1
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Zipursky S, Lee J, Sergeeva A, Ahlsen G, Mannepalli S, Bahna F, Goodman K, Khakh B, Weiner J, Shapiro L, Honig B. Astrocyte morphogenesis requires self-recognition. Res Sq 2024:rs.3.rs-3932947. [PMID: 38463964 PMCID: PMC10925414 DOI: 10.21203/rs.3.rs-3932947/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Self-recognition is a fundamental cellular process across evolution and forms the basis of neuronal self-avoidance1-4. Clustered protocadherins (Pcdh), comprising a large family of isoform-specific homophilic recognition molecules, play a pivotal role in neuronal self-avoidance required for mammalian brain development5-7. The probabilistic expression of different Pcdh isoforms confers unique identities upon neurons and forms the basis for neuronal processes to discriminate between self and non-self5,6,8. Whether this self-recognition mechanism exists in astrocytes, the other predominant cell type of the brain, remains unknown. Here, we report that a specific isoform in the Pcdhγ cluster, γC3, is highly enriched in human and murine astrocytes. Through genetic manipulation, we demonstrate that γC3 acts autonomously to regulate astrocyte morphogenesis in the mouse visual cortex. To determine if γC3 proteins act by promoting recognition between processes of the same astrocyte, we generated pairs of γC3 chimeric proteins capable of heterophilic binding to each other, but incapable of homophilic binding. Co-expressing complementary heterophilic binding isoform pairs in the same γC3 null astrocyte restored normal morphology. By contrast, chimeric γC3 proteins individually expressed in single γC3 null mutant astrocytes did not. These data establish that self-recognition is essential for astrocyte development in the mammalian brain and that, by contrast to neuronal self-recognition, a single Pcdh isoform is both necessary and sufficient for this process.
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Affiliation(s)
| | - John Lee
- University of California Los Angeles
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2
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Sergeeva AP, Katsamba PS, Liao J, Sampson JM, Bahna F, Mannepalli S, Morano NC, Shapiro L, Friesner RA, Honig B. Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. J Mol Biol 2023:168187. [PMID: 37355034 DOI: 10.1016/j.jmb.2023.168187] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
Abstract
The strength of binding between human angiotensin converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of viral spike protein plays a role in the transmissibility of the SARS-CoV-2 virus. In this study we focus on a subset of RBD mutations that have been frequently observed in infected individuals and probe binding affinity changes to ACE2 using surface plasmon resonance (SPR) measurements and free energy perturbation (FEP) calculations. Our SPR results are largely in accord with previous studies but discrepancies do arise due to differences in experimental methods and to protocol differences even when a single method is used. Overall, we find that FEP performance is superior to that of other computational approaches examined as determined by agreement with experiment and, in particular, by its ability to identify stabilizing mutations. Moreover, the calculations successfully predict the observed cooperative stabilization of binding by the Q498R N501Y double mutant present in Omicron variants and offer a physical explanation for the underlying mechanism. Overall, our results suggest that despite the significant computational cost, FEP calculations may offer an effective strategy to understand the effects of interfacial mutations on protein-protein binding affinities and, hence, in a variety of practical applications such as the optimization of neutralizing antibodies.
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Affiliation(s)
- Alina P Sergeeva
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Junzhuo Liao
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Jared M Sampson
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Schrödinger, Inc., New York, NY 10036, USA
| | - Fabiana Bahna
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Seetha Mannepalli
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Nicholas C Morano
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | | | - Barry Honig
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032.
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3
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Xu S, Sergeeva AP, Katsamba PS, Mannepalli S, Bahna F, Bimela J, Zipursky SL, Shapiro L, Honig B, Zinn K. Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules. Cell Rep 2022; 39:110618. [PMID: 35385751 PMCID: PMC9078203 DOI: 10.1016/j.celrep.2022.110618] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/30/2021] [Revised: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
Neurons in the developing brain express many different cell adhesion molecules (CAMs) on their surfaces. CAM-binding affinities can vary by more than 200-fold, but the significance of these variations is unknown. Interactions between the immunoglobulin superfamily CAM DIP-α and its binding partners, Dpr10 and Dpr6, control synaptic targeting and survival of Drosophila optic lobe neurons. We design mutations that systematically change interaction affinity and analyze function in vivo. Reducing affinity causes loss-of-function phenotypes whose severity scales with the magnitude of the change. Synaptic targeting is more sensitive to affinity reduction than is cell survival. Increasing affinity rescues neurons that would normally be culled by apoptosis. By manipulating CAM expression together with affinity, we show that the key parameter controlling circuit assembly is surface avidity, which is the strength of adherence between cell surfaces. We conclude that CAM binding affinities and expression levels are finely tuned for function during development.
