1
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Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.526773. [PMID: 36824741 PMCID: PMC9949092 DOI: 10.1101/2023.02.13.526773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.
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2
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Xie J, DiMaio D. Traptamer screening: a new functional genomics approach to study virus entry and other cellular processes. FEBS J 2022; 289:355-362. [PMID: 33604985 PMCID: PMC8371075 DOI: 10.1111/febs.15775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/26/2021] [Accepted: 02/17/2021] [Indexed: 01/03/2023]
Abstract
Historically, the genetic analysis of mammalian cells entailed the isolation of randomly arising mutant cell lines with altered properties, followed by laborious genetic mapping experiments to identify the mutant gene responsible for the phenotype. In recent years, somatic cell genetics has been revolutionized by functional genomics screens, in which expression of every protein-coding gene is systematically perturbed, and the phenotype of the perturbed cells is determined. We outline here a novel functional genomics screening strategy that differs fundamentally from commonly used approaches. In this strategy, we express libraries of artificial transmembrane proteins named traptamers and select rare cells with the desired phenotype because, by chance, a traptamer specifically perturbs the expression or activity of a target protein. Active traptamers are then recovered from the selected cells and can be used as tools to dissect the biological process under study. We also briefly describe how we have used this new strategy to provide insights into the complex process by which human papillomaviruses enter cells.
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Affiliation(s)
- Jian Xie
- Department of Genetics, Yale School of Medicine, New Haven, CT USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT USA
- Yale Cancer Center, New Haven, CT USA
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3
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Petti LM, Koleske BN, DiMaio D. Activation of the PDGF β Receptor by a Persistent Artificial Signal Peptide. J Mol Biol 2021; 433:167223. [PMID: 34474086 DOI: 10.1016/j.jmb.2021.167223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/25/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Most eukaryotic transmembrane and secreted proteins contain N-terminal signal peptides that mediate insertion of the nascent translation products into the membrane of the endoplasmic reticulum. After membrane insertion, signal peptides typically are cleaved from the mature protein and degraded. Here, we tested whether a small hydrophobic protein selected for growth promoting activity in mammalian cells retained transforming activity while also acting as a signal peptide. We replaced the signal peptide of the PDGF β receptor (PDGFβR) with a previously described 29-residue artificial transmembrane protein named 9C3 that can activate the PDGFβR in trans. We showed that a modified version of 9C3 at the N-terminus of the PDGFβR can function as a signal peptide, as assessed by its ability to support high level expression, glycosylation, and cell surface localization of the PDGFβR. The 9C3 signal peptide retains its ability to interact with the transmembrane domain of the PDGFβR and cause receptor activation and cell proliferation. Cleavage of the 9C3 signal peptide from the mature receptor is not required for these activities. However, signal peptide cleavage does occur in some molecules, and the cleaved signal peptide can persist in cells and activate a co-expressed PDGFβR in trans. Our finding that a hydrophobic sequence can display signal peptide and transforming activity suggest that some naturally occurring signal peptides may also display additional biological activities by interacting with the transmembrane domains of target proteins.
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Affiliation(s)
- Lisa M Petti
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
| | - Benjamin N Koleske
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA; Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, PO Box 208024, New Haven, CT 06520-8024, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA; Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, PO Box 208024, New Haven, CT 06520-8024, USA; Department of Therapeutic Radiology, Yale School of Medicine, PO Box 208040, New Haven, CT 06520-8040, USA; Yale Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA.
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4
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Aptamers in Virology-A Consolidated Review of the Most Recent Advancements in Diagnosis and Therapy. Pharmaceutics 2021; 13:pharmaceutics13101646. [PMID: 34683938 PMCID: PMC8540715 DOI: 10.3390/pharmaceutics13101646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
The use of short oligonucleotide or peptide molecules as target-specific aptamers has recently garnered substantial attention in the field of the detection and treatment of viral infections. Based on their high affinity and high specificity to desired targets, their use is on the rise to replace antibodies for the detection of viruses and viral antigens. Furthermore, aptamers inhibit intracellular viral transcription and translation, in addition to restricting viral entry into host cells. This has opened up a plethora of new targets for the research and development of novel vaccines against viruses. Here, we discuss the advances made in aptamer technology for viral diagnosis and therapy in the past decade.
