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Elazar A, Chandler NJ, Davey AS, Weinstein JY, Nguyen JV, Trenker R, Cross RS, Jenkins MR, Call MJ, Call ME, Fleishman SJ. De novo-designed transmembrane domains tune engineered receptor functions. eLife 2022; 11:75660. [PMID: 35506657 PMCID: PMC9068223 DOI: 10.7554/elife.75660] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/14/2022] [Indexed: 12/20/2022] Open
Abstract
De novo-designed receptor transmembrane domains (TMDs) present opportunities for precise control of cellular receptor functions. We developed a de novo design strategy for generating programmed membrane proteins (proMPs): single-pass α-helical TMDs that self-assemble through computationally defined and crystallographically validated interfaces. We used these proMPs to program specific oligomeric interactions into a chimeric antigen receptor (CAR) that we expressed in mouse primary T cells and found that both in vitro CAR T cell cytokine release and in vivo antitumor activity scaled linearly with the oligomeric state encoded by the receptor TMD, from monomers up to tetramers. All programmed CARs stimulated substantially lower T cell cytokine release relative to the commonly used CD28 TMD, which we show elevated cytokine release through lateral recruitment of the endogenous T cell costimulatory receptor CD28. Precise design using orthogonal and modular TMDs thus provides a new way to program receptor structure and predictably tune activity for basic or applied synthetic biology.
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Affiliation(s)
- Assaf Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Nicholas J Chandler
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ashleigh S Davey
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jonathan Y Weinstein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Julie V Nguyen
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Raphael Trenker
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ryan S Cross
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Misty R Jenkins
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Melissa J Call
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew E Call
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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van T Hag L, de Campo L, Tran N, Sokolova A, Trenker R, Call ME, Call MJ, Garvey CJ, Leung AE, Darwish TA, Krause-Heuer A, Knott R, Meikle TG, Drummond CJ, Mezzenga R, Conn CE. Protein-Eye View of the in Meso Crystallization Mechanism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8344-8356. [PMID: 31122018 DOI: 10.1021/acs.langmuir.9b00647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
For evolving biological and biomedical applications of hybrid protein?lipid materials, understanding the behavior of the protein within the lipid mesophase is crucial. After more than two decades since the invention of the in meso crystallization method, a protein-eye view of its mechanism is still lacking. Numerous structural studies have suggested that integral membrane proteins preferentially partition at localized flat points on the bilayer surface of the cubic phase with crystal growth occurring from a local fluid lamellar L? phase conduit. However, studies to date have, by necessity, focused on structural transitions occurring in the lipid mesophase. Here, we demonstrate using small-angle neutron scattering that the lipid bilayer of monoolein (the most commonly used lipid for in meso crystallization) can be contrast-matched using deuteration, allowing us to isolate scattering from encapsulated peptides during the crystal growth process for the first time. During in meso crystallization, a clear decrease in form factor scattering intensity of the peptides was observed and directly correlated with crystal growth. A transient fluid lamellar L? phase was observed, providing direct evidence for the proposed mechanism for this technique. This suggests that the peptide passes through a transition from the cubic QII phase, via an L? phase to the lamellar crystalline Lc phase with similar layered spacing. When high protein loading was possible, the lamellar crystalline Lc phase of the peptide in the single crystals was observed. These findings show the mechanism of in meso crystallization for the first time from the perspective of integral membrane proteins.
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Affiliation(s)
- Leonie van T Hag
- Department of Health Sciences and Technology , ETH Zurich , CH-8092 Zurich , Switzerland
| | | | - Nhiem Tran
- School of Science, College of Science, Engineering and Health , RMIT University , Melbourne , Victoria 3001 , Australia
| | | | - Raphael Trenker
- Structural Biology Division , The Walter and Eliza Hall Institute of Medical Research , Parkville , Victoria 3052 , Australia
- Department of Medical Biology , The University of Melbourne , Parkville , Victoria 3052 , Australia
| | - Matthew E Call
- Structural Biology Division , The Walter and Eliza Hall Institute of Medical Research , Parkville , Victoria 3052 , Australia
- Department of Medical Biology , The University of Melbourne , Parkville , Victoria 3052 , Australia
| | - Melissa J Call
- Structural Biology Division , The Walter and Eliza Hall Institute of Medical Research , Parkville , Victoria 3052 , Australia
- Department of Medical Biology , The University of Melbourne , Parkville , Victoria 3052 , Australia
| | | | - Anna E Leung
- Scientific Activities Division , European Spallation Source ERIC , Lund 224 84 , Sweden
| | | | | | | | - Thomas G Meikle
- School of Science, College of Science, Engineering and Health , RMIT University , Melbourne , Victoria 3001 , Australia
| | - Calum J Drummond
- School of Science, College of Science, Engineering and Health , RMIT University , Melbourne , Victoria 3001 , Australia
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology , ETH Zurich , CH-8092 Zurich , Switzerland
- Department of Materials , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Charlotte E Conn
- School of Science, College of Science, Engineering and Health , RMIT University , Melbourne , Victoria 3001 , Australia
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Tan C, Byrne EFX, Ah-Cann C, Call MJ, Call ME. A serine in the first transmembrane domain of the human E3 ubiquitin ligase MARCH9 is critical for down-regulation of its protein substrates. J Biol Chem 2018; 294:2470-2485. [PMID: 30554144 DOI: 10.1074/jbc.ra118.004836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/05/2018] [Indexed: 01/29/2023] Open
Abstract
The membrane-associated RING-CH (MARCH) family of membrane-bound E3 ubiquitin ligases regulates the levels of cell-surface membrane proteins, many of which are involved in immune responses. Although their role in ubiquitin-dependent endocytosis and degradation of cell-surface proteins is extensively documented, the features of MARCH proteins and their substrates that drive the molecular recognition events leading to ubiquitin transfer remain poorly defined. In this study, we sought to determine the features of human MARCH9 that are required for regulating the surface levels of its substrate proteins. Consistent with previous studies of other MARCH proteins, we found that susceptibility to MARCH9 activity is encoded in the transmembrane (TM) domains of its substrates. Accordingly, substitutions at specific residues and motifs within MARCH9's TM domains resulted in varying degrees of functional impairment. Most notably, a single serine-to-alanine substitution in the first of its two TM domains rendered MARCH9 completely unable to alter the surface levels of two different substrates: the major histocompatibility class I molecule HLA-A2 and the T-cell co-receptor CD4. Solution NMR analysis of a MARCH9 fragment encompassing the two TM domains and extracellular connecting loop revealed that the residues contributing most to MARCH9 activity are located in the α-helical portions of TM1 and TM2 that are closest to the extracellular face of the lipid bilayer. This observation defines a key region required for substrate regulation. In summary, our biochemical and structural findings demonstrate that specific sequences in the α-helical MARCH9 TM domains make crucial contributions to its ability to down-regulate its protein substrates.
