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  1. Article ; Online: Plate-Focusing Based on a Meta-Molecule of Dendritic Structure in the Visible Frequency.

    Cheng, Suna / An, Di / Chen, Huan / Zhao, Xiaopeng

    Molecules (Basel, Switzerland)

    2018  Volume 23, Issue 6

    Abstract: To study the potential application of metasurfaces in lens technology, we propose a dendritic meta-molecule surface (also referred to as a dendritic metasurface) and realize the focusing effect in the visible spectrum through simulations and experiments. ...

    Abstract To study the potential application of metasurfaces in lens technology, we propose a dendritic meta-molecule surface (also referred to as a dendritic metasurface) and realize the focusing effect in the visible spectrum through simulations and experiments. Using asymmetric dendritic structures, this metasurface can achieve distinct broadband anomalous reflection and refraction. When the metasurface is rotated by 180° around the
    MeSH term(s) Light ; Models, Theoretical ; Molecular Structure
    Language English
    Publishing date 2018-05-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules23061323
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Computational design of non-porous pH-responsive antibody nanoparticles.

    Yang, Erin C / Divine, Robby / Miranda, Marcos C / Borst, Andrew J / Sheffler, Will / Zhang, Jason Z / Decarreau, Justin / Saragovi, Amijai / Abedi, Mohamad / Goldbach, Nicolas / Ahlrichs, Maggie / Dobbins, Craig / Hand, Alexis / Cheng, Suna / Lamb, Mila / Levine, Paul M / Chan, Sidney / Skotheim, Rebecca / Fallas, Jorge /
    Ueda, George / Lubner, Joshua / Somiya, Masaharu / Khmelinskaia, Alena / King, Neil P / Baker, David

    Nature structural & molecular biology

    2024  

    Abstract: Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and is important for targeted delivery of biologics. Here we describe the design of octahedral non-porous nanoparticles with a ... ...

    Abstract Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and is important for targeted delivery of biologics. Here we describe the design of octahedral non-porous nanoparticles with a targeting antibody on the two-fold symmetry axis, a designed trimer programmed to disassemble below a tunable pH transition point on the three-fold axis, and a designed tetramer on the four-fold symmetry axis. Designed non-covalent interfaces guide cooperative nanoparticle assembly from independently purified components, and a cryo-EM density map closely matches the computational design model. The designed nanoparticles can package protein and nucleic acid payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between 5.9 and 6.7. The ability to incorporate almost any antibody into a non-porous pH-dependent nanoparticle opens up new routes to antibody-directed targeted delivery.
    Language English
    Publishing date 2024-05-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-024-01288-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Computational design of non-porous, pH-responsive antibody nanoparticles.

    Yang, Erin C / Divine, Robby / Miranda, Marcos C / Borst, Andrew J / Sheffler, Will / Zhang, Jason Z / Decarreau, Justin / Saragovi, Amijai / Abedi, Mohamad / Goldbach, Nicolas / Ahlrichs, Maggie / Dobbins, Craig / Hand, Alexis / Cheng, Suna / Lamb, Mila / Levine, Paul M / Chan, Sidney / Skotheim, Rebecca / Fallas, Jorge /
    Ueda, George / Lubner, Joshua / Somiya, Masaharu / Khmelinskaia, Alena / King, Neil P / Baker, David

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and important for targeted delivery of biologics. We describe the design of octahedral non-porous nanoparticles with the three ... ...

    Abstract Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and important for targeted delivery of biologics. We describe the design of octahedral non-porous nanoparticles with the three symmetry axes (four-fold, three-fold, and two-fold) occupied by three distinct protein homooligomers: a
    Language English
    Publishing date 2023-04-18
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.17.537263
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Antigen- and scaffold-specific antibody responses to protein nanoparticle immunogens.

    Kraft, John C / Pham, Minh N / Shehata, Laila / Brinkkemper, Mitch / Boyoglu-Barnum, Seyhan / Sprouse, Kaitlin R / Walls, Alexandra C / Cheng, Suna / Murphy, Mike / Pettie, Deleah / Ahlrichs, Maggie / Sydeman, Claire / Johnson, Max / Blackstone, Alyssa / Ellis, Daniel / Ravichandran, Rashmi / Fiala, Brooke / Wrenn, Samuel / Miranda, Marcos /
    Sliepen, Kwinten / Brouwer, Philip J M / Antanasijevic, Aleksandar / Veesler, David / Ward, Andrew B / Kanekiyo, Masaru / Pepper, Marion / Sanders, Rogier W / King, Neil P

    Cell reports. Medicine

    2022  Volume 3, Issue 10, Page(s) 100780

    Abstract: Protein nanoparticle scaffolds are increasingly used in next-generation vaccine designs, and several have established records of clinical safety and efficacy. Yet the rules for how immune responses specific to nanoparticle scaffolds affect the ... ...

