1
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Frank PH, Hong M, Higgins B, Perkins S, Taylor T, Wall VE, Drew M, Waybright T, Gillette W, Esposito D, Messing S. Adapting recombinant bacterial alkaline phosphatase for nucleotide exchange of small GTPases. Protein Expr Purif 2024; 218:106446. [PMID: 38395209 PMCID: PMC11000209 DOI: 10.1016/j.pep.2024.106446] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/29/2023] [Revised: 01/05/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
The small GTPase Rat sarcoma virus proteins (RAS) are key regulators of cell growth and involved in 20-30% of cancers. RAS switches between its active state and inactive state via exchange of GTP (active) and GDP (inactive). Therefore, to study active protein, it needs to undergo nucleotide exchange to a non-hydrolysable GTP analog. Calf intestine alkaline phosphatase bound to agarose beads (CIP-agarose) is regularly used in a nucleotide exchange protocol to replace GDP with a non-hydrolysable analog. Due to pandemic supply problems and product shortages, we found the need for an alternative to this commercially available product. Here we describe how we generated a bacterial alkaline phosphatase (BAP) with an affinity tag bound to an agarose bead. This BAP completely exchanges the nucleotide in our samples, thereby demonstrating an alternative to the commercially available product using generally available laboratory equipment.
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Affiliation(s)
- Peter H Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Min Hong
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brianna Higgins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vanessa E Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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2
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Taylor T, Gillette W. Production of Isotopically Labeled KRAS4b. Methods Mol Biol 2024; 2797:23-34. [PMID: 38570450 DOI: 10.1007/978-1-0716-3822-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Isotopically labelled proteins are important reagents in structural biology as well as in targeted drug development. The field continues to advance with complex multi-isotope labeling. We have combined our experience in high-level soluble KRAS4b expression with protocols for isotope incorporation, to achieve reliable and efficient approaches for several labeling strategies. Typical experiments achieve nearly 100% 15N incorporation, with yields in the range of 1.3-24.6 mg/L (median = 6.4 mg/L, n = 53). Improvements in the growth parameters in the presence of deuterium reduce the standard time of fermentation from 5 days to 3 days by modifying the medium used during the weaning process. The methods described are compatible with multi-isotope labeling and site-specific labeling.
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Affiliation(s)
- Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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3
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Fu Y, da Fonseca Rezende e Mello J, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, Itkin Z, Stanley TB, Hsu A, Dandey V, Sharma K, Gillette W, Taylor T, Ramakrishnan N, Perkins S, Esposito D, Oh E, Susumu K, Wolak M, Ferrer M, Hall MD, Borgnia MJ, Simeonov A. A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike. PLoS One 2022; 17:e0272364. [PMID: 35947606 PMCID: PMC9365158 DOI: 10.1371/journal.pone.0272364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/22/2022] [Accepted: 07/18/2022] [Indexed: 01/11/2023] Open
Abstract
Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Ying Fu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Juliana da Fonseca Rezende e Mello
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Bryan D. Fleming
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Alex Renn
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Catherine Z. Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Quinlin Hanson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Emily M. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Robert Petrovich
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Richard T. Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Thomas B. Stanley
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Allen Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Venkata Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Kedar Sharma
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nitya Ramakrishnan
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Shelley Perkins
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Eunkeu Oh
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Kimihiro Susumu
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
- Jacobs Corporation, Hanover, Maryland, United States of America
| | - Mason Wolak
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail: (MDH); (MJB); (AS)
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- * E-mail: (MDH); (MJB); (AS)
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail: (MDH); (MJB); (AS)
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4
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Chao FA, Dharmaiah S, Taylor T, Messing S, Gillette W, Esposito D, Nissley DV, McCormick F, Byrd RA, Simanshu DK, Cornilescu G. Insights into the Cross Talk between Effector and Allosteric Lobes of KRAS from Methyl Conformational Dynamics. J Am Chem Soc 2022; 144:4196-4205. [PMID: 35213144 PMCID: PMC10430694 DOI: 10.1021/jacs.2c00007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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] [Indexed: 12/21/2022]
Abstract
KRAS is the most frequently mutated RAS protein in cancer patients, and it is estimated that about 20% of the cancer patients in the United States carried mutant RAS proteins. To accelerate therapeutic development, structures and dynamics of RAS proteins had been extensively studied by various biophysical techniques for decades. Although 31P NMR studies revealed population equilibrium of the two major states in the active GMPPNP-bound form, more complex conformational dynamics in RAS proteins and oncogenic mutants subtly modulate the interactions with their downstream effectors. We established a set of customized NMR relaxation dispersion techniques to efficiently and systematically examine the ms-μs conformational dynamics of RAS proteins. This method allowed us to observe varying synchronized motions that connect the effector and allosteric lobes in KRAS. We demonstrated the role of conformational dynamics of KRAS in controlling its interaction with the Ras-binding domain of the downstream effector RAF1, the first kinase in the MAPK pathway. This allows one to explain, as well as to predict, the altered binding affinities of various KRAS mutants, which was neither previously reported nor apparent from the structural perspective.
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Affiliation(s)
- Fa-An Chao
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94158, United States
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
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5
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Fu Y, Mello JDFRE, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, Itkin Z, Stanley T, Hsu A, Dandey V, Gillette W, Taylor T, Ramakrishnan N, Perkins S, Esposito D, Oh E, Susumu K, Wolak M, Ferrer M, Hall MD, Borgnia MJ, Simeonov A. The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2. bioRxiv 2021. [PMID: 34729560 DOI: 10.1101/2021.10.22.465476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants. One-Sentence Summary A cost-effective, high-throughput, adaptable pipeline capable of identifying effective humanized nanobodies against SARS-CoV-2.
