1
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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. bioRxiv 2024:2023.07.10.548257. [PMID: 37502916 PMCID: PMC10369915 DOI: 10.1101/2023.07.10.548257] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Mutations in the tyrosine phosphatase SHP2 are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that, while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8-10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.
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Affiliation(s)
- Anne E. van Vlimmeren
- Department of Chemistry, Columbia University, New York, NY 10027
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Rashmi Voleti
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Ziyuan Jiang
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Deepti Karandur
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
| | - Preston A. Humphries
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY 10027
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2
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Cabanero DC, Kariofillis SK, Johns AC, Kim J, Ni J, Park S, Parker DL, Ramil CP, Roy X, Shah NH, Rovis T. Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light. J Am Chem Soc 2024; 146:1337-1345. [PMID: 38165744 DOI: 10.1021/jacs.3c09545] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
State-of-the-art methods in photoproximity labeling center on the targeted generation and capture of short-lived reactive intermediates to provide a snapshot of local protein environments. Diazirines are the current gold standard for high-resolution proximity labeling, generating short-lived aryl(trifluoromethyl) carbenes. Here, we present a method to access aryl(trifluoromethyl) carbenes from a stable diazo source via tissue-penetrable, deep red to near-infrared light (600-800 nm). The operative mechanism of this activation involves Dexter energy transfer from photoexcited osmium(II) photocatalysts to the diazo, thus revealing an aryl(trifluoromethyl) carbene. The labeling preferences of the diazo probe with amino acids are studied, showing high reactivity toward heteroatom-H bonds. Upon the synthesis of a biotinylated diazo probe, labeling studies are conducted on native proteins as well as proteins conjugated to the Os photocatalyst. Finally, we demonstrate that the conjugation of a protein inhibitor to the photocatalyst also enables selective protein labeling in the presence of spectator proteins and achieves specific labeling of a membrane protein on the surface of mammalian cells via a two-antibody photocatalytic system.
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Affiliation(s)
- David C Cabanero
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Stavros K Kariofillis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Andrew C Johns
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jinwoo Kim
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jizhi Ni
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sangho Park
- Discovery Biology, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Dann L Parker
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carlo P Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Xavier Roy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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3
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Tsai YL, Arias-Badia M, Kadlecek TA, Lwin YM, Srinath A, Shah NH, Wang ZE, Barber D, Kuriyan J, Fong L, Weiss A. TCR signaling promotes formation of an STS1-Cbl-b complex with pH-sensitive phosphatase activity that suppresses T cell function in acidic environments. Immunity 2023; 56:2682-2698.e9. [PMID: 38091950 PMCID: PMC10785950 DOI: 10.1016/j.immuni.2023.11.010] [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: 01/23/2023] [Revised: 08/11/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023]
Abstract
T cell responses are inhibited by acidic environments. T cell receptor (TCR)-induced protein phosphorylation is negatively regulated by dephosphorylation and/or ubiquitination, but the mechanisms underlying sensitivity to acidic environments are not fully understood. Here, we found that TCR stimulation induced a molecular complex of Cbl-b, an E3-ubiquitin ligase, with STS1, a pH-sensitive unconventional phosphatase. The induced interaction depended upon a proline motif in Cbl-b interacting with the STS1 SH3 domain. STS1 dephosphorylated Cbl-b interacting phosphoproteins. The deficiency of STS1 or Cbl-b diminished the sensitivity of T cell responses to the inhibitory effects of acid in an autocrine or paracrine manner in vitro or in vivo. Moreover, the deficiency of STS1 or Cbl-b promoted T cell proliferative and differentiation activities in vivo and inhibited tumor growth, prolonged survival, and improved T cell fitness in tumor models. Thus, a TCR-induced STS1-Cbl-b complex senses intra- or extra-cellular acidity and regulates T cell responses, presenting a potential therapeutic target for improving anti-tumor immunity.
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Affiliation(s)
- Yuan-Li Tsai
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marcel Arias-Badia
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Theresa A Kadlecek
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yee May Lwin
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aahir Srinath
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Zhi-En Wang
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Kuriyan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Lawrence Fong
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arthur Weiss
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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4
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Li A, Voleti R, Lee M, Gagoski D, Shah NH. High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display. eLife 2023; 12:82345. [PMID: 36927728 PMCID: PMC10065799 DOI: 10.7554/elife.82345] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
Tyrosine kinases and SH2 (phosphotyrosine recognition) domains have binding specificities that depend on the amino acid sequence surrounding the target (phospho)tyrosine residue. Although the preferred recognition motifs of many kinases and SH2 domains are known, we lack a quantitative description of sequence specificity that could guide predictions about signaling pathways or be used to design sequences for biomedical applications. Here, we present a platform that combines genetically-encoded peptide libraries and deep sequencing to profile sequence recognition by tyrosine kinases and SH2 domains. We screened several tyrosine kinases against a million-peptide random library and used the resulting profiles to design high-activity sequences. We also screened several kinases against a library containing thousands of human proteome-derived peptides and their naturally-occurring variants. These screens recapitulated independently measured phosphorylation rates and revealed hundreds of phosphosite-proximal mutations that impact phosphosite recognition by tyrosine kinases. We extended this platform to the analysis of SH2 domains and showed that screens could predict relative binding affinities. Finally, we expanded our method to assess the impact of non-canonical and post-translationally modified amino acids on sequence recognition. This specificity profiling platform will shed new light on phosphotyrosine signaling and could readily be adapted to other protein modification/recognition domains.
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Affiliation(s)
- Allyson Li
- Department of Chemistry, Columbia University, New York, United States
| | - Rashmi Voleti
- Department of Chemistry, Columbia University, New York, United States
| | - Minhee Lee
- Department of Chemistry, Columbia University, New York, United States
| | - Dejan Gagoski
- Department of Chemistry, Columbia University, New York, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, United States
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5
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Hong SH, Xi SY, Johns AC, Tang LC, Li A, Hum MN, Chartier CA, Jovanovic M, Shah NH. Mapping the chemical space of active-site targeted covalent ligands for protein tyrosine phosphatases. Chembiochem 2023; 24:e202200706. [PMID: 36893077 DOI: 10.1002/cbic.202200706] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/10/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are an important class of enzymes that modulate essential cellular processes through protein dephosphorylation and are dysregulated in various disease states. There is demand for new compounds that target the active sites of these enzymes, for use as chemical tools to dissect their biological roles or as leads for the development of new therapeutics. In this study, we explore an array of electrophiles and fragment scaffolds to investigate the required chemical parameters for covalent inhibition of tyrosine phosphatases. Our analysis juxtaposes the intrinsic electrophilicity of these compounds with their potency against several classical PTPs, revealing chemotypes that inhibit tyrosine phosphatases while minimizing excessive, potentially non-specific reactivity. We also assess sequence divergence at key residues in PTPs to explain their differential susceptibility to covalent inhibition. We anticipate that our study will inspire new strategies to develop covalent probes and inhibitors for tyrosine phosphatases.
