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  1. AU="Thadani, Nicole N"
  2. AU="Allison E. Norlander" AU="Allison E. Norlander"
  3. AU="Wei, Peifa"
  4. AU="Colak, Errol"
  5. AU="Hassan, Hosni M"
  6. AU="Becker, D T"
  7. AU="Lewis-Lloyd, Christopher A"
  8. AU=Doshi Rupali Kotwal AU=Doshi Rupali Kotwal
  9. AU="Kore Schlottau"
  10. AU="Jamjoom, Mona"
  11. AU="Bergmann, P."
  12. AU="Li, Congju"
  13. AU="Christenson, Robert"
  14. AU="O'Neill, Hugh M"
  15. AU="Vaccaro, Daniel H."
  16. AU=Panchin Yuri V
  17. AU=McIlvennan Colleen K
  18. AU="Khan, Mohammad Afsar"
  19. AU="Zhuang, Hua-Lu"
  20. AU="Lopez, Omar M"
  21. AU=Asfaw Abay
  22. AU="Santana, Ricardo Costa de"
  23. AU="Ortega, Johis"
  24. AU="Sogaolu, Moyosore"
  25. AU="Duchesne, Gabriela"
  26. AU="Sander, Klaus"
  27. AU="Wiegersma, Aline Marileen"
  28. AU=Mehta Yatin
  29. AU="Ki Hwan Kim"
  30. AU="Gulati, Rajiv"
  31. AU="Sullivan, Christopher"
  32. AU="Meier-Stephenson, Vanessa C"
  33. AU=Kim Joo Seop
  34. AU="Mortensen, Jennifer L"
  35. AU="Manthey, Helga D"
  36. AU="Baker, Susan"
  37. AU="Gunasegaram, James R"
  38. AU="Jung, Steffen"
  39. AU="Cairns, Anita"
  40. AU="Fox, Lindsay"

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  1. Artikel ; Online: Learning from prepandemic data to forecast viral escape.

    Thadani, Nicole N / Gurev, Sarah / Notin, Pascal / Youssef, Noor / Rollins, Nathan J / Ritter, Daniel / Sander, Chris / Gal, Yarin / Marks, Debora S

    Nature

    2023  Band 622, Heft 7984, Seite(n) 818–825

    Abstract: Effective pandemic preparedness relies on anticipating viral mutations that are able to evade host immune responses to facilitate vaccine and therapeutic design. However, current strategies for viral evolution prediction are not available early in a ... ...

    Abstract Effective pandemic preparedness relies on anticipating viral mutations that are able to evade host immune responses to facilitate vaccine and therapeutic design. However, current strategies for viral evolution prediction are not available early in a pandemic-experimental approaches require host polyclonal antibodies to test against
    Mesh-Begriff(e) Humans ; Drug Design ; Evolution, Molecular ; Forecasting ; HIV Infections ; Immune Evasion/genetics ; Immune Evasion/immunology ; Influenza, Human ; Lassa virus ; Mutation ; Nipah Virus ; Pandemics ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Viral Vaccines/immunology ; Viruses/genetics ; Viruses/immunology
    Chemische Substanzen Viral Vaccines
    Sprache Englisch
    Erscheinungsdatum 2023-10-11
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-06617-0
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Learning from pre-pandemic data to forecast viral antibody escape

    Thadani, Nicole N / Gurev, Sarah / Notin, Pascal / Youssef, Noor / Rollins, Nathan J / Sander, Chris / Gal, Yarin / Marks, Debora

    bioRxiv

    Abstract: From early detection of variants of concern to vaccine and therapeutic design, pandemic preparedness depends on identifying viral mutations that escape the response of the host immune system. While experimental scans are useful for quantifying escape ... ...

