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García-Arribas AB, Ibáñez-Freire P, Carlero D, Palacios-Alonso P, Cantero-Reviejo M, Ares P, López-Polín G, Yan H, Wang Y, Sarkar S, Chhowalla M, Oksanen HM, Martín-Benito J, de Pablo PJ, Delgado-Buscalioni R. Broad Adaptability of Coronavirus Adhesion Revealed from the Complementary Surface Affinity of Membrane and Spikes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404186. [PMID: 39231361 DOI: 10.1002/advs.202404186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/21/2024] [Indexed: 09/06/2024]
Abstract
Coronavirus stands for a large family of viruses characterized by protruding spikes surrounding a lipidic membrane adorned with proteins. The present study explores the adhesion of transmissible gastroenteritis coronavirus (TGEV) particles on a variety of reference solid surfaces that emulate typical virus-surface interactions. Atomic force microscopy informs about trapping effectivity and the shape of the virus envelope on each surface, revealing that the deformation of TGEV particles spans from 20% to 50% in diameter. Given this large deformation range, experimental Langmuir isotherms convey an unexpectedly moderate variation in the adsorption-free energy, indicating a viral adhesion adaptability which goes beyond the membrane. The combination of an extended Helfrich theory and coarse-grained simulations reveals that, in fact, the envelope and the spikes present complementary adsorption affinities. While strong membrane-surface interaction lead to highly deformed TGEV particles, surfaces with strong spike attraction yield smaller deformations with similar or even larger adsorption-free energies.
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Affiliation(s)
- Aritz B García-Arribas
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pablo Ibáñez-Freire
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Diego Carlero
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología CSIC, Madrid, 28049, Spain
| | - Pablo Palacios-Alonso
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Miguel Cantero-Reviejo
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pablo Ares
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Guillermo López-Polín
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Han Yan
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Yan Wang
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Soumya Sarkar
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Manish Chhowalla
- Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Hanna M Oksanen
- Faculty of Biological and Environmental Sciences, Vijkki Biocenter, University of Helsinki, Helsinki, 00014, Finland
| | - Jaime Martín-Benito
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Rafael Delgado-Buscalioni
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid, Madrid, 28049, Spain
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Bosch A, Guzman HV, Pérez R. Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces. J Chem Inf Model 2024; 64:5977-5990. [PMID: 39083670 PMCID: PMC11323246 DOI: 10.1021/acs.jcim.4c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024]
Abstract
Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.
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Affiliation(s)
- Antonio
M. Bosch
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Horacio V. Guzman
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
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3
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Xiao Y, Zheng B, Ding X, Zheng P. Probing nanomechanical interactions of SARS-CoV-2 variants Omicron and XBB with common surfaces. Chem Commun (Camb) 2023; 59:11268-11271. [PMID: 37664897 DOI: 10.1039/d3cc02721j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The emergence of SARS-CoV-2 variants has further raised concerns about viral transmission. A fundamental understanding of the intermolecular interactions between the coronavirus and different surfaces is needed to address the transmission of SARS-CoV-2 through respiratory droplet-contaminated surfaces or fomites. The receptor-binding domain (RBD) of the spike protein is a key target for the adhesion of SARS-CoV-2 on the surface. To understand the effect of mutations on adhesion, atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) was used to quantify the interactions between wild-type, Omicron, and XBB with several surfaces. The measurement revealed that RBD exhibits relatively higher forces on paper and gold surfaces, with the average force being 1.5 times greater compared to that on plastic surface. In addition, the force elevation on paper and gold surfaces for the variants can reach ∼28% relative to the wild type. These findings enhance our understanding of the nanomechanical interactions of the virus on common surfaces.
