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Carten JD, Khelashvili G, Bidon MK, Straus MR, Tang T, Jaimes JA, Whittaker GR, Weinstein H, Daniel S. A Mechanistic Understanding of the Modes of Ca 2+ Ion Binding to the SARS-CoV-1 Fusion Peptide and Their Role in the Dynamics of Host Membrane Penetration. ACS Infect Dis 2024; 10:398-411. [PMID: 38270149 DOI: 10.1021/acsinfecdis.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The SARS-CoV-1 spike glycoprotein contains a fusion peptide (FP) segment that mediates the fusion of the viral and host cell membranes. Calcium ions are thought to position the FP optimally for membrane insertion by interacting with negatively charged residues in this segment (E801, D802, D812, E821, D825, and D830); however, which residues bind to calcium and in what combinations supportive of membrane insertion are unknown. Using biological assays and molecular dynamics studies, we have determined the functional configurations of FP-Ca2+ binding that likely promote membrane insertion. We first individually mutated the negatively charged residues in the SARS CoV-1 FP to assay their roles in cell entry and syncytia formation, finding that charge loss in the D802A or D830A mutants greatly reduced syncytia formation and pseudoparticle transduction of VeroE6 cells. Interestingly, one mutation (D812A) led to a modest increase in cell transduction, further indicating that FP function likely depends on calcium binding at specific residues and in specific combinations. To interpret these results mechanistically and identify specific modes of FP-Ca2+ binding that modulate membrane insertion, we performed molecular dynamics simulations of the SARS-CoV-1 FP and Ca2+ions. The preferred residue pairs for Ca2+ binding we identified (E801/D802, E801/D830, and D812/E821) include the two residues found to be essential for S function in our biological studies (D802 and D830). The three preferred Ca2+ binding pairs were also predicted to promote FP membrane insertion. We also identified a Ca2+ binding pair (E821/D825) predicted to inhibit FP membrane insertion. We then carried out simulations in the presence of membranes and found that binding of Ca2+ to SARS-CoV-1 FP residue pairs E801/D802 and D812/E821 facilitates membrane insertion by enabling the peptide to adopt conformations that shield the negative charges of the FP to reduce repulsion by the membrane phospholipid headgroups. This calcium binding mode also optimally positions the hydrophobic LLF region of the FP for membrane penetration. Conversely, Ca2+ binding to the FP E801/D802 and D821/D825 pairs eliminates the negative charge screening and instead creates a repulsive negative charge that hinders membrane penetration of the LLF motif. These computational results, taken together with our biological studies, provide an improved and nuanced mechanistic understanding of the dymanics of SARS-CoV-1 calcium binding and their potential effects on host cell entry.
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Affiliation(s)
- Juliana Debrito Carten
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - George Khelashvili
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Miya K Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Marco R Straus
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Javier A Jaimes
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Gary R Whittaker
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
- Public & Ecosystem Health, Cornell University, Ithaca, New York 14853, United States
| | - Harel Weinstein
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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Van Doren SR, Scott BS, Koppisetti RK. SARS-CoV-2 fusion peptide sculpting of a membrane with insertion of charged and polar groups. Structure 2023; 31:1184-1199.e3. [PMID: 37625399 PMCID: PMC10592393 DOI: 10.1016/j.str.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike is essential for infection. How this charged and hydrophobic domain occupies and affects membranes needs clarification. Its depth in zwitterionic, bilayered micelles at pH 5 (resembling late endosomes) was measured by paramagnetic NMR relaxation enhancements used to bias molecular dynamics simulations. Asp830 inserted deeply, along with Lys825 or Lys835. Protonation of Asp830 appeared to enhance agreement of simulated and NMR-measured depths. While the fusion peptide occupied a leaflet of the DMPC bilayer, the opposite leaflet invaginated with influx of water and choline head groups in around Asp830 and bilayer-inserted polar side chains. NMR-detected hydrogen exchange found corroborating hydration of the backbone of Thr827-Phe833 inserted deeply in bicelles. Pinching of the membrane at the inserted charge and the intramembrane hydration of polar groups agree with theory. Formation of corridors of hydrated, inward-turned head groups was accompanied by flip-flop of head groups. Potential roles of the defects are discussed.