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Affiliation(s)
- Suk Ho Hong
- Columbia University, Department of Chemistry, 3000 Broadway, 10027, New York, UNITED STATES
| | - Sarah Y Xi
- Columbia University, Department of Chemistry, 3000 Broadway, 10027, New York, UNITED STATES
| | - Andrew C Johns
- Columbia University, Department of Chemistry, 3000 Broadway, 10027, New York, UNITED STATES
| | - Lauren C Tang
- Columbia University, Department of Biological Sciences, 1212 Amsterdam Avenue, 10027, New York, UNITED STATES
| | - Allyson Li
- Columbia University, Department of Chemistry, 3000 Broadway, 10027, New York, UNITED STATES
| | - Madeleine N Hum
- Columbia University, Department of Chemistry, 3000 Broadway, 10027, New York, UNITED STATES
| | - Cassandra A Chartier
- Columbia University, Department of Chemistry, 3000 Broadway, 10027, New York, UNITED STATES
| | - Marko Jovanovic
- Columbia University, Department of Biological Sciences, 1212 Amsterdam Avenue, 10027, New York, UNITED STATES
| | - Neel H Shah
- Columbia University, Department of Chemistry, 3000 Broadway, 344 Havemeyer Hall, MC 3105, 10027, New York, UNITED STATES
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6
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Lamartina CW, Chartier CA, Lee S, Shah NH, Rovis T. Modular Synthesis of Unnatural Peptides via Rh(III)-Catalyzed Diastereoselective Three-Component Carboamidation Reaction. J Am Chem Soc 2023; 145:1129-1135. [PMID: 36576945 PMCID: PMC10580301 DOI: 10.1021/jacs.2c10793] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herein we report a modular peptide ligation methodology that couples dioxazolones, arylboronic acids, and acrylamides to construct amide bonds in a diastereoselective manner under mild conditions, facilitated by Rh(III) catalysis. By converting the C-terminus of one peptide into a dioxazolone and the N-terminus of a second peptide into an acrylamide, the two pieces can be bridged by an arylboronic acid to construct unnatural phenylalanine, tyrosine, and tryptophan residues at the junction point with diastereoselectivity for their corresponding d-stereocenters. The reaction exhibits excellent functional group tolerance with a large substrate scope and is compatible with a wide array of protected amino acid residues that are utilized in Fmoc solid phase peptide synthesis. The methodology is applied to the synthesis of six diastereomeric proteasome inhibitor analogs, as well as the ligation of two 10-mer oligopeptides to construct a 21-mer polypeptide with an unnatural phenylalanine residue at the center.
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Affiliation(s)
| | - Cassandra A. Chartier
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Sumin Lee
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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7
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Doron-Mandel E, Bokor BJ, Ma Y, Street LA, Tang LC, Abdou AA, Shah NH, Rosenberger GA, Jovanovic M. SEC-TMT facilitates quantitative differential analysis of protein interaction networks. bioRxiv 2023:2023.01.12.523793. [PMID: 36711903 PMCID: PMC9882152 DOI: 10.1101/2023.01.12.523793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/14/2023]
Abstract
The majority of cellular proteins interact with at least one partner or assemble into molecular-complexes to exert their function. This network of protein-protein interactions (PPIs) and the composition of macromolecular machines differ between cell types and physiological conditions. Therefore, characterizing PPI networks and their dynamic changes is vital for discovering novel biological functions and underlying mechanisms of cellular processes. However, producing an in-depth, global snapshot of PPIs from a given specimen requires measuring tens to thousands of LC-MS/MS runs. Consequently, while recent works made seminal contributions by mapping PPIs at great depth, almost all focused on just 1-2 conditions, generating comprehensive but mostly static PPI networks. In this study we report the development of SEC-TMT, a method that enables identifying and measuring PPIs in a quantitative manner from only 4-8 LC-MS/MS runs per biological sample. This was accomplished by incorporating tandem mass tag (TMT) multiplexing with a size exclusion chromatography mass spectrometry (SEC-MS) work-flow. SEC-TMT reduces measurement time by an order of magnitude while maintaining resolution and coverage of thousands of cellular interactions, equivalent to the gold standard in the field. We show that SEC-TMT provides benefits for conducting differential analyses to measure changes in the PPI network between conditions. This development makes it feasible to study dynamic systems at scale and holds the potential to drive more rapid discoveries of PPI impact on cellular processes.
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Affiliation(s)
- Ella Doron-Mandel
- Department of Biological Sciences, Columbia University, New-York, NY, USA
| | - Benjamin J. Bokor
- Department of Biological Sciences, Columbia University, New-York, NY, USA
| | - Yanzhe Ma
- Department of Biological Sciences, Columbia University, New-York, NY, USA
| | - Lena A. Street
- Department of Biological Sciences, Columbia University, New-York, NY, USA
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New-York, NY, USA
| | - Ahmed A. Abdou
- Department of Biological Sciences, Columbia University, New-York, NY, USA
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New-York, NY, USA
| | - George A. Rosenberger
- Herbert Irving Cancer Research Center, Columbia University Medical Center, New-York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New-York, NY, USA
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8
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Rube HT, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BV, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning. Nat Biotechnol 2022; 40:1520-1527. [PMID: 35606422 PMCID: PMC9546773 DOI: 10.1038/s41587-022-01307-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 06/06/2021] [Accepted: 04/04/2022] [Indexed: 01/02/2023]
Abstract
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions. Here we describe a flexible machine learning method, called ProBound, that accurately defines sequence recognition in terms of equilibrium binding constants or kinetic rates. This is achieved using a multi-layered maximum-likelihood framework that models both the molecular interactions and the data generation process. We show that ProBound quantifies transcription factor (TF) behavior with models that predict binding affinity over a range exceeding that of previous resources; captures the impact of DNA modifications and conformational flexibility of multi-TF complexes; and infers specificity directly from in vivo data such as ChIP-seq without peak calling. When coupled with an assay called KD-seq, it determines the absolute affinity of protein-ligand interactions. We also apply ProBound to profile the kinetics of kinase-substrate interactions. ProBound opens new avenues for decoding biological networks and rationally engineering protein-ligand interactions.
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Affiliation(s)
- H Tomas Rube
- Department of Bioengineering, University of California, Merced, Merced, CA, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Basheer Becerra
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lucas A N Melo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Bach Viet Do
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Xiaoting Li
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Hammaad H Adam
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
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9
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Hobbs HT, Shah NH, Shoemaker SR, Amacher JF, Marqusee S, Kuriyan J. Saturation mutagenesis of a predicted ancestral Syk-family kinase. Protein Sci 2022; 31:e4411. [PMID: 36173161 PMCID: PMC9601881 DOI: 10.1002/pro.4411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 04/24/2022] [Revised: 06/27/2022] [Accepted: 07/25/2022] [Indexed: 11/08/2022]
Abstract
Many tyrosine kinases cannot be expressed readily in Escherichia coli, limiting facile production of these proteins for biochemical experiments. We used ancestral sequence reconstruction to generate a spleen tyrosine kinase (Syk) variant that can be expressed in bacteria and purified in soluble form, unlike the human members of this family (Syk and zeta-chain-associated protein kinase of 70 kDa [ZAP-70]). The catalytic activity, substrate specificity, and regulation by phosphorylation of this Syk variant are similar to the corresponding properties of human Syk and ZAP-70. Taking advantage of the ability to express this novel Syk-family kinase in bacteria, we developed a two-hybrid assay that couples the growth of E. coli in the presence of an antibiotic to successful phosphorylation of a bait peptide by the kinase. Using this assay, we screened a site-saturation mutagenesis library of the kinase domain of this reconstructed Syk-family kinase. Sites of loss-of-function mutations identified in the screen correlate well with residues established previously as critical to function and/or structure in protein kinases. We also identified activating mutations in the regulatory hydrophobic spine and activation loop, which are within key motifs involved in kinase regulation. Strikingly, one mutation in an ancestral Syk-family variant increases the soluble expression of the protein by 75-fold. Thus, through ancestral sequence reconstruction followed by deep mutational scanning, we have generated Syk-family kinase variants that can be expressed in bacteria with very high yield.
