1
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Božič A, Podgornik R. Increased preference for lysine over arginine in spike proteins of SARS-CoV-2 BA.2.86 variant and its daughter lineages. PLoS One 2025; 20:e0320891. [PMID: 40193474 PMCID: PMC11975073 DOI: 10.1371/journal.pone.0320891] [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: 11/09/2024] [Accepted: 02/25/2025] [Indexed: 04/09/2025] Open
Abstract
The COVID-19 pandemic offered an unprecedented glimpse into the evolution of its causative virus, SARS-CoV-2. It has been estimated that since its outbreak in late 2019, the virus has explored all possible alternatives in terms of missense mutations for all sites of its polypeptide chain. Spike protein of the virus exhibits the largest sequence variation in particular, with many individual mutations impacting target recognition, cellular entry, and endosomal escape of the virus. Moreover, recent studies unveiled a significant increase in the total charge on the spike protein during the evolution of the virus in the initial period of the pandemic. While this trend has recently come to a halt, we perform a sequence-based analysis of the spike protein of 2665 SARS-CoV-2 variants which shows that mutations in ionizable amino acids continue to occur with the newly emerging variants, with notable differences between lineages from different clades. What is more, we show that within mutations of amino acids which can acquire positive charge, the spike protein of SARS-CoV-2 exhibits a prominent preference for lysine residues over arginine residues. This lysine-to-arginine ratio increased at several points during spike protein evolution, most recently with BA.2.86 and its sublineages, including the recently dominant JN.1, KP.3, and XEC variants. The increased ratio is a consequence of mutations in different structural regions of the spike protein and is now among the highest among viral species in the Coronaviridae family. The impact of high lysine-to-arginine ratio in the spike proteins of BA.2.86 and its daughter lineages on viral fitness remains unclear; we discuss several potential mechanisms that could play a role and that can serve as a starting point for further studies.
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Affiliation(s)
- Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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2
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Domingo M, V Guzman H, Kanduč M, Faraudo J. Electrostatic Interaction between SARS-CoV-2 and Charged Surfaces: Spike Protein Evolution Changed the Game. J Chem Inf Model 2025; 65:240-251. [PMID: 39722544 DOI: 10.1021/acs.jcim.4c01724] [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: 12/28/2024]
Abstract
Previous works show the key role of electrostatics in the SARS-CoV-2 virus in aspects such as virus-cell interactions or virus inactivation by ionic surfactants. Electrostatic interactions depend strongly on the variant since the charge of the Spike protein (responsible for virus-environment interactions) evolved across the variants from the highly negative Wild Type (WT) to the highly positive Omicron variant. The distribution of the charge also evolved from diffuse to highly localized. These facts suggest that SARS-CoV-2 should interact strongly with charged surfaces in a way that changed during the virus evolution. This question is studied here by computing the electrostatic interaction between WT, Delta and Omicron Spike proteins with charged surfaces using a new method (based on Debye-Hückel theory) that provides efficiently general results as a function of the surface charge density σ. We found that the interaction of the WT and Delta variant spikes with charged surfaces is dominated by repulsive image forces proportional to σ2 originating at the protein/water interface. On the contrary, the Omicron variant shows a distinct behavior, being strongly attracted to negatively charged surfaces and repelled from positively charged ones. Therefore, the SARS-CoV-2 virus has evolved from being repelled by charged surfaces to being efficiently adsorbing to negatively charged ones.
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Affiliation(s)
- Marc Domingo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Spain
| | - Horacio V Guzman
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Spain
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Matej Kanduč
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana 1000, Slovenia
| | - Jordi Faraudo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Spain
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3
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Kumar A, Gautam S, Bhatta N, Tafreshi HV, Pourdeyhimi B. Effects of droplet deposition on aerosol capture efficiency of bipolarly charged fibers. SOFT MATTER 2025; 21:198-208. [PMID: 39639707 DOI: 10.1039/d4sm01105h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
Aerosol filters composed of electrostatically charged bipolar fibers are referred to as electret filters. A novel computational model is developed in this work to study the impact of droplet deposition on aerosol capture efficiency of electret fibers. The electret fibers were assumed to have a dipole orientation that was either parallel or perpendicular to the airflow direction. The simulations were conducted using the ANSYS CFD code after it was enhanced with a series of in-house subroutines. Our simulations revealed that droplet deposition on electret fibers decreases their ability to capture airborne particles. More specifically, the simulations were devised to isolate droplet's physical and electrical properties (e.g., surface tension, electrical conductivity…) and quantify their impact on fiber capture efficiency. It was found, in particular, that droplet's electrical conductivity and permittivity have the most adverse impact on the performance of an electret fiber. This is perhaps because higher droplet conductivity results in severe fiber charge neutralization, and higher droplet permittivity leads to a stronger fiber charge shielding. In contrast, fiber wettability was found to have a negligible impact on fiber efficiency. The work presented in this paper offers valuable insights into the complex nature of electret filters used in different industrial and environmental applications.
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Affiliation(s)
- Amit Kumar
- Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, 27606, NC, USA.
| | - Sashank Gautam
- Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, 27606, NC, USA.
| | - Nishant Bhatta
- Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, 27606, NC, USA.
| | - Hooman V Tafreshi
- Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, 27606, NC, USA.
- The Nonwovens Institute, NC State University, Raleigh, 27606, NC, USA
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4
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Golushko IY, Roshal DS, Konevtsova OV, Rochal SB, Podgornik R. Electrostatic interactions and structural transformations in viral shells. NANOSCALE 2024; 16:20182-20193. [PMID: 39380336 DOI: 10.1039/d4nr02612h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
Structural transformations occurring in proteinaceous viral shells (capsids) can be induced by changing the pH of bathing solution, thus modifying the dissociation equilibrium of ionizable amino acids in proteins. To analyze the effects of electrostatic interactions on viral capsids, we construct a model of 2D isotropic elastic shells with embedded point charges located in the centers of mass of individual proteins. We find that modification of the electrostatic interactions between proteins affects not only the size and shape of capsids, but in addition induces substantial deformations of hexamers in capsid structures. Using bacteriophage P22 and Nudarelia capensis omega virus (NωV) as examples, we analyze the capsid faceting and propose an explanation as to why the hexamers in spherical procapsid are skewed, while they acquire a regular shape in the faceted state. Also, we examine the electrostatic and elastic effects that can explain different shapes of coronavirus shells decorated with spikes, which are often localized in compact areas over the shell surface. The proposed mechanism of local curvature generation is supported by the remarkable correspondence between the shell shape and the distribution of spikes in model and observed shells.
