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  1. Article: Critical Negatively Charged Residues Are Important for the Activity of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides.

    Lai, Alex L / Freed, Jack H

    bioRxiv : the preprint server for biology

    2021  

    Abstract: Coronaviruses are a major infectious disease threat, and include the human pathogens of zoonotic origin SARS-CoV ("SARS-1"), SARS-CoV-2 ("SARS-2") and MERS-CoV ("MERS"). Entry of coronaviruses into host cells is mediated by the viral spike (S) protein. ... ...

    Abstract Coronaviruses are a major infectious disease threat, and include the human pathogens of zoonotic origin SARS-CoV ("SARS-1"), SARS-CoV-2 ("SARS-2") and MERS-CoV ("MERS"). Entry of coronaviruses into host cells is mediated by the viral spike (S) protein. Previously, we identified that the domain immediately downstream of the S2' cleavage site is the
    Language English
    Publishing date 2021-12-06
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.11.03.467161
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  2. Article ; Online: Negatively charged residues in the membrane ordering activity of SARS-CoV-1 and -2 fusion peptides.

    Lai, Alex L / Freed, Jack H

    Biophysical journal

    2021  Volume 121, Issue 2, Page(s) 207–227

    Abstract: Entry of coronaviruses into host cells is mediated by the viral spike protein. Previously, we identified the bona fide fusion peptides (FPs) for severe acute respiratory syndrome coronavirus ("SARS-1") and severe acute respiratory syndrome coronavirus-2 ( ...

    Abstract Entry of coronaviruses into host cells is mediated by the viral spike protein. Previously, we identified the bona fide fusion peptides (FPs) for severe acute respiratory syndrome coronavirus ("SARS-1") and severe acute respiratory syndrome coronavirus-2 ("SARS-2") using electron spin resonance spectroscopy. We also found that their FPs induce membrane ordering in a Ca
    MeSH term(s) COVID-19 ; Humans ; Membrane Fusion ; Peptides ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Viral Envelope Proteins/genetics
    Chemical Substances Peptides ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins
    Language English
    Publishing date 2021-12-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2021.12.024
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  3. Article ; Online: SARS-CoV-2 Fusion Peptide has a Greater Membrane Perturbating Effect than SARS-CoV with Highly Specific Dependence on Ca

    Lai, Alex L / Freed, Jack H

    Journal of molecular biology

    2021  Volume 433, Issue 10, Page(s) 166946

    Abstract: Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry of coronaviruses into host cells is mediated by the spike (S) protein. In our ... ...

    Abstract Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry of coronaviruses into host cells is mediated by the spike (S) protein. In our previous ESR studies, the local membrane ordering effect of the fusion peptide (FP) of various viral glycoproteins including the S of SARS-1 and MERS has been consistently observed. We previously determined that the sequence immediately downstream from the S2' cleavage site is the bona fide SARS-1 FP. In this study, we used sequence alignment to identify the SARS-2 FP, and studied its membrane ordering effect. Although there are only three residue differences, SARS-2 FP induces even greater membrane ordering than SARS-1 FP, possibly due to its greater hydrophobicity. This may be a reason that SARS-2 is better able to infect host cells. In addition, the membrane binding enthalpy for SARS-2 is greater. Both the membrane ordering of SARS-2 and SARS-1 FPs are dependent on Ca
    MeSH term(s) Amino Acid Sequence ; Binding Sites ; Calcium/metabolism ; Calcium/pharmacology ; Calorimetry ; Cell Membrane/drug effects ; Cell Membrane/metabolism ; Cell Membrane/virology ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Severe acute respiratory syndrome-related coronavirus/drug effects ; Severe acute respiratory syndrome-related coronavirus/metabolism ; SARS-CoV-2/drug effects ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Thermodynamics ; Viral Fusion Proteins/chemistry ; Viral Fusion Proteins/genetics ; Viral Fusion Proteins/metabolism ; Virus Internalization/drug effects
    Chemical Substances Spike Glycoprotein, Coronavirus ; Viral Fusion Proteins ; spike glycoprotein, SARS-CoV ; spike protein, SARS-CoV-2 ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2021-03-18
    Publishing country Netherlands
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.166946
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  4. Article: Thermal Degradation of Thaumatin at Low pH and Its Prevention Using Alkyl Gallates.