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Affiliation(s)
- Helen T. Hobbs
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCaliforniaUSA
| | - Neel H. Shah
- Department of ChemistryColumbia UniversityNew YorkNew YorkUSA
| | - Sophie R. Shoemaker
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jeanine F. Amacher
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Susan Marqusee
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Kuriyan
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
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10
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Ghanzouri I, Amal S, Ho V, Safarnejad L, Cabot J, Brown-Johnson CG, Leeper N, Asch S, Shah NH, Ross EG. Performance and usability testing of an automated tool for detection of peripheral artery disease using electronic health records. Sci Rep 2022; 12:13364. [PMID: 35922657 PMCID: PMC9349186 DOI: 10.1038/s41598-022-17180-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
Peripheral artery disease (PAD) is a common cardiovascular disorder that is frequently underdiagnosed, which can lead to poorer outcomes due to lower rates of medical optimization. We aimed to develop an automated tool to identify undiagnosed PAD and evaluate physician acceptance of a dashboard representation of risk assessment. Data were derived from electronic health records (EHR). We developed and compared traditional risk score models to novel machine learning models. For usability testing, primary and specialty care physicians were recruited and interviewed until thematic saturation. Data from 3168 patients with PAD and 16,863 controls were utilized. Results showed a deep learning model that utilized time engineered features outperformed random forest and traditional logistic regression models (average AUCs 0.96, 0.91 and 0.81, respectively), P < 0.0001. Of interviewed physicians, 75% were receptive to an EHR-based automated PAD model. Feedback emphasized workflow optimization, including integrating risk assessments directly into the EHR, using dashboard designs that minimize clicks, and providing risk assessments for clinically complex patients. In conclusion, we demonstrate that EHR-based machine learning models can accurately detect risk of PAD and that physicians are receptive to automated risk detection for PAD. Future research aims to prospectively validate model performance and impact on patient outcomes.
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Affiliation(s)
- I Ghanzouri
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - S Amal
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - V Ho
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - L Safarnejad
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - J Cabot
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - C G Brown-Johnson
- Department of Medicine, Primary Care and Population Health, Stanford, CA, USA
| | - N Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - S Asch
- Department of Medicine, Primary Care and Population Health, Stanford, CA, USA
| | - N H Shah
- Department of Medicine, Center for Biomedical Informatics Research, Stanford University School of Medicine, 780 Welch Road, CJ350, Stanford, CA, 94305, USA
| | - E G Ross
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Medicine, Center for Biomedical Informatics Research, Stanford University School of Medicine, 780 Welch Road, CJ350, Stanford, CA, 94305, USA.
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11
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Tsai YL, Badia MA, Kadlecek TA, Shah NH, Fong L, Weiss A. Overcoming inhibitory constraints to TCR signaling by targeting the pH-sensitive phosphatase suppressor of T-cell receptor signaling 1 (STS1). The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.166.14] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
T cells are critically important for adaptive immune responses. Therefore, maintaining their proper homeostasis an d controlling the magnitude of their responses is critical. To control T cell responses, T cell activity is negatively regulated by inhibitory molecules. The Cbl protein family are ubiquitin E3 ligases that suppress TCR signaling by mediating the degradation of TCR signaling molecules. However, studies and our results suggest that Cbl proteins down-regulate phospho-proteins without modulating the total level of target proteins, but the mechanisms are unclear. Here, we show that Cbl-b serves as an adapter to recruit STS1, an unconventional tyrosine phosphatase, to dephosphorylate target proteins and inhibit TCR signaling. STS1 binds to a Cbl-b PPVPP motif via its SH3 domain, and the interaction requires Cbl-b phosphorylation by ZAP70. Elimination of the PPVPP motif compromises Cbl-b suppressive activity, and deletion of STS1 leads to T cell hyper responsiveness to TCR activation which phenocopies Cbl-b deficiency. Furthermore, STS1 uniquely relies on histidine to catalyze dephosphorylation, making it hyperactive in acidic environment. As a result, STS1 and Cbl-b deficient T cells remain hyper responsive and insensitive to low pH whereas WT cells are largely suppressed. Animals with STS1 or Cbl-b deletion show delayed tumor growth and improved survival. Together, these results demonstrate Cbl-b partners with STS1 whose activity is responsive to pH changes to modulate TCR signaling. Moreover, they suggest the pH sensitivity of STS1 is uniquely suited to suppress T cell responses that occur in vivo, such those that occur within inflammatory settings and within tumors, where lower pH conditions may be encountered.
Supported by fellowship from Cancer Research Institute (A133417)
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Affiliation(s)
| | | | - Theresa A Kadlecek
- 1University of California, San Francisco
- 2Howard Hughes Medical Institute
| | | | | | - Arthur Weiss
- 1University of California, San Francisco
- 2Howard Hughes Medical Institute
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12
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Hidalgo F, Nocka LM, Shah NH, Gorday K, Latorraca NR, Bandaru P, Templeton S, Lee D, Karandur D, Pelton JG, Marqusee S, Wemmer D, Kuriyan J. A saturation-mutagenesis analysis of the interplay between stability and activation in Ras. eLife 2022; 11:e76595. [PMID: 35272765 PMCID: PMC8916776 DOI: 10.7554/elife.76595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 01/05/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022] Open
Abstract
Cancer mutations in Ras occur predominantly at three hotspots: Gly 12, Gly 13, and Gln 61. Previously, we reported that deep mutagenesis of H-Ras using a bacterial assay identified many other activating mutations (Bandaru et al., 2017). We now show that the results of saturation mutagenesis of H-Ras in mammalian Ba/F3 cells correlate well with the results of bacterial experiments in which H-Ras or K-Ras are co-expressed with a GTPase-activating protein (GAP). The prominent cancer hotspots are not dominant in the Ba/F3 data. We used the bacterial system to mutagenize Ras constructs of different stabilities and discovered a feature that distinguishes the cancer hotspots. While mutations at the cancer hotspots activate Ras regardless of construct stability, mutations at lower-frequency sites (e.g. at Val 14 or Asp 119) can be activating or deleterious, depending on the stability of the Ras construct. We characterized the dynamics of three non-hotspot activating Ras mutants by using NMR to monitor hydrogen-deuterium exchange (HDX). These mutations result in global increases in HDX rates, consistent with destabilization of Ras. An explanation for these observations is that mutations that destabilize Ras increase nucleotide dissociation rates, enabling activation by spontaneous nucleotide exchange. A further stability decrease can lead to insufficient levels of folded Ras - and subsequent loss of function. In contrast, the cancer hotspot mutations are mechanism-based activators of Ras that interfere directly with the action of GAPs. Our results demonstrate the importance of GAP surveillance and protein stability in determining the sensitivity of Ras to mutational activation.
