principles to improve the biocompatibility of Mg alloys.
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Affiliation(s)
- Hongyan Wang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Haonan Yuan
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Jinming Wang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Engui Zhang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Mingyun Bai
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Yufeng Sun
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Jianfeng Wang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Shijie Zhu
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Yufeng Zheng
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Shaokang Guan
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China; Henan Key Laboratory of Advanced Magnesium Alloys, Zhengzhou 450002, China.
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32
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Song J, Ju Y, Amarasena TH, Lin Z, Mettu S, Zhou J, Rahim MA, Ang CS, Cortez-Jugo C, Kent SJ, Caruso F. Influence of Poly(ethylene glycol) Molecular Architecture on Particle Assembly and Ex Vivo Particle-Immune Cell Interactions in Human Blood. ACS NANO 2021; 15:10025-10038. [PMID: 34009935 DOI: 10.1021/acsnano.1c01642] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Poly(ethylene glycol) (PEG) is widely used in particle assembly to impart biocompatibility and stealth-like properties in vivo for diverse biomedical applications. Previous studies have examined the effect of PEG molecular weight and PEG coating density on the biological fate of various particles; however, there are few studies that detail the fundamental role of PEG molecular architecture in particle engineering and bio-nano interactions. Herein, we engineered PEG particles using a mesoporous silica (MS) templating method and investigated how the PEG building block architecture impacted the physicochemical properties (e.g., surface chemistry and mechanical characteristics) of the PEG particles and subsequently modulated particle-immune cell interactions in human blood. Varying the PEG architecture from 3-arm to 4-arm, 6-arm, and 8-arm generated PEG particles with a denser, stiffer structure, with increasing elastic modulus from 1.5 to 14.9 kPa, inducing an increasing level of immune cell association (from 15% for 3-arm to 45% for 8-arm) with monocytes. In contrast, the precursor PEG particles with the template intact (MS@PEG) were stiffer and generally displayed higher levels of immune cell association but showed the opposite trend-immune cell association decreased with increasing PEG arm numbers. Proteomics analysis demonstrated that the biomolecular corona that formed on the PEG particles minimally influenced particle-immune cell interactions, whereas the MS@PEG particle-cell interactions correlated with the composition of the corona that was abundant in histidine-rich glycoproteins. Our work highlights the role of PEG architecture in the design of stealth PEG-based particles, thus providing a link between the synthetic nature of particles and their biological behavior in blood.
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Affiliation(s)
- Jiaying Song
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Thakshila H Amarasena
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhixing Lin
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Srinivas Mettu
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jiajing Zhou
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Md Arifur Rahim
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christina Cortez-Jugo
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stephen J Kent
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
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Dutta S, Corni S, Brancolini G. Molecular Dynamics Simulations of a Catalytic Multivalent Peptide-Nanoparticle Complex. Int J Mol Sci 2021; 22:3624. [PMID: 33807225 PMCID: PMC8037132 DOI: 10.3390/ijms22073624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide-nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure-function relationship, for technological and nanomedical applications.