    Abstract Protein nanoparticle scaffolds are increasingly used in next-generation vaccine designs, and several have established records of clinical safety and efficacy. Yet the rules for how immune responses specific to nanoparticle scaffolds affect the immunogenicity of displayed antigens have not been established. Here we define relationships between anti-scaffold and antigen-specific antibody responses elicited by protein nanoparticle immunogens. We report that dampening anti-scaffold responses by physical masking does not enhance antigen-specific antibody responses. In a series of immunogens that all use the same nanoparticle scaffold but display four different antigens, only HIV-1 envelope glycoprotein (Env) is subdominant to the scaffold. However, we also demonstrate that scaffold-specific antibody responses can competitively inhibit antigen-specific responses when the scaffold is provided in excess. Overall, our results suggest that anti-scaffold antibody responses are unlikely to suppress antigen-specific antibody responses for protein nanoparticle immunogens in which the antigen is immunodominant over the scaffold.
    MeSH term(s) HIV Antibodies ; Antibody Formation ; HIV-1 ; Nanoparticles ; Glycoproteins ; Vaccines
    Chemical Substances HIV Antibodies ; Glycoproteins ; Vaccines
    Language English
    Publishing date 2022-09-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2666-3791
    ISSN (online) 2666-3791
    DOI 10.1016/j.xcrm.2022.100780
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: De novo

    Roy, Anindya / Shi, Lei / Chang, Ashley / Dong, Xianchi / Fernandez, Andres / Kraft, John C / Li, Jing / Le, Viet Q / Winegar, Rebecca Viazzo / Cherf, Gerald Maxwell / Slocum, Dean / Daniel Poulson, P / Casper, Garrett E / Vallecillo-Zúniga, Mary L / Valdoz, Jonard Corpuz / Miranda, Marcos C / Bai, Hua / Kipnis, Yakov / Olshefsky, Audrey /
    Priya, Tanu / Carter, Lauren / Ravichandran, Rashmi / Chow, Cameron M / Johnson, Max R / Cheng, Suna / Smith, McKaela / Overed-Sayer, Catherine / Finch, Donna K / Lowe, David / Bera, Asim K / Matute-Bello, Gustavo / Birkland, Timothy P / DiMaio, Frank / Raghu, Ganesh / Cochran, Jennifer R / Stewart, Lance J / Campbell, Melody G / Van Ry, Pam M / Springer, Timothy / Baker, David

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between the two closely related integrin proteins and other RGD integrins, ... ...

    Abstract The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between the two closely related integrin proteins and other RGD integrins, stabilize specific conformational states, and have sufficient stability enabling tissue restricted administration could have considerable therapeutic utility. Existing small molecules and antibody inhibitors do not have all of these properties, and hence there is a need for new approaches. Here we describe a method for computationally designing hyperstable RGD-containing miniproteins that are highly selective for a single RGD integrin heterodimer and conformational state, and use this strategy to design inhibitors of αvβ6 and αvβ8 with high selectivity. The αvβ6 and αvβ8 inhibitors have picomolar affinities for their targets, and >1000-fold selectivity over other RGD integrins. CryoEM structures are within 0.6-0.7Å root-mean-square deviation (RMSD) to the computational design models; the designed αvβ6 inhibitor and native ligand stabilize the open conformation in contrast to the therapeutic anti-αvβ6 antibody BG00011 that stabilizes the bent-closed conformation and caused on-target toxicity in patients with lung fibrosis, and the αvβ8 inhibitor maintains the constitutively fixed extended-closed αvβ8 conformation. In a mouse model of bleomycin-induced lung fibrosis, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics when delivered via oropharyngeal administration mimicking inhalation, demonstrating the therapeutic potential of
    Language English
    Publishing date 2023-06-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.06.12.544624
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8.

    Roy, Anindya / Shi, Lei / Chang, Ashley / Dong, Xianchi / Fernandez, Andres / Kraft, John C / Li, Jing / Le, Viet Q / Winegar, Rebecca Viazzo / Cherf, Gerald Maxwell / Slocum, Dean / Poulson, P Daniel / Casper, Garrett E / Vallecillo-Zúniga, Mary L / Valdoz, Jonard Corpuz / Miranda, Marcos C / Bai, Hua / Kipnis, Yakov / Olshefsky, Audrey /
    Priya, Tanu / Carter, Lauren / Ravichandran, Rashmi / Chow, Cameron M / Johnson, Max R / Cheng, Suna / Smith, McKaela / Overed-Sayer, Catherine / Finch, Donna K / Lowe, David / Bera, Asim K / Matute-Bello, Gustavo / Birkland, Timothy P / DiMaio, Frank / Raghu, Ganesh / Cochran, Jennifer R / Stewart, Lance J / Campbell, Melody G / Van Ry, Pam M / Springer, Timothy / Baker, David

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 5660

    Abstract: The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize ... ...

    Abstract The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
    MeSH term(s) Animals ; Mice ; Integrins ; Cell Membrane ; Cryoelectron Microscopy ; Disease Models, Animal ; Pulmonary Fibrosis
    Chemical Substances Integrins
    Language English
    Publishing date 2023-09-13
    Publishing country England
    Document type Journal Article ; 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/s41467-023-41272-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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