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5
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Westerfield JM, Barrera FN. Membrane receptor activation mechanisms and transmembrane peptide tools to elucidate them. J Biol Chem 2019; 295:1792-1814. [PMID: 31879273 DOI: 10.1074/jbc.rev119.009457] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Single-pass membrane receptors contain extracellular domains that respond to external stimuli and transmit information to intracellular domains through a single transmembrane (TM) α-helix. Because membrane receptors have various roles in homeostasis, signaling malfunctions of these receptors can cause disease. Despite their importance, there is still much to be understood mechanistically about how single-pass receptors are activated. In general, single-pass receptors respond to extracellular stimuli via alterations in their oligomeric state. The details of this process are still the focus of intense study, and several lines of evidence indicate that the TM domain (TMD) of the receptor plays a central role. We discuss three major mechanistic hypotheses for receptor activation: ligand-induced dimerization, ligand-induced rotation, and receptor clustering. Recent observations suggest that receptors can use a combination of these activation mechanisms and that technical limitations can bias interpretation. Short peptides derived from receptor TMDs, which can be identified by screening or rationally developed on the basis of the structure or sequence of their targets, have provided critical insights into receptor function. Here, we explore recent evidence that, depending on the target receptor, TMD peptides cannot only inhibit but also activate target receptors and can accommodate novel, bifunctional designs. Furthermore, we call for more sharing of negative results to inform the TMD peptide field, which is rapidly transforming into a suite of unique tools with the potential for future therapeutics.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996.
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6
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He L, Cohen EB, Edwards APB, Xavier-Ferrucio J, Bugge K, Federman RS, Absher D, Myers RM, Kragelund BB, Krause DS, DiMaio D. Transmembrane Protein Aptamer Induces Cooperative Signaling by the EPO Receptor and the Cytokine Receptor β-Common Subunit. iScience 2019; 17:167-181. [PMID: 31279934 PMCID: PMC6614117 DOI: 10.1016/j.isci.2019.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/10/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
The erythropoietin receptor (EPOR) plays an essential role in erythropoiesis and other cellular processes by forming distinct signaling complexes composed of EPOR homodimers or hetero-oligomers between the EPOR and another receptor, but the mechanism of heteroreceptor assembly and signaling is poorly understood. We report here a 46-residue, artificial transmembrane protein aptamer, designated ELI-3, that binds and activates the EPOR and induces growth factor independence in murine BaF3 cells expressing the EPOR. ELI-3 requires the transmembrane domain and JAK2-binding sites of the EPOR for activity, but not the cytoplasmic tyrosines that mediate canonical EPOR signaling. Instead, ELI-3-induced proliferation and activation of JAK/STAT signaling requires the transmembrane and cytoplasmic domains of the cytokine receptor β-common subunit (βcR) in addition to the EPOR. Moreover, ELI-3 fails to induce erythroid differentiation of primary human hematopoietic progenitor cells but inhibits nonhematopoietic cell death induced by serum withdrawal.
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Affiliation(s)
- Li He
- Department of Genetics, Yale School of Medicine, P.O. Box 208005, New Haven, CT 06520-8005, USA
| | - Emily B Cohen
- Department of Genetics, Yale School of Medicine, P.O. Box 208005, New Haven, CT 06520-8005, USA
| | - Anne P B Edwards
- Department of Genetics, Yale School of Medicine, P.O. Box 208005, New Haven, CT 06520-8005, USA
| | - Juliana Xavier-Ferrucio
- Department of Laboratory Medicine, Yale School of Medicine, P.O. Box 208073, New Haven, CT 06520-8073, USA
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and Integrative Structural Biology at University of Copenhagen (ISBUC), Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ross S Federman
- Department of Immunobiology, Yale School of Medicine, P.O. Box 208011, New Haven, CT 06520-8011, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and Integrative Structural Biology at University of Copenhagen (ISBUC), Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Diane S Krause
- Department of Laboratory Medicine, Yale School of Medicine, P.O. Box 208073, New Haven, CT 06520-8073, USA; Yale Cancer Center, P.O. Box 208028, New Haven, CT 06520-8028, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, P.O. Box 208005, New Haven, CT 06520-8005, USA; Department of Therapeutic Radiology, Yale School of Medicine, P.O. Box 208040, New Haven, CT 06520-8040, USA; Department of Molecular Biophysics & Biochemistry, P.O. Box 208114, Yale University, New Haven, CT 06520-8114, USA; Yale Cancer Center, P.O. Box 208028, New Haven, CT 06520-8028, USA.