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Affiliation(s)
- Shuwa Xu
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA.
| | - Alina P Sergeeva
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Seetha Mannepalli
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Fabiana Bahna
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Jude Bimela
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - S Lawrence Zipursky
- Department of Biological Chemistry, HHMI, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Kai Zinn
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA.
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4
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Goodman KM, Katsamba PS, Rubinstein R, Ahlsén G, Bahna F, Mannepalli S, Dan H, Sampogna RV, Shapiro L, Honig B. How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition. eLife 2022; 11:e72416. [PMID: 35253643 PMCID: PMC8901172 DOI: 10.7554/elife.72416] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 07/22/2021] [Accepted: 01/26/2022] [Indexed: 12/30/2022] Open
Abstract
The stochastic expression of fewer than 60 clustered protocadherin (cPcdh) isoforms provides diverse identities to individual vertebrate neurons and a molecular basis for self-/nonself-discrimination. cPcdhs form chains mediated by alternating cis and trans interactions between apposed membranes, which has been suggested to signal self-recognition. Such a mechanism requires that cPcdh cis dimers form promiscuously to generate diverse recognition units, and that trans interactions have precise specificity so that isoform mismatches terminate chain growth. However, the extent to which cPcdh interactions fulfill these requirements has not been definitively demonstrated. Here, we report biophysical experiments showing that cPcdh cis interactions are promiscuous, but with preferences favoring formation of heterologous cis dimers. Trans homophilic interactions are remarkably precise, with no evidence for heterophilic interactions between different isoforms. A new C-type cPcdh crystal structure and mutagenesis data help to explain these observations. Overall, the interaction characteristics we report for cPcdhs help explain their function in neuronal self-/nonself-discrimination.
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Affiliation(s)
- Kerry Marie Goodman
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Phinikoula S Katsamba
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Rotem Rubinstein
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv UniversityTel AvivIsrael
- Sagol School of Neuroscience, Tel Aviv UniversityTel AvivIsrael
| | - Göran Ahlsén
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Fabiana Bahna
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Seetha Mannepalli
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Hanbin Dan
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
| | - Rosemary V Sampogna
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
| | - Barry Honig
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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5
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Madan B, Reddem ER, Wang P, Casner RG, Nair MS, Huang Y, Fahad AS, de Souza MO, Banach BB, López Acevedo SN, Pan X, Nimrania R, Teng I, Bahna F, Zhou T, Zhang B, Yin MT, Ho DD, Kwong PD, Shapiro L, DeKosky BJ. Antibody screening at reduced pH enables preferential selection of potently neutralizing antibodies targeting SARS-CoV-2. AIChE J 2021; 67:e17440. [PMID: 34898670 PMCID: PMC8646896 DOI: 10.1002/aic.17440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 12/28/2022]
Abstract
Antiviral monoclonal antibody (mAb) discovery enables the development of antibody-based antiviral therapeutics. Traditional antiviral mAb discovery relies on affinity between antibody and a viral antigen to discover potent neutralizing antibodies, but these approaches are inefficient because many high affinity mAbs have no neutralizing activity. We sought to determine whether screening for anti-SARS-CoV-2 mAbs at reduced pH could provide more efficient neutralizing antibody discovery. We mined the antibody response of a convalescent COVID-19 patient at both physiological pH (7.4) and reduced pH (4.5), revealing that SARS-CoV-2 neutralizing antibodies were preferentially enriched in pH 4.5 yeast display sorts. Structural analysis revealed that a potent new antibody called LP5 targets the SARS-CoV-2 N-terminal domain supersite via a unique binding recognition mode. Our data combine with evidence from prior studies to support antibody screening at pH 4.5 to accelerate antiviral neutralizing antibody discovery.
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Affiliation(s)
- Bharat Madan
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | - Eswar R. Reddem
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
| | - Pengfei Wang
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ryan G. Casner
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
| | - Manoj S. Nair
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ahmed S. Fahad
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | | | - Bailey B. Banach
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | | | - Xiaoli Pan
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | - Rajani Nimrania
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | - I‐Ting Teng
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Fabiana Bahna
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
| | - Tongqing Zhou
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Baoshan Zhang
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Michael T. Yin
- Department of Medicine, Division of Infectious DiseasesColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - David D. Ho
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Peter D. Kwong
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Brandon J. DeKosky
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
- Department of Chemical EngineeringThe University of KansasLawrenceKansasUSA
- The Ragon Institute of MGHMIT, and Harvard, Cambridge, MA
- Department of Chemical EngineeringMassachusetts Institute of Technology, Cambridge, MA
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6
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Cerutti G, Guo Y, Wang P, Nair MS, Wang M, Huang Y, Yu J, Liu L, Katsamba PS, Bahna F, Reddem ER, Kwong PD, Ho DD, Sheng Z, Shapiro L. Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. Cell Rep 2021; 37:109928. [PMID: 34706271 PMCID: PMC8519878 DOI: 10.1016/j.celrep.2021.109928] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [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: 06/10/2021] [Revised: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023] Open
Abstract
Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here, we report the cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β sandwich. Interestingly, this pocket was previously identified as the binding site for hydrophobic molecules, including heme metabolites, but we observe that their presence does not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains neutralization potency with many variants of concern (VOCs). Overall, we reveal that a hydrophobic pocket in NTD proposed for immune evasion can be used by the immune system for recognition.
