1
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Scott BM, Chen SK, Van Nynatten A, Liu J, Schott RK, Heon E, Peisajovich SG, Chang BSW. Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin. J Mol Evol 2024; 92:61-71. [PMID: 38324225 DOI: 10.1007/s00239-024-10154-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/22/2023] [Indexed: 02/08/2024]
Abstract
Eukaryotic cells use G protein-coupled receptors (GPCRs) to convert external stimuli into internal signals to elicit cellular responses. However, how mutations in GPCR-coding genes affect GPCR activation and downstream signaling pathways remain poorly understood. Approaches such as deep mutational scanning show promise in investigations of GPCRs, but a high-throughput method to measure rhodopsin activation has yet to be achieved. Here, we scale up a fluorescent reporter assay in budding yeast that we engineered to study rhodopsin's light-activated signal transduction. Using this approach, we measured the mutational effects of over 1200 individual human rhodopsin mutants, generated by low-frequency random mutagenesis of the GPCR rhodopsin (RHO) gene. Analysis of the data in the context of rhodopsin's three-dimensional structure reveals that transmembrane helices are generally less tolerant to mutations compared to flanking helices that face the lipid bilayer, which suggest that mutational tolerance is contingent on both the local environment surrounding specific residues and the specific position of these residues in the protein structure. Comparison of functional scores from our screen to clinically identified rhodopsin disease variants found many pathogenic mutants to be loss of function. Lastly, functional scores from our assay were consistent with a complex counterion mechanism involved in ligand-binding and rhodopsin activation. Our results demonstrate that deep mutational scanning is possible for rhodopsin activation and can be an effective method for revealing properties of mutational tolerance that may be generalizable to other transmembrane proteins.
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Affiliation(s)
- Benjamin M Scott
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Steven K Chen
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Jing Liu
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Biology and Centre for Vision Research, York University, Toronto, ON, Canada
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Elise Heon
- Department of Ophthalmology, Hospital for Sick Children, Toronto, ON, Canada
| | - Sergio G Peisajovich
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.
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2
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Chandra S, Manjunath K, Asok A, Varadarajan R. Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA. Protein Sci 2023; 32:e4580. [PMID: 36714997 PMCID: PMC9951195 DOI: 10.1002/pro.4580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/02/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Unlike globular proteins, mutational effects on the function of Intrinsically Disordered Proteins (IDPs) are not well-studied. Deep Mutational Scanning of a yeast surface displayed mutant library yields insights into sequence-function relationships in the CcdA IDP. The approach enables facile prediction of interface residues and local structural signatures of the bound conformation. In contrast to previous titration-based approaches which use a number of ligand concentrations, we show that use of a single rationally chosen ligand concentration can provide quantitative estimates of relative binding constants for large numbers of protein variants. This is because the extended interface of IDP ensures that energetic effects of point mutations are spread over a much smaller range than for globular proteins. Our data also provides insights into the much-debated role of helicity and disorder in partner binding of IDPs. Based on this exhaustive mutational sensitivity dataset, a rudimentary model was developed in an attempt to predict mutational effects on binding affinity of IDPs that form alpha-helical structures upon binding.
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Affiliation(s)
| | | | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of ScienceBangaloreIndia
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3
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Pruvost T, Mathieu M, Dubois S, Maillère B, Vigne E, Nozach H. Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold. MAbs 2023; 15:2175311. [PMID: 36797224 PMCID: PMC9980635 DOI: 10.1080/19420862.2023.2175311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Delineating the precise regions on an antigen that are targeted by antibodies has become a key step for the development of antibody therapeutics. X-ray crystallography and cryogenic electron microscopy are considered the gold standard for providing precise information about these binding sites at atomic resolution. However, they are labor-intensive and a successful outcome is not guaranteed. We used deep mutational scanning (DMS) of the human LAMP-1 antigen displayed on yeast surface and leveraged next-generation sequencing to observe the effect of individual mutants on the binding of two LAMP-1 antibodies and to determine their functional epitopes on LAMP-1. Fine-tuned epitope mapping by DMS approaches is augmented by knowledge of experimental antigen structure. As human LAMP-1 structure has not yet been solved, we used the AlphaFold predicted structure of the full-length protein to combine with DMS data and ultimately finely map antibody epitopes. The accuracy of this method was confirmed by comparing the results to the co-crystal structure of one of the two antibodies with a LAMP-1 luminal domain. Finally, we used AlphaFold models of non-human LAMP-1 to understand the lack of mAb cross-reactivity. While both epitopes in the murine form exhibit multiple mutations in comparison to human LAMP-1, only one and two mutations in the Macaca form suffice to hinder the recognition by mAb B and A, respectively. Altogether, this study promotes a new application of AlphaFold to speed up precision mapping of antibody-antigen interactions and consequently accelerate antibody engineering for optimization.
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Affiliation(s)
- Tiphanie Pruvost
- CEA, INRAE, Medicines and Healthcare Technologies Department, Université Paris-Saclay, SIMoS, France.,Sanofi, Large Molecule Research, Vitry-sur-Seine, France
| | - Magali Mathieu
- Sanofi, Integrated Drug Discovery, Vitry-sur-Seine, France
| | - Steven Dubois
- CEA, INRAE, Medicines and Healthcare Technologies Department, Université Paris-Saclay, SIMoS, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, Université Paris-Saclay, SIMoS, France
| | | | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, Université Paris-Saclay, SIMoS, France
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4
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Vanni I, Iacobone F, D’Agostino C, Giovannelli M, Pirisinu L, Altmeppen HC, Castilla J, Torres JM, Agrimi U, Nonno R. An optimized Western blot assay provides a comprehensive assessment of the physiological endoproteolytic processing of the prion protein. J Biol Chem 2022; 299:102823. [PMID: 36565989 PMCID: PMC9867980 DOI: 10.1016/j.jbc.2022.102823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022] Open
Abstract
The prion protein (PrPC) is subjected to several conserved endoproteolytic events producing bioactive fragments that are of increasing interest for their physiological functions and their implication in the pathogenesis of prion diseases and other neurodegenerative diseases. However, systematic and comprehensive investigations on the full spectrum of PrPC proteoforms have been hampered by the lack of methods able to identify all PrPC-derived proteoforms. Building on previous knowledge of PrPC endoproteolytic processing, we thus developed an optimized Western blot assay able to obtain the maximum information about PrPC constitutive processing and the relative abundance of PrPC proteoforms in a complex biological sample. This approach led to the concurrent identification of the whole spectrum of known endoproteolytic-derived PrPC proteoforms in brain homogenates, including C-terminal, N-terminal and, most importantly, shed PrPC-derived fragments. Endoproteolytic processing of PrPC was remarkably similar in the brain of widely used wild type and transgenic rodent models, with α-cleavage-derived C1 representing the most abundant proteoform and ADAM10-mediated shedding being an unexpectedly prominent proteolytic event. Interestingly, the relative amount of shed PrPC was higher in WT mice than in most other models. Our results indicate that constitutive endoproteolytic processing of PrPC is not affected by PrPC overexpression or host factors other than PrPC but can be impacted by PrPC primary structure. Finally, this method represents a crucial step in gaining insight into pathophysiological roles, biomarker suitability, and therapeutic potential of shed PrPC and for a comprehensive appraisal of PrPC proteoforms in therapies, drug screening, or in the progression of neurodegenerative diseases.