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6
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Kalish H, Klumpp-Thomas C, Hunsberger S, Baus HA, Fay MP, Siripong N, Wang J, Hicks J, Mehalko J, Travers J, Drew M, Pauly K, Spathies J, Ngo T, Adusei KM, Karkanitsa M, Croker JA, Li Y, Graubard BI, Czajkowski L, Belliveau O, Chairez C, Snead KR, Frank P, Shunmugavel A, Han A, Giurgea LT, Rosas LA, Bean R, Athota R, Cervantes-Medina A, Gouzoulis M, Heffelfinger B, Valenti S, Caldararo R, Kolberg MM, Kelly A, Simon R, Shafiq S, Wall V, Reed S, Ford EW, Lokwani R, Denson JP, Messing S, Michael SG, Gillette W, Kimberly RP, Reis SE, Hall MD, Esposito D, Memoli MJ, Sadtler K. Undiagnosed SARS-CoV-2 seropositivity during the first 6 months of the COVID-19 pandemic in the United States. Sci Transl Med 2021; 13:eabh3826. [PMID: 34158410 PMCID: PMC8432952 DOI: 10.1126/scitranslmed.abh3826] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [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: 03/04/2021] [Accepted: 06/16/2021] [Indexed: 12/14/2022]
Abstract
Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates in the United States and elsewhere. To address this, we analyzed seropositivity in 9089 adults in the United States who had not been diagnosed previously with COVID-19. Individuals with characteristics that reflected the U.S. population (n = 27,716) were selected by quota sampling from 462,949 volunteers. Enrolled participants (n = 11,382) provided medical, geographic, demographic, and socioeconomic information and dried blood samples. Survey questions coincident with the Behavioral Risk Factor Surveillance System survey, a large probability-based national survey, were used to adjust for selection bias. Most blood samples (88.7%) were collected between 10 May and 31 July 2020 and were processed using ELISA to measure seropositivity (IgG and IgM antibodies against SARS-CoV-2 spike protein and the spike protein receptor binding domain). The overall weighted undiagnosed seropositivity estimate was 4.6% (95% CI, 2.6 to 6.5%), with race, age, sex, ethnicity, and urban/rural subgroup estimates ranging from 1.1% to 14.2%. The highest seropositivity estimates were in African American participants; younger, female, and Hispanic participants; and residents of urban centers. These data indicate that there were 4.8 undiagnosed SARS-CoV-2 infections for every diagnosed case of COVID-19, and an estimated 16.8 million infections were undiagnosed by mid-July 2020 in the United States.
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Affiliation(s)
- Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Holly Ann Baus
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Nalyn Siripong
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jing Wang
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennifer Hicks
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kyle Pauly
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jacquelyn Spathies
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tran Ngo
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kenneth M Adusei
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Maria Karkanitsa
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jennifer A Croker
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yan Li
- Joint Program in Survey Methodology, Department of Epidemiology and Biostatistics, University of Maryland College Park, College Park, MD 20742, USA
| | - Barry I Graubard
- Division of Cancer Epidemiology and Genetics, Biostatistics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lindsay Czajkowski
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Olivia Belliveau
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Cheryl Chairez
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kelly R Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anandakumar Shunmugavel
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Alison Han
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Luca T Giurgea
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Luz Angela Rosas
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rachel Bean
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rani Athota
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Adriana Cervantes-Medina
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Monica Gouzoulis
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Brittany Heffelfinger
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shannon Valenti
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rocco Caldararo
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Michelle M Kolberg
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Andrew Kelly
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Reid Simon
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Saifullah Shafiq
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Susan Reed
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eric W Ford
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ravi Lokwani
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sam G Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert P Kimberly
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Steven E Reis
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew J Memoli
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA.
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7
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Kalish H, Klumpp-Thomas C, Hunsberger S, Baus HA, Fay MP, Siripong N, Wang J, Hicks J, Mehalko J, Travers J, Drew M, Pauly K, Spathies J, Ngo T, Adusei KM, Karkanitsa M, Croker JA, Li Y, Graubard BI, Czajkowski L, Belliveau O, Chairez C, Snead K, Frank P, Shunmugavel A, Han A, Giurgea LT, Rosas LA, Bean R, Athota R, Cervantes-Medina A, Gouzoulis M, Heffelfinger B, Valenti S, Caldararo R, Kolberg MM, Kelly A, Simon R, Shafiq S, Wall V, Reed S, Ford EW, Lokwani R, Denson JP, Messing S, Michael SG, Gillette W, Kimberly RP, Reis SE, Hall MD, Esposito D, Memoli MJ, Sadtler K. Mapping a Pandemic: SARS-CoV-2 Seropositivity in the United States. medRxiv 2021:2021.01.27.21250570. [PMID: 33532807 PMCID: PMC7852277 DOI: 10.1101/2021.01.27.21250570] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates. To address this, we analyzed seropositivity in US adults who have not previously been diagnosed with COVID-19. Individuals with characteristics that reflect the US population (n = 11,382) and who had not previously been diagnosed with COVID-19 were selected by quota sampling from 241,424 volunteers (ClinicalTrials.gov NCT04334954). Enrolled participants provided medical, geographic, demographic, and socioeconomic information and 9,028 blood samples. The majority (88.7%) of samples were collected between May 10th and July 31st, 2020. Samples were analyzed via ELISA for anti-Spike and anti-RBD antibodies. Estimation of seroprevalence was performed by using a weighted analysis to reflect the US population. We detected an undiagnosed seropositivity rate of 4.6% (95% CI: 2.6 - 6.5%). There was distinct regional variability, with heightened seropositivity in locations of early outbreaks. Subgroup analysis demonstrated that the highest estimated undiagnosed seropositivity within groups was detected in younger participants (ages 18-45, 5.9%), females (5.5%), Black/African American (14.2%), Hispanic (6.1%), and Urban residents (5.3%), and lower undiagnosed seropositivity in those with chronic diseases. During the first wave of infection over the spring/summer of 2020 an estimate of 4.6% of adults had a prior undiagnosed SARS-CoV-2 infection. These data indicate that there were 4.8 (95% CI: 2.8-6.8) undiagnosed cases for every diagnosed case of COVID-19 during this same time period in the United States, and an estimated 16.8 million undiagnosed cases by mid-July 2020.
