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  1. Article ; Online: SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx.

    Kim, Sang Hoon / Kearns, Fiona L / Rosenfeld, Mia A / Votapka, Lane / Casalino, Lorenzo / Papanikolas, Micah / Amaro, Rommie E / Freeman, Ronit

    Cell reports. Physical science

    2023  Volume 4, Issue 4, Page(s) 101346

    Abstract: Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods for detection and mechanisms of action. Here, we investigate the effect of an evolving spike positive charge in SARS-CoV-2 variants and subsequent interactions ...

    Abstract Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods for detection and mechanisms of action. Here, we investigate the effect of an evolving spike positive charge in SARS-CoV-2 variants and subsequent interactions with heparan sulfate and the angiotensin converting enzyme 2 (ACE2) in the glycocalyx. We show that the positively charged Omicron variant evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discover that while the Omicron spike-ACE2 affinity is comparable to that of the Delta variant, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-heparan sulfate-ACE2 with a large proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. This discovery enables us to engineer a second-generation lateral-flow test strip that harnesses both heparin and ACE2 to reliably detect all variants of concern, including Omicron.
    Language English
    Publishing date 2023-04-07
    Publishing country United States
    Document type Journal Article
    ISSN 2666-3864
    ISSN (online) 2666-3864
    DOI 10.1016/j.xcrp.2023.101346
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: An integrated view of p53 dynamics, function, and reactivation.

    Demir, Özlem / Barros, Emilia P / Offutt, Tavina L / Rosenfeld, Mia / Amaro, Rommie E

    Current opinion in structural biology

    2021  Volume 67, Page(s) 187–194

    Abstract: The tumor suppressor p53 plays a vital role in responding to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Expression level alterations and mutational frequency implicates p53 in ... ...

    Abstract The tumor suppressor p53 plays a vital role in responding to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Expression level alterations and mutational frequency implicates p53 in most human cancers. In this review, we show how both computational and experimental methods have been used to provide an integrated view of p53 dynamics, function, and reactivation potential. We argue that p53 serves as an exceptional case study for developing methods in modeling intrinsically disordered proteins. We describe how these methods can be leveraged to improve p53 reactivation molecule design and other novel therapeutic modalities, such as PROteolysis TARgeting Chimeras (PROTACs).
    MeSH term(s) Apoptosis ; Computational Biology ; DNA Damage ; Humans ; Neoplasms/genetics ; Proteolysis ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism
    Chemical Substances Tumor Suppressor Protein p53
    Language English
    Publishing date 2021-01-02
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2020.11.005
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  3. Article ; Online: Spike-heparan sulfate interactions in SARS-CoV-2 infection.

    Kearns, Fiona L / Sandoval, Daniel R / Casalino, Lorenzo / Clausen, Thomas M / Rosenfeld, Mia A / Spliid, Charlotte B / Amaro, Rommie E / Esko, Jeffrey D

    Current opinion in structural biology

    2022  Volume 76, Page(s) 102439

    Abstract: Recent biochemical, biophysical, and genetic studies have shown that heparan sulfate, a major component of the cellular glycocalyx, participates in infection of SARS-CoV-2 by facilitating the so-called open conformation of the spike protein, which is ... ...

    Abstract Recent biochemical, biophysical, and genetic studies have shown that heparan sulfate, a major component of the cellular glycocalyx, participates in infection of SARS-CoV-2 by facilitating the so-called open conformation of the spike protein, which is required for binding to ACE2. This review highlights the involvement of heparan sulfate in the SARS-CoV-2 infection cycle and argues that there is a high degree of coordination between host cell heparan sulfate and asparagine-linked glycans on the spike in enabling ACE2 binding and subsequent infection. The discovery that spike protein binding and infection depends on both viral and host glycans provides insights into the evolution, spread and potential therapies for SARS-CoV-2 and its variants.
    MeSH term(s) Angiotensin-Converting Enzyme 2 ; Asparagine/metabolism ; Binding Sites ; COVID-19 ; Heparitin Sulfate ; Humans ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Asparagine (7006-34-0) ; Heparitin Sulfate (9050-30-0) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2022-07-06
    Publishing country England
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2022.102439
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  4. Article: GlycoGrip

    Kim, Sang Hoon / Kearns, Fiona L / Rosenfeld, Mia A / Casalino, Lorenzo / Papanikolas, Micah J / Simmerling, Carlos / Amaro, Rommie E / Freeman, Ronit

    ACS central science

    2021  Volume 8, Issue 1, Page(s) 22–42

    Abstract: Inspired by the role of cell-surface glycoproteins as coreceptors for pathogens, we report the development ... ...

    Abstract Inspired by the role of cell-surface glycoproteins as coreceptors for pathogens, we report the development of
    Language English
    Publishing date 2021-12-15
    Publishing country United States
    Document type Journal Article
    ISSN 2374-7943
    ISSN 2374-7943
    DOI 10.1021/acscentsci.1c01080
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  5. Article: Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE.