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Affiliation(s)
- Sutapa Dutta
- Dipartimento di Scienze Chimiche, Università di Padova, 35131 Padova, Italy;
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università di Padova, 35131 Padova, Italy;
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Giorgia Brancolini
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
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Mechanistic insights into the adsorption and bioactivity of fibronectin on surfaces with varying chemistries by a combination of experimental strategies and molecular simulations. Bioact Mater 2021; 6:3125-3135. [PMID: 33778193 PMCID: PMC7960943 DOI: 10.1016/j.bioactmat.2021.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
Fibronectin (Fn) is significant to the performance of biomaterials, and the chemistry of biomaterial surface play important roles in Fn adsorption and subsequent cell behavior. However, the "molecular scale" mechanism is still unclear. Herein, we combined experimental strategies with molecular simulations to solve this problem. We prepared self-assembled monolayers with varying chemistries, i.e., SAMs-CH3, SAMs-NH2, SAMs-COOH and SAMs-OH, and characterized Fn adsorption and cell behaviors on them. Next, Monte Carlo method and all-atom molecular dynamics simulations were employed to reveal the orientation/conformation of Fn on surfaces. We found that SAMs-CH3 strongly adsorbed Fn via hydrophobic interactions, but show poor bioactivity as the low exposure of RGD/PHSRN motifs and the deformation of Fn. SAMs-NH2 and SAMs-COOH could adsorb Fn efficiently via vdW interactions, electrostatic interactions, hydrogen bonds and salt bridges. Fn exhibited excellent bioactivity for cell adhesion, proliferation and osteogenic differentiation as high exposure of bioactive motifs on SAMs-NH2, or as the activation of other inferior cell-binding motifs on SAMs-COOH. SAMs-OH showed poor Fn adsorption as the water film. However, the adsorbed Fn displayed non-negligible bioactivity due to high exposure of PHSRN motif and large degree of protein flexibility. We believe that the revealed mechanism presents great potential to rationally design Fn-activating biomaterials.
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Zheng S, Sajib MSJ, Wei Y, Wei T. Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface. J Chem Theory Comput 2021; 17:1874-1882. [PMID: 33586958 DOI: 10.1021/acs.jctc.0c01172] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fundamental understanding of biomolecular interfacial behavior, such as protein adsorption at the microscopic scale, is critical to broad applications in biomaterials, nanomedicine, and nanoparticle-based biosensing techniques. The goal of achieving both computational efficiency and accuracy presents a major challenge for simulation studies at both atomistic and molecular scales. In this work, we developed a unique, accurate, high-throughput simulation method which, by integrating discontinuous molecular dynamics (DMD) simulations with the Go-like protein-surface interaction model, not only solves the dynamics efficiently, but also describes precisely the protein intramolecular and intermolecular interactions at the atomistic scale and the protein-surface interactions at the coarse-grained scale. Using our simulation method and in-house developed software, we performed a systematic study of α-helical ovispirin-1 peptide adsorption on a graphene surface, and our study focused on the effect of surface hydrophobic interactions and π-π stacking on protein adsorption. Our DMD simulations were consistent with full-atom molecular dynamics simulations and showed that a single ovispirin-1 peptide lay down on the flat graphene surface with randomized secondary structure due to strong protein-surface interactions. Peptide aggregates were formed with an internal hydrophobic core driven by strong interactions of hydrophobic residues in the bulk environment. However, upon adsorption, the hydrophobic graphene surface can break the hydrophobic core by denaturing individual peptide structures, leading to disassembling the aggregate structure and further randomizing the ovispirin-1 peptide's secondary structures.
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Affiliation(s)
- Size Zheng
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
| | - Md Symon Jahan Sajib
- Chemical Engineering Department, Howard University, Washington, D.C. 20059, United States
| | - Yong Wei
- Department of Computer Science and Information Systems, University of North Georgia, Dahlonega, Georgia 30597, United States
| | - Tao Wei
- Chemical Engineering Department, Howard University, Washington, D.C. 20059, United States
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36
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Osella S. Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead? NANOMATERIALS 2021; 11:nano11020299. [PMID: 33498961 PMCID: PMC7911014 DOI: 10.3390/nano11020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
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37
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Analysis of binding modes of biopanning heptapeptides with specific affinity to chitosan wrapped MSN. Biochem Biophys Res Commun 2021; 539:64-69. [PMID: 33422941 DOI: 10.1016/j.bbrc.2020.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022]
Abstract
In this work, we demonstrated for the first time that six short heptapeptides screened out by biopanning strategy show affinity binding to chitosan wrapped mesoporous silica nanoparticle (CS/MSN). The interaction between peptide and chitosan-wrapped MSN (CS/MSN) was carefully analyzed with the aid of DLS and ELISA characterization. The results show that π-π stacking and hydrogen bonds account for the strong adsorption under neutral as well as acidic conditions. While hydrophilic and electrostatic interaction are the major modes of the peptide under alkaline condition. These different interaction modes involved in the adsorption of peptides onto CS/MSN could vividly mimic the binding of peptide with chitosan in physiological conditions and help to deeply understand the process of protein adsorption on nanomaterials.