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Affiliation(s)
- Ivan Yu Golushko
- Faculty of Physics, Southern Federal University, Rostov-on-Don, Russia.
| | - Daria S Roshal
- Faculty of Physics, Southern Federal University, Rostov-on-Don, Russia.
| | - Olga V Konevtsova
- Faculty of Physics, Southern Federal University, Rostov-on-Don, Russia.
| | - Sergei B Rochal
- Faculty of Physics, Southern Federal University, Rostov-on-Don, Russia.
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Department of Theoretical Physics, Jozef Stefan Institute, Ljubljana, Slovenia.
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5
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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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6
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Božič A, Podgornik R. Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages. BIOINFORMATICS ADVANCES 2024; 4:vbae053. [PMID: 38645718 PMCID: PMC11031363 DOI: 10.1093/bioadv/vbae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/13/2024] [Accepted: 04/04/2024] [Indexed: 04/23/2024]
Abstract
Motivation Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution. Results We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2200 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment. Availability and implementation The data underlying the article are available in the Supplementary material.
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Affiliation(s)
- Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana 1000, Slovenia
| | - Rudolf Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
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7
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Hristova SH, Zhivkov AM. Three-Dimensional Structural Stability and Local Electrostatic Potential at Point Mutations in Spike Protein of SARS-CoV-2 Coronavirus. Int J Mol Sci 2024; 25:2174. [PMID: 38396850 PMCID: PMC10889838 DOI: 10.3390/ijms25042174] [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: 01/17/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The contagiousness of SARS-CoV-2 β-coronavirus is determined by the virus-receptor electrostatic association of its positively charged spike (S) protein with the negatively charged angiotensin converting enzyme-2 (ACE2 receptor) of the epithelial cells. If some mutations occur, the electrostatic potential on the surface of the receptor-binding domain (RBD) could be altered, and the S-ACE2 association could become stronger or weaker. The aim of the current research is to investigate whether point mutations can noticeably alter the electrostatic potential on the RBD and the 3D stability of the S1-subunit of the S-protein. For this purpose, 15 mutants with different hydrophilicity and electric charge (positive, negative, or uncharged) of the substituted and substituting amino acid residues, located on the RBD at the S1-ACE2 interface, are selected, and the 3D structure of the S1-subunit is reconstructed on the base of the crystallographic structure of the S-protein of the wild-type strain and the amino acid sequence of the unfolded polypeptide chain of the mutants. Then, the Gibbs free energy of folding, isoelectric point, and pH-dependent surface electrostatic potential of the S1-subunit are computed using programs for protein electrostatics. The results show alterations in the local electrostatic potential in the vicinity of the mutant amino acid residue, which can influence the S-ACE2 association. This approach allows prediction of the relative infectivity, transmissibility, and contagiousness (at equal social immune status) of new SARS-CoV-2 mutants by reconstruction of the 3D structure of the S1-subunit and calculation of the surface electrostatic potential.
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Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Street 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Scientific Research Center, “St. Kliment Ohridski” Sofia University, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
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8
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Ruixuan H, Majee A, Dobnikar J, Podgornik R. Electrostatic interactions between charge regulated spherical macroions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:115. [PMID: 38019363 DOI: 10.1140/epje/s10189-023-00373-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023]
Abstract
We study the interaction between two charge regulating spherical macroions with dielectric interior and dissociable surface groups immersed in a monovalent electrolyte solution. The charge dissociation is modelled via the Frumkin-Fowler-Guggenheim isotherm, which allows for multiple adsorption equilibrium states. The interactions are derived from the solutions of the mean-field Poisson-Boltzmann type theory with charge regulation boundary conditions. For a range of conditions we find symmetry breaking transitions from symmetric to asymmetric charge distribution exhibiting annealed charge patchiness, which results in like-charge attraction even in a univalent electrolyte-thus fundamentally modifying the nature of electrostatic interactions in charge-stabilized colloidal suspensions.
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Affiliation(s)
- Hu Ruixuan
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Arghya Majee
- Max Planck Institute for the Physics of Complex Systems, 01187, Dresden, Germany
| | - Jure Dobnikar
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- Songshan Lake Materials Laboratory, Guangdong, 523808, Dongguan, China
| | - Rudolf Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China.
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000, Ljubljana, Slovenia.
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9
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Zhang S, Wang N, Zhang Q, Guan R, Qu Z, Sun L, Li J. The Rise of Electroactive Materials in Face Masks for Preventing Virus Infections. ACS APPLIED MATERIALS & INTERFACES 2023; 15:48839-48854. [PMID: 37815875 DOI: 10.1021/acsami.3c10465] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Air-transmitted pathogens may cause severe epidemics, posing considerable threats to public health and safety. Wearing a face mask is one of the most effective ways to prevent respiratory virus infection transmission. Especially since the new coronavirus pandemic, electroactive materials have received much attention in antiviral face masks due to their highly efficient antiviral capabilities, flexible structural design, excellent sustainability, and outstanding safety. This review first introduces the mechanism for preventing viral infection or the inactivation of viruses by electroactive materials. Then, the applications of electrostatic-, conductive-, triboelectric-, and microbattery-based materials in face masks are described in detail. Finally, the problems of various electroactive antiviral materials are summarized, and the prospects for their future development directions are discussed. In conclusion, electroactive materials have attracted great attention for antiviral face masks, and this review will provide a reference for materials scientists and engineers in antiviral materials and interfaces.