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Affiliation(s)
- Frank Hidalgo
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Laura M Nocka
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Neel H Shah
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Kent Gorday
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - Naomi R Latorraca
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Pradeep Bandaru
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sage Templeton
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - David Lee
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Deepti Karandur
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jeffrey G Pelton
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Susan Marqusee
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - David Wemmer
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - John Kuriyan
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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13
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Hobbs HT, Shah NH, Badroos JM, Gee CL, Marqusee S, Kuriyan J. Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases. Protein Sci 2021; 30:2373-2384. [PMID: 34601763 PMCID: PMC8605373 DOI: 10.1002/pro.4199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/20/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/03/2023]
Abstract
The catalytic activity of Syk-family tyrosine kinases is regulated by a tandem Src homology 2 module (tSH2 module). In the autoinhibited state, this module adopts a conformation that stabilizes an inactive conformation of the kinase domain. The binding of the tSH2 module to phosphorylated immunoreceptor tyrosine-based activation motifs necessitates a conformational change, thereby relieving kinase inhibition and promoting activation. We determined the crystal structure of the isolated tSH2 module of Syk and find, in contrast to ZAP-70, that its conformation more closely resembles that of the peptide-bound state, rather than the autoinhibited state. Hydrogen-deuterium exchange by mass spectrometry, as well as molecular dynamics simulations, reveal that the dynamics of the tSH2 modules of Syk and ZAP-70 differ, with most of these differences occurring in the C-terminal SH2 domain. Our data suggest that the conformational landscapes of the tSH2 modules in Syk and ZAP-70 have been tuned differently, such that the autoinhibited conformation of the Syk tSH2 module is less stable. This feature of Syk likely contributes to its ability to more readily escape autoinhibition when compared to ZAP-70, consistent with tighter control of downstream signaling pathways in T cells.
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Affiliation(s)
- Helen T. Hobbs
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Present address:
Department of Biomedical EngineeringUniversity of CaliforniaIrvineCaliforniaUSA
| | - Neel H. Shah
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Present address:
Department of ChemistryColumbia UniversityNew YorkNew YorkUSA
| | - Jean M. Badroos
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Christine L. Gee
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Susan Marqusee
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - John Kuriyan
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
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14
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Lo WL, Shah NH, Rubin SA, Zhang W, Horkova V, Fallahee IR, Stepanek O, Zon LI, Kuriyan J, Weiss A. Slow phosphorylation of a tyrosine residue in LAT optimizes T cell ligand discrimination. Nat Immunol 2019; 20:1481-1493. [PMID: 31611699 PMCID: PMC6858552 DOI: 10.1038/s41590-019-0502-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/20/2019] [Indexed: 02/07/2023]
Abstract
Self-non-self discrimination is central to T cell-mediated immunity. The kinetic proofreading model can explain T cell antigen receptor (TCR) ligand discrimination; however, the rate-limiting steps have not been identified. Here, we show that tyrosine phosphorylation of the T cell adapter protein LAT at position Y132 is a critical kinetic bottleneck for ligand discrimination. LAT phosphorylation at Y132, mediated by the kinase ZAP-70, leads to the recruitment and activation of phospholipase C-γ1 (PLC-γ1), an important effector molecule for T cell activation. The slow phosphorylation of Y132, relative to other phosphosites on LAT, is governed by a preceding glycine residue (G131) but can be accelerated by substituting this glycine with aspartate or glutamate. Acceleration of Y132 phosphorylation increases the speed and magnitude of PLC-γ1 activation and enhances T cell sensitivity to weaker stimuli, including weak agonists and self-peptides. These observations suggest that the slow phosphorylation of Y132 acts as a proofreading step to facilitate T cell ligand discrimination.
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Affiliation(s)
- Wan-Lin Lo
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Department of Chemistry, Columbia University, New York, NY, USA
| | - Sara A Rubin
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute; Program in Immunology, Harvard Medical School, Boston, MA, USA
| | - Weiguo Zhang
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Veronika Horkova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ian R Fallahee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ondrej Stepanek
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Leonard I Zon
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute; Program in Immunology, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital and Harvard University, Boston, MA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
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15
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Hong SH, Shah NH. Learning from ancestors. eLife 2019; 8:49976. [PMID: 31407665 PMCID: PMC6692129 DOI: 10.7554/elife.49976] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/03/2022] Open
Abstract
Predicting ancestral sequences of protein kinases reveals the molecular details that underlie different modes of activation.
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Affiliation(s)
- Suk Ho Hong
- Department of Chemistry, Columbia University, New York, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, United States
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16
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McSpadden ED, Xia Z, Chi CC, Susa AC, Shah NH, Gee CL, Williams ER, Kuriyan J. Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca 2+ /calmodulin-dependent protein kinase II. Protein Sci 2019; 28:1071-1082. [PMID: 30942928 DOI: 10.1002/pro.3614] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/01/2019] [Indexed: 11/12/2022]
Abstract
The multi-subunit Ca2+ /calmodulin-dependent protein kinase II (CaMKII) holoenzyme plays a critical role in animal learning and memory. The kinase domain of CaMKII is connected by a flexible linker to a C-terminal hub domain that assembles into a 12- or 14-subunit scaffold that displays the kinase domains around it. Studies on CaMKII suggest that the stoichiometry and dynamic assembly/disassembly of hub oligomers may be important for CaMKII regulation. Although CaMKII is a metazoan protein, genes encoding predicted CaMKII-like hub domains, without associated kinase domains, are found in the genomes of some green plants and bacteria. We show that the hub domains encoded by three related green algae, Chlamydomonas reinhardtii, Volvox carteri f. nagarensis, and Gonium pectoral, assemble into 16-, 18-, and 20-subunit oligomers, as assayed by native protein mass spectrometry. These are the largest known CaMKII hub domain assemblies. A crystal structure of the hub domain from C. reinhardtii reveals an 18-subunit organization. We identified four intra-subunit hydrogen bonds in the core of the fold that are present in the Chlamydomonas hub domain, but not in metazoan hubs. When six point mutations designed to recapitulate these hydrogen bonds were introduced into the human CaMKII-α hub domain, the mutant protein formed assemblies with 14 and 16 subunits, instead of the normal 12- and 14-subunit assemblies. Our results show that the stoichiometric balance of CaMKII hub assemblies can be shifted readily by small changes in sequence.
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Affiliation(s)
- Ethan D McSpadden
- Department of Molecular and Cell Biology, University of California, Berkeley, California.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California.,Howard Hughes Medical Institute, University of California, Berkeley, California
| | - Zijie Xia
- Department of Chemistry, University of California, Berkeley, California
| | - Chris C Chi
- Department of Molecular and Cell Biology, University of California, Berkeley, California.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California.,Howard Hughes Medical Institute, University of California, Berkeley, California
| | - Anna C Susa
- Department of Chemistry, University of California, Berkeley, California
| | - Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, California.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California.,Howard Hughes Medical Institute, University of California, Berkeley, California
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, California.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California.,Howard Hughes Medical Institute, University of California, Berkeley, California
| | - Evan R Williams
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California.,Department of Chemistry, University of California, Berkeley, California
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, California.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California.,Howard Hughes Medical Institute, University of California, Berkeley, California.,Department of Chemistry, University of California, Berkeley, California.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
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17
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Abstract
Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.
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Affiliation(s)
- Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jeanine F. Amacher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Laura M. Nocka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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18
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Affiliation(s)
- Byron B. Au-Yeung
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Lin Shen
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, California 94143, USA;,
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, California 94143, USA;,
- Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA
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19
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Shah NH, Löbel M, Weiss A, Kuriyan J. Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen. eLife 2018; 7:35190. [PMID: 29547119 PMCID: PMC5889215 DOI: 10.7554/elife.35190] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 01/19/2018] [Accepted: 03/15/2018] [Indexed: 01/04/2023] Open
Abstract
The specificity of tyrosine kinases is attributed predominantly to localization effects dictated by non-catalytic domains. We developed a method to profile the specificities of tyrosine kinases by combining bacterial surface-display of peptide libraries with next-generation sequencing. Using this, we showed that the tyrosine kinase ZAP-70, which is critical for T cell signaling, discriminates substrates through an electrostatic selection mechanism encoded within its catalytic domain (Shah et al., 2016). Here, we expand this high-throughput platform to analyze the intrinsic specificity of any tyrosine kinase domain against thousands of peptides derived from human tyrosine phosphorylation sites. Using this approach, we find a difference in the electrostatic recognition of substrates between the closely related Src-family kinases Lck and c-Src. This divergence likely reflects the specialization of Lck to act in concert with ZAP-70 in T cell signaling. These results point to the importance of direct recognition at the kinase active site in fine-tuning specificity.