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38
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Deguchi S, Yokoyama R, Maki T, Tomita K, Osugi R, Hakamada M, Mabuchi M. A new mechanism for reduced cell adhesion: Adsorption dynamics of collagen on a nanoporous gold surface. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 119:111461. [PMID: 33321592 DOI: 10.1016/j.msec.2020.111461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 11/24/2022]
Abstract
Nanostructured materials such as nanoparticles and nanoporous materials strongly affect cell behaviors such as cell viability. Because cellular uptake of nanoporous materials does not occur, mechanisms for the effects of nanoporous materials on cells are different from those of nanoparticles. The effects of nanoporous materials on cells are thought to result from large conformational changes in the extracellular matrix (ECM) induced by the nanoporous materials, although the mechanotransduction and the critical focal adhesion cluster size also have an effect on the cell response. However, we show that the adhesion of mesenchymal stem cells to a gold surface is reduced for nanoporous gold (NPG), despite the conformational changes in collagen induced by NPG being below the detection limits of the experimental analyses. The adsorption dynamics of collagen on NPG are investigated by molecular dynamics simulations to determine the origin of the reduced cell adhesion to NPG. The adsorption energy of collagen on NPG is lower than that on flat gold (FG) despite there being little difference between the global conformation of collagen segments adsorbed on NPG compared with FG. This finding is related to the surface strain of NPG and the limited movement of collagen amino acids owing to interchain hydrogen bonds. The results obtained in this study provide new insight into the interactions between nanostructured materials and the ECM.
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Affiliation(s)
- Soichiro Deguchi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan.
| | - Ryo Yokoyama
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Takuya Maki
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Kazuki Tomita
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Ryosuke Osugi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Masataka Hakamada
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Mamoru Mabuchi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
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39
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Armstrong MJ, Rodriguez JB, Dahl P, Salamon P, Hess H, Katira P. Power Law Behavior in Protein Desorption Kinetics Originating from Sequential Binding and Unbinding. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13527-13534. [PMID: 33152250 DOI: 10.1021/acs.langmuir.0c02260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The study of protein adsorption at the single molecule level has recently revealed that the adsorption is reversible, but with a long-tailed residence time distribution which can be approximated with a sum of exponential functions putatively related to distinct adsorption sites. Here it is proposed that the shape of the residence time distribution results from an adsorption process with sequential and reversible steps that contribute to overall binding strength resembling "zippering". In this model, the survival function of the residence time distribution of single proteins varies from an exponential distribution for a single adsorption step to a power law distribution with exponent -1/2 for a large number of adsorption steps. The adsorption of fluorescently labeled fibrinogen to glass surfaces is experimentally studied with single molecule imaging. The experimental residence time distribution can be readily fit by the proposed model. This demonstrates that the observed long residence times can arise from stepwise adsorption rather than rare but strong binding sites and provides guidance for the control of protein adsorption to biomaterials.
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Affiliation(s)
- Megan J Armstrong
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Juan B Rodriguez
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Peter Dahl
- Department of Mechanical Engineering, San Diego State University, San Diego, California 98182, United States
| | - Peter Salamon
- Department of Mathematics and Statistics and Viral Information Institute, San Diego State University, San Diego, California 98182, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, San Diego, California 98182, United States
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40
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Kuang Z, Singh KM, Oliver DJ, Dennis PB, Perry CC, Naik RR. Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets. Nat Commun 2020; 11:5517. [PMID: 33139719 PMCID: PMC7606380 DOI: 10.1038/s41467-020-19233-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/28/2020] [Indexed: 11/26/2022] Open
Abstract
A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 kBT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations. Measuring interaction energies from experimentally measured single-molecular interactions is challenging. Here, the authors report a gamma work distribution applied to single molecule pulling events for estimating peptide absorption free energy.