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Affiliation(s)
- Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Fabiana Bahna
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Eswar R. Reddem
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Peter D. Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA,Corresponding author
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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7
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Blockus H, Rolotti SV, Szoboszlay M, Peze-Heidsieck E, Ming T, Schroeder A, Apostolo N, Vennekens KM, Katsamba PS, Bahna F, Mannepalli S, Ahlsen G, Honig B, Shapiro L, de Wit J, Losonczy A, Polleux F. Synaptogenic activity of the axon guidance molecule Robo2 underlies hippocampal circuit function. Cell Rep 2021; 37:109828. [PMID: 34686348 PMCID: PMC8605498 DOI: 10.1016/j.celrep.2021.109828] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 08/07/2020] [Revised: 07/06/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023] Open
Abstract
Synaptic connectivity within adult circuits exhibits a remarkable degree of cellular and subcellular specificity. We report that the axon guidance receptor Robo2 plays a role in establishing synaptic specificity in hippocampal CA1. In vivo, Robo2 is present and required postsynaptically in CA1 pyramidal neurons (PNs) for the formation of excitatory (E) but not inhibitory (I) synapses, specifically in proximal but not distal dendritic compartments. In vitro approaches show that the synaptogenic activity of Robo2 involves a trans-synaptic interaction with presynaptic Neurexins, as well as binding to its canonical extracellular ligand Slit. In vivo 2-photon Ca2+ imaging of CA1 PNs during spatial navigation in awake behaving mice shows that preventing Robo2-dependent excitatory synapse formation cell autonomously during development alters place cell properties of adult CA1 PNs. Our results identify a trans-synaptic complex linking the establishment of synaptic specificity to circuit function.
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Affiliation(s)
- Heike Blockus
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Sebi V Rolotti
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Miklos Szoboszlay
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Eugénie Peze-Heidsieck
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Tiffany Ming
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Anna Schroeder
- VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Department of Neurosciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Nuno Apostolo
- VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Department of Neurosciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Kristel M Vennekens
- VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Department of Neurosciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Fabiana Bahna
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Seetha Mannepalli
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Goran Ahlsen
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Barry Honig
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Joris de Wit
- VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Department of Neurosciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA.
| | - Franck Polleux
- Department of Neuroscience, Columbia University, New York, NY 10027, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA.
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8
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Cerutti G, Rapp M, Guo Y, Bahna F, Bimela J, Reddem ER, Yu J, Wang P, Liu L, Huang Y, Ho DD, Kwong PD, Sheng Z, Shapiro L. Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies. Structure 2021; 29:655-663.e4. [PMID: 34111408 PMCID: PMC8188728 DOI: 10.1016/j.str.2021.05.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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: 03/04/2021] [Revised: 04/11/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022]
Abstract
Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively, show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of the spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented an immune response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies, such as 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Binding Sites
- Cloning, Molecular
- Cryoelectron Microscopy
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Epitopes/metabolism
- Gene Expression
- HEK293 Cells
- Humans
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Receptors, Virus/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Fabiana Bahna
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Jude Bimela
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Eswar R Reddem
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Cerutti G, Guo Y, Wang P, Nair MS, Huang Y, Yu J, Liu L, Katsamba PS, Bahna F, Reddem ER, Kwong PD, Ho DD, Sheng Z, Shapiro L. Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. bioRxiv 2021:2021.06.29.450397. [PMID: 34230927 PMCID: PMC8259903 DOI: 10.1101/2021.06.29.450397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
UNLABELLED Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here we report the 3.7 Å resolution cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β-sandwich. Interestingly, this pocket has been previously identified as the binding site for hydrophobic molecules including heme metabolites, but we observe their presence to not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains a distinctive neutralization potency with variants of concern (VOC). Overall, we reveal a hydrophobic pocket in NTD proposed for immune evasion can actually be used by the immune system for recognition. HIGHLIGHTS Cryo-EM structure of neutralizing antibody 5-7 in complex with SARS CoV-2 spike5-7 recognizes NTD outside of the previously identified antigenic supersite5-7 binds to a site known to accommodate numerous hydrophobic ligandsStructural basis of 5-7 neutralization tolerance to some variants of concern.