    Pomon, Benjamin / Zhao, Yu / Lai, Alex L / Lin, Tiantian / Freed, Jack H / Abbaspourrad, Alireza

    Food hydrocolloids

    2023  Volume 139

    Abstract: Thaumatin, a potent sweet tasting protein extracted from the Katemfe Plant, is emerging as a natural alternative to synthetic non-nutritive sweeteners and flavor enhancer. As a food additive, its stability within the food matrix during thermal processing ...

    Abstract Thaumatin, a potent sweet tasting protein extracted from the Katemfe Plant, is emerging as a natural alternative to synthetic non-nutritive sweeteners and flavor enhancer. As a food additive, its stability within the food matrix during thermal processing is of great interest to the food industry. When heated under neutral or basic conditions, thaumatin was found to lose its sweetness due to protein aggregation caused by sulfhydryl catalyzed disulfide bond interchange. At lower pH, while thaumatin was also found to lose sweetness after heating, it does so at a slower rate and shows more resistance to sweetness loss. SDS-PAGE indicated that thaumatin fragmented into multiple smaller pieces under heating in acidic pH. Using BEMPO-3, a lipophilic spin trap, we were able to detect the presence of a free-radical within the hydrophobic region of the protein during heating. Protein carbonyl content, a byproduct of protein oxidation, also increased upon heating, providing additional evidence for protein cleavage by a radical pathway. Hexyl gallate successfully inhibited the radical generation as well as protein carbonyl formation of thaumatin during heating.
    Language English
    Publishing date 2023-02-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 742742-6
    ISSN 1873-7137 ; 0268-005X
    ISSN (online) 1873-7137
    ISSN 0268-005X
    DOI 10.1016/j.foodhyd.2023.108544
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  5. Article: Thermal degradation of thaumatin at low pH and its prevention using alkyl gallates

    Pomon, Benjamin / Zhao, Yu / Lai, Alex L. / Lin, Tiantian / Freed, Jack H. / Abbaspourrad, Alireza

    Food hydrocolloids

    2023  Volume 139, Issue -, Page(s) 108544

    Language English
    Document type Article
    ZDB-ID 742742-6
    ISSN 0268-005X
    Database Current Contents Nutrition, Environment, Agriculture

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  6. Article: SARS-CoV-2 Fusion Peptide has a Greater Membrane Perturbating Effect than SARS-CoV with Highly Specific Dependence on Ca2+

    Lai, Alex L / Freed, Jack H

    Journal of molecular biology. 2021 May 14, v. 433, no. 10

    2021  

    Abstract: Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry of coronaviruses into host cells is mediated by the spike (S) protein. In our ... ...