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Affiliation(s)
- Ilaria Vanni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy.
| | - Floriana Iacobone
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Claudia D’Agostino
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Matteo Giovannelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Laura Pirisinu
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Joaquin Castilla
- Basque Research and Technology Alliance (BRTA) - CIC BioGUNE & IKERBasque, Bizkaia, Spain,Centro de Investigación Biomédica en Red de Enfermedades infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Maria Torres
- Centro de Investigación en Sanidad Animal (CISA-INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Umberto Agrimi
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Romolo Nonno
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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5
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Mortberg MA, Zhao HT, Reidenbach AG, Gentile JE, Kuhn E, O'Moore J, Dooley PM, Connors TR, Mazur C, Allen SW, Trombetta BA, McManus AJ, Moore MR, Liu J, Cabin DE, Kordasiewicz HB, Mathews J, Arnold SE, Vallabh SM, Minikel EV. PrP concentration in the central nervous system: regional variability, genotypic effects, and pharmacodynamic impact. JCI Insight 2022; 7:156532. [PMID: 35133987 PMCID: PMC8986079 DOI: 10.1172/jci.insight.156532] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Prion protein (PrP) concentration controls the kinetics of prion replication and is a genetically and pharmacologically validated therapeutic target for prion disease. In order to evaluate PrP concentration as a pharmacodynamic biomarker and assess its contribution to known prion disease risk factors, we developed and validated a plate-based immunoassay reactive for PrP across six species of interest and applicable to brain and cerebrospinal fluid (CSF). PrP concentration varies dramatically between different brain regions in mice, cynomolgus macaques, and humans. PrP expression does not appear to contribute to the known risk factors of age, sex, or common PRNP genetic variants. CSF PrP is lowered in the presence of rare pathogenic PRNP variants, with heterozygous carriers of P102L displaying 55% and of D178N just 31% the CSF PrP concentration of mutation-negative controls. In rodents, pharmacologic reduction of brain Prnp RNA is reflected in brain parenchyma PrP, and in turn in CSF PrP, validating CSF as a sampling compartment for the effect of PrP-lowering therapy. Our findings support the use of CSF PrP as a pharmacodynamic biomarker for PrP-lowering drugs, and suggest that relative reduction from individual baseline CSF PrP concentration may be an appropriate marker for target engagement.
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Affiliation(s)
- Meredith A Mortberg
- Stanley Center for Psychiatric Research, Broad Institute of Harvard & MIT, Cambridge, United States of America
| | - Hien T Zhao
- Neuroscience, Ionis Pharmaceuticals, Inc., Carlsbad, United States of America
| | - Andrew G Reidenbach
- Stanley Center for Psychiatric Research, Broad Institute of Harvard & MIT, Cambridge, United States of America
| | - Juliana E Gentile
- Stanley Center for Psychiatric Research, Broad Institute of Harvard & MIT, Cambridge, United States of America
| | - Eric Kuhn
- Proteomics Platform, Broad Institute of Harvard & MIT, Cambridge, United States of America
| | - Jill O'Moore
- Comparative Medicine, McLaughlin Research Institute, Great Falls, United States of America
| | - Patrick M Dooley
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, United States of America
| | - Theresa R Connors
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, United States of America
| | - Curt Mazur
- Neuroscience, Ionis Pharmaceuticals, Inc., Carlsbad, United States of America
| | - Shona W Allen
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, United States of America
| | - Bianca A Trombetta
- Department of Neurology, Massachusetts General Hospital, Boston, United States of America
| | - Alison J McManus
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, United States of America
| | | | - Jiewu Liu
- Bioagilytix, Bioagilytix, Boston, United States of America
| | - Deborah E Cabin
- Comparative Medicine, McLaughlin Research Institute, Great Falls, United States of America
| | | | - Joel Mathews
- Neuroscience, Ionis Pharmaceuticals, Inc., Carlsbad, United States of America
| | - Steven E Arnold
- Department of Neurology, Massachusetts General Hospital, Boston, United States of America
| | - Sonia M Vallabh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard & MIT, Cambridge, United States of America
| | - Eric Vallabh Minikel
- Stanley Center for Psychiatric Research, Broad Institute of Harvard & MIT, Cambridge, United States of America
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6
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Tosi L, Chaikban L, Larman BH, Rosenfield J, Parekkadan B. Massively parallel DNA target capture using long adapter single stranded oligonucleotide (LASSO) probes assembled through a novel DNA recombinase mediated methodology. Biotechnol J 2022; 17:e2100240. [PMID: 34775678 PMCID: PMC8825753 DOI: 10.1002/biot.202100240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 02/03/2023]
Abstract
In the attempt to bridge the widening gap from DNA sequence to biological function, we developed a novel methodology to assemble Long-Adapter Single-Strand Oligonucleotide (LASSO) probe libraries that enabled the massively multiplexed capture of kilobase-sized DNA fragments for downstream long read DNA sequencing or expression. This method uses short DNA oligonucleotides (pre-LASSO probes) and a plasmid vector that supplies the linker sequence for the mature LASSO probe through Cre-LoxP intramolecular recombination. This strategy generates high quality LASSO probes libraries (≈46% of correct probes). We performed NGS analysis of the post-capture PCR amplification of DNA circles obtained from the LASSO capture of 3087 Escherichia coli ORFs spanning from 400- to 5000 bp. The median enrichment of all targeted ORFs versus untargeted ORFs was 30 times. For ORFs up to 1kb in size, targeted ORFs were enriched up to a median of 260-fold. Here, we show that LASSO probes obtained in this manner, were able to capture full-length open reading frames from total human cDNA. Furthermore, we show that the LASSO capture specificity and sensitivity is sufficient for target capture from total human genomic DNA template. This technology can be used for the preparation of long-read sequencing libraries and for massively multiplexed cloning of human sequences.
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Affiliation(s)
- Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University,
Piscataway, New Jersey 08854, USA
| | - Lamia Chaikban
- Department of Biomedical Engineering, Rutgers University,
Piscataway, New Jersey 08854, USA
| | - Benjamin H. Larman
- Institute of Cell Engineering, Division of Immunology,
Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey Rosenfield
- Cancer Institute of New Jersey, New Brunswick, New Jersey
08854, USA,Department of Pathology, Robert Wood Johnson Medical
School, New Brunswick, NJ 08903, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University,
Piscataway, New Jersey 08854, USA,Cancer Institute of New Jersey, New Brunswick, New Jersey
08854, USA,Correspondence and requests for materials should
be addressed to B.P. (; 599 Taylor
Road, Piscataway, NJ 08854)
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7
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Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021; 43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
Abstract
The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.