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7
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Petti LM, Marlatt SA, Luo Y, Scheideman EH, Shelar A, DiMaio D. Regulation of C-C chemokine receptor 5 (CCR5) stability by Lys 197 and by transmembrane protein aptamers that target it for lysosomal degradation. J Biol Chem 2018; 293:8787-8801. [PMID: 29678881 DOI: 10.1074/jbc.ra117.001067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/06/2018] [Indexed: 12/31/2022] Open
Abstract
C-C motif chemokine receptor 5 (CCR5) is a cell surface-associated, immune-regulatory G protein-coupled receptor (GCPR) with seven transmembrane helices. We previously reported the isolation and initial characterization of short artificial transmembrane protein aptamers, named "traptamers," that specifically down-regulate CCR5 expression and inhibit infection of human T cells by HIV strains that use CCR5 as a co-receptor. Here, we investigated the mechanism of traptamer-mediated CCR5 down-regulation and show that most of the traptamers (designated class 1 traptamers) form a stable complex with CCR5 and target it for lysosome-mediated degradation. The ability of these traptamers to down-regulate CCR5 depended on Lys197 in the fifth transmembrane helix of CCR5. In the absence of traptamers, substitution of Lys197 to an uncharged amino acid increased CCR5 stability, and introduction of a lysine at the homologous position in CCR2b, a related chemokine receptor, decreased CCR2b levels. The prototypic class 2 traptamer BY6M4 also formed a complex with CCR5, but CCR5 down-regulation caused by class 2 traptamers did not depend on the lysosome or on Lys197 These results demonstrate that traptamers use diverse mechanisms to down-regulate CCR5 and identify a specific amino acid that plays a central role in controlling chemokine receptor stability. Further studies of these traptamers are likely to provide new insights into CCR5 metabolism and biology and may suggest new therapeutic approaches to modulate the levels of CCR5 and other GPCRs.
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Affiliation(s)
- Lisa M Petti
- From the Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005
| | - Sara A Marlatt
- From the Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005
| | - Yong Luo
- From the Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005
| | - Elizabeth H Scheideman
- From the Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005
| | - Ashish Shelar
- From the Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005
| | - Daniel DiMaio
- From the Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520-8005, .,the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8024.,the Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut 06520-8040, and.,the Yale Cancer Center, New Haven, Connecticut 06520-8028
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8
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Bala J, Chinnapaiyan S, Dutta RK, Unwalla H. Aptamers in HIV research diagnosis and therapy. RNA Biol 2018; 15:327-337. [PMID: 29431588 PMCID: PMC5927724 DOI: 10.1080/15476286.2017.1414131] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/07/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.
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Affiliation(s)
- Jyoti Bala
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rajib Kumar Dutta
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Hoshang Unwalla
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
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9
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He L, Steinocher H, Shelar A, Cohen EB, Heim EN, Kragelund BB, Grigoryan G, DiMaio D. Single methyl groups can act as toggle switches to specify transmembrane Protein-protein interactions. eLife 2017; 6:27701. [PMID: 28869036 PMCID: PMC5597333 DOI: 10.7554/elife.27701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/01/2017] [Indexed: 01/13/2023] Open
Abstract
Transmembrane domains (TMDs) engage in protein-protein interactions that regulate many cellular processes, but the rules governing the specificity of these interactions are poorly understood. To discover these principles, we analyzed 26-residue model transmembrane proteins consisting exclusively of leucine and isoleucine (called LIL traptamers) that specifically activate the erythropoietin receptor (EPOR) in mouse cells to confer growth factor independence. We discovered that the placement of a single side chain methyl group at specific positions in a traptamer determined whether it associated productively with the TMD of the human EPOR, the mouse EPOR, or both receptors. Association of the traptamers with the EPOR induced EPOR oligomerization in an orientation that stimulated receptor activity. These results highlight the high intrinsic specificity of TMD interactions, demonstrate that a single methyl group can dictate specificity, and define the minimal chemical difference that can modulate the specificity of TMD interactions and the activity of transmembrane proteins.
