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  1. Article ; Online: HIV-1 Envelope Conformation, Allostery, and Dynamics.

    Bennett, Ashley Lauren / Henderson, Rory

    Viruses

    2021  Volume 13, Issue 5

    Abstract: The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the ... ...

    Abstract The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the sole target for broadly neutralizing antibodies, our understanding of these transitions plays a critical role in vaccine immunogen design. Here, we review available experimental data interrogating the HIV-1 Env conformation and detail computational efforts aimed at delineating the series of conformational changes connecting these rearrangements. These studies have provided a structural mapping of prefusion closed, open, and transition intermediate structures, the allosteric elements controlling rearrangements, and state-to-state transition dynamics. The combination of these investigations and innovations in molecular modeling set the stage for advanced studies examining rearrangements at greater spatial and temporal resolution.
    MeSH term(s) Antibodies, Neutralizing/immunology ; HIV Antibodies/immunology ; HIV Envelope Protein gp41/chemistry ; HIV Envelope Protein gp41/genetics ; HIV Envelope Protein gp41/immunology ; HIV-1/chemistry ; HIV-1/genetics ; HIV-1/immunology ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Virus Internalization ; env Gene Products, Human Immunodeficiency Virus/chemistry ; env Gene Products, Human Immunodeficiency Virus/genetics ; env Gene Products, Human Immunodeficiency Virus/immunology ; env Gene Products, Human Immunodeficiency Virus/metabolism
    Chemical Substances Antibodies, Neutralizing ; HIV Antibodies ; HIV Envelope Protein gp41 ; env Gene Products, Human Immunodeficiency Virus
    Language English
    Publishing date 2021-05-07
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13050852
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: HIV-1 Envelope Conformation, Allostery, and Dynamics

    Bennett, Ashley Lauren / Henderson, Rory

    Viruses. 2021 May 07, v. 13, no. 5

    2021  

    Abstract: The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the ... ...

    Abstract The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the sole target for broadly neutralizing antibodies, our understanding of these transitions plays a critical role in vaccine immunogen design. Here, we review available experimental data interrogating the HIV-1 Env conformation and detail computational efforts aimed at delineating the series of conformational changes connecting these rearrangements. These studies have provided a structural mapping of prefusion closed, open, and transition intermediate structures, the allosteric elements controlling rearrangements, and state-to-state transition dynamics. The combination of these investigations and innovations in molecular modeling set the stage for advanced studies examining rearrangements at greater spatial and temporal resolution.
    Keywords antigens ; cell fusion ; glycoproteins ; vaccine development ; vaccines
    Language English
    Dates of publication 2021-0507
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13050852
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: The association between restricted activity and patient outcomes in older adults: systematic literature review and meta-analysis.

    Henderson, Ishbel L / Bone, Rory W / Stevens, Richard / Barnes, Rebecca K / Roberts, Nia / Sheppard, James P / McManus, Richard J

    BMC geriatrics

    2024  Volume 24, Issue 1, Page(s) 316

    Abstract: Background: Restricted activity is a potential early marker of declining health in older adults. Previous studies of this association with patient outcomes have been inconclusive. This review aimed to evaluate the extent to which restricted activity is ... ...

