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Badiee SA, Kumar VG, Moradi M. Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602399. [PMID: 39026831 PMCID: PMC11257422 DOI: 10.1101/2024.07.07.602399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding ability and evasion of the host immune response. In this study, we conducted extensive equilibrium microsecond-level all-atom molecular dynamics (MD) simulations of the HA protein to explore the influence of low pH on its conformational dynamics. Specifically, we investigated the impact of protonation on conserved histidine residues (His106 2 ) located in the hinge region of HA2. Our analysis encompassed comparisons between non-protonated (NP), partially protonated (1P, 2P), and fully-protonated (3P) conditions. Our findings reveal substantial pH-dependent conformational alterations in the HA protein, affecting its receptor-binding capability and immune evasion potential. Notably, the non-protonated form exhibits greater stability compared to protonated states. Conformational shifts in the central helices of HA2 involve outward movement, counterclockwise rotation of protonated helices, and fusion peptide release in protonated systems. Disruption of hydrogen bonds between the fusion peptide and central helices of HA2 drives this release. Moreover, HA1 separation is more likely in the fully-protonated system (3P) compared to non-protonated systems (NP), underscoring the influence of protonation. These insights shed light on influenza virus infection mechanisms and may inform the development of novel antiviral drugs targeting HA protein and pH-responsive drug delivery systems for influenza.
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2
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Karmacharya M, Kumar S, Cho YK. Tuning the Extracellular Vesicles Membrane through Fusion for Biomedical Applications. J Funct Biomater 2023; 14:jfb14020117. [PMID: 36826916 PMCID: PMC9960107 DOI: 10.3390/jfb14020117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Membrane fusion is one of the key phenomena in the living cell for maintaining the basic function of life. Extracellular vesicles (EVs) have the ability to transfer information between cells through plasma membrane fusion, making them a promising tool in diagnostics and therapeutics. This study explores the potential applications of natural membrane vesicles, EVs, and their fusion with liposomes, EVs, and cells and introduces methodologies for enhancing the fusion process. EVs have a high loading capacity, bio-compatibility, and stability, making them ideal for producing effective drugs and diagnostics. The unique properties of fused EVs and the crucial design and development procedures that are necessary to realize their potential as drug carriers and diagnostic tools are also examined. The promise of EVs in various stages of disease management highlights their potential role in future healthcare.
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Affiliation(s)
- Mamata Karmacharya
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sumit Kumar
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Correspondence: (S.K.); (Y.-K.C.)
| | - Yoon-Kyoung Cho
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Correspondence: (S.K.); (Y.-K.C.)
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3
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Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS CENTRAL SCIENCE 2022; 8:1646-1663. [PMID: 36589893 PMCID: PMC9801513 DOI: 10.1021/acscentsci.2c00981] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 05/28/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from convalescent human donor, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
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Affiliation(s)
- Lorenzo Casalino
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Julia Lederhofer
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Yaroslav Tsybovsky
- Electron
Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
Sponsored by the National Cancer Institute, Frederick, Maryland21702, United States
| | - Ian A. Wilson
- Department
of Integrative Structural and Computational Biology and the Skaggs
Institute for Chemical Biology, The Scripps
Research Institute, La Jolla, California92037, United States
| | - Masaru Kanekiyo
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
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Soprano E, Polo E, Pelaz B, del Pino P. Biomimetic cell-derived nanocarriers in cancer research. J Nanobiotechnology 2022; 20:538. [PMID: 36544135 PMCID: PMC9771790 DOI: 10.1186/s12951-022-01748-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Nanoparticles have now long demonstrated capabilities that make them attractive to use in biology and medicine. Some of them, such as lipid nanoparticles (SARS-CoV-2 vaccines) or metallic nanoparticles (contrast agents) are already approved for their use in the clinic. However, considering the constantly growing body of different formulations and the huge research around nanomaterials the number of candidates reaching clinical trials or being commercialized is minimal. The reasons behind being related to the "synthetic" and "foreign" character of their surface. Typically, nanomaterials aiming to develop a function or deliver a cargo locally, fail by showing strong off-target accumulation and generation of adverse responses, which is connected to their strong recognition by immune phagocytes primarily. Therefore, rendering in negligible numbers of nanoparticles developing their intended function. While a wide range of coatings has been applied to avoid certain interactions with the surrounding milieu, the issues remained. Taking advantage of the natural cell membranes, in an approach that resembles a cell transfer, the use of cell-derived surfaces has risen as an alternative to artificial coatings or encapsulation methods. Biomimetic technologies are based on the use of isolated natural components to provide autologous properties to the nanoparticle or cargo being encapsulated, thus, improving their therapeutic behavior. The main goal is to replicate the (bio)-physical properties and functionalities of the source cell and tissue, not only providing a stealthy character to the core but also taking advantage of homotypic properties, that could prove relevant for targeted strategies. Such biomimetic formulations have the potential to overcome the main issues of approaches to provide specific features and identities synthetically. In this review, we provide insight into the challenges of nano-biointerfaces for drug delivery; and the main applications of biomimetic materials derived from specific cell types, focusing on the unique strengths of the fabrication of novel nanotherapeutics in cancer therapy.