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Affiliation(s)
- Kyrin R Hanning
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Mason Minot
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland
| | - Annmaree K Warrender
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland.
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8
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Francino-Urdaniz IM, Whitehead TA. An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies. RSC Chem Biol 2021; 2:1580-1589. [PMID: 34977572 PMCID: PMC8637828 DOI: 10.1039/d1cb00169h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/25/2021] [Indexed: 12/20/2022] Open
Abstract
This mini-review presents a critical survey of techniques used for epitope mapping on the SARS-CoV-2 Spike protein. The sequence and structures for common neutralizing and non-neutralizing epitopes on the Spike protein are described as determined by X-ray crystallography, electron microscopy and linear peptide epitope mapping, among other methods. An additional focus of this mini-review is an analytical appraisal of different deep mutational scanning workflows for conformational epitope mapping and identification of mutants on the Spike protein which escape antibody neutralization. Such a focus is necessary as a critical review of deep mutational scanning for conformational epitope mapping has not been published. A perspective is presented on the use of different epitope determination methods for development of broadly potent antibody therapies and vaccines against SARS-CoV-2.
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Affiliation(s)
- Irene M Francino-Urdaniz
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
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9
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Further Characterization of Glycoform-Selective Prions of Variably Protease-Sensitive Prionopathy. Pathogens 2021; 10:pathogens10050513. [PMID: 33922765 PMCID: PMC8146342 DOI: 10.3390/pathogens10050513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/10/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022] Open
Abstract
Prion is an infectious protein (PrPSc) that is derived from a cellular glycoprotein (PrPC) through a conformational transition and associated with a group of prion diseases in animals and humans. Characterization of proteinase K (PK)-resistant PrPSc by western blotting has been critical to diagnosis and understanding of prion diseases including Creutzfeldt-Jakob disease (CJD) and Gerstmann-Sträussler-Scheinker (GSS) disease in humans. However, formation as well as biochemical and biological properties of the glycoform-selective PrPSc in variably protease-sensitive prionopathy (VPSPr) remain poorly understood. Here we reveal that formation of the ladder-like PrPSc in VPSPr is a PK-dependent two-step process, which is enhanced by basic pH. Two sets of PrPSc fragments can be identified with antibodies directed against an intermediate or a C-terminal domain of the protein. Moreover, antibodies directed against specific PrP glycoforms reveal faster electrophoretic migrations of PrP fragments mono-glycosylated at residue 181 and 197 in VPSPr than those in sporadic CJD (sCJD). Finally, RT-QuIC assay indicates that PrPSc-seeding activity is lower and its lag time is longer in VPSPr than in sCJD. Our results suggest that the glycoform-selective PrPSc in VPSPr is associated with altered glycosylation, resulting in different PK-truncation and aggregation seeding activity compared to PrPSc in sCJD.
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10
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Coelho CH, Tang WK, Burkhardt M, Galson JD, Muratova O, Salinas ND, Alves e Silva TL, Reiter K, MacDonald NJ, Nguyen V, Herrera R, Shimp R, Narum DL, Byrne-Steele M, Pan W, Hou X, Brown B, Eisenhower M, Han J, Jenkins BJ, Doritchamou JYA, Smelkinson MG, Vega-Rodríguez J, Trück J, Taylor JJ, Sagara I, Healy SA, Renn JP, Tolia NH, Duffy PE. A human monoclonal antibody blocks malaria transmission and defines a highly conserved neutralizing epitope on gametes. Nat Commun 2021; 12:1750. [PMID: 33741942 PMCID: PMC7979743 DOI: 10.1038/s41467-021-21955-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
Malaria elimination requires tools that interrupt parasite transmission. Here, we characterize B cell receptor responses among Malian adults vaccinated against the first domain of the cysteine-rich 230 kDa gamete surface protein Pfs230, a key protein in sexual stage development of P. falciparum parasites. Among nine Pfs230 human monoclonal antibodies (mAbs) that we generated, one potently blocks transmission to mosquitoes in a complement-dependent manner and reacts to the gamete surface; the other eight show only low or no blocking activity. The structure of the transmission-blocking mAb in complex with vaccine antigen reveals a large discontinuous conformational epitope, specific to domain 1 of Pfs230 and comprising six structural elements in the protein. The epitope is conserved, suggesting the transmission-blocking mAb is broadly functional. This study provides a rational basis to improve malaria vaccines and develop therapeutic antibodies for malaria elimination.
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Affiliation(s)
- Camila H. Coelho
- grid.94365.3d0000 0001 2297 5165Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Wai Kwan Tang
- grid.94365.3d0000 0001 2297 5165Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Martin Burkhardt
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Jacob D. Galson
- grid.7400.30000 0004 1937 0650Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich (UZH), Zurich, Switzerland ,Alchemab Therapeutics Ltd, 55-56 Russell Square, London, UK
| | - Olga Muratova
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Nichole D. Salinas
- grid.94365.3d0000 0001 2297 5165Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Thiago Luiz Alves e Silva
- grid.94365.3d0000 0001 2297 5165Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD USA
| | - Karine Reiter
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Nicholas J. MacDonald
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Vu Nguyen
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Raul Herrera
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Richard Shimp
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - David L. Narum
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | | | - Wenjing Pan
- grid.429220.fiRepertoire Inc., Huntsville, AL USA
| | - Xiaohong Hou
- grid.429220.fiRepertoire Inc., Huntsville, AL USA
| | | | | | - Jian Han
- grid.429220.fiRepertoire Inc., Huntsville, AL USA
| | - Bethany J. Jenkins
- grid.94365.3d0000 0001 2297 5165Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Justin Y. A. Doritchamou
- grid.94365.3d0000 0001 2297 5165Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Margery G. Smelkinson
- grid.94365.3d0000 0001 2297 5165Biological Imaging Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Joel Vega-Rodríguez
- grid.94365.3d0000 0001 2297 5165Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD USA
| | - Johannes Trück
- grid.7400.30000 0004 1937 0650Division of Immunology and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich (UZH), Zurich, Switzerland
| | - Justin J. Taylor
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Issaka Sagara
- Malaria Research and Training Center, University of Sciences, Techniques, and Technology, Bamako, Mali
| | - Sara A. Healy
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Jonathan P. Renn
- grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Niraj H. Tolia
- grid.94365.3d0000 0001 2297 5165Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Patrick E. Duffy
- grid.94365.3d0000 0001 2297 5165Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA ,grid.94365.3d0000 0001 2297 5165Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
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11
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Ishikawa T. Saccharomyces cerevisiae in neuroscience: how unicellular organism helps to better understand prion protein? Neural Regen Res 2021; 16:489-495. [PMID: 32985470 PMCID: PMC7996030 DOI: 10.4103/1673-5374.293137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The baker’s yeast Saccharomyces (S.) cerevisiae is a single-celled eukaryotic model organism widely used in research on life sciences. Being a unicellular organism, S. cerevisiae has some evident limitations in application to neuroscience. However, yeast prions are extensively studied and they are known to share some hallmarks with mammalian prion protein or other amyloidogenic proteins found in the pathogenesis of Alzheimer’s, Parkinson’s, or Huntington’s diseases. Therefore, the yeast S. cerevisiae has been widely used for basic research on aggregation properties of proteins in cellulo and on their propagation. Recently, a yeast-based study revealed that some regions of mammalian prion protein and amyloid β1–42 are capable of induction and propagation of yeast prions. It is one of the examples showing that evolutionarily distant organisms share common mechanisms underlying the structural conversion of prion proteins making yeast cells a useful system for studying mammalian prion protein. S. cerevisiae has also been used to design novel screening systems for anti-prion compounds from chemical libraries. Yeast-based assays are cheap in maintenance and safe for the researcher, making them a very good choice to perform preliminary screening before further characterization in systems engaging mammalian cells infected with prions. In this review, not only classical red/white colony assay but also yeast-based screening assays developed during last year are discussed. Computational analysis and research carried out using yeast prions force us to expect that prions are widely present in nature. Indeed, the last few years brought us several examples indicating that the mammalian prion protein is no more peculiar protein – it seems that a better understanding of prion proteins nature-wide may aid us with the treatment of prion diseases and other amyloid-related medical conditions.
