1
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Le KC, Jeong H, Tran TM. Theory of transition from brittle to ductile fracture. Phys Rev E 2023; 107:055006. [PMID: 37328972 DOI: 10.1103/physreve.107.055006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/05/2023] [Indexed: 06/18/2023]
Abstract
In this paper, two improvements to the theory of transition from brittle to ductile fracture developed by Langer [J. S. Langer, Phys. Rev. E 103, 063004 (2021)2470-004510.1103/PhysRevE.103.063004] are proposed. First, considering the drastic temperature rise near the crack tip, the temperature dependence of the shear modulus is included to better quantify the thermally sensitive dislocation entanglement. Second, the parameters of the improved theory are identified by the large-scale least-squares method. The comparison between the fracture toughness predicted by the theory and the values obtained in Gumbsch's experiments for tungsten at different temperatures [P. Gumbsch et al., Science 282, 1293 (1998)10.1126/science.282.5392.1293] shows good agreement.
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Affiliation(s)
- K C Le
- Division of Computational Mathematics and Engineering, Institute for Computational Science, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty of Civil Engineering, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
| | - H Jeong
- Lehrstuhl für Mechanik - Materialtheorie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - T M Tran
- Department of Mechanical Engineering, Vietnamese German University, Binh Duong 750000, Vietnam
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2
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Silva RP, Huang Y, Nguyen AW, Hsieh CL, Olaluwoye OS, Kaoud TS, Wilen RE, Qerqez AN, Park JG, Khalil AM, Azouz LR, Le KC, Bohanon AL, DiVenere AM, Liu Y, Lee AG, Amengor DA, Shoemaker SR, Costello SM, Padlan EA, Marqusee S, Martinez-Sobrido L, Dalby KN, D'Arcy S, McLellan JS, Maynard JA. Identification of a conserved S2 epitope present on spike proteins from all highly pathogenic coronaviruses. eLife 2023; 12:e83710. [PMID: 36942851 PMCID: PMC10030117 DOI: 10.7554/elife.83710] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/04/2023] [Indexed: 03/23/2023] Open
Abstract
To address the ongoing SARS-CoV-2 pandemic and prepare for future coronavirus outbreaks, understanding the protective potential of epitopes conserved across SARS-CoV-2 variants and coronavirus lineages is essential. We describe a highly conserved, conformational S2 domain epitope present only in the prefusion core of β-coronaviruses: SARS-CoV-2 S2 apex residues 980-1006 in the flexible hinge. Antibody RAY53 binds the native hinge in MERS-CoV and SARS-CoV-2 spikes on the surface of mammalian cells and mediates antibody-dependent cellular phagocytosis and cytotoxicity against SARS-CoV-2 spike in vitro. Hinge epitope mutations that ablate antibody binding compromise pseudovirus infectivity, but changes elsewhere that affect spike opening dynamics, including those found in Omicron BA.1, occlude the epitope and may evade pre-existing serum antibodies targeting the S2 core. This work defines a third class of S2 antibody while providing insights into the potency and limitations of S2 core epitope targeting.
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Affiliation(s)
- Rui P Silva
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Yimin Huang
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Oladimeji S Olaluwoye
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Rebecca E Wilen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ahlam N Qerqez
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Jun-Gyu Park
- Texas Biomedical Research InstituteSan AntonioUnited States
- Laboratory of Veterinary Zoonosis, College of Veterinary Medicine, Chonnam National UniversityGwangjuRepublic of Korea
| | - Ahmed M Khalil
- Texas Biomedical Research InstituteSan AntonioUnited States
| | - Laura R Azouz
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Amanda L Bohanon
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Yutong Liu
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Alison G Lee
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Dzifa A Amengor
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Sophie R Shoemaker
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, BerkeleyBerkeleyUnited States
| | | | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
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3
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Schaub JM, Chou CW, Kuo HC, Javanmardi K, Hsieh CL, Goldsmith J, DiVenere AM, Le KC, Wrapp D, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Wang N, Lavinder JJ, Ippolito GC, Maynard JA, McLellan JS, Finkelstein IJ. Expression and characterization of SARS-CoV-2 spike proteins. Nat Protoc 2021; 16:5339-5356. [PMID: 34611365 PMCID: PMC9665560 DOI: 10.1038/s41596-021-00623-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/06/2021] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 spike protein is a critical component of coronavirus disease 2019 vaccines and diagnostics and is also a therapeutic target. However, the spike protein is difficult to produce recombinantly because it is a large trimeric class I fusion membrane protein that is metastable and heavily glycosylated. We recently developed a prefusion-stabilized spike variant, termed HexaPro for six stabilizing proline substitutions, that can be expressed with a yield of >30 mg/L in ExpiCHO cells. This protocol describes an optimized workflow for expressing and biophysically characterizing rationally engineered spike proteins in Freestyle 293 and ExpiCHO cell lines. Although we focus on HexaPro, this protocol has been used to purify over a hundred different spike variants in our laboratories. We also provide guidance on expression quality control, long-term storage, and uses in enzyme-linked immunosorbent assays. The entire protocol, from transfection to biophysical characterization, can be completed in 7 d by researchers with basic tissue cell culture and protein purification expertise.