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Affiliation(s)
- Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Holly Ann Baus
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Nalyn Siripong
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jing Wang
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Jennifer Hicks
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Kyle Pauly
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Jacquelyn Spathies
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Tran Ngo
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Kenneth M. Adusei
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Maria Karkanitsa
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Jennifer A Croker
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Yan Li
- Joint Program in Survey Methodology, Department of Epidemiology and Biostatistics, University of Maryland College Park, College Park, MD 20742
| | - Barry I. Graubard
- Division of Cancer Epidemiology & Genetics, Biostatistics Branch, National Cancer Institute, National Institutes of Health, Bethesda MD 20894
| | - Lindsay Czajkowski
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Olivia Belliveau
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Cheryl Chairez
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Anandakumar Shunmugavel
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Alison Han
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Luca T. Giurgea
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Luz Angela Rosas
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Rachel Bean
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Rani Athota
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Adriana Cervantes-Medina
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Monica Gouzoulis
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Brittany Heffelfinger
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Shannon Valenti
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rocco Caldararo
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick MD 21702
| | - Michelle M. Kolberg
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Andrew Kelly
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Reid Simon
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Saifullah Shafiq
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Susan Reed
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Eric W Ford
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ravi Lokwani
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Sam G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Robert P. Kimberly
- Center for Clinical and Translational Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Steven E. Reis
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick MD 21702
| | - Matthew J. Memoli
- Clinical Studies Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
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8
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Klumpp-Thomas C, Kalish H, Drew M, Hunsberger S, Snead K, Fay MP, Mehalko J, Shunmugavel A, Wall V, Frank P, Denson JP, Hong M, Gulten G, Messing S, Hicks J, Michael S, Gillette W, Hall MD, Memoli MJ, Esposito D, Sadtler K. Standardization of ELISA protocols for serosurveys of the SARS-CoV-2 pandemic using clinical and at-home blood sampling. Nat Commun 2021; 12:113. [PMID: 33397956 PMCID: PMC7782755 DOI: 10.1038/s41467-020-20383-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/29/2020] [Indexed: 01/08/2023] Open
Abstract
The extent of SARS-CoV-2 infection throughout the United States population is currently unknown. High quality serology is key to avoiding medically costly diagnostic errors, as well as to assuring properly informed public health decisions. Here, we present an optimized ELISA-based serology protocol, from antigen production to data analyses, that helps define thresholds for IgG and IgM seropositivity with high specificities. Validation of this protocol is performed using traditionally collected serum as well as dried blood on mail-in blood sampling kits. Archival (pre-2019) samples are used as negative controls, and convalescent, PCR-diagnosed COVID-19 patient samples serve as positive controls. Using this protocol, minimal cross-reactivity is observed for the spike proteins of MERS, SARS1, OC43 and HKU1 viruses, and no cross reactivity is observed with anti-influenza A H1N1 HAI. Our protocol may thus help provide standardized, population-based data on the extent of SARS-CoV-2 seropositivity, immunity and infection.
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Affiliation(s)
- Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Anandakumar Shunmugavel
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Min Hong
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Gulcin Gulten
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jennifer Hicks
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Matthew J Memoli
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20894, USA.
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9
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Mehalko J, Drew M, Snead K, Denson JP, Wall V, Taylor T, Sadtler K, Messing S, Gillette W, Esposito D. Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays. Protein Expr Purif 2020; 179:105802. [PMID: 33248226 PMCID: PMC7687410 DOI: 10.1016/j.pep.2020.105802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 01/20/2023]
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection. Improved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parameters. Two versions of RBD show different sensitivity in serology assays. Yields of greater than 50 mg/l obtained under optimal conditions. Magnetic bead purification technology improves throughput of protein production.
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Affiliation(s)
- Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894, USA
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA.
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10
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Mehalko J, Drew M, Snead K, Denson JP, Wall V, Taylor T, Sadtler K, Messing S, Gillette W, Esposito D. Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays. bioRxiv 2020:2020.11.18.388868. [PMID: 33236017 PMCID: PMC7685350 DOI: 10.1101/2020.11.18.388868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection. Highlights: Improved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parametersTwo versions of RBD show different sensitivity in serology assaysYields of greater than 50 mg/l obtained under optimal conditionsMagnetic bead purification technology improves throughput of protein production.
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Affiliation(s)
- Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20894
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
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Esposito D, Mehalko J, Drew M, Snead K, Wall V, Taylor T, Frank P, Denson JP, Hong M, Gulten G, Sadtler K, Messing S, Gillette W. Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays. Protein Expr Purif 2020; 174:105686. [PMID: 32504802 PMCID: PMC7271859 DOI: 10.1016/j.pep.2020.105686] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 11/23/2022]
Abstract
The SARS-CoV-2 spike trimer is the primary antigen for several serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Through this investigation, we developed a simplified and robust purification strategy that consistently yields 5 mg of protein per liter of expression culture for two commonly used forms of the SARS-CoV-2 spike protein. We show that these proteins form well-behaved stable trimers and are consistently functional in serology assays across multiple protein production lots.
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Affiliation(s)
- Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA.
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Min Hong
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Gulcin Gulten
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
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Esposito D, Mehalko J, Drew M, Snead K, Wall V, Taylor T, Frank P, Denson JP, Hong M, Gulten G, Sadtler K, Messing S, Gillette W. Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays. bioRxiv 2020:2020.05.27.120204. [PMID: 32511418 PMCID: PMC7265690 DOI: 10.1101/2020.05.27.120204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The SARS-CoV-2 spike trimer is the primary antigen for several serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Through this investigation, we developed a simplified and robust purification strategy that consistently yields 5 mg of protein per liter of expression culture for two commonly used forms of the SARS-CoV-2 spike protein. We show that these proteins form well-behaved stable trimers and are consistently functional in serology assays across multiple protein production lots.
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Affiliation(s)
- Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Min Hong
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Gulcin Gulten
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702
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13
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Klumpp-Thomas C, Kalish H, Drew M, Hunsberger S, Snead K, Fay MP, Mehalko J, Shunmugavel A, Wall V, Frank P, Denson JP, Hong M, Gulten G, Messing S, Hicks J, Michael S, Gillette W, Hall MD, Memoli M, Esposito D, Sadtler K. Standardization of enzyme-linked immunosorbent assays for serosurveys of the SARS-CoV-2 pandemic using clinical and at-home blood sampling. medRxiv 2020:2020.05.21.20109280. [PMID: 32511472 PMCID: PMC7265693 DOI: 10.1101/2020.05.21.20109280] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The extent of SARS-CoV-2 infection throughout the United States population is currently unknown. High quality serology is a key tool to understanding the spread of infection, immunity against the virus, and correlates of protection. Limited validation and testing of serology assays used for serosurveys can lead to unreliable or misleading data, and clinical testing using such unvalidated assays can lead to medically costly diagnostic errors and improperly informed public health decisions. Estimating prevalence and clinical decision making is highly dependent on specificity. Here, we present an optimized ELISA-based serology protocol from antigen production to data analysis. This protocol defines thresholds for IgG and IgM for determination of seropositivity with estimated specificity well above 99%. Validation was performed using both traditionally collected serum and dried blood on mail-in blood sampling kits, using archival (pre-2019) negative controls and known PCR-diagnosed positive patient controls. Minimal cross-reactivity was observed for the spike proteins of MERS, SARS1, OC43 and HKU1 viruses and no cross reactivity was observed with anti-influenza A H1N1 HAI titer during validation. This strategy is highly specific and is designed to provide good estimates of seroprevalence of SARS-CoV-2 seropositivity in a population, providing specific and reliable data from serosurveys and clinical testing which can be used to better evaluate and understand SARS-CoV-2 immunity and correlates of protection.