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Affiliation(s)
- Shaohua Zhang
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Na Wang
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
- Industrial Research Institute of Nonwovens and Technical Textiles, Shandong Center for Engineered Nonwovens, Qingdao 266071, People's Republic of China
| | - Qian Zhang
- Department of Respirology, Qingdao Women and Children's Hospital, Qingdao 266034, People's Republic of China
| | - Renzheng Guan
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Zhenghai Qu
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Lirong Sun
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Jiwei Li
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
- Industrial Research Institute of Nonwovens and Technical Textiles, Shandong Center for Engineered Nonwovens, Qingdao 266071, People's Republic of China
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Potisk T, Remškar M, Pirker L, Filipič G, Mihelič I, Ješelnik M, Čoko U, Ravnik M. Single-Layer and Double-Layer Filtration Materials Based on Polyvinylidene Fluoride-Co-hexafluoropropylene Nanofibers Coated on Melamine Microfibers. ACS APPLIED NANO MATERIALS 2023; 6:15807-15819. [PMID: 37706065 PMCID: PMC10496027 DOI: 10.1021/acsanm.3c02592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/08/2023] [Indexed: 09/15/2023]
Abstract
In this work, we demonstrate selected optimization changes in the simple design of filtration masks to increase particle removal efficiency (PRE) and filter quality factor by combining experiments and numerical modeling. In particular, we focus on single-layer filters fabricated from uniform thickness fibers and double-layer filters consisting of a layer of highly permeable thick fibers as a support and a thin layer of filtering electrospun nanofibers. For single-layer filters, we demonstrate performance improvement in terms of the quality factor by optimizing the geometry of the composition. We show significantly better PRE performance for filters composed of micrometer-sized fibers covered by a thin layer of electrospun nanofibers. This work is motivated and carried out in collaboration with a targeted industrial development of selected melamine-based filter nano- and micromaterials.
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Affiliation(s)
- Tilen Potisk
- Laboratory
for Molecular Modeling, National Institute
of Chemistry, SI-1001 Ljubljana, Slovenia
- Faculty
of Mathematics and Physics, University of
Ljubljana, SI-1001 Ljubljana, Slovenia
| | - Maja Remškar
- Jožef
Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Luka Pirker
- Jožef
Stefan Institute, SI-1000 Ljubljana, Slovenia
- J. Heyrovsky
Institute of Physical Chemistry, Czech Academy
of Sciences, 182 23 Prague 8, Czech Republic
| | | | | | | | - Urban Čoko
- Laboratory
for Molecular Modeling, National Institute
of Chemistry, SI-1001 Ljubljana, Slovenia
- Faculty
of Mathematics and Physics, University of
Ljubljana, SI-1001 Ljubljana, Slovenia
| | - Miha Ravnik
- Faculty
of Mathematics and Physics, University of
Ljubljana, SI-1001 Ljubljana, Slovenia
- Jožef
Stefan Institute, SI-1000 Ljubljana, Slovenia
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11
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Hristova SH, Zhivkov AM. Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor. Viruses 2023; 15:1752. [PMID: 37632094 PMCID: PMC10460073 DOI: 10.3390/v15081752] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The association of the S-protein of the SARS-CoV-2 beta coronavirus to ACE2 receptors of the human epithelial cells determines its contagiousness and pathogenicity. We computed the pH-dependent electric potential on the surface of the interacting globular proteins and pH-dependent Gibbs free energy at the association of the wild-type strain and the omicron variant. The calculated isoelectric points of the ACE2 receptor (pI 5.4) and the S-protein in trimeric form (pI 7.3, wild type), (pI 7.8, omicron variant), experimentally verified by isoelectric focusing, show that at pH 6-7, the S1-ACE2 association is conditioned by electrostatic attraction of the oppositely charged receptor and viral protein. The comparison of the local electrostatic potentials of the omicron variant and the wild-type strain shows that the point mutations alter the electrostatic potential in a relatively small area on the surface of the receptor-binding domain (RBD) of the S1 subunit. The appearance of seven charge-changing point mutations in RBD (equivalent to three additional positive charges) leads to a stronger S1-ACE2 association at pH 5.5 (typical for the respiratory tract) and a weaker one at pH 7.4 (characteristic of the blood plasma); this reveals the reason for the higher contagiousness but lower pathogenicity of the omicron variant in comparison to the wild-type strain.
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Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Str. 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 11, 1113 Sofia, Bulgaria
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12
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Khunpetch P, Majee A, Ruixuan H, Podgornik R. Curvature effects in interfacial acidity of amphiphilic vesicles. Phys Rev E 2023; 108:024402. [PMID: 37723726 DOI: 10.1103/physreve.108.024402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/11/2023] [Indexed: 09/20/2023]
Abstract
We analyze the changes in the vicinal acidity (pH) at a spherical amphiphilic membrane. The membrane is assumed to contain solvent accessible, embedded, dissociable, charge-regulated moieties. Basing our approach on the linear Debye-Hückel approximation, as well as on the nonlinear Poisson-Boltzmann theory, together with the general Frumkin-Fowler-Guggenheim adsorption isotherm model of the charge-regulation process, we analyze and review the dependence of the local pH on the position, as well as bulk electrolyte concentration, bulk pH, and curvature of the amphiphilic single membrane vesicle. With appropriately chosen adsorption parameters of the charge-regulation model, we find a good agreement with the available experimental data.