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Affiliation(s)
- Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
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12
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Sidore AM, Plesa C, Samson JA, Lubock NB, Kosuri S. DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions. Nucleic Acids Res 2020; 48:e95. [PMID: 32692349 PMCID: PMC7498354 DOI: 10.1093/nar/gkaa600] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/13/2020] [Accepted: 07/11/2020] [Indexed: 01/12/2023] Open
Abstract
Multiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here, we improve DropSynth, a low-cost, multiplexed method that builds gene libraries by compartmentalizing and assembling microarray-derived oligonucleotides in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.
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Affiliation(s)
- Angus M Sidore
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Calin Plesa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joyce A Samson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan B Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.,UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
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13
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Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Eng Des Sel 2019; 32:489-501. [PMID: 32626892 DOI: 10.1093/protein/gzaa012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 01/08/2023] Open
Abstract
Adenylate kinase (AK) orthologs with a range of thermostabilities were subjected to random circular permutation, and deep mutational scanning was used to evaluate where new protein termini were nondisruptive to activity. The fraction of circularly permuted variants that retained function in each library correlated with AK thermostability. In addition, analysis of the positional tolerance to new termini, which increase local conformational flexibility, showed that bonds were either functionally sensitive to cleavage across all homologs, differentially sensitive, or uniformly tolerant. The mobile AMP-binding domain, which displays the highest calculated contact energies, presented the greatest tolerance to new termini across all AKs. In contrast, retention of function in the lid and core domains was more dependent upon AK melting temperature. These results show that family permutation profiling identifies primary structure that has been selected by evolution for dynamics that are critical to activity within an enzyme family. These findings also illustrate how deep mutational scanning can be applied to protein homologs in parallel to differentiate how topology, stability, and local energetics govern mutational tolerance.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, MS-180, Houston, TX 77005, USA.,Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Alicia M Jones
- Biochemistry and Cell Biology Graduate Program, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, 6100 Main Street, MS-140, Houston, TX 77005, USA.,Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, TX 77005, USA.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, TX 77005, USA
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14
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Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biol 2019; 20:223. [PMID: 31679514 PMCID: PMC6827219 DOI: 10.1186/s13059-019-1845-6] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 11/10/2022] Open
Abstract
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB ( https://www.mavedb.org ), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.
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Affiliation(s)
- Daniel Esposito
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jochen Weile
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Frederick P Roth
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
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15
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Atkinson JT, Jones AM, Zhou Q, Silberg JJ. Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis. Nucleic Acids Res 2019; 46:e76. [PMID: 29912470 PMCID: PMC6061844 DOI: 10.1093/nar/gky255] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/28/2018] [Indexed: 12/17/2022] Open
Abstract
Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries of genes created by random circular permutation, an engineering strategy that is used to create open reading frames that express proteins with altered contact order. We describe a new method, termed circular permutation profiling with DNA sequencing (CPP-seq), which combines a one-step transposon mutagenesis protocol for creating libraries with a functional selection, deep sequencing and computational analysis to obtain unbiased insight into a protein's tolerance to circular permutation. Application of this method to an adenylate kinase revealed that CPP-seq creates two types of vectors encoding each circularly permuted gene, which differ in their ability to express proteins. Functional selection of this library revealed that >65% of the sampled vectors that express proteins are enriched relative to those that cannot translate proteins. Mapping enriched sequences onto structure revealed that the mobile AMP binding and rigid core domains display greater tolerance to backbone fragmentation than the mobile lid domain, illustrating how CPP-seq can be used to relate a protein's biophysical characteristics to the retention of activity upon permutation.
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Affiliation(s)
- Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main MS-180, Houston, TX 77005, USA
| | - Alicia M Jones
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, TX 77005, USA
| | - Quan Zhou
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, TX 77005, USA.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, USA
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16
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Wollacott AM, Robinson LN, Ramakrishnan B, Tissire H, Viswanathan K, Shriver Z, Babcock GJ. Structural prediction of antibody-APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data. J Mol Recognit 2019; 32:e2778. [DOI: 10.1002/jmr.2778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/21/2018] [Accepted: 12/06/2018] [Indexed: 12/29/2022]
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17
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A Bioluminescent Cell Assay to Quantify Prion Protein Dimerization. Sci Rep 2018; 8:14178. [PMID: 30242186 PMCID: PMC6155003 DOI: 10.1038/s41598-018-32581-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 09/12/2018] [Indexed: 11/19/2022] Open
Abstract
The prion protein (PrP) is a cell surface protein that in disease misfolds and becomes infectious causing Creutzfeldt-Jakob disease in humans, scrapie in sheep, and chronic wasting disease in deer and elk. Little is known regarding the dimerization of PrP and its role in disease. We developed a bioluminescent prion assay (BPA) to quantify PrP dimerization by bimolecular complementation of split Gaussia luciferase (GLuc) halves that are each fused to PrP. Fusion constructs between PrP and N- and C-terminal GLuc halves were expressed on the surface of RK13 cells (RK13-DC cells) and dimerized to yield a bioluminescent signal that was decreased in the presence of eight different antibodies to PrP. Dimerization of PrP was independent of divalent cations and was induced under stress. Challenge of RK13-DC cells with seven different prion strains did not lead to detectable infection but was measurable by bioluminescence. Finally, we used BPA to screen a compound library for compounds inhibiting PrP dimerization. One of the most potent compounds to inhibit PrP dimerization was JTC-801, which also inhibited prion replication in RML-infected ScN2a and SMB cells with an EC50 of 370 nM and 220 nM, respectively. We show here that BPA is a versatile tool to study prion biology and to identify anti-prion compounds.