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10
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Cerutti G, Guo Y, Zhou T, Gorman J, Lee M, Rapp M, Reddem ER, Yu J, Bahna F, Bimela J, Huang Y, Katsamba PS, Liu L, Nair MS, Rawi R, Olia AS, Wang P, Zhang B, Chuang GY, Ho DD, Sheng Z, Kwong PD, Shapiro L. Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe 2021; 29:819-833.e7. [PMID: 33789084 PMCID: PMC7953435 DOI: 10.1016/j.chom.2021.03.005] [Citation(s) in RCA: 326] [Impact Index Per Article: 108.7] [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: 12/22/2020] [Revised: 02/17/2021] [Accepted: 03/09/2021] [Indexed: 01/12/2023]
Abstract
Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile β-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.
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Affiliation(s)
- Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myungjin Lee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Eswar R Reddem
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Fabiana Bahna
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Jude Bimela
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Phinikoula S Katsamba
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zizhang Sheng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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11
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Cerutti G, Rapp M, Guo Y, Bahna F, Bimela J, Reddem ER, Yu J, Wang P, Liu L, Huang Y, Ho DD, Kwong PD, Sheng Z, Shapiro L. Structural Basis for Accommodation of Emerging B.1.351 and B.1.1.7 Variants by Two Potent SARS-CoV-2 Neutralizing Antibodies. bioRxiv 2021. [PMID: 33655245 DOI: 10.1101/2021.02.21.432168] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented a response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for both ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies like 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape.
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12
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Petropoulou PI, Mosialou I, Shikhel S, Hao L, Panitsas K, Bisikirska B, Luo N, Bahna F, Kim J, Carberry P, Zanderigo F, Simpson N, Bakalian M, Kassir S, Shapiro L, Underwood MD, May CM, Soligapuram Sai KK, Jorgensen MJ, Confavreux CB, Shapses S, Laferrère B, Mintz A, Mann JJ, Rubin M, Kousteni S. Lipocalin-2 is an anorexigenic signal in primates. eLife 2020; 9:58949. [PMID: 33231171 PMCID: PMC7685704 DOI: 10.7554/elife.58949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 05/15/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
In the mouse, the osteoblast-derived hormone Lipocalin-2 (LCN2) suppresses food intake and acts as a satiety signal. We show here that meal challenges increase serum LCN2 levels in persons with normal or overweight, but not in individuals with obesity. Postprandial LCN2 serum levels correlate inversely with hunger sensation in challenged subjects. We further show through brain PET scans of monkeys injected with radiolabeled recombinant human LCN2 (rh-LCN2) and autoradiography in baboon, macaque, and human brain sections, that LCN2 crosses the blood-brain barrier and localizes to the hypothalamus in primates. In addition, daily treatment of lean monkeys with rh-LCN2 decreases food intake by 21%, without overt side effects. These studies demonstrate the biology of LCN2 as a satiety factor and indicator and anorexigenic signal in primates. Failure to stimulate postprandial LCN2 in individuals with obesity may contribute to metabolic dysregulation, suggesting that LCN2 may be a novel target for obesity treatment.
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Affiliation(s)
| | - Ioanna Mosialou
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
| | - Steven Shikhel
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
| | - Lihong Hao
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States
| | - Konstantinos Panitsas
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
| | - Brygida Bisikirska
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
| | - Na Luo
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
| | - Fabiana Bahna
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Jongho Kim
- Department of Radiology, Columbia University Medical Center, New York, United States
| | - Patrick Carberry
- Department of Radiology, Columbia University Medical Center, New York, United States
| | - Francesca Zanderigo
- Department of Psychiatry, Columbia University Medical Center, New York, United States.,Molecular Imaging and Neuropathology Area, New York State Psychiatric Institute, New York, United States
| | - Norman Simpson
- Department of Psychiatry, Columbia University Medical Center, New York, United States
| | - Mihran Bakalian
- Department of Psychiatry, Columbia University Medical Center, New York, United States
| | - Suham Kassir
- Department of Psychiatry, Columbia University Medical Center, New York, United States.,Molecular Imaging and Neuropathology Area, New York State Psychiatric Institute, New York, United States
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Mark D Underwood
- Department of Psychiatry, Columbia University Medical Center, New York, United States.,Molecular Imaging and Neuropathology Area, New York State Psychiatric Institute, New York, United States
| | - Christina M May
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, United States
| | | | - Matthew J Jorgensen
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, United States
| | | | - Sue Shapses
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States.,Department of Medicine, Rutgers - RWJ Medical School, Rutgers University, New Brunswick, United States
| | - Blandine Laferrère
- New York Obesity Nutrition Research Center, Columbia University, New York, United States.,Department of Medicine, Division of Endocrinology, Columbia University Irving Medical Center, New York, United States
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, United States
| | - J John Mann