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Affiliation(s)
- Petch Khunpetch
- Department of Physics, Faculty of Science, Ramkhamhaeng University, Bang Kapi, 10240 Bangkok, Thailand
- School of Physical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Arghya Majee
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Hu Ruixuan
- School of Physical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Rudolf Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190 Beijing, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, 325000 Zhejiang, China
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13
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Božič A, Podgornik R. Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants. Virus Evol 2023; 9:vead040. [PMID: 37583936 PMCID: PMC10424713 DOI: 10.1093/ve/vead040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 08/17/2023] Open
Abstract
The spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for target recognition, cellular entry, and endosomal escape of the virus. At the same time, it is the part of the virus that exhibits the greatest sequence variation across the many variants which have emerged during its evolution. Recent studies have indicated that with progressive lineage emergence, the positive charge on the spike protein has been increasing, with certain positively charged amino acids (AAs) improving the binding of the spike protein to cell receptors. We have performed a detailed analysis of dissociable AAs of more than 1400 different SARS-CoV-2 lineages, which confirms these observations while suggesting that this progression has reached a plateau with Omicron and its subvariants and that the positive charge is not increasing further. Analysis of the nucleocapsid protein shows no similar increase in positive charge with novel variants, which further indicates that positive charge of the spike protein is being evolutionarily selected for. Furthermore, comparison with the spike proteins of known coronaviruses shows that already the wild-type SARS-CoV-2 spike protein carries an unusually large amount of positively charged AAs when compared to most other betacoronaviruses. Our study sheds light on the evolutionary changes in the number of dissociable AAs on the spike protein of SARS-CoV-2, complementing existing studies and providing a stepping stone towards a better understanding of the relationship between the spike protein charge and viral infectivity and transmissibility.
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Affiliation(s)
- Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, Ljubljana SI-1000, Slovenia
| | - Rudolf Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, No. 3 Nanyitiao, Zhongguancun, Haidian District, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, No. 8 3rd South Street, Zhongguancun, Haidian District, Beijing 100190, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, No.1 Jinlian Road, Wenzhou, Zhejiang 325001, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana SI-1000, Slovenia
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14
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Filipič G, Pirker L, Krajnc AP, Ješelnik M, Remškar M. Enhanced Filtration Efficiency of Natural Materials with the Addition of Electrospun Poly(vinylidene fluoride-co-hexafluoropropylene) Fibres. MATERIALS (BASEL, SWITZERLAND) 2023; 16:2314. [PMID: 36984195 PMCID: PMC10054789 DOI: 10.3390/ma16062314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Pollutants and infectious diseases can spread through air with airborne droplets and aerosols. A respiratory mask can decrease the amount of pollutants we inhale and it can protect us from airborne diseases. With the onset of the COVID-19 pandemic, masks became an everyday item used by a lot of people around the world. As most of them are for a single use, the amount of non-recyclable waste increased dramatically. The plastic from which the masks are made pollutes the environment with various chemicals and microplastic. Here, we investigated the time- and size-dependent filtration efficiency (FE) of aerosols in the range of 25.9 to 685.4 nm of five different natural materials whose FE was enhanced using electrospun poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF) fibres. A scanning electron microscope (SEM) was used to determine the morphology and structure of the natural materials as well as the thickness of the PVDF fibres, while the phase of the electrospun fibres was determined by Raman spectroscopy. A thin layer of the electrospun PVDF fibres with the same grammage was sandwiched between two sheets of natural materials, and their FE increased up to 80%. By varying the grammature of the electrospun polymer, we tuned the FE of cotton from 82.6 to 99.9%. Thus, through the optimization of the grammage of the electrospun polymer, the amount of plastic used in the process can be minimized, while achieving sufficiently high FE.
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Affiliation(s)
- Gregor Filipič
- Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
| | - Luka Pirker
- Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
- Department of Electrochemical Materials, J. Heyrovsky Institute of Physical Chemistry, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Anja Pogačnik Krajnc
- Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska Ulica 19, 1000 Ljubljana, Slovenia
| | - Marjan Ješelnik
- smartMelamine d.o.o., Tomšičeva Cesta 9, 1330 Kočevje, Slovenia
| | - Maja Remškar
- Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
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15
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Yang Y, Wang H, Wang C, Chen Y, Dang B, Liu M, Zhang X, Li Y, Sun Q. Dual-Network Structured Nanofibrous Membranes with Superelevated Interception Probability for Extrafine Particles. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 36907989 DOI: 10.1021/acsami.3c01385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Airborne particulate matter (PM) pollution has caused a public health threat, including nanoscale particles, especially with emerging infectious diseases and indoor and vehicular environmental pollution. However, most existing indoor air filtration units are expensive, energy-intensive, and bulky, and there is an unavoidable trade-off between low-efficiency PM0.3/pathogen interception, PM removal, and air resistance. Herein, we designed and synthesized a two-dimensional continuous cellulose-sheath/net with a unique dual-network corrugated architecture to manufacture high-efficiency air filters and even N95 particulate face mask. Combined with its sheath/net structured pores (size 100-200 nm) consisting of a cellulose framework (1-100 nm diameter), the cellulose sheath/net filter offers high-efficiency air filtration (>99.5338%, Extrafine particles; >99.9999%, PM2.5), low-pressure drops, and a robustness quality factor of >0.14 Pa-1, utilizing their ultralight weight of 30 mg/m2 and physical adhesion and sieving behaviors. Simultaneously, masks prepared with cellulose-sheath/net filters are more likely to capture and block smaller particles than the N95 standard. The synthesis of such materials with their nanoscale features and designed macrostructures may suggest new design criteria for a novel generation of high-efficiency air filter media for different applications such as personal protection products and industrial dust removal.
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Affiliation(s)
- Yushan Yang
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
| | - Hanwei Wang
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
| | - Chao Wang
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
| | - Yipeng Chen
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
| | - Baokang Dang
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
| | - Ming Liu
- Guangxi Fenglin Wood Industry Group Co., Ltd., Nanning 530000, P. R. China
| | - Xiaochun Zhang
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
| | - Yingying Li
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
| | - Qingfeng Sun
- College of Chemistry and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, P. R. China
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16
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Choi J, Poudel K, Nam KS, Piri A, Rivera-Piza A, Ku SK, Hwang J, Kim JO, Byeon JH. Aero-manufacture of nanobulges for an in-place anticoronaviral on air filters. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130458. [PMID: 36444810 DOI: 10.1016/j.jhazmat.2022.130458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
The interest in removing contagious viruses from indoor air using ventilation and filtration systems is increasing rapidly because people spend most of the day indoors. The development of an effective platform to regenerate the antiviral function of air filters during use and safe abrogation of used filters containing infectious viruses is a challenging task, because an on-demand safe-by-design manufacture system is essential for in-place antiviral coatings, but it has been rarely investigated. With these considerations, an electrically operable dispenser was prepared for decorating continuous ultrafine Fe-Zn, Fe-Ag, or Fe-Cu particles (<5 nm) onto SiO2 nanobeads (ca. 130 nm) to form nanobulges (i.e., nanoroughness for engaging coronavirus spikes) in the aerosol state for 3 min direct deposition on the air filter surfaces. The resulting nanobulges were exposed to human coronaviruses (HCoV; surrogates of SARS-CoV-2) to assess antiviral function. The results were compared with similar-sized individual Zn, Ag, and Cu particles. The nanobulges exhibited comparable antiviral activity to Zn, Ag, and Cu particles while retaining biosafety in both in vitro and in vivo models because of the significantly smaller metallic fractions. This suggests that the bimetallic bulge structures generate reactive oxygen species and Fenton-mediated hydroxyl radicals for inactivating HCoV.