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Affiliation(s)
- Enrica Soprano
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Ester Polo
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Beatriz Pelaz
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Pablo del Pino
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
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5
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Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.02.502576. [PMID: 35982676 PMCID: PMC9387122 DOI: 10.1101/2022.08.02.502576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from human convalescent plasma, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, United States
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States,Corresponding author.
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Xu H, Cai M, Gao J, Shi Y, Chen J, Wu Q, Zhang J, Jiang J, Wang H. Membrane protein density determining membrane fusion revealed by dynamic fluorescence imaging. Talanta 2021; 226:122091. [PMID: 33676648 DOI: 10.1016/j.talanta.2021.122091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 01/04/2023]
Abstract
Membrane fusion is fundamental to biological activity of cells, so disclosingits relevant mechanism is very important for understanding various cell functions. Although artificial model systems have been developed to uncover the mechanism of membrane fusion, key factors determining the mode of membrane fusion remain unclear. Based on the construction of different types of liposome vesicles, we used a dynamic fluorescence imaging method to investigate the effect of membrane protein distribution density on membrane fusion. Time-resolved imaging revealed that protein-free pure phospholipid vesicles themselves occurred full membrane fusion. Moreover, we prepared proteoliposomes with increasing protein-to-lipid ratio to better reflect the characteristic of membrane structure in vivo. Our data showed that pure phospholipid vesicles no longer fused with the proteoliposomes that in a higher protein proportion, indicating dense membrane proteins may hinder membrane fusion. A further comparative analysis of the interactions of pure phospholipid vesicles with the cell membrane / giant plasma membrane vesicles (GPMVs) / protein-free giant unilamellar vesicles (GUVs) confirmed the inhibitory effect of dense membrane proteins on membrane fusion. Our work demonstrates the membrane protein density influences the mode of membrane fusion and lays a foundation for constructing quasi-native membrane fusion models in vitro.
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Affiliation(s)
- Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China; Graduate University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China
| | - Yan Shi
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China
| | - Junling Chen
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, PR China
| | - Qiang Wu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, PR China
| | - Jinrui Zhang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China
| | - Junguang Jiang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China; University of Science and Technology of China, Hefei, Anhui, 230026, PR China; Laboratory for Marine Biology and Biotechnology, Qing Dao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, PR China.
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7
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Golani G, Leikina E, Melikov K, Whitlock JM, Gamage DG, Luoma-Overstreet G, Millay DP, Kozlov MM, Chernomordik LV. Myomerger promotes fusion pore by elastic coupling between proximal membrane leaflets and hemifusion diaphragm. Nat Commun 2021; 12:495. [PMID: 33479215 PMCID: PMC7820291 DOI: 10.1038/s41467-020-20804-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/08/2020] [Indexed: 01/09/2023] Open
Abstract
Myomerger is a muscle-specific membrane protein involved in formation of multinucleated muscle cells by mediating the transition from the early hemifusion stage to complete fusion. Here, we considered the physical mechanism of the Myomerger action based on the hypothesis that Myomerger shifts the spontaneous curvature of the outer membrane leaflets to more positive values. We predicted, theoretically, that Myomerger generates the outer leaflet elastic stresses, which propagate into the hemifusion diaphragm and accelerate the fusion pore formation. We showed that Myomerger ectodomain indeed generates positive spontaneous curvature of lipid monolayers. We substantiated the mechanism by experiments on myoblast fusion and influenza hemagglutinin-mediated cell fusion. In both processes, the effects of Myomerger ectodomain were strikingly similar to those of lysophosphatidylcholine known to generate a positive spontaneous curvature of lipid monolayers. The control of post-hemifusion stages by shifting the spontaneous curvature of proximal membrane monolayers may be utilized in diverse fusion processes.
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Affiliation(s)
- Gonen Golani
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Evgenia Leikina
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kamran Melikov
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jarred M Whitlock
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dilani G Gamage
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Gracia Luoma-Overstreet
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Douglas P Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Leonid V Chernomordik
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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8
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Zhang LJ, Xia L, Xie HY, Zhang ZL, Pang DW. Quantum Dot Based Biotracking and Biodetection. Anal Chem 2018; 91:532-547. [DOI: 10.1021/acs.analchem.8b04721] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Li-Juan Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
| | - Li Xia
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
| | - Hai-Yan Xie
- School of Life Science, Beijing Institute of Technology, Beijing 100081, P.R. China
| | - Zhi-Ling Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
| | - Dai-Wen Pang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
- College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, P.R. China
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