- Department of Radiology, Columbia University Medical Center, New York, United States.,Department of Psychiatry, Columbia University Medical Center, New York, United States.,Molecular Imaging and Neuropathology Area, New York State Psychiatric Institute, New York, United States
| | - Mishaela Rubin
- New York Obesity Nutrition Research Center, Columbia University, New York, United States
| | - Stavroula Kousteni
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
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13
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Brasch J, Goodman KM, Noble AJ, Rapp M, Mannepalli S, Bahna F, Dandey VP, Bepler T, Berger B, Maniatis T, Potter CS, Carragher B, Honig B, Shapiro L. Visualization of clustered protocadherin neuronal self-recognition complexes. Nature 2019; 569:280-283. [PMID: 30971825 DOI: 10.1038/s41586-019-1089-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/07/2019] [Indexed: 11/09/2022]
Abstract
Neurite self-recognition and avoidance are fundamental properties of all nervous systems1. These processes facilitate dendritic arborization2,3, prevent formation of autapses4 and allow free interaction among non-self neurons1,2,4,5. Avoidance among self neurites is mediated by stochastic cell-surface expression of combinations of about 60 isoforms of α-, β- and γ-clustered protocadherin that provide mammalian neurons with single-cell identities1,2,4-13. Avoidance is observed between neurons that express identical protocadherin repertoires2,5, and single-isoform differences are sufficient to prevent self-recognition10. Protocadherins form isoform-promiscuous cis dimers and isoform-specific homophilic trans dimers10,14-20. Although these interactions have previously been characterized in isolation15,17-20, structures of full-length protocadherin ectodomains have not been determined, and how these two interfaces engage in self-recognition between neuronal surfaces remains unknown. Here we determine the molecular arrangement of full-length clustered protocadherin ectodomains in single-isoform self-recognition complexes, using X-ray crystallography and cryo-electron tomography. We determine the crystal structure of the clustered protocadherin γB4 ectodomain, which reveals a zipper-like lattice that is formed by alternating cis and trans interactions. Using cryo-electron tomography, we show that clustered protocadherin γB6 ectodomains tethered to liposomes spontaneously assemble into linear arrays at membrane contact sites, in a configuration that is consistent with the assembly observed in the crystal structure. These linear assemblies pack against each other as parallel arrays to form larger two-dimensional structures between membranes. Our results suggest that the formation of ordered linear assemblies by clustered protocadherins represents the initial self-recognition step in neuronal avoidance, and thus provide support for the isoform-mismatch chain-termination model of protocadherin-mediated self-recognition, which depends on these linear chains11.
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Affiliation(s)
- Julia Brasch
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kerry M Goodman
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Micah Rapp
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Seetha Mannepalli
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Fabiana Bahna
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Venkata P Dandey
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Tristan Bepler
- Computational and Systems Biology, MIT, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.,Department of Mathematics, MIT, Cambridge, MA, USA
| | - Tom Maniatis
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Barry Honig
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. .,Howard Hughes Medical Institute, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA. .,Department of Medicine, Columbia University, New York, NY, USA.
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA.
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14
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Goodman KM, Rubinstein R, Brasch J, Mannepalli S, Bahna F, Dan H, Maniatis T, Honig B, Shapiro L. Clustered protocadherin molecular assembly and implications for neuronal self-avoidance. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091884] [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: 04/03/2023] Open
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15
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Goodman KM, Rubinstein R, Brasch J, Thu CA, Bahna F, Mannepalli S, Dan H, Sampogna RV, Maniatis T, Honig B, Shapiro L. Clustered protocadherin molecular assembly and implications for neuronal self-avoidance. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317099500] [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: 11/11/2022] Open
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16
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Goodman KM, Rubinstein R, Thu CA, Mannepalli S, Bahna F, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L. γ-Protocadherin structural diversity and functional implications. eLife 2016; 5. [PMID: 27782885 PMCID: PMC5106212 DOI: 10.7554/elife.20930] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 08/23/2016] [Accepted: 10/06/2016] [Indexed: 12/26/2022] Open
Abstract
Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealing trans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depict cis-interacting regions in monomeric form. Together these structures span the entire γ-Pcdh ectodomain. The trans-dimer structures reveal determinants of γ-Pcdh isoform-specific homophilic recognition. We identified and structurally mapped cis-dimerization mutations to the C-terminal ectodomain structures. Biophysical studies showed that Pcdh ectodomains from γB-subfamily isoforms formed cis dimers, whereas γA isoforms did not, but both γA and γB isoforms could interact in cis with α-Pcdhs. Together, these data show how interaction specificity is distributed over all domains of the γ-Pcdh trans interface, and suggest that subfamily- or isoform-specific cis-interactions may play a role in the Pcdh-mediated neuronal self-recognition code.