    Chongsaritsinsuk, Joann / Steigmeyer, Alexandra D / Mahoney, Keira E / Rosenfeld, Mia A / Lucas, Taryn M / Ince, Deniz / Kearns, Fiona L / Battison, Alexandria S / Hollenhorst, Marie A / Shon, D Judy / Tiemeyer, Katherine H / Attah, Victor / Kwon, Catherine / Bertozzi, Carolyn R / Ferracane, Michael J / Amaro, Rommie E / Malaker, Stacy A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key ... ...

    Abstract Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in terms of glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamics (MD) simulations of TIM-3 and -4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.01.526488
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike

    Oliveira, A. Sofia F. / Kearns, Fiona L. / Rosenfeld, Mia A. / Casalino, Lorenzo / Berger, Imre / Schaffitzel, Christiane / Davidson, Andrew D. / Amaro, Rommie E. / Mulholland, Adrian J.

    bioRxiv

    Abstract: The trimeric spike protein plays an essential role in the SARS-CoV-2 virus lifecycle, facilitating virus entry through binding to the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediating viral and host membrane fusion. The SARS-CoV-2 ... ...

    Abstract The trimeric spike protein plays an essential role in the SARS-CoV-2 virus lifecycle, facilitating virus entry through binding to the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediating viral and host membrane fusion. The SARS-CoV-2 spike contains an allosteric fatty acid (FA) binding site at the interface between two neighbouring receptor-binding domains. This site, also found in some other coronaviruses, binds free fatty acids such as linoleic and oleic acid, and other small molecules. Understanding allostery and how this site modulates the behaviour of different regions in this protein could potentiate the development of promising alternative strategies for new coronavirus therapies. Here, we apply dynamical nonequilibrium molecular dynamics (D-NEMD) simulations to investigate allosteric effects and identify the communication pathways in the fully glycosylated spike in the original SARS-CoV-2 ancestral variant. The results reveal the allosteric networks that connect the FA site to important functional regions of the protein, including some more than 40 Angstroms away. These regions include the receptor binding motif, an antigenic supersite in the N-terminal domain, the furin cleavage site, the regions surrounding the fusion peptide and a second allosteric site known to bind heme and biliverdin. The networks identified here highlight the complexity of the allosteric modulation in this protein and reveal a striking and unexpected connection between different allosteric sites. Notably, 65% of amino acid substitutions, deletions and insertions in the Alpha, Beta, Delta, Gamma and Omicron variants map onto or close to the identified allosteric pathways.
    Keywords covid19
    Language English
    Publishing date 2023-11-08
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.11.06.565757
    Database COVID19

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  7. Article ; Online: Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE.

    Chongsaritsinsuk, Joann / Steigmeyer, Alexandra D / Mahoney, Keira E / Rosenfeld, Mia A / Lucas, Taryn M / Smith, Courtney M / Li, Alice / Ince, Deniz / Kearns, Fiona L / Battison, Alexandria S / Hollenhorst, Marie A / Judy Shon, D / Tiemeyer, Katherine H / Attah, Victor / Kwon, Catherine / Bertozzi, Carolyn R / Ferracane, Michael J / Lemmon, Mark A / Amaro, Rommie E /
    Malaker, Stacy A

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6169

    Abstract: Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key ... ...

    Abstract Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key regulators in cellular immunity. However, their dense O-glycosylation remains enigmatic, primarily due to the challenges associated with studying mucin domains. Here, we demonstrate that the mucinase SmE has a unique ability to cleave at residues bearing very complex glycans. SmE enables improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we perform molecular dynamics (MD) simulations of TIM-3 and -4 to understand how glycosylation affects structural features of these proteins. Finally, we use these models to investigate the functional relevance of glycosylation for TIM-3 function and ligand binding. Overall, we present a powerful workflow to better understand the detailed molecular structures and functions of the mucinome.
    MeSH term(s) Hepatitis A Virus Cellular Receptor 2 ; Mucins/metabolism ; Polysaccharide-Lyases ; Polysaccharides/chemistry
    Chemical Substances hyaluronate lyase (EC 4.2.2.1) ; Hepatitis A Virus Cellular Receptor 2 ; Mucins ; Polysaccharide-Lyases (EC 4.2.2.-) ; Polysaccharides
    Language English
    Publishing date 2023-10-04
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-41756-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens

    Nuqui, Xandra / Casalino, Lorenzo / Zhou, Ling / Shehata, Mohamed / Wang, Albert / Tse, Alexandra L. / Ojha, Anupam / Kearns, Fiona L. / Rosenfeld, Mia A. / Miller, Emily Happy / Acreman, Cory M. / Ahn, Surl-Hee / Chandran, Kartik / McLellan, Jason S. / Amaro, Rommie E

    bioRxiv

    Abstract: The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 ... ...