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Affiliation(s)
- Jisoo Choi
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Kishwor Poudel
- College of Pharmacy, Yeungnam University, Gyeongsan 38511, Republic of Korea; Wellman Center for Photomedicine, Department of Dermatology, Meassachusetts General Hospital, Harvard Medical School, MA 02114, USA
| | - Kang Sik Nam
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Amin Piri
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Adriana Rivera-Piza
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sae Kwang Ku
- College of Korean Medicine, Daegu Haany University, Gyeongsan 38610 Republic of Korea
| | - Jungho Hwang
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jong Oh Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38511, Republic of Korea.
| | - Jeong Hoon Byeon
- School of Mechanical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea.
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17
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Mantri D, Wymenga L, van Turnhout J, van Zeijl H, Zhang G. Manipulation, Sampling and Inactivation of the SARS-CoV-2 Virus Using Nonuniform Electric Fields on Micro-Fabricated Platforms: A Review. MICROMACHINES 2023; 14:345. [PMID: 36838044 PMCID: PMC9967285 DOI: 10.3390/mi14020345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/21/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Micro-devices that use electric fields to trap, analyze and inactivate micro-organisms vary in concept, design and application. The application of electric fields to manipulate and inactivate bacteria and single-celled organisms has been described extensively in the literature. By contrast, the effect of such fields on viruses is not well understood. This review explores the possibility of using existing methods for manipulating and inactivating larger viruses and bacteria, for smaller viruses, such as SARS-CoV-2. It also provides an overview of the theoretical background. The findings may be used to implement new ideas and frame experimental parameters that optimize the manipulation, sampling and inactivation of SARS-CoV-2 electrically.
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Affiliation(s)
- Devashish Mantri
- Department Biomedical Engineering, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Luutzen Wymenga
- Department Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Jan van Turnhout
- Department Material Science Engineering, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Henk van Zeijl
- Department Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Guoqi Zhang
- Department Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
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18
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Konevtsova OV, Golushko IY, Podgornik R, Rochal SB. Hidden symmetry of the flavivirus protein shell and pH-controlled reconstruction of the viral surface. Biomater Sci 2022; 11:225-234. [PMID: 36426630 DOI: 10.1039/d2bm01562e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Using recent Zika virus structural data we reveal a hidden symmetry of protein order in immature and mature flavivirus shells, violating the Caspar-Klug paradigmatic model of capsid structures. We show that proteins of the outer immature shell layer exhibit trihexagonal tiling, while proteins from inner and outer layers conjointly form a double-shelled close-packed structure, based on a common triangular spherical lattice. Within the proposed structural model, we furthermore rationalize the structural organization of misassembled non-infectious subviral particles that have no inner capsid. We consider a pH-controlled structural reconstruction of the outer shell from the trimeric to the dimeric state, and demonstrate that this transition, occurring during the virus maturation, can be induced by changes in protein charges at lower pH, leading to a decrease in the electrostatic interaction free energy. This transition could also be assisted by electrostatic attraction of shell proteins to the interposed lipid membrane substrate separating the shells.
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Affiliation(s)
- Olga V Konevtsova
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| | - Ivan Yu Golushko
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. .,Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Sergei B Rochal
- Physics Faculty, Southern Federal University, Rostov-on-Don, Russia.
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19
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Barroso da Silva FL, Giron CC, Laaksonen A. Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule. J Phys Chem B 2022; 126:6835-6852. [PMID: 36066414 DOI: 10.1021/acs.jpcb.2c04225] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This "RBD charge rule" should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
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Affiliation(s)
- Fernando L Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Av. Getúlio Guaritá, 38025-440 Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, 210009, P. R. China.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden.,Department of Chemical and Geological Sciences, Campus Monserrato, University of Cagliari, SS 554 bivio per Sestu, 09042 Monserrato, Italy
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20
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Adherence of SARS-CoV-2 Delta variant to a surgical mask and N95 respirators. Future Sci OA 2022; 8:FSO808. [PMID: 36248067 PMCID: PMC9540236 DOI: 10.2144/fsoa-2022-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
The use of facial protection has been adopted globally due to the COVID-19 pandemic. We dissected four respirators and one surgical mask into layers to determine whether or not the virus adheres to them. These individual layers were contaminated with the SARS-CoV-2 Delta variant, and its release by vortexing was performed. Samples were used to infect Vero cells, and a plaque assay was used to evaluate the adherence of the virus to the layers. Results showed that a cumulative log reduction of the layers reduced the load of the virus by at least sixfold. Our study confirms the effectiveness of facial protection in reducing the transmission and/or infection of SARS-CoV-2. The use of facial protection, including masks and respirators, has been adopted globally due to the COVID-19 pandemic. These products have been demonstrated to be effective in reducing the transmission of the virus. This study tested whether the virus can adhere to the different layers of respirators and a surgical mask. These individual layers were contaminated with the COVID-19 Delta variant, and we determined the degree of release after applying a mechanical force. Samples were used to infect cells, and the adherence of the virus to the layers was assessed. Results showed that a significant reduction in the number of viruses was observed. Our study confirms the effectiveness of facial protection in reducing the transmission and or infection of SARS-CoV-2.