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18
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Medina-Cucurella AV, Zhu Y, Bowen SJ, Bergeron LM, Whitehead TA. Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies. Biotechnol Bioeng 2018; 115:1925-1937. [PMID: 29663315 DOI: 10.1002/bit.26706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 01/19/2023]
Abstract
Nerve growth factor (NGF) plays a central role in multiple chronic pain conditions. As such, anti-NGF monoclonal antibodies (mAbs) that function by antagonizing NGF downstream signaling are leading drug candidates for non-opioid pain relief. To evaluate anti-canine NGF (cNGF) mAbs we sought a yeast surface display platform of cNGF. Both mature cNGF and pro-cNGF displayed on the yeast surface but bound conformationally sensitive mAbs at most 2.5-fold in mean fluorescence intensity above background, suggesting that cNGF was mostly misfolded. To improve the amount of folded, displayed cNGF, we used comprehensive mutagenesis, FACS, and deep sequencing to identify point mutants in the pro-region of canine NGF that properly enhance the folded protein displayed on the yeast surface. Out of 1,737 tested single point mutants in the pro region, 49 increased the amount of NGF recognized by conformationally sensitive mAbs. These gain-of-function mutations cluster around residues A-61-P-26. Gain-of-function mutants were additive, and a construct containing three mutations increased amount of folded cNGF to 23-fold above background. Using this new cNGF construct, fine conformational epitopes for tanezumab and three anti-cNGF mAbs were evaluated. The epitope revealed by the yeast experiments largely overlapped with the tanezumab epitope previously determined by X-ray crystallography. The other mAbs showed site-specific differences with tanezumab. As the number of binding epitopes of functionally neutralizing anti-NGF mAbs on NGF are limited, subtle differences in the individual interacting residues on NGF that bind each mAb contribute to the understanding of each antibody and variations in its neutralizing activity. These results demonstrate the potential of deep sequencing-guided protein engineering to improve the production of folded surface-displayed protein, and the resulting cNGF construct provides a platform to map conformational epitopes for other anti-neurotrophin mAbs.
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Affiliation(s)
- Angélica V Medina-Cucurella
- Department of Chemical Engineering and Materials Science, Michigan State University Engineering Building, East Lansing, Michigan
| | - Yaqi Zhu
- Zoetis Global Therapeutic Research, Veterinary Medicine Research and Development, Kalamazoo, Michigan
| | - Scott J Bowen
- Zoetis Global Therapeutic Research, Veterinary Medicine Research and Development, Kalamazoo, Michigan
| | - Lisa M Bergeron
- Zoetis Global Therapeutic Research, Veterinary Medicine Research and Development, Kalamazoo, Michigan
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University Engineering Building, East Lansing, Michigan.,Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan
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19
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Medina-Cucurella AV, Whitehead TA. Characterizing Protein-Protein Interactions Using Deep Sequencing Coupled to Yeast Surface Display. Methods Mol Biol 2018; 1764:101-121. [PMID: 29605911 DOI: 10.1007/978-1-4939-7759-8_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this chapter, we discuss a method to determine the affinity and specificity of nearly all single-point mutants for a full-length protein binder. This method combines deep sequencing, comprehensive mutagenesis, yeast surface display, and fluorescence-activated cell sorting. This approach has been used to study sequence-function relationships for protein-protein interactions. The data can be used to determine the fine conformational epitope on the protein binder.
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Affiliation(s)
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA. .,Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, USA.
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20
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Wrenbeck EE, Faber MS, Whitehead TA. Deep sequencing methods for protein engineering and design. Curr Opin Struct Biol 2017; 45:36-44. [PMID: 27886568 PMCID: PMC5440218 DOI: 10.1016/j.sbi.2016.11.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/01/2016] [Indexed: 11/27/2022]
Abstract
The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition. Examples include the creation of multiple dual-affinity Fabs targeting structurally dissimilar epitopes and engineering of a broad germline-targeted anti-HIV-1 immunogen. Additionally, we highlight the generation of enzyme fitness landscapes for conducting fundamental studies of protein behavior and evolution. We conclude with discussion of technological advances.
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Affiliation(s)
- Emily E Wrenbeck
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, United States
| | - Matthew S Faber
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, United States; Departments of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, United States.
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21
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Wu B, McDonald AJ, Markham K, Rich CB, McHugh KP, Tatzelt J, Colby DW, Millhauser GL, Harris DA. The N-terminus of the prion protein is a toxic effector regulated by the C-terminus. eLife 2017; 6:e23473. [PMID: 28527237 PMCID: PMC5469617 DOI: 10.7554/elife.23473] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/17/2017] [Indexed: 12/23/2022] Open
Abstract
PrPC, the cellular isoform of the prion protein, serves to transduce the neurotoxic effects of PrPSc, the infectious isoform, but how this occurs is mysterious. Here, using a combination of electrophysiological, cellular, and biophysical techniques, we show that the flexible, N-terminal domain of PrPC functions as a powerful toxicity-transducing effector whose activity is tightly regulated in cis by the globular C-terminal domain. Ligands binding to the N-terminal domain abolish the spontaneous ionic currents associated with neurotoxic mutants of PrP, and the isolated N-terminal domain induces currents when expressed in the absence of the C-terminal domain. Anti-PrP antibodies targeting epitopes in the C-terminal domain induce currents, and cause degeneration of dendrites on murine hippocampal neurons, effects that entirely dependent on the effector function of the N-terminus. NMR experiments demonstrate intramolecular docking between N- and C-terminal domains of PrPC, revealing a novel auto-inhibitory mechanism that regulates the functional activity of PrPC.