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Affiliation(s)
- Kerry Marie Goodman
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Rotem Rubinstein
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Department of Systems Biology, Columbia University, New York, United States
| | - Chan Aye Thu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Seetha Mannepalli
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Fabiana Bahna
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Göran Ahlsén
- Department of Systems Biology, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Chelsea Rittenhouse
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, United States
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Department of Systems Biology, Columbia University, New York, United States.,Howard Hughes Medical Institute, Columbia University, New York, United States.,Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, United States.,Department of Medicine, Columbia University, New York, United States
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Department of Systems Biology, Columbia University, New York, United States.,Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, United States
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17
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Goodman KM, Rubinstein R, Thu CA, Bahna F, Mannepalli S, Ahlsén G, Rittenhouse C, Maniatis T, Honig B, Shapiro L. Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins. Neuron 2016; 90:709-23. [PMID: 27161523 DOI: 10.1016/j.neuron.2016.04.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/22/2016] [Accepted: 03/30/2016] [Indexed: 10/21/2022]
Abstract
Clustered protocadherin proteins (α-, β-, and γ-Pcdhs) provide a high level of cell-surface diversity to individual vertebrate neurons, engaging in highly specific homophilic interactions to mediate important roles in mammalian neural circuit development. How Pcdhs bind homophilically through their extracellular cadherin (EC) domains among dozens of highly similar isoforms has not been determined. Here, we report crystal structures for extracellular regions from four mouse Pcdh isoforms (α4, α7, β6, and β8), revealing a canonical head-to-tail interaction mode for homophilic trans dimers comprising primary intermolecular EC1:EC4 and EC2:EC3 interactions. A subset of trans interface residues exhibit isoform-specific conservation, suggesting roles in recognition specificity. Mutation of these residues, along with trans-interacting partner residues, altered the specificities of Pcdh interactions. Together, these data show how sequence variation among Pcdh isoforms encodes their diverse strict homophilic recognition specificities, which are required for their key roles in neural circuit assembly.
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Affiliation(s)
- Kerry Marie Goodman
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Rotem Rubinstein
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Chan Aye Thu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Fabiana Bahna
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Seetha Mannepalli
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Göran Ahlsén
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Chelsea Rittenhouse
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10032, USA
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10032, USA.
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18
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Rubinstein R, Thu CA, Goodman KM, Wolcott HN, Bahna F, Mannepalli S, Ahlsen G, Chevee M, Halim A, Clausen H, Maniatis T, Shapiro L, Honig B. Molecular logic of neuronal self-recognition through protocadherin domain interactions. Cell 2015; 163:629-42. [PMID: 26478182 DOI: 10.1016/j.cell.2015.09.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/17/2015] [Accepted: 08/27/2015] [Indexed: 12/27/2022]
Abstract
Self-avoidance, a process preventing interactions of axons and dendrites from the same neuron during development, is mediated in vertebrates through the stochastic single-neuron expression of clustered protocadherin protein isoforms. Extracellular cadherin (EC) domains mediate isoform-specific homophilic binding between cells, conferring cell recognition through a poorly understood mechanism. Here, we report crystal structures for the EC1-EC3 domain regions from four protocadherin isoforms representing the α, β, and γ subfamilies. All are rod shaped and monomeric in solution. Biophysical measurements, cell aggregation assays, and computational docking reveal that trans binding between cells depends on the EC1-EC4 domains, which interact in an antiparallel orientation. We also show that the EC6 domains are required for the formation of cis-dimers. Overall, our results are consistent with a model in which protocadherin cis-dimers engage in a head-to-tail interaction between EC1-EC4 domains from apposed cell surfaces, possibly forming a zipper-like protein assembly, and thus providing a size-dependent self-recognition mechanism.
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Affiliation(s)
- Rotem Rubinstein
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Chan Aye Thu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Kerry Marie Goodman
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Holly Noelle Wolcott
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Fabiana Bahna
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Seetha Mannepalli
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Goran Ahlsen
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Maxime Chevee
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA.