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Affiliation(s)
- Zhifeng Kuang
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Kristi M Singh
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Daniel J Oliver
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Patrick B Dennis
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Rajesh R Naik
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA.
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41
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Watanabe G, Eimura H, Abbott NL, Kato T. Biomolecular Binding at Aqueous Interfaces of Langmuir Monolayers of Bioconjugated Amphiphilic Mesogenic Molecules: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12281-12287. [PMID: 32970447 DOI: 10.1021/acs.langmuir.0c02191] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We report a molecular dynamics (MD) simulation study of protein binding at the aqueous-liquid crystal (LC) interfaces of bioconjugated mesogenic molecules. As a simple model of these interfaces, we use monolayers composed of biotin-conjugated or biotin-free amphiphilic mesogenic molecules and streptavidin in water. The all-atom MD simulations reveal that the binding of streptavidin to the biotin mesogenic monolayer is significantly stronger than that to biotin-free mesogenic monolayers. Although specific protein binding marginally increases the overall orientational order and the tilt of the biotin-conjugated mesogenic molecules of the monolayer, significant changes in tilt were observed near the bound protein (in contrast to the protein interaction with the monolayer without biotin). We also observe that specific protein binding changes the dynamic properties of the mesogens within the monolayer (e.g., lateral diffusion coefficients) and associated water. Overall, these MD simulations advance our understanding of the molecular-level phenomena involved in the binding of biomolecules and subsequent dynamic changes at the aqueous-LC interfaces. These results provide guidance to future molecular-level designs of biofunctional LC interfaces.
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Affiliation(s)
- Go Watanabe
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Hiroki Eimura
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Nicholas L Abbott
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Takashi Kato
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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42
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Wang X, Lan PC, Ma S. Metal-Organic Frameworks for Enzyme Immobilization: Beyond Host Matrix Materials. ACS CENTRAL SCIENCE 2020; 6:1497-1506. [PMID: 32999925 PMCID: PMC7517118 DOI: 10.1021/acscentsci.0c00687] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 05/15/2023]
Abstract
Enzyme immobilization in metal-organic frameworks (MOFs) as a promising strategy is attracting the interest of scientists from different disciplines with the expansion of MOFs' development. Different from other traditional host materials, their unique strengths of high surface areas, large yet adjustable pore sizes, functionalizable pore walls, and diverse architectures make MOFs an ideal platform to investigate hosted enzymes, which is critical to the industrial and commercial process. In addition to the protective function of MOFs, the extensive roles of MOFs in the enzyme immobilization are being well-explored by making full use of their remarkable properties like well-defined structure, high porosity, and tunable functionality. Such development shifts the focus from the exploration of immobilization strategies toward functionalization. Meanwhile, this would undoubtedly contribute to a better understanding of enzymes in regards to the structural transformation after being hosted in a confinement environment, particularly to the orientation and conformation change as well as the interplay between enzyme and matrix MOFs. In this Outlook, we target a comprehensive review of the role diversities of the host matrix MOF based on the current enzyme immobilization research, along with proposing an outlook toward the future development of this field, including the representatives of potential techniques and methodologies being capable of studying the hosted enzymes.