    Abstract From early detection of variants of concern to vaccine and therapeutic design, pandemic preparedness depends on identifying viral mutations that escape the response of the host immune system. While experimental scans are useful for quantifying escape potential, they remain laborious and impractical for exploring the combinatorial space of mutations. Here we introduce a biologically grounded model to quantify the viral escape potential of mutations at scale. Our method - EVEscape - brings together fitness predictions from evolutionary models, structure-based features that assess antibody binding potential, and distances between mutated and wild-type residues. Unlike other models that predict variants of concern based on newly observed variants, EVEscape has no reliance on recent community prevalence, and is applicable before surveillance sequencing or experimental scans are broadly available. We validate EVEscape predictions against experimental data on H1N1, HIV and SARS-CoV-2, including data on immune escape. For SARS-CoV-2, we show that EVEscape anticipates mutation frequency, strain prevalence, and escape mutations. Drawing from GISAID, we provide continually updated escape predictions for all current strains of SARS-CoV-2.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2022-07-22
    Verlag Cold Spring Harbor Laboratory
    Dokumenttyp Artikel ; Online
    DOI 10.1101/2022.07.21.501023
    Datenquelle COVID19

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  3. Artikel: Simultaneous enhancement of multiple functional properties using evolution-informed protein design.

    Fram, Benjamin / Truebridge, Ian / Su, Yang / Riesselman, Adam J / Ingraham, John B / Passera, Alessandro / Napier, Eve / Thadani, Nicole N / Lim, Samuel / Roberts, Kristen / Kaur, Gurleen / Stiffler, Michael / Marks, Debora S / Bahl, Christopher D / Khan, Amir R / Sander, Chris / Gauthier, Nicholas P

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Designing optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of ... ...

    Abstract Designing optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of mutations, while maintaining structure and enhancing function. Homologous protein sequences contain extensive information about various protein properties and activities that have emerged over billions of years of evolution. Evolutionary models of sequence co-variation, derived from a set of homologous sequences, have proven effective in a range of applications including structure determination and mutation effect prediction. In this work we apply one of these models (EVcouplings) to computationally design highly divergent variants of the model protein TEM-1 β-lactamase, and characterize these designs experimentally using multiple biochemical and biophysical assays. Nearly all designed variants were functional, including one with 84 mutations from the nearest natural homolog. Surprisingly, all functional designs had large increases in thermostability and most had a broadening of available substrates. These property enhancements occurred while maintaining a nearly identical structure to the wild type enzyme. Collectively, this work demonstrates that evolutionary models of sequence co-variation (1) are able to capture complex epistatic interactions that successfully guide large sequence departures from natural contexts, and (2) can be applied to generate functional diversity useful for many applications in protein design.
    Sprache Englisch
    Erscheinungsdatum 2023-05-09
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.05.09.539914
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells.

    Veling, Mike T / Nguyen, Dan T / Thadani, Nicole N / Oster, Michela E / Rollins, Nathan J / Brock, Kelly P / Bethel, Neville P / Lim, Samuel / Baker, David / Way, Jeffrey C / Marks, Debora S / Chang, Roger L / Silver, Pamela A

    ACS synthetic biology

    2022  Band 11, Heft 3, Seite(n) 1292–1302

    Abstract: Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. ...

    Abstract Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis-protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlights the ability of DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.
    Mesh-Begriff(e) Animals ; Apoptosis ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Tardigrada/metabolism
    Chemische Substanzen Intrinsically Disordered Proteins
    Sprache Englisch
    Erscheinungsdatum 2022-02-18
    Erscheinungsland United States
    Dokumenttyp 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.
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.1c00572
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Site-Specific Post-translational Surface Modification of Adeno-Associated Virus Vectors Using Leucine Zippers.

    Thadani, Nicole N / Yang, Joanna / Moyo, Buhle / Lee, Ciaran M / Chen, Maria Y / Bao, Gang / Suh, Junghae

    ACS synthetic biology

    2020  Band 9, Heft 3, Seite(n) 461–467

    Abstract: Adeno-associated virus (AAV) is widely favored as a gene therapy vector, tested in over 200 clinical trials internationally. To improve targeted delivery a variety of genetic capsid modifications, such as insertion of targeting proteins/peptides into the ...

