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Erramilli SK, Dominik PK, Deneka D, Tokarz P, Kim SS, Reddy BG, Skrobek BM, Dalmas O, Perozo E, Kossiakoff AA. Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA. J Mol Biol 2023; 435:168192. [PMID: 37394032 PMCID: PMC10529903 DOI: 10.1016/j.jmb.2023.168192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023]
Abstract
CorA, the primary magnesium ion channel in prokaryotes and archaea, is a prototypical homopentameric ion channel that undergoes ion-dependent conformational transitions. CorA adopts five-fold symmetric non-conductive states in the presence of high concentrations of Mg2+, and highly asymmetric flexible states in its complete absence. However, the latter were of insufficient resolution to be thoroughly characterized. In order to gain additional insights into the relationship between asymmetry and channel activation, we exploited phage display selection strategies to generate conformation-specific synthetic antibodies (sABs) against CorA in the absence of Mg2+. Two sABs from these selections, C12 and C18, showed different degrees of Mg2+-sensitivity. Through structural, biochemical, and biophysical characterization, we found the sABs are both conformation-specific but probe different features of the channel under open-like conditions. C18 is highly specific to the Mg2+-depleted state of CorA and through negative-stain electron microscopy (ns-EM), we show sAB binding reflects the asymmetric arrangement of CorA protomers in Mg2+-depleted conditions. We used X-ray crystallography to determine a structure at 2.0 Å resolution of sAB C12 bound to the soluble N-terminal regulatory domain of CorA. The structure shows C12 is a competitive inhibitor of regulatory magnesium binding through its interaction with the divalent cation sensing site. We subsequently exploited this relationship to capture and visualize asymmetric CorA states in different [Mg2+] using ns-EM. We additionally utilized these sABs to provide insights into the energy landscape that governs the ion-dependent conformational transitions of CorA.
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Affiliation(s)
- Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Dawid Deneka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Piotr Tokarz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Bharat G Reddy
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Blazej M Skrobek
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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2
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Erramilli SK, Dominik PK, Ogbu CP, Kossiakoff AA, Vecchio AJ. Cryo-EM structures of a synthetic antibody against 22 kDa claudin-4 reveal its complex with Clostridium perfringens enterotoxin. bioRxiv 2023:2023.06.12.544689. [PMID: 37398044 PMCID: PMC10312657 DOI: 10.1101/2023.06.12.544689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Claudins are a family of ∼25 kDa membrane proteins that integrate into tight junctions to form molecular barriers at the paracellular spaces between endothelial and epithelial cells. Humans have 27 subtypes, which homo- and hetero-oligomerize to impart distinct properties and physiological functions to tissues and organs. As the structural and functional backbone of tight junctions, claudins are attractive targets for therapeutics capable of modulating tissue permeability to deliver drugs or treat disease. However, structures of claudins are limited due to their small sizes and physicochemical properties-these traits also make therapy development a challenge. We have developed a synthetic antibody fragment (sFab) that binds human claudin-4 and used it to resolve structures of its complex with Clostridium perfringens enterotoxin (CpE) using cryogenic electron microscopy (cryo-EM). The resolution of the structures reveals the architectures of 22 kDa claudin-4, the 14 kDa C-terminal domain of CpE, and the mechanism by which this sFab binds claudins. Further, we elucidate the biochemical and biophysical bases of sFab binding and demonstrate that this molecule exhibits subtype-selectivity by assaying homologous claudins. Our results provide a framework for developing sFabs against hard-to-target claudins and establishes the utility of sFabs as fiducial markers for determining cryo-EM structures of this small membrane protein family at resolutions that surpass X-ray crystallography. Taken together, this work highlights the ability of sFabs to elucidate claudin structure and function and posits their potential as therapeutics for modulating tight junctions by targeting specific claudin subtypes.