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Affiliation(s)
- Jeffrey M Schaub
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jory Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020. [PMID: 32703906 DOI: 10.1126/science:abd0826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Alison G Lee
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Juyeon Park
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Dzifa Amengor
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Oncology, Dell Medical School, University of Texas, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
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5
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020; 369:1501-1505. [PMID: 32703906 PMCID: PMC7402631 DOI: 10.1126/science.abd0826] [Citation(s) in RCA: 792] [Impact Index Per Article: 198.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Alison G Lee
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Christy K Hjorth
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - John Ludes-Meyers
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Juyeon Park
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Dzifa Amengor
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Department of Oncology, Dell Medical School, University of Texas, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AGW, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes. bioRxiv 2020:2020.05.30.125484. [PMID: 32577660 PMCID: PMC7302215 DOI: 10.1101/2020.05.30.125484] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ~10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
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Affiliation(s)
- Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jory A. Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jeffrey M. Schaub
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andrea M. DiVenere
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kevin C. Le
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Alison Gene-Wei Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Yutong Liu
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Patrick O. Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Christy K. Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - John Ludes-Meyers
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Annalee W. Nguyen
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Juyeon Park
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Dzifa Amengor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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Nguyen AW, Le KC, Maynard JA. Identification of high affinity HER2 binding antibodies using CHO Fab surface display. Protein Eng Des Sel 2019; 31:91-101. [PMID: 29566240 DOI: 10.1093/protein/gzy004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/02/2018] [Indexed: 12/27/2022] Open
Abstract
Discovery of monoclonal antibodies is most commonly performed using phage or yeast display but mammalian cells are used for production because of the complex antibody structure, including the multiple disulfide bonds and glycosylation, required for function. As this transition between host organisms is often accompanied by impaired binding, folding or expression, development pipelines include laborious plate-based screening or engineering strategies to adapt an antibody to mammalian expression. To circumvent these problems, we developed a plasmid-based Fab screening platform on Chinese hamster ovary (CHO) cells which allows for antibody selection in the production host and in the presence of the same post-translational modifications as the manufactured product. A hu4D5 variant with low affinity for the human epidermal growth factor receptor (HER2) growth factor receptor was mutagenized and this library of ~10(6) unique clones was screened to identify variants with up to 400-fold enhanced HER2 binding. After two rounds of fluorescence activated cell sorting (FACS), four unique clones exhibited improved antigen binding when expressed on the CHO surface or as purified human IgG. Three of the four clones contained free cysteines in third complementarity determining region of the antibody heavy chain, which did not impair expression or cause aggregation. The improved clones had similar yields and stabilities as hu4D5 and similar sub-nanomolar affinities as measured by equilibrium binding to target cells. The limited size of mammalian libraries restricts the utility of this approach for naïve antibody library screening, but it is a powerful approach for antibody affinity maturation or specificity enhancement and is readily generalizable to engineering other surface receptors, including T-cell receptors and chimeric antigen receptors.
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Affiliation(s)
- Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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8
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Abstract
The thermodynamic dislocation theory developed for nonuniform plastic deformations is used here to simulate the stress-strain curves for crystals subjected to antiplane shear-controlled load reversal. We show that the presence of the positive back stress during the load reversal reduces the magnitude of shear stress required to pull excess dislocations back to the center of the specimen. There, the excess dislocations of opposite signs meet and annihilate each other leading to the Bauschinger effect.