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Affiliation(s)
- Bei Wu
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
| | - Alex J McDonald
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
| | - Kathleen Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, United States
| | - Celeste B Rich
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
| | - Kyle P McHugh
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, United States
| | - Jörg Tatzelt
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - David W Colby
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, United States
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, United States
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, United States
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22
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Wang X, Stapleton JA, Klesmith JR, Hewlett EL, Whitehead TA, Maynard JA. Fine Epitope Mapping of Two Antibodies Neutralizing the Bordetella Adenylate Cyclase Toxin. Biochemistry 2017; 56:1324-1336. [PMID: 28177609 DOI: 10.1021/acs.biochem.6b01163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenylate cyclase toxin (ACT) is an important Bordetella pertussis virulence factor that is not included in current acellular pertussis vaccines. We previously demonstrated that immunization with the repeat-in-toxin (RTX) domain of ACT elicits neutralizing antibodies in mice and discovered the first two antibodies to neutralize ACT activities by occluding the receptor-binding site. Here, we fully characterize these antibodies and their epitopes. Both antibodies bind ACT with low nanomolar affinity and cross-react with ACT homologues produced by B. parapertussis and B. bronchiseptica. Antibody M1H5 binds B. pertussis RTX751 ∼100-fold tighter than RTX751 from the other two species, while antibody M2B10 has similar affinity for all three variants. To initially map the antibody epitopes, we generated a series of ACT chimeras and truncation variants, which implicated the repeat blocks II-III. To identify individual epitope residues, we displayed randomly mutated RTX751 libraries on yeast and isolated clones with decreased antibody binding by flow cytometry. Next-generation sequencing identified candidate epitope residues on the basis of enrichment of clones with mutations at specific positions. These epitopes form two adjacent surface patches on a predicted structural model of the RTX751 domain, one for each antibody. Notably, the cellular receptor also binds within blocks II-III and shares at least one residue with the M1H5 epitope. The RTX751 model supports the notion that the antibody and receptor epitopes overlap. These data provide insight into mechanisms of ACT neutralization and guidance for engineering more stable RTX variants that may be more appropriate vaccine antigens.
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Affiliation(s)
- Xianzhe Wang
- Department of Chemical Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - James A Stapleton
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan 48824, United States
| | - Justin R Klesmith
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| | - Erik L Hewlett
- Department of Medicine, University of Virginia , Charlottesville, Virginia 22906, United States
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan 48824, United States.,Department of Biosystems and Agricultural Engineering, Michigan State University , East Lansing, Michigan 48824, United States
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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23
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Cellular prion protein is present in mitochondria of healthy mice. Sci Rep 2017; 7:41556. [PMID: 28148964 PMCID: PMC5288712 DOI: 10.1038/srep41556] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/13/2016] [Indexed: 01/04/2023] Open
Abstract
Cellular prion protein (PrPC) is a mammalian glycoprotein which is usually found anchored to the plasma membrane via a glycophosphatidylinositol (GPI) anchor. PrPC misfolds to a pathogenic isoform PrPSc, the causative agent of neurodegenerative prion diseases. The precise function of PrPC remains elusive but may depend upon its cellular localization. Here we show that PrPC is present in brain mitochondria from 6–12 week old wild-type and transgenic mice in the absence of disease. Mitochondrial PrPC was fully processed with mature N-linked glycans and did not require the GPI anchor for localization. Protease treatment of purified mitochondria suggested that mitochondrial PrPC exists as a transmembrane isoform with the C-terminus facing the mitochondrial matrix and the N-terminus facing the intermembrane space. Taken together, our data suggest that PrPC can be found in mitochondria in the absence of disease, old age, mutation, or overexpression and that PrPC may affect mitochondrial function.
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24
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Adams RM, Mora T, Walczak AM, Kinney JB. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. eLife 2016; 5. [PMID: 28035901 PMCID: PMC5268739 DOI: 10.7554/elife.23156] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/27/2016] [Indexed: 11/30/2022] Open
Abstract
Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody’s amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects of antibody expression and stability that arise in standard deep mutational scanning assays. We demonstrate Tite-Seq on the CDR1H and CDR3H regions of a well-studied scFv antibody. Our data shed light on the structural basis for antigen binding affinity and suggests a role for secondary CDR loops in establishing antibody stability. Tite-Seq fills a large gap in the ability to measure critical aspects of the adaptive immune system, and can be readily used for studying sequence-affinity landscapes in other protein systems. DOI:http://dx.doi.org/10.7554/eLife.23156.001 Antibodies are proteins produced by cells of the immune system to tag or neutralize potential threats to the body, such as foreign substances and disease-causing microbes. Antibodies do this by binding to target molecules called antigens. An antibody’s ability to bind to an antigen depends on the sequence of amino acids – the building blocks of proteins – that make up the antibody. Through a process that randomizes this sequence of amino acids, the immune system generates a vast pool of antibodies that are able to target almost any foreign antigen that exists in nature. Currently, little is understood about how the sequence of amino acids in an antibody determines how strongly that antibody binds to its antigen target – a property referred to as the antibody’s binding affinity. Answering this fundamental question requires techniques that can measure the affinities of many different antibodies at the same time. However, previous high-throughput methods have been unable to provide quantitative measurements of binding affinities. These kinds of measurements are difficult because an antibody’s amino acid sequence governs more than just binding affinity: it also affects how easy it is to produce that antibody, and what fraction of antibody molecules work properly. Adams et al. now describe a new method, named “Tite-Seq”, that overcomes these issues. First, thousands of different antibodies are displayed on the surface of yeast cells, with each cell carrying a single kind of antibody. These cells are then incubated with fluorescently labeled antigen at a wide range of different concentrations. Next, the yeast cells are sorted based on how brightly they glow; brighter cells have more antigen bound to them, and so it is possible to calculate how much of the antigen is bound to each kind of antibody at each concentration. Plotting these data provides a “binding curve” for each antibody, which is then used to read off the antibody’s binding affinity in a way that is not affected by the factors that have plagued other high-throughput methods. Tite-Seq is thus able to measure the binding affinities for thousands of different antibodies at the same time. This will potentially allow researchers to address many fundamental and yet unanswered questions about how the immune system works. Tite-Seq can also be used to measure how amino acid sequence affects the binding affinity of proteins other than antibodies. DOI:http://dx.doi.org/10.7554/eLife.23156.002
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Affiliation(s)
- Rhys M Adams
- Laboratoire de Physique Théorique, UMR8549, CNRS, École Normale Supérieure, Paris, France.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS, École Normale Supérieure, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS, École Normale Supérieure, Paris, France
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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25
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van Rosmalen M, Janssen BMG, Hendrikse NM, van der Linden AJ, Pieters PA, Wanders D, de Greef TFA, Merkx M. Affinity Maturation of a Cyclic Peptide Handle for Therapeutic Antibodies Using Deep Mutational Scanning. J Biol Chem 2016; 292:1477-1489. [PMID: 27974464 DOI: 10.1074/jbc.m116.764225] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/29/2016] [Indexed: 11/06/2022] Open
Abstract
Meditopes are cyclic peptides that bind in a specific pocket in the antigen-binding fragment of a therapeutic antibody such as cetuximab. Provided their moderate affinity can be enhanced, meditope peptides could be used as specific non-covalent and paratope-independent handles in targeted drug delivery, molecular imaging, and therapeutic drug monitoring. Here we show that the affinity of a recently reported meditope for cetuximab can be substantially enhanced using a combination of yeast display and deep mutational scanning. Deep sequencing was used to construct a fitness landscape of this protein-peptide interaction, and four mutations were identified that together improved the affinity for cetuximab 10-fold to 15 nm Importantly, the increased affinity translated into enhanced cetuximab-mediated recruitment to EGF receptor-overexpressing cancer cells. Although in silico Rosetta simulations correctly identified positions that were tolerant to mutation, modeling did not accurately predict the affinity-enhancing mutations. The experimental approach reported here should be generally applicable and could be used to develop meditope peptides with low nanomolar affinity for other therapeutic antibodies.