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Affiliation(s)
- Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD, 20850
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Heather Kalish
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute for Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20894
| | - Kelly Snead
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Michael P Fay
- Biostatistics Research Branch, National Institute for Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20894
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Anandakumar Shunmugavel
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Vanessa Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - John-Paul Denson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Min Hong
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Gulcin Gulten
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Simon Messing
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jennifer Hicks
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD, 20850
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD, 20850
| | - Matthew Memoli
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute for Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20894
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Kaitlyn Sadtler
- Section on Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda MD 20894
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14
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Sherekar M, Han SW, Messing S, Drew M, Ye X, Gillette W, Juneja P, O’Neill H, Stanley C, Ramanathan A, de Val N, Lorenzo C, McCormick F, Esposito D. Abstract PR08: Biochemical and structural analysis of the neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-pr08] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Neurofibromin is the 320-kilodalton protein product of the NF1 gene that is mutated in the Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to abrogation of the GTPase-activating activity of the protein, leading to aberrant signaling through the RAS-MAPK pathway. Very little is known about the function of the majority of the NF1 protein—to date, only the GAP domain and a region containing a Sec-PH motif have detailed structural information. To better understand the role of this large protein, we have carried out a series of biochemical and biophysical studies that clearly show that full-length NF1 protein exists primarily as a dimer. Data from in vivo experiments confirmed that this dimerization also occurs in cells, and presumably has biologic implications. A model was generated from negative-stain EM data that suggests that NF1 monomers form both intermolecular contacts to form dimers and intramolecular contacts that stabilize the individual monomers. Deletion analysis permitted us to map these two interacting domains to different parts of the NF1 protein, and crosslinking studies coupled with mass spectrometry helped to identify regions of possible interaction. In addition, introduction of point mutations observed in patients with NF diseases caused a dramatic decrease in the stability of proteins both in vitro and in vivo, potentially arguing for a rationale for loss of NF1 activity by these single mutations.
This abstract is also being presented as Poster A03.
Citation Format: Mukul Sherekar, Sae-Won Han, Simon Messing, Matthew Drew, Xiaoying Ye, William Gillette, Puneet Juneja, Hugh O’Neill, Christopher Stanley, Arvind Ramanathan, Natalia de Val, Claire Lorenzo, Frank McCormick, Dominic Esposito. Biochemical and structural analysis of the neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr PR08.
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Affiliation(s)
- Mukul Sherekar
- 1Frederick National Laboratory for Cancer Research, Frederick, MD,
| | - Sae-Won Han
- 2University of California San Francisco, San Francisco, CA,
| | - Simon Messing
- 1Frederick National Laboratory for Cancer Research, Frederick, MD,
| | - Matthew Drew
- 1Frederick National Laboratory for Cancer Research, Frederick, MD,
| | - Xiaoying Ye
- 1Frederick National Laboratory for Cancer Research, Frederick, MD,
| | - William Gillette
- 1Frederick National Laboratory for Cancer Research, Frederick, MD,
| | | | | | | | | | - Natalia de Val
- 1Frederick National Laboratory for Cancer Research, Frederick, MD,
| | - Claire Lorenzo
- 2University of California San Francisco, San Francisco, CA,
| | | | - Dominic Esposito
- 1Frederick National Laboratory for Cancer Research, Frederick, MD,
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15
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Kopra K, Vuorinen E, Abreu-Blanco M, Wang Q, Eskonen V, Gillette W, Pulliainen AT, Holderfield M, Härmä H. Homogeneous Dual-Parametric-Coupled Assay for Simultaneous Nucleotide Exchange and KRAS/RAF-RBD Interaction Monitoring. Anal Chem 2020; 92:4971-4979. [PMID: 32106676 PMCID: PMC7143314 DOI: 10.1021/acs.analchem.9b05126] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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] [Indexed: 02/07/2023]
Abstract
We have developed a rapid and sensitive single-well dual-parametric method introduced in linked RAS nucleotide exchange and RAS/RAF-RBD interaction assays. RAS mutations are frequent drivers of multiple different human cancers, but the development of therapeutic strategies has been challenging. Traditionally, efforts to disrupt the RAS function have focused on nucleotide exchange inhibitors, GTP-RAS interaction inhibitors, and activators increasing GTPase activity of mutant RAS proteins. As the amount of biological knowledge grows, targeted biochemical assays enabling high-throughput screening have become increasingly interesting. We have previously introduced a homogeneous quenching resonance energy transfer (QRET) assay for nucleotide binding studies with RAS and heterotrimeric G proteins. Here, we introduce a novel homogeneous signaling technique called QTR-FRET, which combine QRET technology and time-resolved Förster resonance energy transfer (TR-FRET). The dual-parametric QTR-FRET technique enables the linking of guanine nucleotide exchange factor-induced Eu3+-GTP association to RAS, monitored at 615 nm, and subsequent Eu3+-GTP-loaded RAS interaction with RAF-RBD-Alexa680 monitored at 730 nm. Both reactions were monitored in a single-well assay applicable for inhibitor screening and real-time reaction monitoring. This homogeneous assay enables separable detection of both nucleotide exchange and RAS/RAF interaction inhibitors using low nanomolar protein concentrations. To demonstrate a wider applicability as a screening and real-time reaction monitoring method, the QTR-FRET technique was also applied for G(i)α GTP-loading and pertussis toxin-catalyzed ADP-ribosylation of G(i)α, for which we synthesized a novel γ-GTP-Eu3+ molecule. The study indicates that the QTR-FRET detection technique presented here can be readily applied to dual-parametric assays for various targets.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Emmiliisa Vuorinen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Maria Abreu-Blanco
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Qi Wang
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - William Gillette
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Arto T Pulliainen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Matthew Holderfield
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
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16
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Agamasu C, Frank P, Perkins S, Waybright T, Messing S, Gillette W, Stephen AG. Fully Processed Recombinant KRAS4b: Isolating and Characterizing the Farnesylated and Methylated Protein. J Vis Exp 2020. [PMID: 32009649 DOI: 10.3791/60703] [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] [Indexed: 10/31/2022] Open
Abstract
Protein prenylation is a key modification that is responsible for targeting proteins to intracellular membranes. KRAS4b, which is mutated in 22% of human cancers, is processed by farnesylation and carboxymethylation due to the presence of a 'CAAX' box motif at the C-terminus. An engineered baculovirus system was used to express farnesylated and carboxymethylated KRAS4b in insect cells and has been described previously. Here, we describe the detailed, practical purification and biochemical characterization of the protein. Specifically, affinity and ion exchange chromatography were used to purify the protein to homogeneity. Intact and native mass spectrometry was used to validate the correct modification of KRAS4b and to verify nucleotide binding. Finally, membrane association of farnesylated and carboxymethylated KRAS4b to liposomes was measured using surface plasmon resonance spectroscopy.