    Abstract Background: Restricted activity is a potential early marker of declining health in older adults. Previous studies of this association with patient outcomes have been inconclusive. This review aimed to evaluate the extent to which restricted activity is associated with decline in health.
    Methods: A search was conducted for studies including people over 65 years old which investigated the association between measures of restricted activity and hospitalisation, cognitive decline, and mortality. Following data extraction by two reviewers, eligible studies were summarised using Inverse Variance Heterogeneity meta-analysis.
    Results: The search identified 8,434 unique publications, with 11 eligible studies. Three measures of restricted activity were identified: bed rest, restricted movement, and dependency for activities of daily living (ADL). Three studies looked at hospitalisations, with two finding a significant association with bed rest or restricted movement and one showing no evidence of an association. Restricted activity was associated with a significant increase in mortality across all three measures (bed rest odds ratio [OR] 6.34, 95%CI 2.51-16.02, I2 = 76%; restricted movement OR 5.38 95%CI 2.60-11.13, I2 = 69%; general ADL dependency OR 4.65 95%CI 2.25-9.26, I2 = 84%). The significant heterogeneity observed could not be explained by restricting the analysis by length of follow-up, or measure of restricted activity. No meta-analysis was conducted on the limited evidence for cognitive decline outcomes.
    Conclusions: Limited studies have considered the prognostic value of restricted activity in terms of predicting future declining health. Current evidence suggests restricted activity is associated with hospitalisation and mortality, and therefore could identify a group for whom early intervention might be possible.
    MeSH term(s) Humans ; Aged ; Activities of Daily Living ; Hospitalization
    Language English
    Publishing date 2024-04-04
    Publishing country England
    Document type Systematic Review ; Meta-Analysis ; Journal Article
    ZDB-ID 2059865-8
    ISSN 1471-2318 ; 1471-2318
    ISSN (online) 1471-2318
    ISSN 1471-2318
    DOI 10.1186/s12877-024-04866-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Improved Surface Functional and Photocatalytic Properties of Hybrid ZnO-MoS

    Rameshkumar, Saranya / Henderson, Rory / Padamati, Ramesh Babu

    Membranes

    2020  Volume 10, Issue 5

    Abstract: The synergistic mechanism of photocatalytic-assisted dye degradation has been demonstrated using a hybrid ZnO- ... ...

    Abstract The synergistic mechanism of photocatalytic-assisted dye degradation has been demonstrated using a hybrid ZnO-MoS
    Language English
    Publishing date 2020-05-21
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2077-0375
    ISSN 2077-0375
    DOI 10.3390/membranes10050106
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The addition of lopinavir-ritonavir to carfilzomib-based triplets can induce meaningful clinical response in carfilzomib-refractory myeloma patients: a single-center experience.

    Bennett, Rory / Chan, Henry / Henderson, Ross / Merriman, Eileen / Hanna, Merit / Elinder-Camburn, Anna / Simpson, David

    Leukemia & lymphoma

    2022  Volume 63, Issue 7, Page(s) 1738–1741

    MeSH term(s) Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Dexamethasone/therapeutic use ; Humans ; Lopinavir/therapeutic use ; Multiple Myeloma/diagnosis ; Multiple Myeloma/drug therapy ; Neoplasm Recurrence, Local/drug therapy ; Oligopeptides ; Ritonavir/therapeutic use
    Chemical Substances Oligopeptides ; Lopinavir (2494G1JF75) ; carfilzomib (72X6E3J5AR) ; Dexamethasone (7S5I7G3JQL) ; Ritonavir (O3J8G9O825)
    Language English
    Publishing date 2022-02-11
    Publishing country United States
    Document type Letter
    ZDB-ID 1042374-6
    ISSN 1029-2403 ; 1042-8194
    ISSN (online) 1029-2403
    ISSN 1042-8194
    DOI 10.1080/10428194.2022.2038374
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Microsecond dynamics control the HIV-1 Envelope conformation.

    Bennett, Ashley L / Edwards, Robert / Kosheleva, Irina / Saunders, Carrie / Bililign, Yishak / Williams, Ashliegh / Bubphamala, Pimthada / Manosouri, Katayoun / Anasti, Kara / Saunders, Kevin O / Alam, S Munir / Haynes, Barton F / Acharya, Priyamvada / Henderson, Rory

    Science advances

    2024  Volume 10, Issue 5, Page(s) eadj0396

    Abstract: The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond ... ...

    Abstract The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.
    MeSH term(s) env Gene Products, Human Immunodeficiency Virus/chemistry ; HIV-1 ; HIV Antibodies ; Molecular Conformation ; Protein Multimerization ; Protein Conformation
    Chemical Substances env Gene Products, Human Immunodeficiency Virus ; HIV Antibodies
    Language English
    Publishing date 2024-02-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adj0396
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage.

    Henderson, Rory / Zhou, Ye / Stalls, Victoria / Wiehe, Kevin / Saunders, Kevin O / Wagh, Kshitij / Anasti, Kara / Barr, Maggie / Parks, Robert / Alam, S Munir / Korber, Bette / Haynes, Barton F / Bartesaghi, Alberto / Acharya, Priyamvada

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 2782

    Abstract: Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for ... ...