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Affiliation(s)
- Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Mark Löbel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Arthur Weiss
- Department of Medicine, Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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20
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Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. eLife 2017; 6:e27810. [PMID: 28686159 PMCID: PMC5538825 DOI: 10.7554/elife.27810] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [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: 04/14/2017] [Accepted: 07/05/2017] [Indexed: 02/02/2023] Open
Abstract
Ras proteins are highly conserved signaling molecules that exhibit regulated, nucleotide-dependent switching between active and inactive states. The high conservation of Ras requires mechanistic explanation, especially given the general mutational tolerance of proteins. Here, we use deep mutational scanning, biochemical analysis and molecular simulations to understand constraints on Ras sequence. Ras exhibits global sensitivity to mutation when regulated by a GTPase activating protein and a nucleotide exchange factor. Removing the regulators shifts the distribution of mutational effects to be largely neutral, and reveals hotspots of activating mutations in residues that restrain Ras dynamics and promote the inactive state. Evolutionary analysis, combined with structural and mutational data, argue that Ras has co-evolved with its regulators in the vertebrate lineage. Overall, our results show that sequence conservation in Ras depends strongly on the biochemical network in which it operates, providing a framework for understanding the origin of global selection pressures on proteins.
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Affiliation(s)
- Pradeep Bandaru
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Moitrayee Bhattacharyya
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - John P Barton
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States,Department of Physics, Massachusetts Institute of Technology, Cambridge, United States,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Yasushi Kondo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Arup K Chakraborty
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States,Department of Physics, Massachusetts Institute of Technology, Cambridge, United States,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
| | - Rama Ranganathan
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States,Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States, (RR)
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States, (JK)
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21
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Shah NH, Wang Q, Yan Q, Karandur D, Kadlecek TA, Fallahee IR, Russ WP, Ranganathan R, Weiss A, Kuriyan J. An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor. eLife 2016; 5. [PMID: 27700984 PMCID: PMC5089863 DOI: 10.7554/elife.20105] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [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: 07/27/2016] [Accepted: 10/03/2016] [Indexed: 12/15/2022] Open
Abstract
The sequence of events that initiates T cell signaling is dictated by the specificities and order of activation of the tyrosine kinases that signal downstream of the T cell receptor. Using a platform that combines exhaustive point-mutagenesis of peptide substrates, bacterial surface-display, cell sorting, and deep sequencing, we have defined the specificities of the first two kinases in this pathway, Lck and ZAP-70, for the T cell receptor ζ chain and the scaffold proteins LAT and SLP-76. We find that ZAP-70 selects its substrates by utilizing an electrostatic mechanism that excludes substrates with positively-charged residues and favors LAT and SLP-76 phosphosites that are surrounded by negatively-charged residues. This mechanism prevents ZAP-70 from phosphorylating its own activation loop, thereby enforcing its strict dependence on Lck for activation. The sequence features in ZAP-70, LAT, and SLP-76 that underlie electrostatic selectivity likely contribute to the specific response of T cells to foreign antigens. DOI:http://dx.doi.org/10.7554/eLife.20105.001 A class of enzymes known as tyrosine kinases relay signals in cells by adding phosphate groups onto specific sites (called 'tyrosine residues') in other proteins. Most tyrosine kinases can phosphorylate many targets (or 'substrates'); they can also phosphorylate and thereby activate themselves, when given the right signal. Many tyrosine kinases select their substrates on the basis of their location; once recruited to and activated at a specific site, these enzymes will typically phosphorylate many nearby proteins. A tyrosine kinase called ZAP-70 is found in immune cells known as T cells. ZAP-70 works together with another kinase called Lck to activate T cells, which enables the cells to mount an immune response when they encounter foreign molecules. This pathway is precisely controlled, with Lck activated first, followed by ZAP-70. Unlike most other tyrosine kinases, ZAP-70 cannot activate itself, and it will only phosphorylate a narrow range of substrates. The origin of these constraints are not understood, but they are thought to be crucial for ensuring that T cells readily respond to foreign molecules but not to healthy cells. Shah et al. developed a high-throughput technique to investigate which features ZAP-70 and Lck use to select their substrates. First, hundreds of different sequences based on natural substrates were genetically encoded and introduced into bacterial cells, with one type per bacterium. The bacteria displayed these sequence variants on their surface, and Shah et al. then treated the bacteria with either ZAP-70 or Lck. Cell sorting was used to isolate those bacterial cells with variants that were phosphorylated, and high-throughput DNA sequencing was used to identify the phosphorylated sequences. This approach revealed that ZAP-70 was deterred from phosphorylating sites that carry a positive charge and strongly preferred sites that are negatively-charged, such as those found in its two major substrates. Shah et al. also showed that Lck, which behaves like a typical tyrosine kinase, could not phosphorylate the substrates of ZAP-70 because of their substantial negative charge. This lack of cross-reactivity between Lck and the ZAP-70 substrates prevents premature signaling in T cells. Using simulations, Shah et al. went on to show that a positively-charged region on ZAP-70 (which is more prominent than in other tyrosine kinases) helps ZAP-70 interact with negatively-charged substrates. This region also deters the kinase from activating itself, making it dependent instead upon Lck for activation. Together, these results identify the distinctive features of ZAP-70 that are important for ensuring that T cells are activated only when they sense foreign molecules on unhealthy cells. The work will lead to future studies exploring the tightly controlled signaling events carried out by tyrosine kinases in T cells in more detail. DOI:http://dx.doi.org/10.7554/eLife.20105.002
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Affiliation(s)
- Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Qingrong Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Theresa A Kadlecek
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, United States
| | - Ian R Fallahee
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - William P Russ
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Rama Ranganathan
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Arthur Weiss
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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22
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Abstract
Protein trans-splicing (PTS) by split inteins has found widespread use in chemical biology and biotechnology. Herein, we describe the use of a consensus design approach to engineer a split intein with enhanced stability and activity that make it more robust than any known PTS system. Using batch mutagenesis, we first conduct a detailed analysis of the difference in splicing rates between the Npu (fast) and Ssp (slow) split inteins of the DnaE family and find that most impactful residues lie on the second shell of the protein, directly adjacent to the active site. These residues are then used to generate an alignment of 73 naturally occurring DnaE inteins that are predicted to be fast. The consensus sequence from this alignment (Cfa) demonstrates both rapid protein splicing and unprecedented thermal and chaotropic stability. Moreover, when fused to various proteins including antibody heavy chains, the N-terminal fragment of Cfa exhibits increased expression levels relative to other N-intein fusions. The durability and efficiency of Cfa should improve current intein based technologies and may provide a platform for the development of new protein chemistry techniques.