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Affiliation(s)
- Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
| | - Peter Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research;
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17
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Sherekar M, Han SW, Ghirlando R, Messing S, Drew M, Rabara D, Waybright T, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV, Gillette W, McCormick F, Esposito D. Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49919-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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18
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Sherekar M, Han SW, Ghirlando R, Messing S, Drew M, Rabara D, Waybright T, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV, Gillette W, McCormick F, Esposito D. Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer. J Biol Chem 2019; 295:1105-1119. [PMID: 31836666 PMCID: PMC6983858 DOI: 10.1074/jbc.ra119.010934] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/10/2019] [Indexed: 12/28/2022] Open
Abstract
Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS–mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH motif. To better understand the role of this large protein, here we carried out a series of biochemical and biophysical experiments, including size-exclusion chromatography–multiangle light scattering (SEC-MALS), small-angle X-ray and neutron scattering, and analytical ultracentrifugation, indicating that full-length neurofibromin forms a high-affinity dimer. We observed that neurofibromin dimerization also occurs in human cells and likely has biological and clinical implications. Analysis of purified full-length and truncated neurofibromin variants by negative-stain EM revealed the overall architecture of the dimer and predicted the potential interactions that contribute to the dimer interface. We could reconstitute structures resembling high-affinity full-length dimers by mixing N- and C-terminal protein domains in vitro. The reconstituted neurofibromin was capable of GTPase activation in vitro, and co-expression of the two domains in human cells effectively recapitulated the activity of full-length neurofibromin. Taken together, these results suggest how neurofibromin dimers might form and be stabilized within the cell.
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Affiliation(s)
- Mukul Sherekar
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Sae-Won Han
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158.,Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Matthew Drew
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Puneet Juneja
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia 30322
| | - Hugh O'Neill
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | | | | | | | - Sriram Subramaniam
- Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702.,Department of Biochemistry, Life Sciences Center, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702.,Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
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19
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Tran T, Dharmaiah S, Yan W, Chan A, Waybright T, Gillette W, Esposito D, Stephen A, Nissley D, McCormick F, Simanshu DK. Abstract 960: Structures of oncogenic KRAS mutants in the active state and complexed with RasGAP provide new insights into targeting RAS-driven cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-960] [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] [Indexed: 11/16/2022]
Abstract
Abstract
RAS proteins are responsible for a third of all cancer cases and are involved in both early onset and progression of the deadliest cancers, including lung, colon, and pancreatic cancers. RAS proteins act as binary molecular switches that cycle between active GTP-bound and inactive GDP-bound states. The conversion from inactive to the active form is stimulated by guanine nucleotide-exchange factors (GEFs). Conversion back to the inactive form is mediated by GTPase-activating proteins (GAPs). In the GTP-bound state, RAS proteins interact with a variety of effector proteins such as RAF Kinase, PI 3-Kinase, and RalGDS, leading to activation of several signaling cascades within the cell. Among the three RAS isoforms - HRAS, KRAS, and NRAS, KRAS is the most commonly mutated gene. 98% of oncogenic RAS mutations are found at amino acid positions G12, G13, and Q61, which impair intrinsic and GAP-mediated GTPase function resulting in accumulation of constitutively GTP-bound RAS in cells. To gain insights into the effect of oncogenic mutations on overall structure and GTP hydrolysis, we solved high-resolution crystal structures of wild-type and six oncogenic mutants (G12C, G12D, G12V, G13D, Q61L, and Q61R) of KRAS4b in complex with GMPPNP (a non-hydrolysable GTP analog) and magnesium. Structural comparison of mutants vs. wild-type KRA4b in complex with GMPPNP/Mg2+ and KRAS4b mutants vs. WT-HRAS bound to RASA1-GAP provides a rationale for impaired intrinsic and GAP-mediated GTP hydrolysis in the KRAS mutants. Interestingly, we noticed variations in the conformation of the switch I region which contacts both nucleotide and many downstream effector proteins. In the structure of three KRAS mutants, the switch I region adopts a partially open conformation known as the state I. Importantly, the state I structures reveal new pockets that could be exploited for structure-based drug design. Recently we have also solved the structures of GMPPNP-bound wild-type and Q61 mutants of KRAS in complex with RasGAPs. Structural analysis of KRAS Q61 mutants bound to RasGAPs provides a rationale for impaired GAP-mediated GTP hydrolysis and new insights for designing small molecules that could potentially restore GAP-mediated GTPase activity in these mutants.
Citation Format: Timothy Tran, Srisathiyanarayanan Dharmaiah, Wupeng Yan, Albert Chan, Timothy Waybright, William Gillette, Dominic Esposito, Andrew Stephen, Dwight Nissley, Frank McCormick, Dhirendra K. Simanshu. Structures of oncogenic KRAS mutants in the active state and complexed with RasGAP provide new insights into targeting RAS-driven cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 960.
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Affiliation(s)
- Timothy Tran
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | - Wupeng Yan
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Albert Chan
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | - William Gillette
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dominic Esposito
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Andrew Stephen
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dwight Nissley
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Frank McCormick
- Frederick National Laboratory for Cancer Research, Frederick, MD
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20
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Sherekar M, Han SW, Messing S, Drew M, Gillette W, Lorenzo C, McCormick F, Esposito D. Abstract 1768: Biochemical and structural analysis of the Neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1768] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Neurofibromin is the 320 kilodalton protein product of the NF1 gene which is mutated in the Rasopathy disease Neurofibromatosis Type I. Defects in NF1 lead to abrogation of the GTPase activating activity of the protein, leading to aberrant signaling through the RAS-MAPK pathway. Very little is known about the function of the majority of the NF1 protein—to date only the GAP domain and a region containing a Sec-PH motif have detailed structural information. To better understand the role of this large protein, we have carried out a series of biochemical and biophysical studies which clearly show that full length NF1 protein exists primarily as a dimer. Data from in vivo experiments confirmed that this dimerization also occurs in cells, and presumably has biological implications. A model was generated from negative-stain EM data which suggests that NF1 monomers form both intermolecular contacts to form dimers and intramolecular contacts which stabilize the individual monomers. Deletion analysis permitted us to map these two interacting domains to different parts of the NF1 protein, and crosslinking studies coupled with mass spectrometry helped to identify regions of possible interaction. In addition, introduction of point mutations observed in patients with NF diseases caused a dramatic decrease in the stability of proteins both in vitro and in vivo, potentially arguing for a rationale for loss of NF1 activity by these single mutations
Citation Format: Mukul Sherekar, Sae-Won Han, Simon Messing, Matthew Drew, William Gillette, Claire Lorenzo, Frank McCormick, Dominic Esposito. Biochemical and structural analysis of the Neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1768.