    Abstract Adeno-associated virus (AAV) is widely favored as a gene therapy vector, tested in over 200 clinical trials internationally. To improve targeted delivery a variety of genetic capsid modifications, such as insertion of targeting proteins/peptides into the capsid shell, have been explored with some success but larger insertions often have unpredictable deleterious impacts on capsid formation and gene delivery. Here, we demonstrate a modular platform for the integration of exogenous peptides and proteins onto the AAV capsid post-translationally while preserving vector functionality. We decorated the AAV capsid with leucine-zipper coiled-coil binding motifs that exhibit specific noncovalent heterodimerization. AAV capsids successfully display hexahistidine tagged-peptides using this approach, as demonstrated through nickel column affinity. This protein display platform may facilitate the incorporation of biological moieties on the AAV surface, expanding possibilities for vector enhancement and engineering.
    Mesh-Begriff(e) Animals ; CHO Cells ; Capsid/metabolism ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Cricetulus ; Dependovirus/genetics ; Genetic Engineering/methods ; Genetic Vectors/genetics ; Genetic Vectors/metabolism ; Histidine/genetics ; Human Umbilical Vein Endothelial Cells ; Humans ; Leucine Zippers/genetics ; Protein Processing, Post-Translational ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Transduction, Genetic
    Chemische Substanzen Capsid Proteins ; Recombinant Proteins ; Histidine (4QD397987E)
    Sprache Englisch
    Erscheinungsdatum 2020-02-18
    Erscheinungsland United States
    Dokumenttyp 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.
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.9b00341
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Reprogramming the Activatable Peptide Display Function of Adeno-Associated Virus Nanoparticles.

    Thadani, Nicole N / Dempsey, Christopher / Zhao, Julia / Vasquez, Sonya M / Suh, Junghae

    ACS nano

    2017  Band 12, Heft 2, Seite(n) 1445–1454

    Abstract: We harnessed an intrinsic activatable peptide display behavior shared by several parvoviruses, including the adeno-associated virus (AAV), in order to design protein-based nanodevices that can carry out an exogenous functional output in response to ... ...

    Abstract We harnessed an intrinsic activatable peptide display behavior shared by several parvoviruses, including the adeno-associated virus (AAV), in order to design protein-based nanodevices that can carry out an exogenous functional output in response to stimulus detection. Specifically, we generated truncated viral capsid subunits that, when combined with native capsid components into mosaic capsids, can perform robust activatable peptide display. By modulating the ratio of subunits in the mosaic capsid, properties of the activatable peptide display function can be optimized. Interestingly, the truncated subunits can form homomeric capsids not observed in nature, but at the price of losing the ability to carry out activatable peptide display. Collectively, our results demonstrate the importance of capsid mosaicism when activatable peptide display is desired and help explain why the wild-type AAV capsid exists as a mosaic of different subunits. This proof-of-concept study illustrates a strategy for reprogramming a particular conformational output behavior of AAV in pursuit of the long-term vision of creating stimulus-responsive nanodevices.
    Mesh-Begriff(e) Dependovirus/chemistry ; Dependovirus/genetics ; Dependovirus/isolation & purification ; Humans ; Mutation ; Nanoparticles/chemistry ; Peptides/chemistry
    Chemische Substanzen Peptides
    Sprache Englisch
    Erscheinungsdatum 2017-12-26
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.7b07804
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus.

    Thadani, Nicole N / Zhou, Qin / Reyes Gamas, Kiara / Butler, Susan / Bueno, Carlos / Schafer, Nicholas P / Morcos, Faruck / Wolynes, Peter G / Suh, Junghae

    Biophysical journal

    2020  Band 120, Heft 3, Seite(n) 489–503

    Abstract: Adeno-associated virus (AAV) is a promising gene therapy vector because of its efficient gene delivery and relatively mild immunogenicity. To improve delivery target specificity, researchers use combinatorial and rational library design strategies to ... ...