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3
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Erramilli SK, Dominik PK, Deneka D, Tokarz P, Kim SS, Reddy BG, Skrobek BM, Dalmas O, Perozo E, Kossiakoff AA. Conformation-specific synthetic antibodies discriminate multiple functional states of the ion channel CorA. bioRxiv 2023:2023.05.07.539746. [PMID: 37205530 PMCID: PMC10187328 DOI: 10.1101/2023.05.07.539746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
CorA, the primary magnesium ion channel in prokaryotes and archaea, is a prototypical homopentameric ion channel that undergoes ion-dependent conformational transitions. CorA adopts five-fold symmetric non-conductive states in the presence of high concentrations of Mg 2+ , and highly asymmetric flexible states in its complete absence. However, the latter were of insufficient resolution to be thoroughly characterized. In order to gain additional insights into the relationship between asymmetry and channel activation, we exploited phage display selection strategies to generate conformation-specific synthetic antibodies (sABs) against CorA in the absence of Mg 2+ . Two sABs from these selections, C12 and C18, showed different degrees of Mg 2+ -sensitivity. Through structural, biochemical, and biophysical characterization, we found the sABs are both conformation-specific but probe different features of the channel under open-like conditions. C18 is highly specific to the Mg 2+ -depleted state of CorA and through negative-stain electron microscopy (ns-EM), we show sAB binding reflects the asymmetric arrangement of CorA protomers in Mg 2+ -depleted conditions. We used X-ray crystallography to determine a structure at 2.0 Å resolution of sAB C12 bound to the soluble N-terminal regulatory domain of CorA. The structure shows C12 is a competitive inhibitor of regulatory magnesium binding through its interaction with the divalent cation sensing site. We subsequently exploited this relationship to capture and visualize asymmetric CorA states in different [Mg 2+ ] using ns-EM. We additionally utilized these sABs to provide insights into the energy landscape that governs the ion-dependent conformational transitions of CorA.
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4
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Orlando BJ, Dominik PK, Roy S, Ogbu CP, Erramilli SK, Kossiakoff AA, Vecchio AJ. Development, structure, and mechanism of synthetic antibodies that target claudin and Clostridium perfringens enterotoxin complexes. J Biol Chem 2022; 298:102357. [PMID: 35952760 PMCID: PMC9463536 DOI: 10.1016/j.jbc.2022.102357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
Strains of Clostridium perfringens produce a two-domain enterotoxin (CpE) that afflicts humans and domesticated animals, causing prevalent gastrointestinal illnesses. CpE’s C-terminal domain (cCpE) binds cell surface receptors, followed by a restructuring of its N-terminal domain to form a membrane-penetrating β-barrel pore, which is toxic to epithelial cells of the gut. The claudin family of membrane proteins are known receptors for CpE and also control the architecture and function of cell-cell contacts (tight junctions) that create barriers to intercellular molecular transport. CpE binding and assembly disables claudin barrier function and induces cytotoxicity via β-pore formation, disrupting gut homeostasis; however, a structural basis of this process and strategies to inhibit the claudin–CpE interactions that trigger it are both lacking. Here, we used a synthetic antigen-binding fragment (sFab) library to discover two sFabs that bind claudin-4 and cCpE complexes. We established these sFabs’ mode of molecular recognition and binding properties and determined structures of each sFab bound to claudin-4–cCpE complexes using cryo-EM. The structures reveal that the sFabs bind a shared epitope, but conform distinctly, which explains their unique binding equilibria. Mutagenesis of antigen/sFab interfaces observed therein result in binding changes, validating the structures, and uncovering the sFab’s targeting mechanism. From these insights, we generated a model for CpE’s claudin-bound β-pore that predicted sFabs would not prevent cytotoxicity, which we then verified in vivo. Taken together, this work demonstrates the development and mechanism of claudin/cCpE-binding sFabs that provide a framework and strategy for obstructing claudin/CpE assembly to treat CpE-linked gastrointestinal diseases.
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Affiliation(s)
- Benjamin J Orlando
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824 USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637 USA
| | - Sourav Roy
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588 USA
| | - Chinemerem P Ogbu
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588 USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637 USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637 USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588 USA.