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Affiliation(s)
- Mukul Sherekar
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Sae-Won Han
- 2University of California San Francisco, San Francisco, CA
| | - Simon Messing
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Matthew Drew
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Gillette
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Claire Lorenzo
- 2University of California San Francisco, San Francisco, CA
| | | | - Dominic Esposito
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
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21
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Gillette W, Frank P, Perkins S, Drew M, Grose C, Esposito D. Production of Farnesylated and Methylated Proteins in an Engineered Insect Cell System. Methods Mol Biol 2019; 2009:259-277. [PMID: 31152410 DOI: 10.1007/978-1-4939-9532-5_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein prenylation is a common posttranslational modification that enhances the ability of proteins to interact with membrane components within the cell. In many cases, these prenylated proteins are involved in important human diseases, including aging-related disorders and cancer. To effectively study these proteins or develop therapeutics, large quantities of properly modified proteins are required. Historically, production of fully modified farnesylated and methylated proteins at high yield has been challenging. Recently, an engineered insect cell system which is capable of producing authentically modified KRAS protein was used to generate material for structural studies and assay development. Here we describe protocols for extending this work to other farnesylated and methylated substrates.
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Affiliation(s)
- William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Peter Frank
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shelley Perkins
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Matthew Drew
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Carissa Grose
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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22
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Stephen AG, Van Q, Tonelli M, Gillette W, Esposito D, Niu B, Gross M, Heinrich F, Ramanathan A, Stanley C. Abstract 5238: Structural and biochemical characterization of membrane bound KRAS. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5238] [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] [Indexed: 11/16/2022]
Abstract
Abstract
KRAS4b functions as a molecular switch cycling between an active GTP bound state and inactive GDP state. Active KRAS4b binds tightly to RAF1 via its Ras binding domain (RBD), however activation of RAF1 competent for MAPK signal transduction requires membrane bound KRAS4b. Using recombinant farnesylated and methylated KRAS4b (KRAS4b-FMe) we have used a variety of biophysical methodologies including paramagnetic relaxation enhancement NMR, neutron reflectivity, small angle neutron and x-ray scattering and protein footprinting to gain insights into the orientation and structure of KRAS-FMe bound to a membrane. In these experiments we have used Nanodiscs or tethered lipid bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline or -serine (70% POPC 30% POPS). Our data indicate that KRAS-FMe is oriented perpendicular to the membrane with minimal direct contacts to the membrane. The nucleotide bound state does not significantly change the orientation relative to the membrane. We will also present data on the effect of the RBD domain of RAF1 binding to KRAS-FMe at the membrane.
Citation Format: Andrew G. Stephen, Que Van, Marco Tonelli, William Gillette, Dominic Esposito, Ben Niu, Michael Gross, Frank Heinrich, Arvind Ramanathan, Christopher Stanley. Structural and biochemical characterization of membrane bound KRAS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5238. doi:10.1158/1538-7445.AM2017-5238
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Affiliation(s)
| | - Que Van
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Marco Tonelli
- 2National Magnet Resource Facility at Madison, Madison, WI
| | - William Gillette
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dominic Esposito
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Ben Niu
- 3Washington University in St. Louis, St. Louis, MO
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Tran T, Dharmaiah S, Chertov O, Waybright T, Gillette W, Esposito D, Nissley D, McCormick F, Stephen A, Simanshu D. Abstract 1366: Structural basis of impaired GTP hydrolysis in oncogenic mutants of KRAS. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1366] [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] [Indexed: 11/16/2022]
Abstract
Abstract
RAS mutations are found in one-third of all human cancers. Among the three RAS isoforms - HRAS, KRAS and NRAS, KRAS is the most commonly mutated gene (in 86% of RAS-driven cancers) and the mutations are often detected in pancreatic, colorectal and lung cancers. RAS proteins function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. The active or inactive state of RAS proteins is regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In the GTP-bound state, RAS proteins interact with a variety of effector proteins, such as Raf, PI3K, and RalGDS, leading to activation of several signaling cascades within the cell. In 98% of the cases, oncogenic RAS mutations are found at amino acid positions G12, G13, and Q61 which impair intrinsic and GAP-mediated GTPase function resulting in accumulation of constitutively GTP-bound RAS in cells. To gain insights into the effect of oncogenic mutations on overall structure and GTP hydrolysis, we solved high-resolution crystal structures of wild type and six oncogenic mutants (G12C, G12D, G12V, G13D, Q61L and Q61R) of KRAS4b in complex with GMPPNP (a non-hydrolysable GTP analog) and magnesium. Comparison of GDP and GMPPNP bound structures of wild type (WT) KRAS4b suggests conformational changes that occur when KRAS4b transitions from inactive to active state. Comparison of mutant and wild-type KRAS structures has shown the appearance of new pockets in some cases that could be exploited for structure-based drug design. Structural superposition of mutants vs. wild type KRAS4b in complex with GMPPNP/Mg2+, and KRAS4b mutants vs. WT-HRAS bound to RASA1-GAP provides a rationale for impaired intrinsic and GAP-mediated GTP hydrolysis in the KRAS mutants.