    Abstract Coronaviruses are a major infectious disease threat, and include the zoonotic-origin human pathogens SARS-CoV-2, SARS-CoV, and MERS-CoV (SARS-2, SARS-1, and MERS). Entry of coronaviruses into host cells is mediated by the spike (S) protein. In our previous ESR studies, the local membrane ordering effect of the fusion peptide (FP) of various viral glycoproteins including the S of SARS-1 and MERS has been consistently observed. We previously determined that the sequence immediately downstream from the S2′ cleavage site is the bona fide SARS-1 FP. In this study, we used sequence alignment to identify the SARS-2 FP, and studied its membrane ordering effect. Although there are only three residue differences, SARS-2 FP induces even greater membrane ordering than SARS-1 FP, possibly due to its greater hydrophobicity. This may be a reason that SARS-2 is better able to infect host cells. In addition, the membrane binding enthalpy for SARS-2 is greater. Both the membrane ordering of SARS-2 and SARS-1 FPs are dependent on Ca²⁺, but that of SARS-2 shows a greater response to the presence of Ca²⁺. Both FPs bind two Ca²⁺ ions as does SARS-1 FP, but the two Ca²⁺ binding sites of SARS-2 exhibit greater cooperativity. This Ca²⁺ dependence by the SARS-2 FP is very ion-specific. These results show that Ca²⁺ is an important regulator that interacts with the SARS-2 FP and thus plays a significant role in SARS-2 viral entry. This could lead to therapeutic solutions that either target the FP-calcium interaction or block the Ca²⁺ channel.
    Keywords Coronavirus infections ; Severe acute respiratory syndrome coronavirus 2 ; calcium ; enthalpy ; glycoproteins ; humans ; hydrophobicity ; molecular biology ; peptides ; sequence alignment ; therapeutics
    Language English
    Dates of publication 2021-0514
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.166946
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Critical Negatively Charged Residues Are Important for the Activity of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides

    Lai, Alex L. / Freed, Jack H

    bioRxiv

    Abstract: Coronaviruses are a major infectious disease threat, and include the human pathogens of zoonotic origin SARS-CoV ("SARS-1"), SARS-CoV-2 ("SARS-2") and MERS-CoV ("MERS"). Entry of coronaviruses into host cells is mediated by the viral spike (S) protein. ... ...

    Abstract Coronaviruses are a major infectious disease threat, and include the human pathogens of zoonotic origin SARS-CoV ("SARS-1"), SARS-CoV-2 ("SARS-2") and MERS-CoV ("MERS"). Entry of coronaviruses into host cells is mediated by the viral spike (S) protein. Previously, we identified that the domain immediately downstream of the S29 cleavage site is the bona fide FP (amino acids 798-835) for SARS-1 using ESR spectroscopy technology. We also found that the SARS-1 FP induces membrane ordering in a Ca<sup>2+</sup> dependent fashion. In this study, we want to know which residues are involved in this Ca<sup>2+</sup> binding, to build a topological model and to understand the role of the Ca<sup>2+</sup>. We performed a systematic mutation study on the negatively charged residues on the SARS-1 FP. While all six negatively charged residues contributes to the membrane ordering activity of the FP to some extent, D812 is the most important residue. We provided a topological model of how the FP binds Ca<sup>2+</sup> ions: both FP1 and FP2 bind one Ca<sup>2+</sup> ion, and there are two binding sites in FP1 and three in FP2. We also found that the corresponding residue D830 in the SARS-2 FP plays a similar critical role. ITC experiments show that the binding energies between the FP and Ca<sup>2+</sup> as well as between the FP and membranes also decreases for all mutants. The binding of Ca<sup>2+</sup>, the folding of FP and the ordering activity correlated very well across the mutants, suggesting that the function of the Ca<sup>2+</sup> is to help to folding of FP in membranes to enhance its activity. Using a novel pseudotyped virus particle (PP)-liposome methodology, we monitored the membrane ordering induced by the FPs in the whole S proteins in its trimer form in real time. We found that the SARS-1 and SARS-2 PPs also induce membrane ordering as the separate FPs do, and the mutations of the negatively charged residues also greatly reduce the membrane ordering activity. However, the difference in kinetic between the PP and FP indicates a possible role of FP trimerization. This finding could lead to therapeutic solutions that either target the FP-calcium interaction or block the Ca<sup>2+</sup> channel to combat the ongoing COVID-19 pandemic.
    Keywords covid19
    Language English
    Publishing date 2021-12-06
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.11.03.467161
    Database COVID19

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  8. Article ; Online: Thermal degradation of thaumatin at low pH and its prevention using alkyl gallates

    Pomon, Benjamin / Zhao, Yu / Lai, Alex L. / Lin, Tiantian / Freed, Jack H. / Abbaspourrad, Alireza

    Food Hydrocolloids. 2023 May, v. 139 p.108544-

    2023  

    Abstract: Thaumatin, a potent sweet tasting protein extracted from the Katemfe Plant, is emerging as a natural alternative to synthetic non-nutritive sweeteners and flavor enhancer. As a food additive, its stability within the food matrix during thermal processing ...