    Abstract Adeno-associated virus (AAV) is a promising gene therapy vector because of its efficient gene delivery and relatively mild immunogenicity. To improve delivery target specificity, researchers use combinatorial and rational library design strategies to generate novel AAV capsid variants. These approaches frequently propose high proportions of nonforming or noninfective capsid protein sequences that reduce the effective depth of synthesized vector DNA libraries, thereby raising the discovery cost of novel vectors. We evaluated two computational techniques for their ability to estimate the impact of residue mutations on AAV capsid protein-protein interactions and thus predict changes in vector fitness, reasoning that these approaches might inform the design of functionally enriched AAV libraries and accelerate therapeutic candidate identification. The Frustratometer computes an energy function derived from the energy landscape theory of protein folding. Direct-coupling analysis (DCA) is a statistical framework that captures residue coevolution within proteins. We applied the Frustratometer to select candidate protein residues predicted to favor assembled or disassembled capsid states, then predicted mutation effects at these sites using the Frustratometer and DCA. Capsid mutants were experimentally assessed for changes in virus formation, stability, and transduction ability. The Frustratometer-based metric showed a counterintuitive correlation with viral stability, whereas a DCA-derived metric was highly correlated with virus transduction ability in the small population of residues studied. Our results suggest that coevolutionary models may be able to elucidate complex capsid residue-residue interaction networks essential for viral function, but further study is needed to understand the relationship between protein energy simulations and viral capsid metastability.
    Mesh-Begriff(e) Capsid ; Capsid Proteins/genetics ; Dependovirus/genetics ; Gene Transfer Techniques ; Genetic Vectors ; Transduction, Genetic
    Chemische Substanzen Capsid Proteins
    Sprache Englisch
    Erscheinungsdatum 2020-12-25
    Erscheinungsland United States
    Dokumenttyp 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 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2020.12.018
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Preparation and catalytic evaluation of ruthenium-nickel dendrimer encapsulated nanoparticles via intradendrimer redox displacement of nickel nanoparticles.

    Marvin, Katherine A / Thadani, Nicole N / Atkinson, Corinne A / Keller, Emily L / Stevenson, Keith J

    Chemical communications (Cambridge, England)

    2012  Band 48, Heft 50, Seite(n) 6289–6291

    Abstract: Ru and Ru(x)Ni(30) dendrimer encapsulated nanoparticles (DENs) were synthesized using a redox-displacement method. DEN catalytic activity for the reduction of p-nitrophenol was evaluated and found to be dependent on the ratio of metals present. ...

    Abstract Ru and Ru(x)Ni(30) dendrimer encapsulated nanoparticles (DENs) were synthesized using a redox-displacement method. DEN catalytic activity for the reduction of p-nitrophenol was evaluated and found to be dependent on the ratio of metals present.
    Mesh-Begriff(e) Catalysis ; Dendrimers/chemistry ; Metal Nanoparticles/chemistry ; Nickel/chemistry ; Oxidation-Reduction ; Ruthenium/chemistry
    Chemische Substanzen Dendrimers ; Nickel (7OV03QG267) ; Ruthenium (7UI0TKC3U5)
    Sprache Englisch
    Erscheinungsdatum 2012-06-25
    Erscheinungsland England
    Dokumenttyp Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c2cc31370g
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel: Preparation and catalytic evaluation of ruthenium–nickel dendrimer encapsulated nanoparticles via intradendrimer redox displacement of nickel nanoparticles

    Marvin, Katherine A / Atkinson, Corinne A / Keller, Emily L / Stevenson, Keith J / Thadani, Nicole N

    Chemical communications. 2012 May 28, v. 48, no. 50

    2012  

    Abstract: Ru and RuxNi30 dendrimer encapsulated nanoparticles (DENs) were synthesized using a redox-displacement method. DEN catalytic activity for the reduction of p-nitrophenol was evaluated and found to be dependent on the ratio of metals present. ...

    Abstract Ru and RuxNi30 dendrimer encapsulated nanoparticles (DENs) were synthesized using a redox-displacement method. DEN catalytic activity for the reduction of p-nitrophenol was evaluated and found to be dependent on the ratio of metals present.
    Schlagwörter catalytic activity ; chemical communication ; chemical reactions ; dendrimers ; encapsulation ; nanoparticles ; nickel ; p-nitrophenol
    Sprache Englisch
    Erscheinungsverlauf 2012-0528
    Umfang p. 6289-6291.
    Erscheinungsort The Royal Society of Chemistry
    Dokumenttyp Artikel
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c2cc31370g
    Datenquelle NAL Katalog (AGRICOLA)

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