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Hutchings CJ, Colussi P, Clark TG. Ion channels as therapeutic antibody targets. MAbs 2018; 11:265-296. [PMID: 30526315 PMCID: PMC6380435 DOI: 10.1080/19420862.2018.1548232] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/01/2018] [Accepted: 11/03/2018] [Indexed: 12/12/2022] Open
Abstract
It is now well established that antibodies have numerous potential benefits when developed as therapeutics. Here, we evaluate the technical challenges of raising antibodies to membrane-spanning proteins together with enabling technologies that may facilitate the discovery of antibody therapeutics to ion channels. Additionally, we discuss the potential targeting opportunities in the anti-ion channel antibody landscape, along with a number of case studies where functional antibodies that target ion channels have been reported. Antibodies currently in development and progressing towards the clinic are highlighted.
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Affiliation(s)
| | | | - Theodore G. Clark
- TetraGenetics Inc, Arlington Massachusetts, USA
- Department of Microbiology and Immunology, Cornell University, Ithaca New York, USA
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2
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Araman C, Thompson RE, Wang S, Hackl S, Payne RJ, Becker CFW. Semisynthetic prion protein (PrP) variants carrying glycan mimics at position 181 and 197 do not form fibrils. Chem Sci 2017; 8:6626-6632. [PMID: 28989689 PMCID: PMC5625290 DOI: 10.1039/c7sc02719b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/18/2017] [Indexed: 12/12/2022] Open
Abstract
Semisynthesis and characterization of homogeneously mono- and di-PEGylated full length PrP variants to study the impact of PEGylation (as N-glycan mimics) on protein folding and aggregation.
The prion protein (PrP) is an N-glycosylated protein attached to the outer leaflet of eukaryotic cell membranes via a glycosylphosphatidylinositol (GPI) anchor. Different prion strains have distinct glycosylation patterns and the extent of glycosylation of potentially pathogenic misfolded prion protein (PrPSc) has a major impact on several prion-related diseases (transmissible spongiform encephalopathies, TSEs). Based on these findings it is hypothesized that posttranslational modifications (PTMs) of PrP influence conversion of cellular prion protein (PrPC) into PrPSc and, as such, modified PrP variants are critical tools needed to investigate the impact of PTMs on the pathogenesis of TSEs. Here we report a semisynthetic approach to generate PrP variants modified with monodisperse polyethyleneglycol (PEG) units as mimics of N-glycans. Incorporating PEG at glycosylation sites 181 and 197 in PrP induced only small changes to the secondary structure when compared to unmodified, wildtype PrP. More importantly, in vitro aggregation was abrogated for all PEGylated PrP variants under conditions at which wildtype PrP aggregated. Furthermore, the addition of PEGylated PrP as low as 10 mol% to wildtype PrP completely blocked aggregation. A similar effect was observed for synthetic PEGylated PrP segments comprising amino acids 179–231 alone if these were added to wildtype PrP in aggregation assays. This behavior raises the question if large N-glycans interfere with aggregation in vivo and if PEGylated PrP peptides could serve as potential therapeutics.
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Affiliation(s)
- Can Araman
- Institute of Biological Chemistry , Department of Chemistry , University of Vienna , Waehringer Strasse 38 , 1090 , Vienna-AT , Austria .
| | - Robert E Thompson
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Siyao Wang
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Stefanie Hackl
- Institute of Biological Chemistry , Department of Chemistry , University of Vienna , Waehringer Strasse 38 , 1090 , Vienna-AT , Austria .
| | - Richard J Payne
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Christian F W Becker
- Institute of Biological Chemistry , Department of Chemistry , University of Vienna , Waehringer Strasse 38 , 1090 , Vienna-AT , Austria .