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21
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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22
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Wu S, Dong T, Li Y, Sun M, Qi Y, Liu J, Kuss MA, Chen S, Duan B. State-of-the-art review of advanced electrospun nanofiber yarn-based textiles for biomedical applications. APPLIED MATERIALS TODAY 2022; 27:101473. [PMID: 35434263 PMCID: PMC8994858 DOI: 10.1016/j.apmt.2022.101473] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 05/02/2023]
Abstract
The pandemic of the coronavirus disease 2019 (COVID-19) has made biotextiles, including face masks and protective clothing, quite familiar in our daily lives. Biotextiles are one broad category of textile products that are beyond our imagination. Currently, biotextiles have been routinely utilized in various biomedical fields, like daily protection, wound healing, tissue regeneration, drug delivery, and sensing, to improve the health and medical conditions of individuals. However, these biotextiles are commonly manufactured with fibers with diameters on the micrometer scale (> 10 μm). Recently, nanofibrous materials have aroused extensive attention in the fields of fiber science and textile engineering because the fibers with nanoscale diameters exhibited obviously superior performances, such as size and surface/interface effects as well as optical, electrical, mechanical, and biological properties, compared to microfibers. A combination of innovative electrospinning techniques and traditional textile-forming strategies opens a new window for the generation of nanofibrous biotextiles to renew and update traditional microfibrous biotextiles. In the last two decades, the conventional electrospinning device has been widely modified to generate nanofiber yarns (NYs) with the fiber diameters less than 1000 nm. The electrospun NYs can be further employed as the primary processing unit for manufacturing a new generation of nano-textiles using various textile-forming strategies. In this review, starting from the basic information of conventional electrospinning techniques, we summarize the innovative electrospinning strategies for NY fabrication and critically discuss their advantages and limitations. This review further covers the progress in the construction of electrospun NY-based nanotextiles and their recent applications in biomedical fields, mainly including surgical sutures, various scaffolds and implants for tissue engineering, smart wearable bioelectronics, and their current and potential applications in the COVID-19 pandemic. At the end, this review highlights and identifies the future needs and opportunities of electrospun NYs and NY-based nanotextiles for clinical use.
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Key Words
- CNT, carbon nanotube
- COVID-19, coronavirus disease 2019
- ECM, extracellular matrix
- Electrospinning
- FDA, food and drug administration
- GF, gauge factor
- GO, graphene oxide
- HAVIC, human aortic valve interstitial cell
- HAp, hydroxyapatite
- MSC, mesenchymal stem cell
- MSC-SC, MSC derived Schwann cell-like cell
- MWCNT, multiwalled carbon nanotube
- MY, microfiber yarn
- MeGel, methacrylated gelatin
- NGC, nerve guidance conduit
- NHMR, neutral hollow metal rod
- NMD, neutral metal disc
- NY, nanofiber yarn
- Nanoyarns
- PA6, polyamide 6
- PA66, polyamide 66
- PAN, polyacrylonitrile
- PANi, polyaniline
- PCL, polycaprolactone
- PEO, polyethylene oxide
- PGA, polyglycolide
- PHBV, poly(3-hydroxybutyrate-co-3-hydroxyvalerate)
- PLCL, poly(L-lactide-co-ε-caprolactone)
- PLGA, poly(lactic-co-glycolic acid)
- PLLA, poly(L-lactic acid)
- PMIA, poly(m-phenylene isophthalamide)
- PPDO, polydioxanone
- PPy, polypyrrole
- PSA, poly(sulfone amide)
- PU, polyurethane
- PVA, poly(vinyl alcohol)
- PVAc, poly(vinyl acetate)
- PVDF, poly(vinylidene difluoride)
- PVDF-HFP, poly(vinylidene floride-co-hexafluoropropylene)
- PVDF-TrFE, poly(vinylidene fluoride trifluoroethylene)
- PVP, poly(vinyl pyrrolidone)
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SC, Schwann cell
- SF, silk fibroin
- SWCNT, single-walled carbon nanotube
- TGF-β1, transforming growth factor-β1
- Textile-forming technique
- Tissue scaffolds
- VEGF, vascular endothelial growth factor
- Wearable bioelectronics
- bFGF, basic fibroblast growth factor
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Affiliation(s)
- Shaohua Wu
- College of Textiles & Clothing, Qingdao University, Qingdao, China
| | - Ting Dong
- College of Textiles & Clothing, Qingdao University, Qingdao, China
| | - Yiran Li
- College of Textiles & Clothing, Qingdao University, Qingdao, China
| | - Mingchao Sun
- College of Textiles & Clothing, Qingdao University, Qingdao, China
| | - Ye Qi
- College of Textiles & Clothing, Qingdao University, Qingdao, China
| | - Jiao Liu
- College of Textiles & Clothing, Qingdao University, Qingdao, China
| | - Mitchell A Kuss
- Mary & Dick Holland Regenerative Medicine Program and Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Surgery, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shaojuan Chen
- College of Textiles & Clothing, Qingdao University, Qingdao, China
| | - Bin Duan
- Mary & Dick Holland Regenerative Medicine Program and Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Surgery, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
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23
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Impact of Wearing on Filtration Performance of Electrostatic Filter Face Masks. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095032. [PMID: 35564426 PMCID: PMC9100139 DOI: 10.3390/ijerph19095032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023]
Abstract
Certified disposable respirators afford important protection from hazardous aerosols but lose performance as they are worn. This study examines the effect of wear time on filtration efficiency. Disposable respirators were worn by CSIRO staff over a period of 4 weeks in early 2020. Participants wore the respirator masks for given times up to eight hours whilst working in laboratory/office environments. At that time COVID-19 precautions required staff to wear surgical (or other) masks and increase use of hand sanitizer from dispenser stations. Results obtained from a test group of ten individuals without health preconditions show an increasing number of masks failing with wear time, while the remainder continue to perform nearly unaffected for up to 8 h. Some masks were found to retain filtration performance better than others, possibly due to the type of challenge they were subjected to by the wearer. However, the rate and extent of decay are expected to differ between environments since there are many contributing factors and properties of the aerosol challenge cannot be controlled in a live trial. Penetration and variability increased during wear; the longer the wear time, the more deleterious to particle removal, particularly after approximately 2 h of wear. This behavior is captured in a descriptive statistical model based on results from a trial with this test group. The effectiveness of the masks in preventing the penetration of KCl particles was determined before and after wearing, with the analysis focusing on the most penetrating particles in a size range of 0.3–0.5 µm diameter where respirator masks are most vulnerable. The basic elements of the study, including the approach to filter testing and sample sanitization, are broadly applicable. Conclusions also have applicability to typical commercially available single-use respirator masks manufactured from melt blown polypropylene as they are reliant on the same physical principles for particle capture and electrostatic enhancement was comparable for the particle size range used for detection.