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Yen YC, Schafer CT, Gustavsson M, Eberle SA, Dominik PK, Deneka D, Zhang P, Schall TJ, Kossiakoff AA, Tesmer JJG, Handel TM. Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. Sci Adv 2022; 8:eabn8063. [PMID: 35857509 PMCID: PMC9278869 DOI: 10.1126/sciadv.abn8063] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/26/2022] [Indexed: 05/12/2023]
Abstract
Both CXC chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3) are activated by the chemokine CXCL12 yet evoke distinct cellular responses. CXCR4 is a canonical G protein-coupled receptor (GPCR), whereas ACKR3 is intrinsically biased for arrestin. The molecular basis for this difference is not understood. Here, we describe cryo-EM structures of ACKR3 in complex with CXCL12, a more potent CXCL12 variant, and a small-molecule agonist. The bound chemokines adopt an unexpected pose relative to those established for CXCR4 and observed in other receptor-chemokine complexes. Along with functional studies, these structures provide insight into the ligand-binding promiscuity of ACKR3, why it fails to couple to G proteins, and its bias toward β-arrestin. The results lay the groundwork for understanding the physiological interplay of ACKR3 with other GPCRs.
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Affiliation(s)
- Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Christopher T. Schafer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stefanie A. Eberle
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Pawel K. Dominik
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Dawid Deneka
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Department of Biophysics, Jagiellonian University, Krakow, Poland
| | - Penglie Zhang
- ChemoCentryx Inc., 835 Industrial Rd., Suite 600, San Carlos, CA 94070, USA
| | - Thomas J. Schall
- ChemoCentryx Inc., 835 Industrial Rd., Suite 600, San Carlos, CA 94070, USA
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - John J. G. Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Molecular Pharmacology and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
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Yen Y, Schafer CT, Gustavsson M, Eberle SA, Dominik PK, Deneka D, Zhang P, Schall TJ, Kossiakoff AA, Handel TM, Tesmer JJ. Seven structures of atypical chemokine receptor 3 reveal the molecular bases for its promiscuity and signaling bias. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Martin Gustavsson
- University of California, San DiegoLa JollaCA
- University of CopenhagenCopenhagen
| | | | | | - Dawid Deneka
- University of ChicagoChicagoIL
- Dept of BiophysicsJagiellonian UniversityKrakow
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Orlando BJ, Dominik PK, Roy S, Ogbu C, Erramilli SK, Kossiakoff AA, Vecchio AJ. Cryo-EM structures of human claudin-4 in complex with its bacterial toxin antagonist enabled by synthetic antibody fragments reveal targeting mechanisms and therapeutic potential. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Chen SH, Dominik PK, Stanfield J, Ding S, Yang W, Kurd N, Llewellyn R, Heyen J, Wang C, Melton Z, Van Blarcom T, Lindquist KC, Chaparro-Riggers J, Salek-Ardakani S. Dual checkpoint blockade of CD47 and PD-L1 using an affinity-tuned bispecific antibody maximizes antitumor immunity. J Immunother Cancer 2021; 9:jitc-2021-003464. [PMID: 34599020 PMCID: PMC8488710 DOI: 10.1136/jitc-2021-003464] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND T cell checkpoint immunotherapies have shown promising results in the clinic, but most patients remain non-responsive. CD47-signal regulatory protein alpha (SIRPα) myeloid checkpoint blockade has shown early clinical activity in hematologic malignancies. However, CD47 expression on peripheral blood limits αCD47 antibody selectivity and thus efficacy in solid tumors. METHODS To improve the antibody selectivity and therapeutic window, we developed a novel affinity-tuned bispecific antibody targeting CD47 and programmed death-ligand 1 (PD-L1) to antagonize both innate and adaptive immune checkpoint pathways. This PD-L1-targeted CD47 bispecific antibody was designed with potent affinity for PD-L1 and moderate affinity for CD47 to achieve preferential binding on tumor and myeloid cells expressing PD-L1 in the tumor microenvironment (TME). RESULTS The antibody design reduced binding on red blood cells and enhanced selectivity to the TME, improving the therapeutic window compared with αCD47 and its combination with αPD-L1 in syngeneic tumor models. Mechanistically, both myeloid and T cells were activated and contributed to antitumor activity of αCD47/PD-L1 bispecific antibody. Distinct from αCD47 and αPD-L1 monotherapies or combination therapies, single-cell RNA sequencing (scRNA-seq) and gene expression analysis revealed that the bispecific treatment resulted in unique innate activation, including pattern recognition receptor-mediated induction of type I interferon pathways and antigen presentation in dendritic cells and macrophage populations. Furthermore, treatment increased the Tcf7+ stem-like progenitor CD8 T cell population in the TME and promoted its differentiation to an effector-like state. Consistent with mouse data, the compounds were well tolerated and demonstrated robust myeloid and T cell activation in non-human primates (NHPs). Notably, RNA-seq analysis in NHPs provided evidence that the innate activation was mainly contributed by CD47-SIRPα but not PD-L1-PD-1 blockade from the bispecific antibody. CONCLUSION These findings provide novel mechanistic insights into how myeloid and T cells can be uniquely modulated by the dual innate and adaptive checkpoint antibody and demonstrate its potential in clinical development (NCT04881045) to improve patient outcomes over current PD-(L)1 and CD47-targeted therapies.