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Howorka S. Building membrane nanopores. NATURE NANOTECHNOLOGY 2017; 12:619-630. [PMID: 28681859 DOI: 10.1038/nnano.2017.99] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 04/19/2017] [Indexed: 05/28/2023]
Abstract
Membrane nanopores-hollow nanoscale barrels that puncture biological or synthetic membranes-have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
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Jacobsen MT, Erickson PW, Kay MS. Aligator: A computational tool for optimizing total chemical synthesis of large proteins. Bioorg Med Chem 2017; 25:4946-4952. [PMID: 28651912 DOI: 10.1016/j.bmc.2017.05.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 12/14/2022]
Abstract
The scope of chemical protein synthesis (CPS) continues to expand, driven primarily by advances in chemical ligation tools (e.g., reversible solubilizing groups and novel ligation chemistries). However, the design of an optimal synthesis route can be an arduous and fickle task due to the large number of theoretically possible, and in many cases problematic, synthetic strategies. In this perspective, we highlight recent CPS tool advances and then introduce a new and easy-to-use program, Aligator (Automated Ligator), for analyzing and designing the most efficient strategies for constructing large targets using CPS. As a model set, we selected the E. coli ribosomal proteins and associated factors for computational analysis. Aligator systematically scores and ranks all feasible synthetic strategies for a particular CPS target. The Aligator script methodically evaluates potential peptide segments for a target using a scoring function that includes solubility, ligation site quality, segment lengths, and number of ligations to provide a ranked list of potential synthetic strategies. We demonstrate the utility of Aligator by analyzing three recent CPS projects from our lab: TNFα (157 aa), GroES (97 aa), and DapA (312 aa). As the limits of CPS are extended, we expect that computational tools will play an increasingly important role in the efficient execution of ambitious CPS projects such as production of a mirror-image ribosome.
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Affiliation(s)
- Michael T Jacobsen
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, United States
| | - Patrick W Erickson
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, United States
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, United States.
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Asymmetric perturbations of signalling oligomers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:153-69. [PMID: 24650570 DOI: 10.1016/j.pbiomolbio.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.
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Manor J, Arkin IT. Gaining insight into membrane protein structure using isotope-edited FTIR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012. [PMID: 23196348 DOI: 10.1016/j.bbamem.2012.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
FTIR spectroscopy has long been used as a tool used to gain average structural information on proteins. With the advent of stable isotope editing, FTIR can be used to derive accurate information on isolated amino acids. In particular, in an anisotropic sample such as membrane layers, it is possible to measure the orientation of the peptidic carbonyl groups. Herein, we review the theory that enables one to obtain accurate restraints from FTIR spectroscopy, alongside considerations for sample suitability and general applicability. We also propose approaches that may be used to generate structural models of simple membrane proteins based on FTIR orientational restraints. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Joshua Manor
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem, 91904, Israel
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Tada S, Kitajima T, Ito Y. Design and synthesis of binding growth factors. Int J Mol Sci 2012; 13:6053-6072. [PMID: 22754349 PMCID: PMC3382770 DOI: 10.3390/ijms13056053] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/10/2012] [Accepted: 05/09/2012] [Indexed: 01/01/2023] Open
Abstract
Growth factors play important roles in tissue regeneration. However, because of their instability and diffusible nature, improvements in their performance would be desirable for therapeutic applications. Conferring binding affinities would be one way to improve their applicability. Here we review techniques for conjugating growth factors to polypeptides with particular affinities. Conjugation has been designed at the level of gene fusion and of polypeptide ligation. We summarize and discuss the designs and applications of binding growth factors prepared by such conjugation approaches.
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Affiliation(s)
- Seiichi Tada
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takashi Kitajima
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Ito Y. Elaborate Synthesis of Biological Macromolecules. Chembiochem 2012; 13:1100-2. [DOI: 10.1002/cbic.201200183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Indexed: 11/10/2022]
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Devaraneni PK, Devereaux JJ, Valiyaveetil FI. In vitro folding of KvAP, a voltage-gated K+ channel. Biochemistry 2011; 50:10442-50. [PMID: 22044112 DOI: 10.1021/bi2012965] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this contribution, we report in vitro folding of the archaebacterial voltage-gated K(+) channel, K(v)AP. We show that in vitro folding of the K(v)AP channel from the extensively unfolded state requires lipid vesicles and that the refolded channel is biochemically and functionally similar to the native channel. The in vitro folding process is slow at room temperature, and the folding yield depends on the composition of the lipid bilayer. The major factor influencing refolding is temperature, and almost quantitative refolding of the K(v)AP channel is observed at 80 °C. To differentiate between insertion into the bilayer and folding within the bilayer, we developed a cysteine protection assay. Using this assay, we demonstrate that insertion of the unfolded protein into the bilayer is relatively fast at room temperature and independent of lipid composition, suggesting that temperature and bilayer composition influence folding within the bilayer. Further, we demonstrate that in vitro folding provides an effective method for obtaining high yields of the native channel. Our studies suggest that the K(v)AP channel provides a good model system for investigating the folding of a multidomain integral membrane protein.
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Affiliation(s)
- Prasanna K Devaraneni
- The Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, Oregon 97239, United States
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Brehs M, Bäuml K, Becker CFW. Chemical Synthesis of an Integral Membrane Enzyme - The Challenges of Diacylglycerol Kinase. Isr J Chem 2011. [DOI: 10.1002/ijch.201100090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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