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Lavigne A, Géhin T, Gilquin B, Jousseaume V, Veillerot M, Botella C, Chevalier C, Jamois C, Chevolot Y, Phaner-Goutorbe M, Yeromonahos C. Effect of Silane Monolayers and Nanoporous Silicon Surfaces on the Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Detection of Sepsis Metabolites Biomarkers Mixed in Solution. ACS OMEGA 2023; 8:28898-28909. [PMID: 37576693 PMCID: PMC10413469 DOI: 10.1021/acsomega.3c04266] [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: 06/15/2023] [Accepted: 07/07/2023] [Indexed: 08/15/2023]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) is a promising strategy for clinical diagnosis based on metabolite detection. However, several bottlenecks (such as the lack of reproducibility in analysis, the presence of an important background in low-mass range, and the lack of organic matrix for some molecules) prevent its transfer to clinical cases. These limitations can be addressed by using nanoporous silicon surfaces chemically functionalized with silane monolayers. In the present study, sepsis metabolite biomarkers were used to investigate the effects of silane monolayers and porous silicon substrates on MALDI-ToF MS analysis (signal-to-noise value (S/N), relative standard deviation of the S/N of triplicate samples (STDmean), and intra-substrates uniformity). Also, the impact of the physicochemical properties of metabolites, with different isoelectric points and hydrophobic-hydrophilic balances, was assessed. Four different silane molecules, with various alkyl chain lengths and head-group charges, were self-assembled in monolayers on plane and porous silicon surfaces. Their surface coverage and conformity were investigated by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The seven metabolites detected on the stainless-steel target plate (lysophosphatidylcholine, caffeine, phenylalanine, creatinine, valine, arginine, and glycerophosphocholine) are also detected on the silanized and bare, plane and porous silicon surfaces. Moreover, two metabolites, glycine and alanine, which are not detected on the stainless-steel target plate, are detected on all silanized surfaces, except glycine which is not detected on CH3 short-modified porous silicon and on the bare plane silicon substrate. In addition, whatever the metabolites (except phenylalanine and valine), at least one of the silicon surfaces allows to increase the S/N value in comparison with the stainless-steel target plate. Also, the heterogeneity of matrix crystallization features is linked to the STDmean which is poor on the NH3+ monolayer on plane substrate and better on the NH3+ monolayer on porous substrate, for most of the metabolites. Nevertheless, matrix crystallization features are not sufficient to systematically get high STDmean and uniformity in MALDI-ToF MS analysis. Indeed, the physicochemical properties of metabolites and surfaces, limitations in metabolite extraction from the pores, and improvement in metabolite desorption due to the pores are shown to significantly impact MS analysis. In particular, in the case of the most hydrophobic metabolites studied, the highest S/N values and the best STDmean and uniformity (the lowest values) are reached by using porous substrates, while in the case of the most hydrophilic metabolites studied, plane substrates demonstrated the highest S/N and the lowest STDmean. No clear trend of surface chemistry was evidenced.
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Affiliation(s)
- Antonin Lavigne
- Univ
Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69134 Ecully Cedex, France
| | - Thomas Géhin
- Univ
Lyon, CNRS, Ecole Centrale de Lyon, INSA Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69134 Ecully Cedex, France
| | - Benoît Gilquin
- Univ
Grenoble Alpes, CEA, LETI, F-38000 Grenoble, France
| | | | - Marc Veillerot
- Univ
Grenoble Alpes, CEA, LETI, F-38000 Grenoble, France
| | - Claude Botella
- Univ
Lyon, CNRS, Ecole Centrale de Lyon, INSA Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69134 Ecully Cedex, France
| | - Céline Chevalier
- Univ
Lyon, INSA Lyon, CNRS, Ecole Centrale de Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69621 Villeurbanne Cedex, France
| | - Cécile Jamois
- Univ
Lyon, INSA Lyon, CNRS, Ecole Centrale de Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69621 Villeurbanne Cedex, France
| | - Yann Chevolot
- Univ
Lyon, CNRS, Ecole Centrale de Lyon, INSA Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69134 Ecully Cedex, France
| | - Magali Phaner-Goutorbe
- Univ
Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69134 Ecully Cedex, France
| | - Christelle Yeromonahos
- Univ
Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude
Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69134 Ecully Cedex, France
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Lavigne A, Gilquin B, Géhin T, Jousseaume V, Veillerot M, Chevolot Y, Phaner-Goutorbe M, Yeromonahos C. Effects of Silane Monolayers on Lysophosphatidylcholine (LysoPC) Detection by Desorption Ionization on Silicon Mass Spectrometry (DIOS-MS) in Solution and Plasma. ACS APPLIED MATERIALS & INTERFACES 2023; 15:18685-18693. [PMID: 37014887 DOI: 10.1021/acsami.3c01181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Desorption ionization on silicon mass spectrometry (DIOS-MS) enables high throughput analysis of low-molecular-weight biomolecules. However, detection of metabolite biomarkers in complex fluids such as plasma requires sample pretreatment, limiting clinical application. Here, we show that porous silicon, chemically modified using monolayers of n-propyldimethylmethoxysilane molecules, is a good candidate for fingerprinting lysophosphatidylcholine (lysoPC) in plasma, without sample pretreatment, for DIOS-MS-based diagnosis (e.g., sepsis). Results were correlated to lysoPC molecule location inside/outside the pores, determined by time-of-flight secondary ion mass spectrometry profiling, and to physicochemical properties.