    Abstract Thaumatin, a potent sweet tasting protein extracted from the Katemfe Plant, is emerging as a natural alternative to synthetic non-nutritive sweeteners and flavor enhancer. As a food additive, its stability within the food matrix during thermal processing is of great interest to the food industry. When heated under neutral or basic conditions, thaumatin was found to lose its sweetness due to protein aggregation caused by sulfhydryl catalyzed disulfide bond interchange. At lower pH, while thaumatin was also found to lose sweetness after heating, it does so at a slower rate and shows more resistance to sweetness loss. SDS-PAGE indicated that thaumatin fragmented into multiple smaller pieces under heating in acidic pH. Using BEMPO-3, a lipophilic spin trap, we were able to detect the presence of a free-radical within the hydrophobic region of the protein during heating. Protein carbonyl content, a byproduct of protein oxidation, also increased upon heating, providing additional evidence for protein cleavage by a radical pathway. Hexyl gallate successfully inhibited the radical generation as well as protein carbonyl formation of thaumatin during heating.
    Keywords byproducts ; catalytic activity ; disulfide bonds ; flavor enhancers ; food additives ; food industry ; food matrix ; heat ; hydrocolloids ; hydrophobicity ; lipophilicity ; oxidation ; pH ; polyacrylamide gel electrophoresis ; sweetness ; thermal degradation ; Radical organic species ; Thaumatin ; Spin probes ; BEMPO-3 ; Antioxidants ; EPR
    Language English
    Dates of publication 2023-05
    Publishing place Elsevier Ltd
    Document type Article ; Online
    ZDB-ID 742742-6
    ISSN 1873-7137 ; 0268-005X
    ISSN (online) 1873-7137
    ISSN 0268-005X
    DOI 10.1016/j.foodhyd.2023.108544
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Characterization of Two Highly Specific Monoclonal Antibodies Targeting the Glycan Loop of the Zika Virus Envelope Protein.

    McLaury, Alex R / Haun, Brien K / To, Albert / Mayerlen, Ludwig / Medina, Liana O / Lai, Chih-Yun / Wong, Teri Ann S / Nakano, Eileen / Strange, Daniel / Aquino, Draven / Huang, Yan-Jang S / Higgs, Stephen / Vanlandingham, Dana L / Garcia, Alan / Berestecky, John M / Lehrer, Axel T

    Viral immunology

    2024  Volume 37, Issue 3, Page(s) 167–175

    Abstract: Zika virus (ZIKV) is an emerging flavivirus associated with several neurological diseases such as Guillain-Barré syndrome in adults and microcephaly in newborn children. Its distribution and mode of transmission ( ... ...

    Abstract Zika virus (ZIKV) is an emerging flavivirus associated with several neurological diseases such as Guillain-Barré syndrome in adults and microcephaly in newborn children. Its distribution and mode of transmission (via
    MeSH term(s) Animals ; Infant, Newborn ; Humans ; Zika Virus ; Zika Virus Infection ; Viral Envelope Proteins ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Flavivirus ; Aedes
    Chemical Substances Viral Envelope Proteins ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral
    Language English
    Publishing date 2024-04-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639075-4
    ISSN 1557-8976 ; 0882-8245
    ISSN (online) 1557-8976
    ISSN 0882-8245
    DOI 10.1089/vim.2023.0153
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  10. Article ; Online: Erratum for Thorsen et al., "Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering".

    Thorsen, Michael K / Lai, Alex / Lee, Michelle W / Hoogerheide, David P / Wong, Gerard C L / Freed, Jack H / Heldwein, Ekaterina E

    mBio

    2022  Volume 13, Issue 1, Page(s) e0367321

    Language English
    Publishing date 2022-01-18
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.03673-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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