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Affiliation(s)
- K C Le
- Lehrstuhl für Mechanik-Materialtheorie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - T M Tran
- Lehrstuhl für Mechanik-Materialtheorie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Abstract
The statistical-thermodynamic dislocation theory developed in previous papers is used here in an analysis of high-temperature deformation of aluminum and steel. Using physics-based parameters that we expect theoretically to be independent of strain rate and temperature, we are able to fit experimental stress-strain curves for three different strain rates and three different temperatures for each of these two materials. Our theoretical curves include yielding transitions at zero strain in agreement with experiment. We find that thermal softening effects are important even at the lowest temperatures and smallest strain rates.
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Affiliation(s)
- K C Le
- Lehrstuhl für Mechanik-Materialtheorie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - T M Tran
- Lehrstuhl für Mechanik-Materialtheorie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - J S Langer
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106-9530, USA
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Langsjoen RM, Auguste AJ, Rossi SL, Roundy CM, Penate HN, Kastis M, Schnizlein MK, Le KC, Haller SL, Chen R, Watowich SJ, Weaver SC. Host oxidative folding pathways offer novel anti-chikungunya virus drug targets with broad spectrum potential. Antiviral Res 2017; 143:246-251. [PMID: 28461071 DOI: 10.1016/j.antiviral.2017.04.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/05/2017] [Indexed: 11/15/2022]
Abstract
Alphaviruses require conserved cysteine residues for proper folding and assembly of the E1 and E2 envelope glycoproteins, and likely depend on host protein disulfide isomerase-family enzymes (PDI) to aid in facilitating disulfide bond formation and isomerization in these proteins. Here, we show that in human HEK293 cells, commercially available inhibitors of PDI or modulators thereof (thioredoxin reductase, TRX-R; endoplasmic reticulum oxidoreductin-1, ERO-1) inhibit the replication of CHIKV chikungunya virus (CHIKV) in vitro in a dose-dependent manner. Further, the TRX-R inhibitor auranofin inhibited Venezuelan equine encephalitis virus and the flavivirus Zika virus replication in vitro, while PDI inhibitor 16F16 reduced replication but demonstrated notable toxicity. 16F16 significantly altered the viral genome: plaque-forming unit (PFU) ratio of CHIKV in vitro without affecting relative intracellular viral RNA quantities and inhibited CHIKV E1-induced cell-cell fusion, suggesting that PDI inhibitors alter progeny virion infectivity through altered envelope function. Auranofin also increased the extracellular genome:PFU ratio but decreased the amount of intracellular CHIKV RNA, suggesting an alternative mechanism of action. Finally, auranofin reduced footpad swelling and viremia in the C57BL/6 murine model of CHIKV infection. Our results suggest that targeting oxidative folding pathways represents a potential new anti-alphavirus therapeutic strategy.
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Affiliation(s)
- Rose M Langsjoen
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Shannan L Rossi
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Christopher M Roundy
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Heidy N Penate
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Maria Kastis
- Center in Environmental Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Kevin C Le
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Sherry L Haller
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rubing Chen
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Stanley J Watowich
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Center in Environmental Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
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11
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Abstract
Thermal nucleation of two-dimensional charges is studied. It is argued that the probability of N charge pairs to appear has a simple asymptotics for large N: p(N)=[q(c,beta,micro)](N)/Z(beta,micro), where q(c,beta,micro) is a function of charge concentration c, inverse temperature beta, and chemical potential micro, and Z(beta,micro) is the partition function. We present q(c,beta,micro) as a limit value of some functional integral and find an approximate value of this limit. This provides thermodynamic description of nucleation transition. The probability distribution of charge positions is studied within the same approximation. The behavior of the probability distribution indicates that for small charge concentration the transition is of Kosterlitz-Thouless type, i.e., the dipoles nucleated dissociate and form a neutral plasma, while at larger charge concentration the transition corresponds to nucleation of dipoles that may remain bounded. A transition with respect to chemical potential is observed, for micro<micro(cr) the charge nucleation is a transition of infinite order, while for micro>micro(cr) it becomes a first-order transition.
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