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Affiliation(s)
- Antonin Lavigne
- CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Univ Lyon, Ecole Centrale de Lyon, 69134 Ecully Cedex, France
| | - Benoît Gilquin
- CEA, LETI, Clinatec, Univ. Grenoble Alpes, 38000 Grenoble, France
| | - Thomas Géhin
- INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Univ Lyon, CNRS, Ecole Centrale de Lyon, 69134 Ecully Cedex, France
| | | | - Marc Veillerot
- CEA, LETI, Univ Grenoble Alpes, F-38000 Grenoble, France
| | - Yann Chevolot
- INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Univ Lyon, CNRS, Ecole Centrale de Lyon, 69134 Ecully Cedex, France
| | - Magali Phaner-Goutorbe
- CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Univ Lyon, Ecole Centrale de Lyon, 69134 Ecully Cedex, France
| | - Christelle Yeromonahos
- CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Univ Lyon, Ecole Centrale de Lyon, 69134 Ecully Cedex, France
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Zhang Z, Qiao M, Zhao H, Ran Q, Yuan S. Effect of sodium alkyl sulfate chain length on foam stability: A molecular dynamics study. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2022.130394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Corregidor D, Tabraue R, Colchero L, Daza R, Elices M, Guinea GV, Pérez-Rigueiro J. High-Yield Characterization of Single Molecule Interactions with DeepTip TM Atomic Force Microscopy Probes. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010226. [PMID: 36615422 PMCID: PMC9822271 DOI: 10.3390/molecules28010226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Single molecule interactions between biotin and streptavidin were characterized with functionalized DeepTipTM probes and used as a model system to develop a comprehensive methodology for the high-yield identification and analysis of single molecular events. The procedure comprises the covalent binding of the target molecule to a surface and of the sensing molecule to the DeepTipTM probe, so that the interaction between both chemical species can be characterized by obtaining force-displacement curves in an atomic force microscope. It is shown that molecular resolution is consistently attained with a percentage of successful events higher than 90% of the total number of recorded curves, and a very low level of unspecific interactions. The combination of both features is a clear indication of the robustness and versatility of the proposed methodology.
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Affiliation(s)
- Daniel Corregidor
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Raquel Tabraue
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Luis Colchero
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Rafael Daza
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Manuel Elices
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Gustavo V. Guinea
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Biomaterials and Regenerative Medicine Group, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Calle Prof. Martín Lagos s/n, 28040 Madrid, Spain
| | - José Pérez-Rigueiro
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain
- Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Biomaterials and Regenerative Medicine Group, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Calle Prof. Martín Lagos s/n, 28040 Madrid, Spain
- Correspondence:
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Dutta S, Gagliardi M, Bellucci L, Agostini M, Corni S, Cecchini M, Brancolini G. Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study. Front Mol Biosci 2022; 9:1006525. [DOI: 10.3389/fmolb.2022.1006525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.