Citation Format: Timothy Tran, Sathiya Dharmaiah, Oleg Chertov, Timothy Waybright, William Gillette, Dominic Esposito, Dwight Nissley, Frank McCormick, Andrew Stephen, Dhirendra Simanshu. Structural basis of impaired GTP hydrolysis in oncogenic mutants of KRAS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1366. doi:10.1158/1538-7445.AM2017-1366
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Affiliation(s)
- Timothy Tran
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Sathiya Dharmaiah
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Oleg Chertov
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Timothy Waybright
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Gillette
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dominic Esposito
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dwight Nissley
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Frank McCormick
- 2Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Andrew Stephen
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dhirendra Simanshu
- 1NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD
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Esposito D, Mehalko J, Wall V, Grose C, Gillette W, Stephens R. Abstract 1872: Development of reference reagents to accelerate research on the RAS pathway. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1872] [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] [Indexed: 11/16/2022]
Abstract
Abstract
The RAS Reference Reagents program within the NCI RAS Initiative is produces and distributes qualified DNA vectors, cell lines, and viruses to the external community to facilitate research into RAS biology and development of RAS cancer therapeutics. DNA vectors representing a variety of RAS mutations, as well as a complete collection of 180 genes in the RAS pathway are available as Gateway-compatible Entry clones. These clones represent the most commonly expressed transcript forms of the 180 genes, many of which were not previously available in full-length, wildtype forms. The vectors can be used with the FNLCR combinatorial cloning library to easily generate a large number of different types of expression clones with various promoters, fusion tags, and plasmid backbones. Additional reagents under construction include validated plasmid and lentiviral reagents for shRNA and CRISPR delivery, qualified cell lines for use in research into the RAS pathway, and systems for the generation of highly purified and characterized Ras and Ras-related proteins. A highlight of these reagents are materials for the high yield production of properly processed, prenylated KRAS protein using an engineered insect cell expression system. This system could be used to produce other prenylated small GTPases at levels not previously attainable. All of the resources of the RAS Reference Reagents program are readily available to the academic community through simple mechanisms, and can be licensed to industry scientists as well. The program is also interested in identifying the needs of the community for additional RAS-related resources, and is developing methods for vetting requests from the outside to provide additional reagents.
Citation Format: Dominic Esposito, Jennifer Mehalko, Vanessa Wall, Carissa Grose, William Gillette, Robert Stephens. Development of reference reagents to accelerate research on the RAS pathway. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1872.
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Affiliation(s)
- Dominic Esposito
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Jennifer Mehalko
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Vanessa Wall
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Carissa Grose
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Gillette
- Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert Stephens
- Frederick National Laboratory for Cancer Research, Frederick, MD
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Dharmaiah S, Bindu L, Frank P, Gillette W, Esposito D, Nissley D, McCormick F, Stephen A, Simanshu D. Abstract 4373: Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4373] [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] [Indexed: 11/16/2022]
Abstract
Abstract
KRAS is the most frequently mutated member of RAS superfamily in all human cancers. Post-translational farnesylation and methylation of KRAS at its C-terminal end plays an important role in its trafficking to proper subcellular compartments for cell signaling events. PDEδ acts as a chaperone for farnesylated members of the RAS superfamily and plays a key role in their trafficking from the place of biosynthesis or post-translational modification to a transport vesicle or plasma membrane. We solved the structures of wild-type full-length KRAS4b (farnesylated and methylated) in complex with PDEδ in two different crystal forms at 2 Ang resolution. Our structure showed that only the last six amino acids of hypervariable region (and not the G-domain) of KRAS4b interact with PDEδ. Farnesyl and methyl groups present on Cys185 bind tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we could see all amino acids present in the hypervariable region of KRAS4b, thus providing atomic details of hypervariable region of KRAS4b for the first time. Comparison of the two crystal forms suggests how PDEδ could bind to both farnesylated as well as geranylgeranylated KRAS4b. The structure provides the rationale for nucleotide-independent binding of KRAS4b to PDEδ and its interaction with other farnesylated but not palmitoylated members of RAS superfamily.
Citation Format: Sathiya Dharmaiah, Lakshman Bindu, Peter Frank, William Gillette, Dominic Esposito, Dwight Nissley, Frank McCormick, Andrew Stephen, Dhirendra Simanshu. Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4373.
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Affiliation(s)
| | - Lakshman Bindu
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Peter Frank
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Gillette
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dominic Esposito
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Dwight Nissley
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Frank McCormick
- 2Frederick National Laboratory for Cancer Research and University of California San Francisco, San Francisco, CA
| | - Andrew Stephen
- 1Frederick National Laboratory for Cancer Research, Frederick, MD
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Labo N, Miley W, Marshall V, Gillette W, Esposito D, Bess M, Turano A, Uldrick T, Polizzotto MN, Wyvill KM, Bagni R, Yarchoan R, Whitby D. Heterogeneity and breadth of host antibody response to KSHV infection demonstrated by systematic analysis of the KSHV proteome. PLoS Pathog 2014; 10:e1004046. [PMID: 24675986 PMCID: PMC3968157 DOI: 10.1371/journal.ppat.1004046] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 08/26/2013] [Accepted: 02/17/2014] [Indexed: 01/15/2023] Open
Abstract
The Kaposi sarcoma associated herpesvirus (KSHV) genome encodes more than 85 open reading frames (ORFs). Serological evaluation of KSHV infection now generally relies on reactivity to just one latent and/or one lytic protein (commonly ORF73 and K8.1). Most of the other polypeptides encoded by the virus have unknown antigenic profiles. We have systematically expressed and purified products from 72 KSHV ORFs in recombinant systems and analyzed seroreactivity in US patients with KSHV-associated malignancies, and US blood donors (low KSHV seroprevalence population). We identified several KSHV proteins (ORF38, ORF61, ORF59 and K5) that elicited significant responses in individuals with KSHV-associated diseases. In these patients, patterns of reactivity were heterogeneous; however, HIV infection appeared to be associated with breadth and intensity of serological responses. Improved antigenic characterization of additional ORFs may increase the sensitivity of serologic assays, lead to more rapid progresses in understanding immune responses to KSHV, and allow for better comprehension of the natural history of KSHV infection. To this end, we have developed a bead-based multiplex assay detecting antibodies to six KSHV antigens.
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Affiliation(s)
- Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Wendell Miley
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - William Gillette
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Dominic Esposito
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Matthew Bess
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Alexandra Turano
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Thomas Uldrick
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mark N. Polizzotto
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kathleen M. Wyvill
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Rachel Bagni
- Protein Expression Laboratory, Advanced Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail:
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Hopkins R, Esposito D, Gillette W. Widening the bottleneck: increasing success in protein expression and purification. J Struct Biol 2010; 172:14-20. [PMID: 20650317 DOI: 10.1016/j.jsb.2010.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/11/2010] [Accepted: 07/15/2010] [Indexed: 11/24/2022]
Abstract
The number of variables at play in the expression and purification of a single protein dwarf those involved in sequencing a genome. Although certain trends are apparent, there is no one-size-fits-all approach to the process of purifying proteins. Thus, whereas numerous genome sequencing projects are providing an overwhelming number of interesting open reading frames for structural biologists to study, fully realizing the potential of this resource is still only a distant hope. We will discuss several current approaches to high throughput expression and purification as well as strategies that have served us well to quickly identify lead protein expression constructs in the context of a core service protein expression and purification laboratory. The use of the baculovirus expression vector system and implementation of a purification screening method will be emphasized.