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24
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Chen D, Tang L, Wang Y, Tan Y, Fu Y, Cai W, Yu Z, Sun S, Zheng J, Cui J, Wang G, Liu Y, Zhou H. Speaking-Induced Charge-Laden Face Masks with Durable Protectiveness and Wearing Breathability. ACS APPLIED MATERIALS & INTERFACES 2022; 14:17774-17782. [PMID: 35362941 PMCID: PMC8982734 DOI: 10.1021/acsami.2c01077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/22/2022] [Indexed: 05/17/2023]
Abstract
Face masks, which serve as personal protection equipment, have become ubiquitous for combating the ongoing COVID-19. However, conventional electrostatic-based mask filters are disposable and short-term effective with high breathing resistance, causing respiratory ailments and massive consumption (129 billion monthly), intensifying global environmental pollution. In an effort to address these challenges, the introduction of a piezoelectric polymer was adopted to realize the charge-laden melt-blown via the melt-blowing method. The charge-laden melt-blown could be applied to manufacture face masks and to generate charges triggered by mechanical and acoustic energy originated from daily speaking. Through an efficient and scalable industrial melt-blown process, our charge-laden mask is capable of overcoming the inevitable electrostatic attenuation, even in a high-humidity atmosphere by long-wearing (prolonging from 4 to 72 h) and three-cycle common decontamination methods. Combined with outstanding protective properties (PM2.5 filtration efficiency >99.9%), breathability (differential pressure <17 Pa/cm2), and mechanical strength, the resultant charge-laden mask could enable the decreased replacement of masks, thereby lowering to 94.4% of output masks worldwide (∼122 billion monthly) without substituting the existing structure or assembling process.
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Affiliation(s)
- Dan Chen
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Lianwei Tang
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Yunming Wang
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Yongyao Tan
- Department of Ophthalmology, Tongji Hospital, Tongji
Medical College, Huazhong University of Science and Technology,
Wuhan 430074, China
| | - Yue Fu
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Weihao Cai
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Zhaohan Yu
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Shuang Sun
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Jiaqi Zheng
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Jingqiang Cui
- Henan Key Laboratory of Medical Polymer
Materials Technology and Application, TuoRen Medical Device Research & Development
Institute Co., Ltd., Health Technology Industry Park Changyuan County,
Changyuan, Henan 453000, China
| | - Guosheng Wang
- Henan Key Laboratory of Medical Polymer
Materials Technology and Application, TuoRen Medical Device Research & Development
Institute Co., Ltd., Health Technology Industry Park Changyuan County,
Changyuan, Henan 453000, China
| | - Yang Liu
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
| | - Huamin Zhou
- State Key Laboratory of Materials Processing and Die
& Mould Technology, School of Materials Science and Engineering, Huazhong
University of Science and Technology, Wuhan 430074,
China
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25
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Kang M, Jang NY, Kim YJ, Ro HJ, Kim D, Kim Y, Kim HT, Kwon HM, Ahn JH, Choi BO, Cho NH, Kim SW. Virus blocking textile for SARS-CoV-2 using human body triboelectric energy harvesting. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:100813. [PMID: 35309284 PMCID: PMC8920588 DOI: 10.1016/j.xcrp.2022.100813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 01/10/2022] [Accepted: 02/23/2022] [Indexed: 05/13/2023]
Abstract
Effective mitigation technology to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required before achieving population immunity through vaccines. Here we demonstrate a virus-blocking textile (VBT) that repulses SARS-CoV-2 by applying repulsive Coulomb force to respiratory particles, powered by human body triboelectric energy harvesting. We show that SARS-CoV-2 has negative charges, and a human body generates high output current of which peak-to-peak value reaches 259.6 μA at most, based on triboelectric effect. Thereby, the human body can sustainably power a VBT to have negative electrical potential, and the VBT highly blocks SARS-CoV-2 by repulsion. In an acrylic chamber study, we found that the VBT blocks SARS-CoV-2 by 99.95%, and SARS-CoV-2 in the VBT is 13-fold reduced. Our work provides technology that may prevent the spread of virus based on repulsive Coulomb force and triboelectric energy harvesting.
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Affiliation(s)
- Minki Kang
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Na-Yoon Jang
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Young-Jun Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Hyo-Jin Ro
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Dabin Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Yuri Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hyoung Taek Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Hye Mi Kwon
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jin-Hyun Ahn
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Stem Cell and Regenerative Medicine Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
- Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University (SKKU), Seoul 06351, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Institute of Endemic Disease, Seoul National University Medical Research Center and Bundang Hospital, Seoul 13620, Republic of Korea
| | - Sang-Woo Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University (SKKU), Seoul 06351, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
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26
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Khunpetch P, Majee A, Podgornik R. Curvature effects in charge-regulated lipid bilayers. SOFT MATTER 2022; 18:2597-2610. [PMID: 35294512 DOI: 10.1039/d1sm01665b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We formulate a theory of electrostatic interactions in lipid bilayer membranes where both monolayer leaflets contain dissociable moieties that are subject to charge regulation. We specifically investigate the coupling between membrane curvature and charge regulation of a lipid bilayer vesicle using both the linear Debye-Hückel (DH) and the non-linear Poisson-Boltzmann (PB) theory. We find that charge regulation of an otherwise symmetric bilayer membrane can induce charge symmetry breaking, non-linear flexoelectricity and anomalous curvature dependence of free energy. The pH effects investigated go beyond the paradigm of electrostatic renormalization of the mechano-elastic properties of membranes.