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Affiliation(s)
- Adam J Stevens
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Zachary Z Brown
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Neel H Shah
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
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23
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Harpaz R, DuMochel W, Shah NH. Big Data and Adverse Drug Reaction Detection. Clin Pharmacol Ther 2015; 99:268-70. [PMID: 26575203 DOI: 10.1002/cpt.302] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 11/06/2022]
Abstract
Big Data holds the promise of fundamentally transforming the manner in which adverse drug reactions can be identified and evaluated. This commentary discusses new data sources that are envisioned to form a Big Data-enabled pharmacovigilance system and the role of these data in powering the future of adverse drug reactions detection.
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Affiliation(s)
- R Harpaz
- Oracle Health Sciences, Bedford, Massachusetts, USA
| | - W DuMochel
- Oracle Health Sciences, Bedford, Massachusetts, USA
| | - N H Shah
- Stanford University, Stanford, California, USA
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24
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Affiliation(s)
- H M S Khan
- Islamia University Bahawalpur, The Islamia University of Bahawalpur, Pakistan
| | - H Butt
- Islamia University Bahawalpur, The Islamia University of Bahawalpur, Pakistan
| | - N H Shah
- Bahauddin Zakarya University, Multan, Pakistan
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25
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Abstract
Protein splicing is a posttranslational modification where intervening proteins (inteins) cleave themselves from larger precursor proteins and ligate their flanking polypeptides (exteins) through a multistep chemical reaction. First thought to be an anomaly found in only a few organisms, protein splicing by inteins has since been observed in microorganisms from all domains of life. Despite this broad phylogenetic distribution, all inteins share common structural features such as a horseshoe-like pseudo two-fold symmetric fold, several canonical sequence motifs, and similar splicing mechanisms. Intriguingly, the splicing efficiencies and substrate specificity of different inteins vary considerably, reflecting subtle changes in the chemical mechanism of splicing, linked to their local structure and dynamics. As intein chemistry has widespread use in protein chemistry, understanding the structural and dynamical aspects of inteins is crucial for intein engineering and the improvement of intein-based technologies.
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Affiliation(s)
- Ertan Eryilmaz
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
| | - Neel H Shah
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - Tom W Muir
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - David Cowburn
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
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26
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Abstract
Inteins are auto-processing domains found in organisms from all domains of life. These proteins carry out a process known as protein splicing, which is a multi-step biochemical reaction comprised of both the cleavage and formation of peptide bonds. While the endogenous substrates of protein splicing are specific essential proteins found in intein-containing host organisms, inteins are also functional in exogenous contexts and can be used to chemically manipulate virtually any polypeptide backbone. Given this, protein chemists have exploited various facets of intein reactivity to modify proteins in myriad ways for both basic biological research as well as potential therapeutic applications. Here, we review the intein field, first focusing on the biological context and phylogenetic diversity of inteins, followed by a description of intein structure and biochemical function. Finally, we discuss prevalent inteinbased technologies, focusing on their applications in chemical biology, followed by persistent caveats of intein chemistry and approaches to alleviate these shortcomings. The findings summarized herein describe two and a half decades of research, leading from a biochemical curiosity to the development of powerful protein engineering tools.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, United States
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27
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Abstract
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Split
inteins are a class of naturally occurring proteins that
carry out protein splicing in trans. The chemical
mechanism of protein trans-splicing is well-understood
and has been exploited to develop several powerful protein engineering
technologies. Split intein chemistry is preceded by efficient molecular
recognition between two protomers that become intertwined in their
bound state. It is currently unclear how this unique topology is achieved
upon fragment association. Using biophysical techniques in conjunction
with protein engineering methods, including segmental isotopic labeling,
we show that one split intein fragment is partly folded, while the
other is completely disordered. These polypeptides capture each other
through their disordered regions and form an ordered intermediate
with native-like structure at their interface. This intermediate then
collapses into the canonical intein fold. This mechanism provides
insight into the evolutionary constraints on split intein assembly
and should enhance the development of split intein-based technologies.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
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28
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Harpaz R, DuMouchel W, LePendu P, Bauer-Mehren A, Ryan P, Shah NH. Response to "Logistic regression in signal detection: another piece added to the puzzle". Clin Pharmacol Ther 2013; 94:313. [PMID: 23756371 DOI: 10.1038/clpt.2013.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Abstract
With increasing adoption of electronic health records (EHRs), there is an opportunity to use the free-text portion of EHRs for pharmacovigilance. We present novel methods that annotate the unstructured clinical notes and transform them into a deidentified patient-feature matrix encoded using medical terminologies. We demonstrate the use of the resulting high-throughput data for detecting drug-adverse event associations and adverse events associated with drug-drug interactions. We show that these methods flag adverse events early (in most cases before an official alert), allow filtering of spurious signals by adjusting for potential confounding, and compile prevalence information. We argue that analyzing large volumes of free-text clinical notes enables drug safety surveillance using a yet untapped data source. Such data mining can be used for hypothesis generation and for rapid analysis of suspected adverse event risk.
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Affiliation(s)
- P LePendu
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA.
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30
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Abstract
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Split
inteins play an important role in modern protein semisynthesis
techniques. These naturally occurring protein splicing domains can
be used for in vitro and in vivo protein modification, peptide and
protein cyclization, segmental isotopic labeling, and the construction
of biosensors. The most well-characterized family of split inteins,
the cyanobacterial DnaE inteins, show particular promise, as many
of these can splice proteins in less than 1 min. Despite this fact,
the activity of these inteins is context-dependent: certain peptide
sequences surrounding their ligation junction (called local N- and
C-exteins) are strongly preferred, while other sequences cause a dramatic
reduction in the splicing kinetics and yield. These sequence constraints
limit the utility of inteins, and thus, a more detailed understanding
of their participation in protein splicing is needed. Here we present
a thorough kinetic analysis of the relationship between C-extein composition
and split intein activity. The results of these experiments were used
to guide structural and molecular dynamics studies, which revealed
that the motions of catalytic residues are constrained by the second
C-extein residue, likely forcing them into an active conformation
that promotes rapid protein splicing. Together, our structural and
functional studies also highlight a key region of the intein structure
that can be re-engineered to increase intein promiscuity.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
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31
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Abstract
Chemically modified proteins are invaluable tools for studying the molecular details of biological processes, and they also hold great potential as new therapeutic agents. Several methods have been developed for the site-specific modification of proteins, one of the most widely used being expressed protein ligation (EPL) in which a recombinant α-thioester is ligated to an N-terminal Cys-containing peptide. Despite the widespread use of EPL, the generation and isolation of the required recombinant protein α-thioesters remain challenging. We describe here a new method for the preparation and purification of recombinant protein α-thioesters using engineered versions of naturally split DnaE inteins. This family of autoprocessing enzymes is closely related to the inteins currently used for protein α-thioester generation, but they feature faster kinetics and are split into two inactive polypeptides that need to associate to become active. Taking advantage of the strong affinity between the two split intein fragments, we devised a streamlined procedure for the purification and generation of protein α-thioesters from cell lysates and applied this strategy for the semisynthesis of a variety of proteins including an acetylated histone and a site-specifically modified monoclonal antibody.