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Affiliation(s)
- Xiaoliang Wang
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Pui Ching Lan
- Department
of Chemistry, University of North Texas, 1508 West Mulberry Street, Denton, Texas 76201, United States
| | - Shengqian Ma
- Department
of Chemistry, University of North Texas, 1508 West Mulberry Street, Denton, Texas 76201, United States
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
- E-mail:
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43
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Wang X, Yang X, Chen H, Yang X, Xu Z. Entropy-Enthalpy Compensation in Peptide Adsorption on Solid Surfaces: Dependence on Surface Hydration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10822-10829. [PMID: 32813538 DOI: 10.1021/acs.langmuir.0c01845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although protein adsorption at the solid-water interface is of immense importance, understanding the crucial role of the water phase in mediating protein-surface interactions is lacking, particularly due to the lack of fundamental thermodynamic data. Herein, we have performed complicated free energy calculations and successfully extracted the entropy and enthalpy changes of molecular adsorption on solids. Using the gold and graphene as the surface models with distinct affinities to the water phase, we successfully unravel the sharply opposite manners of entropy-enthalpy compensation in driving water and tripeptide adsorptions on two surfaces. Though the thermodynamic features of water adsorption on surface are enthalpically dominated based on the positions of free energy barriers and minima, the favorable entropy term significantly decreases the free energy barrier and further stabilizes the adsorbate at the adsorption site on the graphene surface. For the peptide, the shape of the adsorption free energy profile is jointly determined by the enthalpy and entropy changes, which, however, alternatively act the driving force to promote the peptide adsorption on the Au surface and graphene surface. The distinct structural and dynamic properties of solid-liquid interfaces account for the special role of the interfacial water phase in regulating the competitive relationship between the entropy and enthalpy variations.
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Affiliation(s)
- Xiang Wang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Xiao Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Huijun Chen
- Obstetrics and Gynecology Department, Zhongnan Hospital of Wuhan University, #169 East Lake Road, Wuchang District, Wuhan 430017, China
| | - Xiaoning Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Zhijun Xu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
- Zhangjiagang Institute of Nanjing Tech University, Jiangfanlu 8, Zhangjiagang 215699, China
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44
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Insight into vitronectin structural evolution on material surface chemistries: The mediation for cell adhesion. Bioact Mater 2020; 5:1044-1052. [PMID: 32695935 PMCID: PMC7358734 DOI: 10.1016/j.bioactmat.2020.06.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/18/2022] Open
Abstract
Biomaterial surface chemistry engenders profound consequences on cell adhesion and the ultimate tissue response by adsorbing proteins from extracellular matrix, where vitronectin (Vn) is involved as one of the crucial mediator proteins. Deciphering the adsorption behaviors of Vn in molecular scale provides a useful account of how to design biomaterial surfaces. But the details of structural dynamics and consequential biological effect remain elusive. Herein, both experimental and computational approaches were applied to delineate the conformational and orientational evolution of Vn during adsorption onto self-assembled monolayers (SAMs) terminating with -COOH, -NH2, -CH3 and -OH. To unravel the interplay between cell binding and the charge and wettability of material surface, somatomedin-B (SMB) domain of Vn holding the RGD cell-binding motif was employed in molecular dynamics (MD) simulations, with orientation initialized by Monte Carlo (MC) method. Experimental evidences including protein adsorption, cell adhesion and integrin gene expressions were thoroughly investigated. The adsorption of Vn on different surface chemistries showed very complex profiles. Cell adhesion was enabled on all Vn-adsorbed surfaces but with distinct mechanisms mostly determined by conformational change induced reorientation. Higher amount of Vn was observed on negatively charged surface (COOH) and hydrophobic surface (CH3). However, advantageous orientations defined by RGD loop conditions were only obtained on the charged surfaces (COOH and NH2). Specifically, COOH surface straightened up the Vn molecules and accumulated them into a higher density, whereas CH3 surface squashed Vn and stacked them into higher density multilayer by tracking adsorption but with the RGD loops restrained. These findings may have a broad implication on the understanding of Vn functionality and would help develop new strategies for designing advanced biomaterials. Unfolded straighten structure of Vn unbinds RGD loop on negatively charged surface. Unfolded Vn forms compact multilayers by tracking adsorption on hydrophobic surface. Accessible RGD loop of adsorbed Vn endows better cell affinity for charged surface.