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19
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Harrison OJ, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM, Troyanovsky RB, Ben-Shaul A, Frank J, Troyanovsky SM, Shapiro L, Honig B. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure 2011; 19:244-56. [PMID: 21300292 DOI: 10.1016/j.str.2010.11.016] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 11/24/2022]
Abstract
Adherens junctions, which play a central role in intercellular adhesion, comprise clusters of type I classical cadherins that bind via extracellular domains extended from opposing cell surfaces. We show that a molecular layer seen in crystal structures of E- and N-cadherin ectodomains reported here and in a previous C-cadherin structure corresponds to the extracellular architecture of adherens junctions. In all three ectodomain crystals, cadherins dimerize through a trans adhesive interface and are connected by a second, cis, interface. Assemblies formed by E-cadherin ectodomains coated on liposomes also appear to adopt this structure. Fluorescent imaging of junctions formed from wild-type and mutant E-cadherins in cultured cells confirm conclusions derived from structural evidence. Mutations that interfere with the trans interface ablate adhesion, whereas cis interface mutations disrupt stable junction formation. Our observations are consistent with a model for junction assembly involving strong trans and weak cis interactions localized in the ectodomain.
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Affiliation(s)
- Oliver J Harrison
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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20
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Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol 2011; 18:693-700. [PMID: 21572446 PMCID: PMC3113550 DOI: 10.1038/nsmb.2051] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 02/24/2011] [Indexed: 02/02/2023]
Abstract
Cell adhesion by classical cadherins is mediated by dimerization of their EC1 domains through the “swapping” of N-terminal β-strands. We use molecular simulations, measurements of binding affinities, and x-ray crystallography to provide a detailed picture of the structural and energetic factors that control the adhesive dimerization of cadherins. We show that strand swapping in EC1 is driven by conformational strain in cadherin monomers which arises from the anchoring of their short N-terminal strand at one end by the conserved Trp2 and at the other by ligation to Ca2+ ions. We also demonstrate that a conserved pro-pro motif functions to avoid the formation of an overly tight interface where affinity differences between different cadherins, crucial at the cellular level, are lost. We use these findings to design site-directed mutations which transform a monomeric EC2-EC3 domain cadherin construct, into a strand-swapped dimer.
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Affiliation(s)
- Jeremie Vendome
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. Howard Hughes Medical Institute, Columbia University, New York, New York, USA
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21
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Koehnke J, Katsamba PS, Ahlsen G, Bahna F, Vendome J, Honig B, Shapiro L, Jin X. Splice form dependence of beta-neurexin/neuroligin binding interactions. Neuron 2010; 67:61-74. [PMID: 20624592 DOI: 10.1016/j.neuron.2010.06.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2010] [Indexed: 11/25/2022]
Abstract
Alternatively spliced beta-neurexins (beta-NRXs) and neuroligins (NLs) are thought to have distinct extracellular binding affinities, potentially providing a beta-NRX/NL synaptic recognition code. We utilized surface plasmon resonance to measure binding affinities between all combinations of alternatively spliced beta-NRX 1-3 and NL 1-3 ectodomains. Binding was observed for all beta-NRX/NL pairs. The presence of the NL1 B splice insertion lowers beta-NRX binding affinity by approximately 2-fold, while beta-NRX splice insertion 4 has small effects that do not synergize with NL splicing. New structures of glycosylated beta-NRXs 1 and 2 containing splice insertion 4 reveal that the insertion forms a new beta strand that replaces the beta10 strand, leaving the NL binding site intact. This helps to explain the limited effect of splice insert 4 on NRX/NL binding affinities. These results provide new structural insights and quantitative binding information to help determine whether and how splice isoform choice plays a role in beta-NRX/NL-mediated synaptic recognition.
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Affiliation(s)
- Jesko Koehnke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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22
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Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison OJ, Brasch J, Jin X, Posy S, Vendome J, Ranscht B, Jessell TM, Honig B, Shapiro L. T-cadherin structures reveal a novel adhesive binding mechanism. Nat Struct Mol Biol 2010; 17:339-47. [PMID: 20190755 DOI: 10.1038/nsmb.1781] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 11/24/2009] [Indexed: 11/09/2022]
Abstract
Vertebrate genomes encode 19 classical cadherins and about 100 nonclassical cadherins. Adhesion by classical cadherins depends on binding interactions in their N-terminal EC1 domains, which swap N-terminal beta-strands between partner molecules from apposing cells. However, strand-swapping sequence signatures are absent from nonclassical cadherins, raising the question of how these proteins function in adhesion. Here, we show that T-cadherin, a glycosylphosphatidylinositol (GPI)-anchored cadherin, forms dimers through an alternative nonswapped interface near the EC1-EC2 calcium-binding sites. Mutations within this interface ablate the adhesive capacity of T-cadherin. These nonadhesive T-cadherin mutants also lose the ability to regulate neurite outgrowth from T-cadherin-expressing neurons. Our findings reveal the likely molecular architecture of the T-cadherin homophilic interface and its requirement for axon outgrowth regulation. The adhesive binding mode used by T-cadherin may also be used by other nonclassical cadherins.