    Abstract The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 subunit. S2, in contrast, is the most evolutionarily conserved region of the spike and can elicit broadly neutralizing and protective antibodies. Yet, the usage of S2 as an alternative vaccine strategy is hampered by its general instability. Here, we use a simulation-driven approach to design highly stable S2-only antigens retaining a closed prefusion conformation. Weighted ensemble simulations provide mechanistic characterization of the S2 trimer opening, informing the design of tryptophan substitutions that impart kinetic and thermodynamic stabilization. Alchemical free energy perturbation calculations and a corroborating set of experiments confirm that V991W and T998W in the central helices of S2 stabilize the trimer in the closed prefusion conformation, producing an antigen with increased protein expression, superior thermostability, and preserved immunogenicity against sarbecoviruses.
    Keywords covid19
    Language English
    Publishing date 2023-10-25
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.10.24.563841
    Database COVID19

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  9. Article: NIDCD/VA hearing aid clinical trial and follow-up: background.

    Bratt, Gene W / Rosenfeld, Mia A L / Williams, David W

    Journal of the American Academy of Audiology

    2007  Volume 18, Issue 4, Page(s) 274–281

    Abstract: This report provides background regarding the Long Term Follow-Up of Patients in the NIDCD/VA Hearing Aid Clinical Trial study and serves as an introduction to the detailed reports that follow in this issue of Journal of the American Academy of Audiology. ...

    Abstract This report provides background regarding the Long Term Follow-Up of Patients in the NIDCD/VA Hearing Aid Clinical Trial study and serves as an introduction to the detailed reports that follow in this issue of Journal of the American Academy of Audiology. The authors investigated five- to seven-year benefit/satisfaction in participants from the original NIDCDNA Hearing Aid Clinical Trial. The new study was designed to investigate current use of the original study hearing aids, to compare changes in selected audiological measures, and to assess possible predictors of long-term hearing aid use. The outcome measures included estimates of speech intelligibility in quiet and noise, self-reported patterns of hearing aid usage, self-reported estimates of activity limitations and quality-of-life issues, estimates of hearing aid satisfaction, and self-reported hearing aid benefit. Overall, the short-term benefits of hearing aid use observed during the original trial were noted to persist in the long term.
    MeSH term(s) Clinical Trials as Topic ; Follow-Up Studies ; Hearing Aids ; Hearing Loss, Sensorineural/rehabilitation ; Humans ; Research Design ; United States
    Language English
    Publishing date 2007-05-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1132599-9
    ISSN 2157-3107 ; 1050-0545
    ISSN (online) 2157-3107
    ISSN 1050-0545
    DOI 10.3766/jaaa.18.4.2
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    Zs.A 3529: Show issues Location:
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  10. Article ; Online: Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection.

    Oh, Chang-Ki / Nakamura, Tomohiro / Beutler, Nathan / Zhang, Xu / Piña-Crespo, Juan / Talantova, Maria / Ghatak, Swagata / Trudler, Dorit / Carnevale, Lauren N / McKercher, Scott R / Bakowski, Malina A / Diedrich, Jolene K / Roberts, Amanda J / Woods, Ashley K / Chi, Victor / Gupta, Anil K / Rosenfeld, Mia A / Kearns, Fiona L / Casalino, Lorenzo /
    Shaabani, Namir / Liu, Hejun / Wilson, Ian A / Amaro, Rommie E / Burton, Dennis R / Yates, John R / Becker, Cyrus / Rogers, Thomas F / Chatterjee, Arnab K / Lipton, Stuart A

    Nature chemical biology

    2022  Volume 19, Issue 3, Page(s) 275–283

    Abstract: Prevention of infection and propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a high priority in the Coronavirus Disease 2019 (COVID-19) pandemic. Here we describe S-nitrosylation of multiple proteins involved in SARS-CoV-2 ... ...

    Abstract Prevention of infection and propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a high priority in the Coronavirus Disease 2019 (COVID-19) pandemic. Here we describe S-nitrosylation of multiple proteins involved in SARS-CoV-2 infection, including angiotensin-converting enzyme 2 (ACE2), the receptor for viral entry. This reaction prevents binding of ACE2 to the SARS-CoV-2 spike protein, thereby inhibiting viral entry, infectivity and cytotoxicity. Aminoadamantane compounds also inhibit coronavirus ion channels formed by envelope (E) protein. Accordingly, we developed dual-mechanism aminoadamantane nitrate compounds that inhibit viral entry and, thus, the spread of infection by S-nitrosylating ACE2 via targeted delivery of the drug after E protein channel blockade. These non-toxic compounds are active in vitro and in vivo in the Syrian hamster COVID-19 model and, thus, provide a novel avenue to pursue therapy.
    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2/metabolism ; Angiotensin-Converting Enzyme 2/metabolism ; Protein Binding ; Peptidyl-Dipeptidase A/metabolism
    Chemical Substances spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Peptidyl-Dipeptidase A (EC 3.4.15.1)
    Language English
    Publishing date 2022-09-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-022-01149-6
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