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Huang B, Li M, Mo H, Chen C, Chen K. Effects of Substitution Ratios of Zinc-Substituted Hydroxyapatite on Adsorption and Desorption Behaviors of Bone Morphogenetic Protein-2. Int J Mol Sci 2022; 23:ijms231710144. [PMID: 36077541 PMCID: PMC9456158 DOI: 10.3390/ijms231710144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022] Open
Abstract
Understanding interactions between bone morphogenetic proteins (BMPs) and biomaterials is of great significance in preserving the structure and bioactivity of BMPs when utilized in clinical applications. Currently, bone morphogenetic protein-2 (BMP-2) is one of the most important growth factors in bone tissue engineering; however, atomistic interactions between BMP-2 and zinc-substituted hydroxyapatite (Zn-HAP, commonly used in artificial bone implants) have not been well clarified until now. Thus, in this work, the interaction energies, binding/debinding states, and molecular structures of BMP-2 upon a series of Zn-HAP surfaces (Zn-HAPs, 1 at%, 2.5 at%, 5 at%, and 10 at% substitution) were investigated by hybrid molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. Meanwhile, cellular studies including alkaline phosphatase (ALP) activity and reverse transcription-polymerase chain reaction (RT-PCR) assay were performed to verify the theoretical modeling findings. It was found that, compared to pure HAP, Zn-HAPs exhibited a higher binding affinity of BMP-2 at the adsorption process; meanwhile, the detachment of BMP-2 upon Zn-HAPs was more difficult at the desorption process. In addition, molecular structures of BMP-2 could be well stabilized upon Zn-HAPs, especially for Zn10-HAP (with a 10 at% substitution), which showed both the higher stability of cystine-knots and less change in the secondary structures of BMP-2 than those upon HAP. Cellular studies confirmed that higher ALP activity and osteogenic marker gene expression were achieved upon BMP-2/Zn-HAPs than those upon BMP-2/HAP. These findings verified that Zn-HAPs favor the adsorption of BMP-2 and leverage the bioactivity of BMP-2. Together, this work clarified the interaction mechanisms between BMP-2 and Zn-HAPs at the atom level, which could provide new molecular-level insights into the design of BMP-2-loaded biomaterials for bone tissue engineering.
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Ma Y, Hua T, Trinh TA, Wang R, Chew JW. Molecular dynamics simulation of the competitive adsorption behavior of effluent organic matters by heated aluminum oxide particles (HAOPs). Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.120961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Martí D, Martín-Martínez E, Torras J, Betran O, Turon P, Alemán C. In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold. Colloids Surf B Biointerfaces 2022; 213:112400. [PMID: 35158221 PMCID: PMC8820101 DOI: 10.1016/j.colsurfb.2022.112400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/26/2022]
Abstract
The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.
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Affiliation(s)
- Didac Martí
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Eduard Martín-Martínez
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
| | - Juan Torras
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain.
| | - Oscar Betran
- Departament de Física, EETAC, Universitat Politècnica de Catalunya (UPC), c/ Esteve Terrades, 7, 08860 Castelldefels, Spain
| | - Pau Turon
- B. Braun Surgical, S.A.U. Carretera de Terrasa 121, Rubí, 08191 Barcelona, Spain.
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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10
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Ayan E, Yuksel B, Destan E, Ertem FB, Yildirim G, Eren M, Yefanov OM, Barty A, Tolstikova A, Ketawala GK, Botha S, Dao EH, Hayes B, Liang M, Seaberg MH, Hunter MS, Batyuk A, Mariani V, Su Z, Poitevin F, Yoon CH, Kupitz C, Cohen A, Doukov T, Sierra RG, Dağ Ç, DeMirci H. Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature. Commun Biol 2022; 5:73. [PMID: 35058563 PMCID: PMC8776744 DOI: 10.1038/s42003-021-02903-7] [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: 05/18/2021] [Accepted: 10/28/2021] [Indexed: 11/11/2022] Open
Abstract
Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.
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Affiliation(s)
- Esra Ayan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Busra Yuksel
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Fatma Betul Ertem
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Gunseli Yildirim
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Meryem Eren
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | | | - Anton Barty
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Gihan K Ketawala
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Aina Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Çağdaş Dağ
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research, Koc University, 34450, Istanbul, Turkey
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey.
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey.