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Affiliation(s)
- Martijn van Rosmalen
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Brian M G Janssen
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Natalie M Hendrikse
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ardjan J van der Linden
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A Pieters
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Dave Wanders
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Tom F A de Greef
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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26
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Kowalsky CA, Whitehead TA. Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing. Proteins 2016; 84:1914-1928. [PMID: 27699856 DOI: 10.1002/prot.25175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/05/2016] [Accepted: 09/27/2016] [Indexed: 12/27/2022]
Abstract
The comprehensive sequence determinants of binding affinity for type I cohesin toward dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2970 and 2778 single point mutants of C. thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with the three independent experimental methods. This reconstruction results in a narrow dynamic range of -0.8-0.5 kcal/mol. The computational software packages FoldX and Rosetta were used to predict mutations that disrupt binding by more than 0.4 kcal/mol. The area under the curve of receiver operator curves was 0.82 for FoldX and 0.77 for Rosetta, showing reasonable agreements between predictions and experimental results. Destabilizing mutations to core and rim positions were predicted with higher accuracy than support positions. This benchmark dataset may be useful for developing new computational prediction tools for the prediction of the mutational effect on binding affinities for protein-protein interactions. Experimental considerations to improve precision and range of the reconstruction method are discussed. Proteins 2016; 84:1914-1928. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Caitlin A Kowalsky
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, 48824
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, 48824
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27
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Gaiotto T, Hufton SE. Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. PLoS One 2016; 11:e0164296. [PMID: 27741319 PMCID: PMC5065140 DOI: 10.1371/journal.pone.0164296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
Cross-neutralising monoclonal antibodies against influenza hemagglutinin (HA) are of considerable interest as both therapeutics and diagnostic tools. We have recently described five different single domain antibodies (nanobodies) which share this cross-neutralising activity and suggest their small size, high stability, and cleft binding properties may present distinct advantages over equivalent conventional antibodies. We have used yeast display in combination with deep mutational scanning to give residue level resolution of positions in the antibody-HA interface which are crucial for binding. In addition, we have mapped positions within HA predicted to have minimal effect on antibody binding when mutated. Our cross-neutralising nanobodies were shown to bind to a highly conserved pocket in the HA2 domain of A(H1N1)pdm09 influenza virus overlapping with the fusion peptide suggesting their mechanism of action is through the inhibition of viral membrane fusion. We also note that the epitope overlaps with that of CR6261 and F10 which are human monoclonal antibodies in clinical development as immunotherapeutics. Although all five nanobodies mapped to the same highly conserved binding pocket we observed differences in the size of the epitope footprint which has implications in comparing the relative genetic barrier each nanobody presents to a rapidly evolving influenza virus. To further refine our epitope map, we have re-created naturally occurring mutations within this HA stem epitope and tested their effect on binding using yeast display. We have shown that a D46N mutation in the HA2 stem domain uniquely interferes with binding of R2b-E8. Further testing of this substitution in the context of full length purified HA from 1918 H1N1 pandemic (Spanish flu), 2009 H1N1 pandemic (swine flu) and highly pathogenic avian influenza H5N1 demonstrated binding which correlated with D46 whereas binding to seasonal H1N1 strains carrying N46 was absent. In addition, our deep sequence analysis predicted that binding to the emerging H1N1 strain (A/Christchurch/16/2010) carrying the HA2-E47K mutation would not affect binding was confirmed experimentally. This demonstrates yeast display, in combination with deep sequencing, may be able to predict antibody reactivity to emerging influenza strains so assisting in the preparation for future influenza pandemics.
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Affiliation(s)
- Tiziano Gaiotto
- Biotherapeutics Group, National Institute for Biological Standards and Control, a centre of the Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar, Herts, EN6 3QG, United Kingdom
| | - Simon E. Hufton
- Biotherapeutics Group, National Institute for Biological Standards and Control, a centre of the Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar, Herts, EN6 3QG, United Kingdom
- * E-mail:
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28
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The power of multiplexed functional analysis of genetic variants. Nat Protoc 2016; 11:1782-7. [PMID: 27583640 DOI: 10.1038/nprot.2016.135] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022]
Abstract
New technologies have recently enabled saturation mutagenesis and functional analysis of nearly all possible variants of regulatory elements or proteins of interest in single experiments. Here we discuss the past, present, and future of such multiplexed (functional) assays for variant effects (MAVEs). MAVEs provide detailed insight into sequence-function relationships, and they may prove critical for the prospective clinical interpretation of genetic variants.
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29
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Strømland Ø, Jakubec M, Furse S, Halskau Ø. Detection of misfolded protein aggregates from a clinical perspective. J Clin Transl Res 2016; 2:11-26. [PMID: 30873457 PMCID: PMC6410640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
Neurodegenerative Protein Misfolding Diseases (PMDs), such as Alzheimer's (AD), Parkinson's (PD) and prion diseases, are generally difficult to diagnose before irreversible damage to the central nervous system damage has occurred. Detection of the misfolded proteins that ultimately lead to these conditions offers a means for providing early detection and diagnosis of this class of disease. In this review, we discuss recent developments surrounding protein misfolding diseases with emphasis on the cytotoxic oligomers implicated in their aetiology. We also discuss the relationship of misfolded proteins with biological membranes. Finally, we discuss how far techniques for providing early diagnoses for PMDs have advanced and describe promising clinical approaches. We conclude that antibodies with specificity towards oligomeric species of AD and PD and lectins with specificity for particular glycosylation, show promise. However, it is not clear which approach may yield a reliable clinical test first. Relevance for patients: Individuals suffering from protein misfolding diseases will likely benefit form earlier, less- or even non-invasive diagnosis techniques. The current state and possible future directions for these are subject of this review.