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Affiliation(s)
- Miquel Vila-Perelló
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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32
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Shah NH, Dann GP, Vila-Perelló M, Liu Z, Muir TW. Ultrafast protein splicing is common among cyanobacterial split inteins: implications for protein engineering. J Am Chem Soc 2012; 134:11338-41. [PMID: 22734434 DOI: 10.1021/ja303226x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe the first systematic study of a family of inteins, the split DnaE inteins from cyanobacteria. By measuring in vivo splicing efficiencies and in vitro kinetics, we demonstrate that several inteins can catalyze protein trans-splicing in tens of seconds rather than hours, as is commonly observed for this autoprocessing protein family. Furthermore, we show that when artificially fused, these inteins can be used for rapid generation of protein α-thioesters for expressed protein ligation. This comprehensive survey of split inteins provides indispensable information for the development and improvement of intein-based tools for chemical biology.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, 325 Frick Chemistry Laboratory, Princeton, New Jersey 08544, USA
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33
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Abstract
An important goal of the health system is to identify new adverse drug events (ADEs) in the postapproval period. Datamining methods that can transform data into meaningful knowledge to inform patient safety have proven essential for this purpose. New opportunities have emerged to harness data sources that have not been used within the traditional framework. This article provides an overview of recent methodological innovations and data sources used to support ADE discovery and analysis.
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Affiliation(s)
- R Harpaz
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA.
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34
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Shah NH. Translational bioinformatics embraces big data. Yearb Med Inform 2012; 7:130-134. [PMID: 22890354 PMCID: PMC4370941] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
We review the latest trends and major developments in translational bioinformatics in the year 2011-2012. Our emphasis is on highlighting the key events in the field and pointing at promising research areas for the future. The key take-home points are: • Translational informatics is ready to revolutionize human health and healthcare using large-scale measurements on individuals. • Data-centric approaches that compute on massive amounts of data (often called "Big Data") to discover patterns and to make clinically relevant predictions will gain adoption. • Research that bridges the latest multimodal measurement technologies with large amounts of electronic healthcare data is increasing; and is where new breakthroughs will occur.
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Affiliation(s)
- N H Shah
- Stanford University School of Medicine, 1265 Welch Road, Room X-229, Stanford, CA 94305, USA. E-mail:
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35
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Abstract
Split inteins carry out a naturally occurring process known as protein trans-splicing, where two protein fragments bind to form a catalytically competent enzyme, then catalyze their own excision and the ligation of their flanking sequences. In the past thirteen years since their discovery, chemists and biologists have utilized split inteins in exogenous contexts for a number of biotechnological applications centered around the formation of native peptide bonds. While many protein trans-splicing technologies have emerged and flourished in recent years, several factors still limit their wide-spread practical use. Here, we discuss the development, applications, and limitations of split intein-based technologies and propose that further advancement in this field will require a more fundamental understanding of split intein structure and function.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, 325 Frick Laboratory, Princeton, New Jersey 08544, USA, Telephone: 609-258-5778
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36
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Affiliation(s)
| | | | - Mikki G. Boswell
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
| | | | - Fanny G. Yeung
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
| | | | - Christian Wolf
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
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37
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Shah NH, Vila-Perelló M, Muir TW. Kinetic control of one-pot trans-splicing reactions by using a wild-type and designed split intein. Angew Chem Int Ed Engl 2011; 50:6511-5. [PMID: 21656885 DOI: 10.1002/anie.201102909] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Indexed: 01/28/2023]
Affiliation(s)
- Neel H Shah
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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38
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Shah NH, Vila-Perelló M, Muir TW. Kinetic Control of One-Pot Trans-Splicing Reactions by Using a Wild-Type and Designed Split Intein. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102909] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Shah NH, Butterfoss GL, Nguyen K, Yoo B, Bonneau R, Rabenstein DL, Kirshenbaum K. Oligo(N-aryl glycines): A New Twist on Structured Peptoids. J Am Chem Soc 2008; 130:16622-32. [DOI: 10.1021/ja804580n] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Neel H. Shah
- Department of Chemistry, Center for Genomics & Systems Biology, and Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, New York 10003, and Department of Chemistry, University of California, Riverside, California 92521
| | - Glenn L. Butterfoss
- Department of Chemistry, Center for Genomics & Systems Biology, and Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, New York 10003, and Department of Chemistry, University of California, Riverside, California 92521
| | - Khanh Nguyen
- Department of Chemistry, Center for Genomics & Systems Biology, and Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, New York 10003, and Department of Chemistry, University of California, Riverside, California 92521
| | - Barney Yoo
- Department of Chemistry, Center for Genomics & Systems Biology, and Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, New York 10003, and Department of Chemistry, University of California, Riverside, California 92521
| | - Richard Bonneau
- Department of Chemistry, Center for Genomics & Systems Biology, and Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, New York 10003, and Department of Chemistry, University of California, Riverside, California 92521
| | - Dallas L. Rabenstein
- Department of Chemistry, Center for Genomics & Systems Biology, and Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, New York 10003, and Department of Chemistry, University of California, Riverside, California 92521
| | - Kent Kirshenbaum
- Department of Chemistry, Center for Genomics & Systems Biology, and Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, New York 10003, and Department of Chemistry, University of California, Riverside, California 92521
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40
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Musen MA, Shah NH, Noy NF, Dai BY, Dorf M, Griffith N, Buntrok J, Jonquet C, Montegut MJ, Rubin DL. BioPortal: ontologies and data resources with the click of a mouse. AMIA Annu Symp Proc 2008:1223-1224. [PMID: 18999306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/15/2008] [Revised: 07/15/2008] [Indexed: 05/27/2023]
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41
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Shah NH, Kirshenbaum K. Direct Generation of Polymer Films on Copper Surfaces through Azide‐Alkyne Cycloaddition Reactions between Peptidomimetic Oligomers. Macromol Rapid Commun 2008. [DOI: 10.1002/marc.200800042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Shah NH, Sundaram RO, Velusamy A, Braithwaite IJ. Five-year functional outcome analysis of ankle fracture fixation. Injury 2007; 38:1308-12. [PMID: 17888434 DOI: 10.1016/j.injury.2007.06.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 05/13/2007] [Accepted: 06/04/2007] [Indexed: 02/02/2023]
Abstract
This study examines retrospectively the functional outcome of patients at 5 years following their ankle fracture surgery using the Olerud-Molander Ankle Score (OMAS) and SF-12 questionnaire. Of 69 patients, 43 were females and 26 males. The mean age was 50.7 years. There were 74 and 26% of Weber 'B' and 'C' fractures, respectively. The mean OMAS was 75.2. About 63% of the patients were still complaining of stiffness, around 45% patients were still complaining of ankle swelling, 50% of patients still had some sort of pain, 39% still thought that they had not fully recovered and 38% did not return to their pre-injury sporting activity. Apart from the age, no significant difference was seen in the OMAS due to gender, fracture type or timing of surgery. Our findings show that many patients who have had surgery for ankle fractures will still have some functional limitations even 5 years after the injury.
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Affiliation(s)
- N H Shah
- Department of Trauma & Orthopaedic Surgery, Countess of Chester Hospital NHS Foundation Trust, Liverpool Road, Chester, Cheshire CH2 1UL, England, United Kingdom.
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44
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Abstract
MOTIVATION Experimental design, hypothesis-testing and model-building in the current data-rich environment require the biologists' to collect, evaluate and integrate large amounts of information of many disparate kinds. Developing a unified framework for the representation and conceptual integration of biological data and processes is a major challenge in bioinformatics because of the variety of available data and the different levels of detail at which biological processes can be considered. RESULTS We have developed the HyBrow (Hypothesis Browser) system as a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. HyBrow consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology and programs to perform hypothesis design and evaluation. We demonstrate the HyBrow prototype using the galactose gene network in Saccharomyces cerevisiae as our test system, and evaluate alternative hypotheses for consistency with stored information. AVAILABILITY www.hybrow.org
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Affiliation(s)
- S A Racunas
- The Huck Institute for Life Sciences, Penn State University, University Park, PA 16801, USA
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45
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Abstract
Eight cases of hepatitis E acquired in the UK are reported. These cases presented to an inner city hospital in Birmingham, UK, over a 5-month period in 2005. HEV is considered unusual in the UK and generally occurs after travel to endemic regions. Only five cases of hepatitis E acquired in the UK have been reported in the literature. This series represents an increase in the local incidence of hepatitis E, particularly that of UK-acquired infection. HEV should be considered in all patients with acute hepatitis, irrespective of travel history.