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Affiliation(s)
- Shih-Hsun Chen
- Cancer Immunology Discovery, Pfizer Inc, San Diego, California, USA
| | | | | | - Sheng Ding
- BioMedicine Design, Pfizer Inc, San Diego, California, USA
| | - Wenjing Yang
- Computational Biology, Pfizer Inc, San Diego, California, USA
| | - Nadia Kurd
- Cancer Immunology Discovery, Pfizer Inc, San Diego, California, USA
| | - Ryan Llewellyn
- Cancer Immunology Discovery, Pfizer Inc, San Diego, California, USA
| | | | - Carole Wang
- BioMedicine Design, Pfizer Inc, San Diego, California, USA
| | - Zea Melton
- BioMedicine Design, Pfizer Inc, San Diego, California, USA
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Liu W, Maben Z, Wang C, Lindquist KC, Li M, Rayannavar V, Lopez Armenta I, Nager A, Pascua E, Dominik PK, Oyen D, Wang H, Roach RC, Allan CM, Mosyak L, Chaparro-Riggers J. Structural delineation and phase-dependent activation of the costimulatory CD27:CD70 complex. J Biol Chem 2021; 297:101102. [PMID: 34419446 PMCID: PMC8484739 DOI: 10.1016/j.jbc.2021.101102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022] Open
Abstract
CD27 is a tumor necrosis factor (TNF) receptor, which stimulates lymphocytes and promotes their differentiation upon activation by TNF ligand CD70. Activation of the CD27 receptor provides a costimulatory signal to promote T cell, B cell, and NK cell activity to facilitate antitumor and anti-infection immunity. Aberrant increased and focused expression of CD70 on many tumor cells renders CD70 an attractive therapeutic target for direct tumor killing. However, despite their use as drug targets to treat cancers, the molecular basis and atomic details of CD27 and CD70 interaction remain elusive. Here we report the crystal structure of human CD27 in complex with human CD70. Analysis of our structure shows that CD70 adopts a classical TNF ligand homotrimeric assembly to engage CD27 receptors in a 3:3 stoichiometry. By combining structural and rational mutagenesis data with reported disease-correlated mutations, we identified the key amino acid residues of CD27 and CD70 that control this interaction. We also report increased potency for plate-bound CD70 constructs compared with solution-phase ligand in a functional activity to stimulate T-cells in vitro. These findings offer new mechanistic insight into this critical costimulatory interaction.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Hui Wang
- Pfizer, Inc, La Jolla, California, USA
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10
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Kintzer AF, Green EM, Dominik PK, Bridges M, Armache JP, Deneka D, Kim SS, Hubbell W, Kossiakoff AA, Cheng Y, Stroud RM. Structural basis for activation of voltage sensor domains in an ion channel TPC1. Proc Natl Acad Sci U S A 2018; 115:E9095-E9104. [PMID: 30190435 PMCID: PMC6166827 DOI: 10.1073/pnas.1805651115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Voltage-sensing domains (VSDs) couple changes in transmembrane electrical potential to conformational changes that regulate ion conductance through a central channel. Positively charged amino acids inside each sensor cooperatively respond to changes in voltage. Our previous structure of a TPC1 channel captured an example of a resting-state VSD in an intact ion channel. To generate an activated-state VSD in the same channel we removed the luminal inhibitory Ca2+-binding site (Cai2+), which shifts voltage-dependent opening to more negative voltage and activation at 0 mV. Cryo-EM reveals two coexisting structures of the VSD, an intermediate state 1 that partially closes access to the cytoplasmic side but remains occluded on the luminal side and an intermediate activated state 2 in which the cytoplasmic solvent access to the gating charges closes, while luminal access partially opens. Activation can be thought of as moving a hydrophobic insulating region of the VSD from the external side to an alternate grouping on the internal side. This effectively moves the gating charges from the inside potential to that of the outside. Activation also requires binding of Ca2+ to a cytoplasmic site (Caa2+). An X-ray structure with Caa2+ removed and a near-atomic resolution cryo-EM structure with Cai2+ removed define how dramatic conformational changes in the cytoplasmic domains may communicate with the VSD during activation. Together four structures provide a basis for understanding the voltage-dependent transition from resting to activated state, the tuning of VSD by thermodynamic stability, and this channel's requirement of cytoplasmic Ca2+ ions for activation.