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Affiliation(s)
- Cyrus Tan
- From the Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 3052 Parkville, Victoria, Australia.,the Department of Medical Biology, University of Melbourne, 3052 Parkville, Victoria, Australia
| | - Eamon F X Byrne
- the Department of Bioengineering, Stanford University, Stanford, California 94305, and
| | - Casey Ah-Cann
- the Department of Medical Biology, University of Melbourne, 3052 Parkville, Victoria, Australia.,the ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 3052 Parkville, Victoria, Australia
| | - Melissa J Call
- From the Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 3052 Parkville, Victoria, Australia, .,the Department of Medical Biology, University of Melbourne, 3052 Parkville, Victoria, Australia
| | - Matthew E Call
- From the Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 3052 Parkville, Victoria, Australia, .,the Department of Medical Biology, University of Melbourne, 3052 Parkville, Victoria, Australia
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4
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A conserved αβ transmembrane interface forms the core of a compact T-cell receptor-CD3 structure within the membrane. Proc Natl Acad Sci U S A 2016; 113:E6649-E6658. [PMID: 27791034 DOI: 10.1073/pnas.1611445113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The T-cell antigen receptor (TCR) is an assembly of eight type I single-pass membrane proteins that occupies a central position in adaptive immunity. Many TCR-triggering models invoke an alteration in receptor complex structure as the initiating event, but both the precise subunit organization and the pathway by which ligand-induced alterations are transferred to the cytoplasmic signaling domains are unknown. Here, we show that the receptor complex transmembrane (TM) domains form an intimately associated eight-helix bundle organized by a specific interhelical TCR TM interface. The salient features of this core structure are absolutely conserved between αβ and γδ TCR sequences and throughout vertebrate evolution, and mutations at key interface residues caused defects in the formation of stable TCRαβ:CD3δε:CD3γε:ζζ complexes. These findings demonstrate that the eight TCR-CD3 subunits form a compact and precisely organized structure within the membrane and provide a structural basis for further investigation of conformationally regulated models of transbilayer TCR signaling.
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van 't Hag L, Knoblich K, Seabrook SA, Kirby NM, Mudie ST, Lau D, Li X, Gras SL, Mulet X, Call ME, Call MJ, Drummond CJ, Conn CE. Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0125. [PMID: 27298442 PMCID: PMC4920275 DOI: 10.1098/rsta.2015.0125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 05/19/2023]
Abstract
The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the DAP12-TM peptide using synchrotron small angle X-ray scattering (SAXS) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso, from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput SAXS analysis of in meso grown crystals.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'.
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Affiliation(s)
- Leonie van 't Hag
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Konstantin Knoblich
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Shane A Seabrook
- CSIRO Manufacturing Flagship, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Nigel M Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Stephen T Mudie
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Deborah Lau
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Xu Li
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia
| | - Sally L Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3052, Australia The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xavier Mulet
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia
| | - Matthew E Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Melissa J Call
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Calum J Drummond
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton, Victoria 3169, Australia School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Charlotte E Conn
- School of Applied Sciences, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
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Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly. Cell Rep 2015; 11:1184-92. [PMID: 25981043 DOI: 10.1016/j.celrep.2015.04.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/09/2015] [Accepted: 04/21/2015] [Indexed: 11/20/2022] Open
Abstract
The membrane-spanning α helices of single-pass receptors play crucial roles in stabilizing oligomeric structures and transducing biochemical signals across the membrane. Probing intermolecular transmembrane interactions in single-pass receptors presents unique challenges, reflected in a gross underrepresentation of their membrane-embedded domains in structural databases. Here, we present two high-resolution structures of transmembrane assemblies from a eukaryotic single-pass protein crystallized in a lipidic membrane environment. Trimeric and tetrameric structures of the immunoreceptor signaling module DAP12, determined to 1.77-Å and 2.14-Å resolution, respectively, are organized by the same polar surfaces that govern intramembrane assembly with client receptors. We demonstrate that, in addition to the well-studied dimeric form, these trimeric and tetrameric structures are made in cells, and their formation is competitive with receptor association in the ER. The polar transmembrane sequences therefore act as primary determinants of oligomerization specificity through interplay between charge shielding and sequestration of polar surfaces within helix interfaces.
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