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Affiliation(s)
- Ralph Hopkins
- Protein Expression Laboratory, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
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Gillette W, Patrick TB. Medical identity theft: an emerging problem for informatics. AMIA Annu Symp Proc 2007:964. [PMID: 18694064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 07/30/2007] [Accepted: 10/11/2007] [Indexed: 05/26/2023]
Abstract
This poster reports a preliminary review of medical identity theft. Financial identity theft has received a great deal of media attention. Medical identity theft is a particular kind of identity theft that has received little attention. There are two main subtypes of medical identity theft. In the first type the stolen medical identity is used to receive medical services, and in the second type the stolen medical identity is used to commit healthcare fraud.
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Affiliation(s)
- William Gillette
- Healthcare Administration and Informatics, College of Health Sciences, University of Wisconsin-Milwaukee, USA
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Schmeisser H, Kontsek P, Esposito D, Gillette W, Schreiber G, Zoon KC. Binding Characteristics of IFN-alpha Subvariants to IFNAR2-EC and Influence of the 6-Histidine Tag. J Interferon Cytokine Res 2007; 26:866-76. [PMID: 17238829 DOI: 10.1089/jir.2006.26.866] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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] [Indexed: 11/12/2022] Open
Abstract
The expression, purification, detection, and assay of recombinant proteins have been made more convenient and rapid by the use of small affinity tags. To facilitate the purification of interferon-alpha2c (IFN-alpha2c) by metal chelate affinity chromatography, N-terminal 6-histidine tag was introduced via genetic manipulation. Two preparations of IFN material were purified; one contained IFN-alpha2c with the 6-histidine tag, and the other contained IFN-alpha2c without the 6-histidine tag. The antigenic properties of the human IFN-alpha2c subvariant with and without the 6-histidine tag, as well as the effects of the N-terminal 6-histidine tag on IFN-alpha2c interaction with the extracellular domain of human IFN-alpha receptor chain 2 (IFNAR2-EC) were examined. For the purposes of this study, IFNs were characterized by Western blots with anti-IFN monoclonal antibodies (mAb) and bioassays. Immunoblot analyses showed differences between IFN-alpha2c-6-histidine tag and IFN-alpha2a, b, c in their interaction with IFNAR2-EC. We also observed differences between IFN-alpha2c-6-histidine tag and IFN-alpha2a, b, c in bioactivities. This study is the first report that shows that an N-terminal 6-histidine tag on IFN-alpha2c can affect its interaction with receptor and cause a different bioactivity.
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Boeshans KM, Wolf R, Voscopoulos C, Gillette W, Esposito D, Mueser TC, Yuspa SH, Ahvazi B. Purification, crystallization and preliminary X-ray diffraction of human S100A15. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:467-70. [PMID: 16682778 PMCID: PMC2219979 DOI: 10.1107/s1744309106012838] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 04/08/2006] [Indexed: 11/10/2022]
Abstract
Human S100A15 is a novel member of the S100 family of EF-hand calcium-binding proteins and was recently identified in psoriasis, where it is significantly upregulated in lesional skin. The protein is implicated as an effector in calcium-mediated signal transduction pathways. Although its biological function is unclear, the association of the 11.2 kDa S100A15 with psoriasis suggests that it contributes to the pathogenesis of the disease and could provide a molecular target for therapy. To provide insight into the function of S100A15, the protein was crystallized to visualize its structure and to further the understanding of how the many similar calcium-binding mediator proteins in the cell distinguish their cognate target molecules. The S100A15 protein has been cloned, expressed and purified to homogeneity and produced two crystal forms. Crystals of form I are triclinic, with unit-cell parameters a = 33.5, b = 44.3, c = 44.8 angstroms, alpha = 71.2, beta = 68.1, gamma = 67.8 degrees and an estimated two molecules in the asymmetric unit, and diffract to 1.7 angstroms resolution. Crystals of form II are monoclinic, with unit-cell parameters a = 82.1, b = 33.6, c = 52.2 angstroms, beta = 128.2 degrees and an estimated one molecule in the asymmetric unit, and diffract to 2.0 angstroms resolution. This structural analysis of the human S100A15 will further aid in the phylogenic comparison between the other members of the S100 protein family, especially the highly homologous paralog S100A7.
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Affiliation(s)
- Karen M. Boeshans
- X-ray Crystallography Facility, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald Wolf
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher Voscopoulos
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William Gillette
- Protein Expression Laboratory, Research Technology Program, National Cancer Institute, SAIC-Frederick Inc., Frederick, MD 21702, USA
| | - Dominic Esposito
- Protein Expression Laboratory, Research Technology Program, National Cancer Institute, SAIC-Frederick Inc., Frederick, MD 21702, USA
| | - Timothy C. Mueser
- Department of Chemistry, University of Toledo, Toledo, OH 43606, USA
| | - Stuart H. Yuspa
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bijan Ahvazi
- X-ray Crystallography Facility, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
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Yang Q, Huang W, Jozwik C, Lin Y, Glasman M, Caohuy H, Srivastava M, Esposito D, Gillette W, Hartley J, Pollard HB. Cardiac glycosides inhibit TNF-alpha/NF-kappaB signaling by blocking recruitment of TNF receptor-associated death domain to the TNF receptor. Proc Natl Acad Sci U S A 2005; 102:9631-6. [PMID: 15983368 PMCID: PMC1160519 DOI: 10.1073/pnas.0504097102] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [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] [Indexed: 01/03/2023] Open
Abstract
Digitoxin and structurally related cardiac glycoside drugs potently block activation of the TNF-alpha/NF-kappaB signaling pathway. We have hypothesized that the mechanism might be discovered by searching systematically for selective inhibitory action through the entire pathway. We report that the common action of these drugs is to block the TNF-alpha-dependent binding of TNF receptor 1 to TNF receptor-associated death domain. This drug action can be observed with native cells, such as HeLa, and reconstituted systems prepared in HEK293 cells. All other antiinflammatory effects of digitoxin on NF-kappaB and c-Jun N-terminal kinase pathways appear to follow from the blockade of this initial upstream signaling event.
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Affiliation(s)
- Qingfeng Yang
- Department of Anatomy, Physiology, and Genetics and Institute for Molecular Medicine, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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Scopp IW, Gillette W, Kumar V, Larato D. Treatment of oral lesions with topically applied vancomycin hydrochloride. Oral Surg Oral Med Oral Pathol 1967; 24:703-6. [PMID: 4862230 DOI: 10.1016/0030-4220(67)90220-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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