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Affiliation(s)
- Alexander F Kintzer
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
| | - Evan M Green
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
| | - Pawel K Dominik
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Michael Bridges
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Jean-Paul Armache
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
| | - Dawid Deneka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Wayne Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143;
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94143
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143;
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11
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Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA. Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination. J Mol Biol 2017; 430:337-347. [PMID: 29273204 DOI: 10.1016/j.jmb.2017.12.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/05/2017] [Accepted: 12/13/2017] [Indexed: 01/01/2023]
Abstract
Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones.
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Affiliation(s)
- Lucas J Bailey
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kimberly M Sheehy
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wenguang G Liang
- Ben May Institute for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Michael Clark
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Mateusz Jaskolowski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; University of Gdansk and Medical University of Gdansk, International Faculty of Biotechnology, Gdansk, Poland
| | - Yejoon Kim
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Dawid Deneka
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Krakow, Poland
| | - Wei-Jen Tang
- Ben May Institute for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
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12
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Matthies D, Dalmas O, Borgnia MJ, Dominik PK, Merk A, Rao P, Reddy BG, Islam S, Bartesaghi A, Perozo E, Subramaniam S. Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating. Cell 2016; 164:747-56. [PMID: 26871634 DOI: 10.1016/j.cell.2015.12.055] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/10/2015] [Accepted: 12/23/2015] [Indexed: 11/30/2022]
Abstract
CorA, the major Mg(2+) uptake system in prokaryotes, is gated by intracellular Mg(2+) (KD ∼ 1-2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg(2+)-bound and Mg(2+)-free conditions, but EPR spectroscopic studies reveal large Mg(2+)-driven quaternary conformational changes. Here, we determined cryo-EM structures of CorA in the Mg(2+)-bound closed conformation and in two open Mg(2+)-free states at resolutions of 3.8, 7.1, and 7.1 Å, respectively. In the absence of bound Mg(2+), four of the five subunits are displaced to variable extents (∼ 10-25 Å) by hinge-like motions as large as ∼ 35° at the stalk helix. The transition between a single 5-fold symmetric closed state and an ensemble of low Mg(2+), open, asymmetric conformational states is, thus, the key structural signature of CorA gating. This mechanism is likely to apply to other structurally similar divalent ion channels.
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Affiliation(s)
- Doreen Matthies
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Mario J Borgnia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Prashant Rao
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Bharat G Reddy
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Shahidul Islam
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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13
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Matthies D, Dalmas O, Borgnia MJ, Dominik PK, Merk A, Rao P, Reddy BG, Islam S, Bartesaghi A, Perozo E, Subramaniam S. Single-Particle Cryo-EM Studies of a 200-kDa Magnesium Ion Channel Reveal Large Structural Changes Upon Gating. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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14
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Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA. Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs. Structure 2015; 24:300-9. [PMID: 26749445 DOI: 10.1016/j.str.2015.11.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 01/18/2023]
Abstract
A major challenge in membrane biophysics is to define the mechanistic linkages between a protein's conformational transitions and its function. We describe a novel approach to stabilize transient functional states of membrane proteins in native-like lipid environments allowing for their structural and biochemical characterization. This is accomplished by combining the power of antibody Fab-based phage display selection with the benefits of embedding membrane protein targets in lipid-filled nanodiscs. In addition to providing a stabilizing lipid environment, nanodiscs afford significant technical advantages over detergent-based formats. This enables the production of a rich pool of high-performance Fab binders that can be used as crystallization chaperones, as fiducial markers for single-particle cryoelectron microscopy, and as probes of different conformational states. Moreover, nanodisc-generated Fabs can be used to identify detergents that best mimic native membrane environments for use in biophysical studies.
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Affiliation(s)
- Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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15
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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