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Affiliation(s)
- G J Sadler
- Department of Gastroenterology, The Heart of England Foundation Trust, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, United Kingdom
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Shah NH, Walton NP, Sudhahar TA, Donell ST. Screening time for extra-capsular proximal femoral fracture fixation; the difference between extra-medullary and intra-medullary implant usage. Injury 2004; 35:1010-4. [PMID: 15351668 DOI: 10.1016/j.injury.2003.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2003] [Indexed: 02/02/2023]
Abstract
The aim of this study was to compare the fluoroscopic screening time used for treatment of fractures of the trochanteric region of the femur using two different implant systems. Data were collected from 277 proximal femoral fracture fixations. A dynamic hip screw (DHS) was used in 145, and an intra-medullary hip screw (IMHS) was used in 132. There was no difference between the two groups with respect to age, gender or side. Altogether, there were 42% two parts, 35% were three parts and 23% were four parts extra-capsular neck fractures. There was no statistical difference in ionising radiation exposure in closed reduction of these fractures regardless of the fracture configuration or surgical experience of the surgeon. The mean screening time to implant a DHS in two part fractures was 0.48 min, for three part fractures it was 0.45 min and for four part fractures it was 0.46 min. The mean screening time to implant IMHS was 1.02 min for two part fractures, 0.96 min for three part fractures and 1.03 min for four part fractures. These differences were statistically significant (P < or = 0.05).
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Affiliation(s)
- N H Shah
- Department of Trauma and Orthopaedic Surgery, Institute of Orthopaedics, Norfolk and Norwich University Hospital NHS Trust, Colney Lane, Norwich NR4, UK.
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Abstract
SUMMARY Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes, none of them accept Arabidopsis thaliana data. In order to address this need for A.thaliana community, we have developed a program that retrieves GO annotations for A.thaliana genes and performs functional category analysis for lists of genes selected by the user. AVAILABILITY http://www.personal.psu.edu/nhs109/Clench
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Affiliation(s)
- N H Shah
- The Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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Abstract
We describe two sets of programs for expediting routine tasks in analysis of cDNA microarray data and promoter sequences. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in three different ways. It allows combining of result files into comprehensive data sets, evaluation of the quality of both technical and biological replicates and row and/or column standardization of data matrices. The second set supports mapping ESTs in the genome, identifying the corresponding genes and recovering their promoters, analyzing promoters for transcription factor binding sites, and visual representation of the results. The programs are designed primarily for Arabidopsis thaliana researchers, but can be adapted readily for other model systems. Availability and Supplementary information: http://www.personal.psu.edu/nhs109/Programs/
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Affiliation(s)
- N H Shah
- The Huck Institute of Life Sciences and The Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Abstract
The use of a wax-based vehicle is one approach to stabilize a drug which is susceptible to hydrolysis and/or oxidation. The drug used in the study, as a microfine powder, is dispersed in the wax mixture and encapsulated in a soft gelatin capsule. To ensure reproducibility of drug content uniformity and encapsulability of the soft gelatin capsule dosage form, optimal viscosity and lot to lot uniformity of the viscosity of the suspension are required. The objective of the study was to identify the critical processing factors which could affect the rheological behavior of the wax based vehicle. Rheological behavior of the vehicle at temperatures ranging from 15 to 90 degrees C was evaluated using a CSL Rheometer equipped with parallel plates and a shear rate sweep mode, unless otherwise specified. Viscosity vs. temperature profiles of the vehicle were determined using the same conditions at different cooling rates ranging from 1.3 to 20 degrees C per min. Three distinct regions of phase transition of the wax mixture can be seen in the Arrhenius plot: (i) a sol region at temperatures above 50 degrees C, (ii) a transition of gel to sol at temperatures ranging from 30 to 45 degrees C, and (iii) a gel region at temperatures below 30 degrees C. The vehicle in a sol region behaved as a Newtonian fluid, indicating minimal interactions between the hydrocarbon chains of the vehicle. The vehicle in a gel region behaved thixotropic in nature, as indicated by a hysteresis loop. The shear rate had a more pronounced effect on the area of thixotropy than the shear time. The cooling rate had a pronounced effect on the resultant viscosity. At the same applied shear rate, the vehicle which was cooled at a faster rate, may cause a recrystallization of the wax mixture in different crystalline forms, resulting in a higher viscosity than the vehicle cooled at a slower rate. This effect was more pronounced when the shear was applied at a lower rate. The results of this study indicate that shear rate and cooling rate are the critical processing factors in controlling the viscosity of the final product and must be well controlled in the manufacturing procedure.
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Affiliation(s)
- W Phuapradit
- Pharmaceutical and Analytical R&D, Nutley, NJ 07110, USA
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Shah NH, Jacobs AA, Shah NH, de Graaf FK. Safety and efficacy of an oil-adjuvant vaccine against haemorrhagic septicaemia in buffalo calves: cross-protection between the serotypes B:2,5 and E:2,5. Vet Rec 2001; 149:583-7. [PMID: 11730166 DOI: 10.1136/vr.149.19.583] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The safety, efficacy and duration of immunity of an improved oil-adjuvant vaccine against haemorrhagic septicaemia, containing inactivated cells of Pasteurella multocida serotype B:2,5, were tested in young buffalo calves in Pakistan. For safety testing, five buffalo calves were vaccinated intramuscularly with twice the normal dose, and six weeks later with a normal dose. Except for a transient rise in rectal temperature at six hours after the vaccinations, no systemic reactions were observed. The buffaloes remained in good condition and had a normal appetite. No local reactions were observed at the injection site. For efficacy testing two trials were carried out. In the first, buffalo calves were vaccinated intramuscularly either with two doses two-and-a-half months apart, or with a single dose, or left unvaccinated. They were challenged subcutaneously with virulent P multocida after eight, 13 or 15 months. After challenge at eight months the four buffaloes given two doses and the buffalo given one dose were protected, whereas the control animal developed the typical signs of the disease. After the challenges at 13 and 15 months, the vaccinated animals were still protected whereas the control animals died. In the second trial, buffalo calves were vaccinated intramuscularly either with two doses two months apart, or with a single dose at two months or left unvaccinated. The buffaloes were challenged after eight or 14 months. After challenge at eight months the four control animals died, whereas three of the four buffaloes given a single dose were protected. After challenge at 14 months, the three control animals died, whereas four of the five buffaloes given two doses and both the buffaloes given a single dose were protected. To test for cross-protection against the heterologous serotypes E:2,5 and B:3,4, groups of mice were vaccinated once or left unvaccinated. Four weeks later, the vaccinated and control groups were challenged with a dilution series of the different challenge cultures. The vaccine appeared to induce protection against challenge with different strains of serotypes B:2,5 and E:2,5 but not against strains of serotype B:3,4.
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Affiliation(s)
- N H Shah
- Centre of Animal Biotechnology, Veterinary Research Institute, Peshawar, Pakistan
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