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Affiliation(s)
- Li He
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Helena Steinocher
- Department of Biology, Structural and NMR Laboratory, University of Copenhagen, Copenhagen, Denmark
| | - Ashish Shelar
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Emily B Cohen
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Erin N Heim
- Department of Genetics, Yale School of Medicine, New Haven, United States
| | - Birthe B Kragelund
- Department of Biology, Structural and NMR Laboratory, University of Copenhagen, Copenhagen, Denmark
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, United States
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, United States.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, United States.,Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, United States.,Yale Cancer Center, New Haven, United States
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10
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Zeng X, Wu P, Yao C, Liang J, Zhang S, Yin H. Small Molecule and Peptide Recognition of Protein Transmembrane Domains. Biochemistry 2017; 56:2076-2085. [DOI: 10.1021/acs.biochem.6b00909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Xianfeng Zeng
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Peiyao Wu
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Chengbo Yao
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Jiaqi Liang
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Shuting Zhang
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
- School
of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Hang Yin
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
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11
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Abstract
The majority of therapeutics target membrane proteins, accessible on the surface of cells, to alter cellular signaling. Cells use membrane proteins to transduce signals into cells, transport ions and molecules, bind cells to a surface or substrate, and catalyze reactions. Newly devised technologies allow us to drug conventionally "undruggable" regions of membrane proteins, enabling modulation of protein-protein, protein-lipid, and protein-nucleic acid interactions. In this review, we survey the state of the art of high-throughput screening and rational design in drug discovery, and we evaluate the advances in biological understanding and technological capacity that will drive pharmacotherapy forward against unorthodox membrane protein targets.
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Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry.,BioFrontiers Institute, and.,Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Aaron D Flynn
- BioFrontiers Institute, and.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309; ,
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12
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Cohen EB, Jun SJ, Bears Z, Barrera FN, Alonso M, Engelman DM, DiMaio D. Mapping the homodimer interface of an optimized, artificial, transmembrane protein activator of the human erythropoietin receptor. PLoS One 2014; 9:e95593. [PMID: 24788775 PMCID: PMC4005772 DOI: 10.1371/journal.pone.0095593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/28/2014] [Indexed: 01/20/2023] Open
Abstract
Transmembrane proteins constitute a large fraction of cellular proteins, and specific interactions involving membrane-spanning protein segments play an important role in protein oligomerization, folding, and function. We previously isolated an artificial, dimeric, 44-amino acid transmembrane protein that activates the human erythropoietin receptor (hEPOR) in trans. This artificial protein supports limited erythroid differentiation of primary human hematopoietic progenitor cells in vitro, even though it does not resemble erythropoietin, the natural ligand of this receptor. Here, we used a directed-evolution approach to explore the structural basis for the ability of transmembrane proteins to activate the hEPOR. A library that expresses thousands of mutants of the transmembrane activator was screened for variants that were more active than the original isolate at inducing growth factor independence in mouse cells expressing the hEPOR. The most active mutant, EBC5-16, supports erythroid differentiation in human cells with activity approaching that of EPO, as assessed by cell-surface expression of glycophorin A, a late-stage marker of erythroid differentiation. EBC5-16 contains a single isoleucine to serine substitution at position 25, which increases its ability to form dimers. Genetic studies confirmed the importance of dimerization for activity and identified the residues constituting the homodimer interface of EBC5-16. The interface requires a GxxxG dimer packing motif and a small amino acid at position 25 for maximal activity, implying that tight packing of the EBC5-16 dimer is a crucial determinant of activity. These experiments identified an artificial protein that causes robust activation of its target in a natural host cell, demonstrated the importance of dimerization of this protein for engagement of the hEPOR, and provided the framework for future structure-function studies of this novel mechanism of receptor activation.
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Affiliation(s)
- Emily B. Cohen
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Susan J. Jun
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Zachary Bears
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Francisco N. Barrera
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
| | - Miriam Alonso
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Donald M. Engelman
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, New Haven, Connecticut, United States of America
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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13
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Abstract
Many viruses encode short transmembrane proteins that play vital roles in virus replication or virulence. Because many of these proteins are less than 50 amino acids long and not homologous to cellular proteins, their open reading frames were often overlooked during the initial annotation of viral genomes. Some of these proteins oligomerize in membranes and form ion channels. Other miniproteins bind to cellular transmembrane proteins and modulate their activity, whereas still others have an unknown mechanism of action. Based on the underlying principles of transmembrane miniprotein structure, it is possible to build artificial small transmembrane proteins that modulate a variety of biological processes. These findings suggest that short transmembrane proteins provide a versatile mechanism to regulate a wide range of cellular activities, and we speculate that cells also express many similar proteins that have not yet been discovered.