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11
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Lecot S, Chevolot Y, Phaner-Goutorbe M, Yeromonahos C. Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations. J Phys Chem B 2021; 125:11078-11090. [PMID: 34570497 DOI: 10.1021/acs.jpcb.1c06050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the context of the COVID-19 outbreak since December 2019, antigenic tests are widely used, for diagnosis purposes, to detect the SARS-CoV-2 spike protein in nasopharyngeal fluid through its interactions with specific antibodies. However, the SARS-CoV-2 spike protein is subject to rapid mutations yielding more and more variants that might lose their affinity toward the currently used antibodies. The virus entry into the host cell involves interactions between the angiotensin-converting enzyme 2 (ACE2) and the SARS-CoV-2 spike protein receptor-binding domain. Consequently, ACE2 could be a target with limited mutation escaping possibilities. However, as the enzyme has not evolved to recognize the virus, its affinity with the spike protein receptor-binding domain is lower than that with specific antibodies. The present molecular dynamics simulations study suggests that the adsorption of the ACE2 on specific silane monolayers could increase its affinity toward the spike protein receptor-binding domain. Indeed, silane monolayers, combining silane molecules with short alkyl chains and positively charged head groups and silane molecules without charged head groups, could adsorb the ACE2 while maintaining its bioactivity (orientation compatible with the spike protein trapping, low conformational changes) and increasing its interactions with the spike protein receptor-binding domain (number of hydrogen bonds and electrostatic interactions) to lead to an increase by 20% both in the binding free energy and in the enzyme /receptor-binding domain rupture force. This work could help develop biosensing tools efficient toward any variants of the SARS-CoV-2 spike protein.
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Affiliation(s)
- Solène Lecot
- Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Université de Lyon, Ecully 69130, France
| | - Yann Chevolot
- Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Université de Lyon, Ecully 69130, France
| | - Magali Phaner-Goutorbe
- Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Université de Lyon, Ecully 69130, France
| | - Christelle Yeromonahos
- Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, Université de Lyon, Ecully 69130, France
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Ma Y, Velioğlu S, Yin Z, Wang R, Chew JW. Molecular dynamics investigation of membrane fouling in organic solvents. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Ma Y, Zydney AL, Wang R, Chew JW. Molecular dynamics study on membrane fouling by oppositely charged proteins. AIChE J 2021. [DOI: 10.1002/aic.17335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yunqiao Ma
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
| | - Andrew L. Zydney
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania USA
| | - Rong Wang
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
- School of Civil and Environmental Engineering Nanyang Technological University Singapore Singapore
| | - Jia Wei Chew
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
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Lecot S, Lavigne A, Yang Z, Chevolot Y, Phaner-Goutorbe M, Yeromonahos C. Effects of the Chemical and Structural Properties of Silane Monolayers on the Organization of Water Molecules and Ions at Interfaces, from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5563-5572. [PMID: 33914530 DOI: 10.1021/acs.langmuir.1c00338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the organization of the hydration layer at functionalized silica surfaces is relevant for a large range of biosensing applications or surface phenomena such as biomolecule adsorption. Silane monolayers are widely used to functionalize silica surfaces. Using molecular dynamics simulations, we have investigated the role of silane molecule head-group charge, alkyl chain length, and surface coverage in the structural organization and dynamic properties of Na+ ions, Cl- ions, and water molecules at the interface. The silane molecules studied are 3-aminopropyldimethylethoxysilane, n-propyldimethylmethoxysilane, octadecyldimethylmethoxysilane, and (dimethylamino)dimethylsilylundecanoate. Our results suggest that the distribution of interfacial ions is sensitive to the 2D dispersion of the silane-charged head groups. Also, while charged silane monolayers show a strong orientation of interfacial water molecules, which leads to a rupture in the hydrogen bond network and disturbs their tetrahedral organization, the arrangement of water molecules at the interface with uncharged silane monolayers seems to be related to the surface roughness and to alkyl chain length. In line with these results, the diffusion of ions and water molecules is higher at the CH3 long monolayer interface than at the CH3 short monolayer interface and at the charged monolayer interfaces. Also, whatever the silane molecules studied, bulk properties are recovered around 0.7 nm above the interface. The interfacial water organization is known to impact biomolecule adsorption. Therefore, these results could further help in optimizing the functionalization layers to capture analytes.
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Affiliation(s)
- Solène Lecot
- Université de Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, INL, UMR5270, 69130 Ecully, France
| | - Antonin Lavigne
- Université de Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, INL, UMR5270, 69130 Ecully, France
| | - Zihua Yang
- Université de Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, INL, UMR5270, 69130 Ecully, France
| | - Yann Chevolot
- Université de Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, INL, UMR5270, 69130 Ecully, France
| | - Magali Phaner-Goutorbe
- Université de Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, INL, UMR5270, 69130 Ecully, France
| | - Christelle Yeromonahos
- Université de Lyon, Ecole Centrale de Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, INL, UMR5270, 69130 Ecully, France
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Affiliation(s)
- Yunqiao Ma
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
| | - Andrew L. Zydney
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania USA
| | - Jia Wei Chew
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
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