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Affiliation(s)
- Petch Khunpetch
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Arghya Majee
- Max Planck Institute for Intelligent Systems, Stuttgart, Germany
- IV. Institute for Theoretical Physics, University of Stuttgart, Stuttgart, Germany.
| | - Rudolf Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
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27
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Bakhshandeh A, Frydel D, Levin Y. Reactive Monte Carlo simulations for charge regulation of colloidal particles. J Chem Phys 2022; 156:014108. [PMID: 34998334 DOI: 10.1063/5.0077956] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We use a reactive Monte Carlo simulation method and the primitive model of electrolyte to study acid-base equilibrium that controls charge regulation in colloidal systems. The simulations are performed in a semi-grand canonical ensemble in which colloidal suspension is in contact with a reservoir of salt and strong acid. The interior of colloidal particles is modeled as a low dielectric medium, different from the surrounding water. The effective colloidal charge is calculated for different numbers of surface acidic groups, pH, salt concentrations, and types of electrolyte. In the case of potassium chloride, the titration curves are compared with the experimental measurements obtained using potentiometric titration. A good agreement is found between simulations and experiments. In the case of lithium chloride, the specific ionic adsorption is taken into account through the partial dehydration of lithium ion.
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Affiliation(s)
- Amin Bakhshandeh
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Derek Frydel
- Department of Chemistry, Universidad Técnica Federico Santa María, Campus San Joaquin, 7820275 Santiago, Chile
| | - Yan Levin
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970 Porto Alegre, RS, Brazil
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28
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Pawłowski PH. Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. Infect Drug Resist 2021; 14:5099-5105. [PMID: 34880635 PMCID: PMC8647725 DOI: 10.2147/idr.s342068] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022] Open
Abstract
The change in the formal charge of 34 SARS-CoV-2 lineages from September 2020 to June 2021 was analyzed according to the monthly evidence of the European agency. The reported point mutations and small insertions are electrically neutral (17), positive (12), or negative (3). They had been found in the spike glycoprotein S, in the RBD and S1/S2 regions, crucial for initiation of viral infection. The most often observed were positive mutations, especially D614G and E484K, located in the region of S1/S2 junction, and in the receptor-binding domain (RBD), respectively. They are related to G and A switching. Positive mutations are stretching equally in both areas, but in the RBD region, they are more dispersed. In the set of analyzed virus variants, the increasing tendency in the number of positively charged residues in spike protein was observed. Furthermore, the well-documented WHO classes show an increase in the COVID-19 percentage case fatality with the positive increase in the spike crucial region’s total charge. The data mining, applying classifier algorithm based on the artificial neuronal network, confirms that the value and the distribution of additional positive charge in S may be important factors enabling virus impact to immunity. This may be promoted by the stronger long-range electrostatic attraction of the virus particle to the host cell, preceding the infection. The estimation of the potential energy for the RBD approaching the angiotensin-converting enzyme (ACE2) was presented.
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Affiliation(s)
- Piotr H Pawłowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
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29
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Dung DN, Phan AD, Nguyen TT, Lam VD. Effects of surface charge and environmental factors on the electrostatic interaction of fiber with virus-like particle: A case of coronavirus. AIP ADVANCES 2021; 11:105008. [PMID: 34646585 PMCID: PMC8501974 DOI: 10.1063/5.0065147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/25/2021] [Indexed: 05/09/2023]
Abstract
We propose a theoretical model to elucidate intermolecular electrostatic interactions between a virus and a substrate. Our model treats the virus as a homogeneous particle having surface charge and the polymer fiber of the respirator as a charged plane. Electric potentials surrounding the virus and fiber are influenced by the surface charge distribution of the virus. We use Poisson-Boltzmann equations to calculate electric potentials. Then, Derjaguin's approximation and a linear superposition of the potential function are extended to determine the electrostatic force. In this work, we apply this model for coronavirus or SARS-CoV-2 case and numerical results quantitatively agree with prior simulation. We find that the influence of fiber's potential on the surface charge of the virus is important and is considered in interaction calculations to obtain better accuracy. The electrostatic interaction significantly decays with increasing separation distance, and this curve becomes steeper when adding more salt. Although the interaction force increases with heating, one can observe the repulsive-attractive transition when the environment is acidic.
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Affiliation(s)
- D. N. Dung
- Faculty of Materials Science and Engineering, Phenikaa University, Yen Nghia, Ha Dong, Ha Noi 12116, Vietnam
| | - Anh D. Phan
- Author to whom correspondence should be addressed:
| | - Toan T. Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems, and Department of Theoretical Physics, Faculty of Physics, VNU University of Science, Vietnam National University—Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 10000, Vietnam
| | - Vu D. Lam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
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30
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Wang N, Ferhan AR, Yoon BK, Jackman JA, Cho NJ, Majima T. Chemical design principles of next-generation antiviral surface coatings. Chem Soc Rev 2021; 50:9741-9765. [PMID: 34259262 DOI: 10.1039/d1cs00317h] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has accelerated efforts to develop high-performance antiviral surface coatings while highlighting the need to build a strong mechanistic understanding of the chemical design principles that underpin antiviral surface coatings. Herein, we critically summarize the latest efforts to develop antiviral surface coatings that exhibit virus-inactivating functions through disrupting lipid envelopes or protein capsids. Particular attention is focused on how cutting-edge advances in material science are being applied to engineer antiviral surface coatings with tailored molecular-level properties to inhibit membrane-enveloped and non-enveloped viruses. Key topics covered include surfaces functionalized with organic and inorganic compounds and nanoparticles to inhibit viruses, and self-cleaning surfaces that incorporate photocatalysts and triplet photosensitizers. Application examples to stop COVID-19 are also introduced and demonstrate how the integration of chemical design principles and advanced material fabrication strategies are leading to next-generation surface coatings that can help thwart viral pandemics and other infectious disease threats.
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Affiliation(s)
- Nan Wang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
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