    Abstract Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affinity maturation and reveal solutions for these that will inform immunogen design aimed at eliciting a broadly neutralizing immune response by vaccination.
    MeSH term(s) Humans ; HIV Infections/prevention & control ; HIV-1/genetics ; Antibodies, Neutralizing ; HIV Antibodies ; Polysaccharides
    Chemical Substances Antibodies, Neutralizing ; HIV Antibodies ; Polysaccharides
    Language English
    Publishing date 2023-05-15
    Publishing country England
    Document type Journal Article ; 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 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-38108-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Microsecond dynamics control the HIV-1 envelope conformation.

    Bennett, Ashley L / Edwards, R J / Kosheleva, Irina / Saunders, Carrie / Bililign, Yishak / Williams, Ashliegh / Manosouri, Katayoun / Saunders, Kevin O / Haynes, Barton F / Acharya, Priyamvada / Henderson, Rory

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although significant progress has been made in understanding the structures of various Env conformations and transition ... ...

    Abstract The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although significant progress has been made in understanding the structures of various Env conformations and transition intermediates that occur within the millisecond timescale, faster transitions in the microsecond timescale have not yet been observed. In this study, we employed time-resolved, temperature-jump small angle X-ray scattering to monitor structural rearrangements in an HIV-1 Env ectodomain construct with microsecond precision. We detected a transition correlated with Env opening that occurs in the hundreds of microseconds range and another more rapid transition that preceded this opening. Model fitting indicated that the early rapid transition involved an order-to-disorder transition in the trimer apex loop contacts, suggesting that conventional conformation-locking design strategies that target the allosteric machinery may be ineffective in preventing this movement. Utilizing this information, we engineered an envelope that locks the apex loop contacts to the adjacent protomer. This modification resulted in significant angle-of-approach shifts in the interaction of a neutralizing antibody. Our findings imply that blocking the intermediate state could be crucial for inducing antibodies with the appropriate bound state orientation through vaccination.
    Language English
    Publishing date 2023-05-18
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.17.541130
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition.

    Zhang, Qianyi E / Lindenberger, Jared / Parsons, Ruth / Thakur, Bhishem / Parks, Rob / Park, Chan Soo / Huang, Xiao / Sammour, Salam / Janowska, Katarzyna / Spence, Taylor N / Edwards, Robert J / Martin, Mitchell / Williams, Wilton B / Gobeil, Sophie / Montefiori, David C / Korber, Bette / Saunders, Kevin O'Neil / Haynes, Barton F / Henderson, Rory /
    Acharya, Priyamvada

    bioRxiv : the preprint server for biology

    2024  

    Abstract: A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. ...

    Abstract A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryo-EM structures of XBB.1.5, XBB.1.16, EG.5 and EG.5.1 spike (S) ectodomains to reveal reinforced 3-RBD-down receptor inaccessible closed states mediated by interprotomer receptor binding domain (RBD) interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters including stability, receptor binding and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.
    Language English
    Publishing date 2024-03-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.12.580004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design.

    Manrique, Pedro D / Chakraborty, Srirupa / Henderson, Rory / Edwards, Robert J / Mansbach, Rachael / Nguyen, Kien / Stalls, Victoria / Saunders, Carrie / Mansouri, Katayoun / Acharya, Priyamvada / Korber, Bette / Gnanakaran, S

    iScience

    2022  Volume 26, Issue 1, Page(s) 105855

    Abstract: The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which ...

    Abstract The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which the virus enters human cells, while simultaneously sporting mutations responsible for immune escape. These functional and escape processes are regulated by complex molecular-level interactions. Our study presents quantitative insights on domain and residue contributions to allosteric communication, immune evasion, and local- and global-level control of functions through the derivation of a weighted graph representation from all-atom MD simulations. Focusing on the ancestral form and the D614G-variant, we provide evidence of the utility of our approach by guiding the selection of a mutation that alters the spike's stability. Taken together, the network approach serves as a valuable tool to evaluate communication "hot-spots" in proteins to guide design of stable immunogens.
    Language English
    Publishing date 2022-12-26
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.105855
    Database MEDical Literature Analysis and Retrieval System OnLINE

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