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Affiliation(s)
- Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520;
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14
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15
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Abstract
All cellular proteins are derived from preexisting ones by natural selection. Because of the random nature of this process, many potentially useful protein structures never arose or were discarded during evolution. Here, we used a single round of genetic selection in mouse cells to isolate chemically simple, biologically active transmembrane proteins that do not contain any amino acid sequences from preexisting proteins. We screened a retroviral library expressing hundreds of thousands of proteins consisting of hydrophobic amino acids in random order to isolate four 29-aa proteins that induced focus formation in mouse and human fibroblasts and tumors in mice. These proteins share no amino acid sequences with known cellular or viral proteins, and the simplest of them contains only seven different amino acids. They transformed cells by forming a stable complex with the platelet-derived growth factor β receptor transmembrane domain and causing ligand-independent receptor activation. We term this approach de novo selection and suggest that it can be used to generate structures and activities not observed in nature, create prototypes for novel research reagents and therapeutics, and provide insight into cell biology, transmembrane protein-protein interactions, and possibly virus evolution and the origin of life.
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16
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Compensatory mutants of the bovine papillomavirus E5 protein and the platelet-derived growth factor β receptor reveal a complex direct transmembrane interaction. J Virol 2013; 87:10936-45. [PMID: 23926343 DOI: 10.1128/jvi.01475-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 44-amino-acid E5 protein of bovine papillomavirus is a dimeric transmembrane protein that exists in a stable complex with the platelet-derived growth factor (PDGF) β receptor, causing receptor activation and cell transformation. The transmembrane domain of the PDGF β receptor is required for complex formation, but it is not known if the two proteins contact one another directly. Here, we studied a PDGF β receptor mutant containing a leucine-to-isoleucine substitution in its transmembrane domain, which prevents complex formation with the wild-type E5 protein in mouse BaF3 cells and inhibits receptor activation by the E5 protein. We selected E5 mutants containing either a small deletion or multiple substitution mutations that restored binding to the mutant PDGF β receptor, resulting in receptor activation and growth factor independence. These E5 mutants displayed lower activity with PDGF β receptor mutants containing other transmembrane substitutions in the vicinity of the original mutation, and one of them cooperated with a receptor mutant containing a distal mutation in the juxtamembrane domain. These results provide strong genetic evidence that the transmembrane domains of the E5 protein and the PDGF β receptor contact one another directly. They also demonstrate that different mutations in the E5 protein allow it to tolerate the same mutation in the PDGF β receptor transmembrane domain and that a mutation in the E5 protein can allow it to tolerate different mutations in the PDGF β receptor. Thus, the rules governing direct interactions between transmembrane helices are complex and not restricted to local interactions.
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DiMaio D, Petti LM. The E5 proteins. Virology 2013; 445:99-114. [PMID: 23731971 DOI: 10.1016/j.virol.2013.05.006] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/01/2013] [Accepted: 05/03/2013] [Indexed: 12/23/2022]
Abstract
The E5 proteins are short transmembrane proteins encoded by many animal and human papillomaviruses. These proteins display transforming activity in cultured cells and animals, and they presumably also play a role in the productive virus life cycle. The E5 proteins are thought to act by modulating the activity of cellular proteins. Here, we describe the biological activities of the best-studied E5 proteins and discuss the evidence implicating specific protein targets and pathways in mediating these activities. The primary target of the 44-amino acid BPV1 E5 protein is the PDGF β receptor, whereas the EGF receptor appears to be an important target of the 83-amino acid HPV16 E5 protein. Both E5 proteins also bind to the vacuolar ATPase and affect MHC class I expression and cell-cell communication. Continued studies of the E5 proteins will elucidate important aspects of transmembrane protein-protein interactions, cellular signal transduction, cell biology, virus replication, and tumorigenesis.
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Affiliation(s)
- Daniel DiMaio
- Department of Genetics, Yale School of Medicine, USA; Department of Therapeutic Radiology, Yale School of Medicine, USA; Department of Molecular Biophysics & Biochemistry, Yale University, USA; Yale Cancer Center, USA.
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Lluis MW, Godfroy JI, Yin H. Protein engineering methods applied to membrane protein targets. Protein Eng Des Sel 2012; 26:91-100. [DOI: 10.1093/protein/gzs079] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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