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Affiliation(s)
- Steven R Van Doren
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA.
| | - Benjamin S Scott
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Rama K Koppisetti
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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3
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Fani M, Moossavi M, Bakhshi H, Jahrodi AN, Khazdair MR, Zardast AH, Ghafari S. Targeting host calcium channels and viroporins: a promising strategy for SARS-CoV-2 therapy. Future Virol 2023:10.2217/fvl-2022-0203. [PMID: 37700758 PMCID: PMC10494978 DOI: 10.2217/fvl-2022-0203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
Despite passing the pandemic phase of the COVID-19, researchers are still investigating various drugs. Previous evidence suggests that blocking the calcium channels may be a suitable treatment option. Ca2+ is required to enhance the fusion process of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Also, some important inflammatory factors during SARS-CoV-2 infection are dependent on Ca2+ level. On the other hand, viroporins have emerged as attractive targets for antiviral therapy due to their essential role in viral replication and pathogenesis. By inhibiting the host calcium channels and viroporins, it is possible to limit the spread of infection. Therefore, calcium channel blockers (CCBs) and drugs targeting Viroporins can be considered an effective option in the fight against SARS-CoV-2.
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Affiliation(s)
- Mona Fani
- Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
- North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Maryam Moossavi
- Department of Immunology, Birjand University of Medical Sciences, Birjand, Iran
| | - Hasan Bakhshi
- Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | | | - Mohammad Reza Khazdair
- Pharmaceutical Science & Clinical Physiology, Cardiovascular Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | | | - Shokouh Ghafari
- Cellular & Molecular Research Center, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, 8815713471, Iran
- Department of Microbiology & Immunology, School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, 8815713471, Iran
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4
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Ma Y, Li P, Hu Y, Qiu T, Wang L, Lu H, Lv K, Xu M, Zhuang J, Liu X, He S, He B, Liu S, Liu L, Wang Y, Yue X, Zhai Y, Luo W, Mai H, Kuang Y, Chen S, Ye F, Zhou N, Zhao W, Chen J, Chen S, Xiong X, Shi M, Pan JA, Chen YQ. Spike substitution T813S increases Sarbecovirus fusogenicity by enhancing the usage of TMPRSS2. PLoS Pathog 2023; 19:e1011123. [PMID: 37196033 DOI: 10.1371/journal.ppat.1011123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/30/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
SARS-CoV Spike (S) protein shares considerable homology with SARS-CoV-2 S, especially in the conserved S2 subunit (S2). S protein mediates coronavirus receptor binding and membrane fusion, and the latter activity can greatly influence coronavirus infection. We observed that SARS-CoV S is less effective in inducing membrane fusion compared with SARS-CoV-2 S. We identify that S813T mutation is sufficient in S2 interfering with the cleavage of SARS-CoV-2 S by TMPRSS2, reducing spike fusogenicity and pseudoparticle entry. Conversely, the mutation of T813S in SARS-CoV S increased fusion ability and viral replication. Our data suggested that residue 813 in the S was critical for the proteolytic activation, and the change from threonine to Serine at 813 position might be an evolutionary feature adopted by SARS-2-related viruses. This finding deepened the understanding of Spike fusogenicity and could provide a new perspective for exploring Sarbecovirus' evolution.