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30
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Reimann RR, Sonati T, Hornemann S, Herrmann US, Arand M, Hawke S, Aguzzi A. Differential Toxicity of Antibodies to the Prion Protein. PLoS Pathog 2016; 12:e1005401. [PMID: 26821311 PMCID: PMC4731068 DOI: 10.1371/journal.ppat.1005401] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/22/2015] [Indexed: 11/25/2022] Open
Abstract
Antibodies against the prion protein PrPC can antagonize prion replication and neuroinvasion, and therefore hold promise as possible therapeutics against prion diseases. However, the safety profile of such antibodies is controversial. It was originally reported that the monoclonal antibody D13 exhibits strong target-related toxicity, yet a subsequent study contradicted these findings. We have reported that several antibodies against certain epitopes of PrPC, including antibody POM1, are profoundly neurotoxic, yet antibody ICSM18, with an epitope that overlaps with POM1, was reported to be innocuous when injected into mouse brains. In order to clarify this confusing situation, we assessed the neurotoxicity of antibodies D13 and ICSM18 with dose-escalation studies using diffusion-weighted magnetic resonance imaging and various histological techniques. We report that both D13 and ICSM18 induce rapid, dose-dependent, on-target neurotoxicity. We conclude that antibodies directed to this region may not be suitable as therapeutics. No such toxicity was found when antibodies against the flexible tail of PrPC were administered. Any attempt at immunotherapy or immunoprophylaxis of prion diseases should account for these potential untoward effects.
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Affiliation(s)
- Regina R. Reimann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Tiziana Sonati
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Uli S. Herrmann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Michael Arand
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Simon Hawke
- Vascular Immunology Laboratory, Department of Pathology, University of Sydney, Camperdown, Australia
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
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31
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Rosenfeld L, Shirian J, Zur Y, Levaot N, Shifman JM, Papo N. Combinatorial and Computational Approaches to Identify Interactions of Macrophage Colony-stimulating Factor (M-CSF) and Its Receptor c-FMS. J Biol Chem 2015; 290:26180-93. [PMID: 26359491 PMCID: PMC4646268 DOI: 10.1074/jbc.m115.671271] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/06/2015] [Indexed: 01/06/2023] Open
Abstract
The molecular interactions between macrophage colony-stimulating factor (M-CSF) and the tyrosine kinase receptor c-FMS play a key role in the immune response, bone metabolism, and the development of some cancers. Because no x-ray structure is available for the human M-CSF · c-FMS complex, the binding epitope for this complex is largely unknown. Our goal was to identify the residues that are essential for binding of the human M-CSF to c-FMS. For this purpose, we used a yeast surface display (YSD) approach. We expressed a combinatorial library of monomeric M-CSF (M-CSFM) single mutants and screened this library to isolate variants with reduced affinity for c-FMS using FACS. Sequencing yielded a number of single M-CSFM variants with mutations both in the direct binding interface and distant from the binding site. In addition, we used computational modeling to map the identified mutations onto the M-CSFM structure and to classify the mutations into three groups as follows: those that significantly decrease protein stability; those that destroy favorable intermolecular interactions; and those that decrease affinity through allosteric effects. To validate the YSD and computational data, M-CSFM and three variants were produced as soluble proteins; their affinity and structure were analyzed; and very good correlations with both YSD data and computational predictions were obtained. By identifying the M-CSFM residues critical for M-CSF · c-FMS interactions, we have laid down the basis for a deeper understanding of the M-CSF · c-FMS signaling mechanism and for the development of target-specific therapeutic agents with the ability to sterically occlude the M-CSF·c-FMS binding interface.
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Affiliation(s)
- Lior Rosenfeld
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, and
| | - Jason Shirian
- the Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yuval Zur
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, and the Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer-Sheva 8410501 and
| | - Noam Levaot
- the Department of Physiology and Cell Biology, Ben-Gurion University of the Negev, Beer-Sheva 8410501 and
| | - Julia M Shifman
- the Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Niv Papo
- From the Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, and
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32
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De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries. Nat Commun 2015; 6:8351. [PMID: 26387459 PMCID: PMC4595759 DOI: 10.1038/ncomms9351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 08/12/2015] [Indexed: 12/13/2022] Open
Abstract
Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants. This paper described a new and efficient method for de novo assembly of multiple DNA sequence information from mutagenized clone libraries. Using codon-barcoded libraries and calling the method JigsawSeq, the authors overcome limitations of short-read sequencing assembly from next-generation sequencing.
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33
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Kowalsky CA, Faber MS, Nath A, Dann HE, Kelly VW, Liu L, Shanker P, Wagner EK, Maynard JA, Chan C, Whitehead TA. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J Biol Chem 2015; 290:26457-70. [PMID: 26296891 DOI: 10.1074/jbc.m115.676635] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 12/29/2022] Open
Abstract
Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.
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Affiliation(s)
| | | | | | - Hailey E Dann
- From the Department of Chemical Engineering and Materials Science
| | - Vince W Kelly
- From the Department of Chemical Engineering and Materials Science
| | - Li Liu
- Department of Microbiology and Molecular Genetics, and
| | - Purva Shanker
- From the Department of Chemical Engineering and Materials Science
| | - Ellen K Wagner
- the Department of Chemical Engineering, University of Texas, Austin, Texas 78712
| | - Jennifer A Maynard
- the Department of Chemical Engineering, University of Texas, Austin, Texas 78712
| | - Christina Chan
- From the Department of Chemical Engineering and Materials Science, Department of Biochemistry and Molecular Biology, Genetics Graduate Program
| | - Timothy A Whitehead
- From the Department of Chemical Engineering and Materials Science, Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan 48824 and
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34
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Didonna A, Venturini AC, Hartman K, Vranac T, Čurin Šerbec V, Legname G. Characterization of four new monoclonal antibodies against the distal N-terminal region of PrP(c). PeerJ 2015; 3:e811. [PMID: 25802800 PMCID: PMC4369333 DOI: 10.7717/peerj.811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/11/2015] [Indexed: 12/15/2022] Open
Abstract
Prion diseases are a group of fatal neurodegenerative disorders that affect humans and animals. They are characterized by the accumulation in the central nervous system of a pathological form of the host-encoded prion protein (PrPC). The prion protein is a membrane glycoprotein that consists of two domains: a globular, structured C-terminus and an unstructured N-terminus. The N-terminal part of the protein is involved in different functions in both health and disease. In the present work we discuss the production and biochemical characterization of a panel of four monoclonal antibodies (mAbs) against the distal N-terminus of PrPC using a well-established methodology based on the immunization of Prnp0/0 mice. Additionally, we show their ability to block prion (PrPSc) replication at nanomolar concentrations in a cell culture model of prion infection. These mAbs represent a promising tool for prion diagnostics and for studying the physiological role of the N-terminal domain of PrPC.
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Affiliation(s)
- Alessandro Didonna
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Anja Colja Venturini
- Department for Production of Diagnostic Reagents and Research, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Katrina Hartman
- Department for Production of Diagnostic Reagents and Research, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Tanja Vranac
- Department for Production of Diagnostic Reagents and Research, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Vladka Čurin Šerbec
- Department for Production of Diagnostic Reagents and Research, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.,ELETTRA-Sincrotrone Trieste S.C.p.A, Trieste, Italy
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