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45
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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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46
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Nanocrystal facet modulation to enhance transferrin binding and cellular delivery. Nat Commun 2020; 11:1262. [PMID: 32152269 PMCID: PMC7062909 DOI: 10.1038/s41467-020-14972-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Binding of biomolecules to crystal surfaces is critical for effective biological applications of crystalline nanomaterials. Here, we present the modulation of exposed crystal facets as a feasible approach to enhance specific nanocrystal–biomolecule associations for improving cellular targeting and nanomaterial uptake. We demonstrate that facet-engineering significantly enhances transferrin binding to cadmium chalcogenide nanocrystals and their subsequent delivery into cancer cells, mediated by transferrin receptors, in a complex biological matrix. Competitive adsorption experiments coupled with theoretical calculations reveal that the (100) facet of cadmoselite and (002) facet of greenockite preferentially bind with transferrin via inner-sphere thiol complexation. Molecular dynamics simulation infers that facet-dependent transferrin binding is also induced by the differential affinity of crystal facets to water molecules in the first solvation shell, which affects access to exposed facets. Overall, this research underlines the promise of facet engineering to improve the efficacy of crystalline nanomaterials in biological applications. Modulation of exposed crystal facets enhances transferrin binding to chalcogenide nanocrystals and their subsequent delivery into cancer cells. Facet-dependent protein binding occurs through inner-sphere thiol complexation and is affected by the structure of the first solvation shell.
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47
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Zhang C, Li X, Wang Z, Huang X, Ge Z, Hu B. Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications. J Phys Chem B 2020; 124:684-694. [PMID: 31880460 DOI: 10.1021/acs.jpcb.9b10192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.
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Affiliation(s)
- Chi Zhang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xiaoyi Li
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zichen Wang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xuqi Huang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhenpeng Ge
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Benfeng Hu
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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48
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Hasoň S, Ostatná V, Fojta M. Simultaneous voltammetric determination of free tryptophan, uric acid, xanthine and hypoxanthine in plasma and urine. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2019.135132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Liu S, Yin X, Zhou H, Zhou B, Shao Q, Yang Z, Zhou R. Different platinum crystal surfaces show very distinct protein denaturation capabilities. NANOSCALE 2019; 11:19352-19361. [PMID: 31620747 DOI: 10.1039/c9nr03682b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface. This surprising difference originates from the distinct water behavior in the first solvation shell (FSS) of the two Pt crystal surfaces. Within the FSS of the Pt(100) crystal surface, water molecules form a very compact and stable monolayer through a highly uniform rhombic hydrogen-bond network. This water monolayer prefers the adsorption of acidic residues (such as Glu and Asp) and acts as a shield to prevent other residues from directly coming into contact with the metal surface. On the other hand, the hydrogen bond network in the water monolayer in the FSS of the Pt(111) crystal surface is very sparse and quite defective, which makes it more vulnerable to the penetration of various residues, particularly those with planar side chains such as Phe, Trp and Arg due to strong dispersion interactions, leading to subsequent protein unfolding. The binding free energy calculations for some key amino acids on the two different crystal surfaces further uncover the molecular origin behind their distinct protein denaturation capability. Our study reveals the vital importance of interfacial water in determining the structure of proteins when binding to different metal crystal surfaces. The discovered molecular mechanisms may be helpful for the future development of a bio-assisted programmable synthetic strategy of sophisticated Pt nanostructures for biomedical applications.
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Affiliation(s)
- Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Xiuhua Yin
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Bo Zhou
- School of Electronic Engineering, Chengdu Technological University, Chengdu 611730, China
| | - Qiwen Shao
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China. and IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA and Department of Chemistry, Columbia University, New York, NY 10027, USA
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50
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Kroutil O, Kabeláč M, Dorčák V, Vacek J. Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study. ELECTROANAL 2019. [DOI: 10.1002/elan.201900314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ondřej Kroutil
- Institute of Physics and Biophysics, Faculty of ScienceUniversity of South Bohemia Branisovska 1760 370 05 Ceske Budejovice Czech Republic
| | - Martin Kabeláč
- Department of Chemistry, Faculty of ScienceUniversity of South Bohemia Branisovska 31 370 05 Ceske Budejovice Czech Republic
| | - Vlastimil Dorčák
- Institute of Biophysics of the CAS Kralovopolska 135 612 65 Brno Czech Republic
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and DentistryPalacky University Hnevotinska 3 775 15 Olomouc Czech Republic
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