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Affiliation(s)
- Yong Ma
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Pengbin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yunqi Hu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongjie Lu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Mengxin Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Zhuang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Suhua He
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Bing He
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shuning Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xinyu Yue
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanmei Zhai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Wanyu Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Haoting Mai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yu Kuang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shifeng Chen
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Feng Ye
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Na Zhou
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Wenjing Zhao
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mang Shi
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Sun Yat-sen University, Guanzhou, China
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Sardar A, Bera T, Kumar Samal S, Dewangan N, Kamble M, Guha S, Tarafdar PK. C-Terminal Lipidation of SARS-CoV-2 Fusion Peptide Reinstates Superior Membrane Fusion Catalytic Ability. Chemistry 2023; 29:e202203034. [PMID: 36422064 DOI: 10.1002/chem.202203034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022]
Abstract
The spike (S) protein of severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) mediates a critical stage in infection, the fusion between viral and host membranes. The protein is categorized as a class I viral fusion protein and has two distinct cleavage sites that can be activated by proteases. The activation deploys the fusion peptide (FP) for insertion into the target cell membranes. Recent studies including our experiments showed that the FP was unable to modulate the kinetics of fusion at a low peptide-to-lipid ratio akin to the spike density at the viral surface. Therefore, we modified the C terminus of FP and attached a myristoyl chain (C-myr-FP) to restrict the C terminus near to the interface, bridge both membranes, and increase the effective local concentration. The lipidated FP (C-myr-FP) of SARS-CoV-2 greatly accelerates membrane fusion at a low peptide-to-lipid ratio as compared to the FP with no lipidation. Biophysical experiments suggest that C-myr-FP adopts a helical structure, perturbs the membrane interface, and increases water penetration to catalyze fusion. Scrambled peptide (C-myr-sFP) and truncated peptide (C-myr-8FP) could not significantly catalyze the fusion, thus suggesting the important role of myristoylation and the N terminus. C-myr-FP enhances murine coronavirus infection by promoting syncytia formation in L2 cells. The C-terminal lipidation of the FP might be a useful strategy to induce artificial fusion in biomedical applications.
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Affiliation(s)
- Avijit Sardar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741246, Mohanpur, India
| | - Tapas Bera
- Department of Chemistry, Jadavpur University, 700032, Kolkata, India
| | - Santosh Kumar Samal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, 741246, Mohanpur, India
| | - Nikesh Dewangan
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741246, Mohanpur, India
| | - Mithila Kamble
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, 741246, Mohanpur, India
| | - Samit Guha
- Department of Chemistry, Jadavpur University, 700032, Kolkata, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741246, Mohanpur, India
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Birtles D, Oh AE, Lee J. Exploring the
pH
dependence of the
SARS‐CoV
‐2 complete fusion domain and the role of its unique structural features. Protein Sci 2022. [PMCID: PMC9538437 DOI: 10.1002/pro.4390] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
SARS‐CoV‐2 may enter target cells through the process of membrane fusion at either the plasma (~pH 7.4–7.0) or endosomal (~pH 6.5–5.0) membrane in order to deliver its genetic information. The fusion domain (FD) of the spike glycoprotein is responsible for initiating fusion and is thus integral to the viral life cycle. The FD of SARS‐CoV‐2 is unique in that it consists of two structurally distinctive regions referred to as the fusion peptide (FP) and the fusion loop (FL); yet the molecular mechanisms behind how this FD perturbs the membrane to initiate fusion remains unclear. In this study via solution NMR, we witnessed only a slight conformational change in the FD between pH 7.4 and pH 5.0, resulting in a minor elongation of helix 1. However, we found that the FD's ability to mediate membrane fusion has a large and significant pH dependence, with fusion events being more readily induced at low pH. Interestingly, a biphasic relationship between the environmental pH and fusogenicity was discovered, suggesting a preference for the FD to initiate fusion at the late endosomal membrane. Furthermore, the conserved disulfide bond and hydrophobic motif “LLF” were found to be critical for the function of the complete FD, with minimal activity witnessed when either was perturbed. In conclusion, these findings indicate that the SARS‐CoV‐2 FD preferably initiates fusion at a pH similar to the late endosome through a mechanism that heavily relies on the internal disulfide bond of the FL and hydrophobic LLF motif within the FP.
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Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
| | - Anna E. Oh
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
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