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Affiliation(s)
- Carlo Ciatto
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
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23
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Harrison OJ, Bahna F, Katsamba PS, Jin X, Brasch J, Vendome J, Ahlsen G, Carroll KJ, Price SR, Honig B, Shapiro L. Two-step adhesive binding by classical cadherins. Nat Struct Mol Biol 2010; 17:348-57. [PMID: 20190754 DOI: 10.1038/nsmb.1784] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 02/02/2010] [Indexed: 11/09/2022]
Abstract
Crystal structures of classical cadherins have revealed two dimeric configurations. In the first, N-terminal beta-strands of EC1 domains 'swap' between partner molecules. The second configuration (the 'X dimer'), also observed for T-cadherin, is mediated by residues near the EC1-EC2 calcium binding sites, and N-terminal beta-strands of partner EC1 domains, though held adjacent, do not swap. Here we show that strand-swapping mutants of type I and II classical cadherins form X dimers. Mutant cadherins impaired for X-dimer formation show no binding in short-time frame surface plasmon resonance assays, but in long-time frame experiments, they have homophilic binding affinities close to that of wild type. Further experiments show that exchange between monomers and dimers is slowed in these mutants. These results reconcile apparently disparate results from prior structural studies and suggest that X dimers are binding intermediates that facilitate the formation of strand-swapped dimers.
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Affiliation(s)
- Oliver J Harrison
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
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24
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Miloushev VZ, Bahna F, Ciatto C, Ahlsen G, Honig B, Shapiro L, Palmer AG. Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. Structure 2008; 16:1195-205. [PMID: 18682221 DOI: 10.1016/j.str.2008.05.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 04/29/2008] [Accepted: 05/20/2008] [Indexed: 11/29/2022]
Abstract
Cadherin-mediated cell adhesion is achieved through dimerization of cadherin N-terminal extracellular (EC1) domains presented from apposed cells. The dimer state is formed by exchange of N-terminal beta strands and insertion of conserved tryptophan indole side chains from one monomer into hydrophobic acceptor pockets of the partner molecule. The present work characterizes individual monomer and dimer states and the monomer-dimer equilibrium of the mouse Type II cadherin-8 EC1 domain using NMR spectroscopy. Limited picosecond-to-nanosecond timescale dynamics of the tryptophan indole moieties for both monomer and dimer states are consistent with well-ordered packing of the N-terminal beta strands intramolecularly and intermolecularly, respectively. However, pronounced microsecond-to-millisecond timescale dynamics of the side chains are observed for the monomer but not the dimer state, suggesting that monomers transiently sample configurations in which the indole moieties are exposed. The results suggest possible kinetic mechanisms for EC1 dimerization.
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Affiliation(s)
- Vesselin Z Miloushev
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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25
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Patel SD, Ciatto C, Chen CP, Bahna F, Rajebhosale M, Arkus N, Schieren I, Jessell TM, Honig B, Price SR, Shapiro L. Type II cadherin ectodomain structures: implications for classical cadherin specificity. Cell 2006; 124:1255-68. [PMID: 16564015 DOI: 10.1016/j.cell.2005.12.046] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 12/01/2005] [Accepted: 12/29/2005] [Indexed: 11/16/2022]
Abstract
Type I and II classical cadherins help to determine the adhesive specificities of animal cells. Crystal-structure determination of ectodomain regions from three type II cadherins reveals adhesive dimers formed by exchange of N-terminal beta strands between partner extracellular cadherin-1 (EC1) domains. These interfaces have two conserved tryptophan side chains that anchor each swapped strand, compared with one in type I cadherins, and include large hydrophobic regions unique to type II interfaces. The EC1 domains of type I and type II cadherins appear to encode cell adhesive specificity in vitro. Moreover, perturbation of motor neuron segregation with chimeric cadherins depends on EC1 domain identity, suggesting that this region, which includes the structurally defined adhesive interface, encodes type II cadherin functional specificity in vivo.
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Affiliation(s)
- Saurabh D Patel
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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26
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Abstract
The cadherins comprise a family of single-pass transmembrane proteins critical for cell-cell adhesion in vertebrates and invertebrates. The recently determined structure of the whole ectodomain from C-cadherin suggests that the adhesion of cadherins presented by juxtaposed cells is mediated by a strand-swapped dimer in which core hydrophobic elements are exchanged between the partner molecules. Sequence analysis suggests that several cadherin subfamilies share this adhesive mechanism. Recent work has shed new light on the molecular basis of cadherin adhesion, although understanding the specificity of these interactions remains a major challenge.
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Affiliation(s)
- Saurabh D Patel
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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27
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Affiliation(s)
- Arhonda Gogos
- Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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