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Affiliation(s)
- Yuelong Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Xuan Ding
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
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Domingo M, Faraudo J. Effect of surfactants on SARS-CoV-2: Molecular dynamics simulations. J Chem Phys 2023; 158:114107. [PMID: 36948819 DOI: 10.1063/5.0135251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Surfactants are commonly used as disinfection agents in personal care products against bacteria and viruses, including SARS-CoV-2. However, there is a lack of understanding of the molecular mechanisms of the inactivation of viruses by surfactants. Here, we employ coarse grain (CG) and all-atom (AA) molecular dynamics simulations to investigate the interaction between general families of surfactants and the SARS-CoV-2 virus. To this end, we considered a CG model of a full virion. Overall, we found that surfactants have only a small impact on the virus envelope, being inserted into the envelope without dissolving it or generating pores, at the conditions considered here. However, we found that surfactants may induce a deep impact on the spike protein of the virus (responsible for its infectivity), easily covering it and inducing its collapse over the envelope surface of the virus. AA simulations confirmed that both negatively and positively charged surfactants are able to extensively adsorb over the spike protein and get inserted into the virus envelope. Our results suggest that the best strategy for the design of surfactants as virucidal agents will be to focus on those strongly interacting with the spike protein.
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Affiliation(s)
- Marc Domingo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Jordi Faraudo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
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Khavani M, Mehranfar A, Mofrad MRK. On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study. J Chem Inf Model 2023; 63:1276-1292. [PMID: 36735895 PMCID: PMC9924083 DOI: 10.1021/acs.jcim.2c01378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/05/2023]
Abstract
The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.
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Affiliation(s)
- Mohammad Khavani
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and
Mechanical Engineering, University of California Berkeley,
Berkeley, California94720, United States
| | - Aliyeh Mehranfar
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and
Mechanical Engineering, University of California Berkeley,
Berkeley, California94720, United States
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and
Mechanical Engineering, University of California Berkeley,
Berkeley, California94720, United States
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Sahihi M, Faraudo J. Computer Simulation of the Interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14673-14685. [PMID: 36418228 PMCID: PMC9730903 DOI: 10.1021/acs.langmuir.2c02120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/07/2022] [Indexed: 06/16/2023]
Abstract
A prominent feature of the SARS-CoV-2 virus is the presence of a large glycoprotein spike protruding from the virus envelope. The spike determines the interaction of the virus with the environment and the host. Here, we used an all-atom molecular dynamics simulation method to investigate the interaction of up- and down-conformations of the S1 subunit of the SARS-CoV-2 spike with the (100) surface of Au, Ag, and Cu. Our results revealed that the spike protein is adsorbed onto the surface of these metals, with Cu being the metal with the highest interaction with the spike. In our simulations, we considered the spike protein in both its up-conformation Sup (one receptor binding domain exposed) and down-conformation Sdown (no exposed receptor binding domain). We found that the affinity of the metals for the up-conformation was higher than their affinity for the down-conformation. The structural changes in the spike in the up-conformation were also larger than the changes in the down-conformation. Comparing the present results for metals with those obtained in our previous MD simulations of Sup with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in Sup, larger than those obtained in our previous studies.
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Sahihi M, Faraudo J. Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface. J Chem Inf Model 2022; 62:3814-3824. [PMID: 35926227 PMCID: PMC9364975 DOI: 10.1021/acs.jcim.2c00562] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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A prominent feature of coronaviruses is the presence
of a large
glycoprotein spike (S) protruding from the viral particle. The specific
interactions of a material with S determine key aspects such as its
possible role for indirect transmission or its suitability as a virucidal
material. Here, we consider all-atom molecular dynamics simulations
of the interaction between a polymer surface (polystyrene) and S in
its up and down conformations. Polystyrene is a commonly used plastic
found in electronics, toys, and many other common objects. Also, previous
atomic force microscopy (AFM) experiments showed substantial adhesion
of S over polystyrene, stronger than in other common materials. Our
results show that the main driving forces for the adsorption of the
S protein over polystyrene were hydrophobic and π–π
interactions with S amino acids and glycans. The interaction was stronger
for the case of S in the up conformation, which exposes one highly
flexible receptor binding domain (RBD) that adjusts its conformation
to interact with the polymer surface. In this case, the interaction
has similar contributions from the RBD and glycans. In the case of
S in the down conformation, the interaction with the polystyrene surface
was weaker and it was dominated by glycans located near the RBD. We
do not find significant structural changes in the conformation of
S, a result which is in deep contrast to our previous results with
another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2
virions may adsorb strongly over plastic surfaces without significantly
affecting their infectivity.
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Affiliation(s)
- Mehdi Sahihi
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, E-08193 Barcelona, Spain
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, E-08193 Barcelona, Spain
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