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Sakai T, Mashima T, Kobayashi N, Ogata H, Duan L, Fujiki R, Hengphasatporn K, Uda T, Shigeta Y, Hifumi E, Hirota S. Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping. Nat Commun 2023; 14:7807. [PMID: 38065949 PMCID: PMC10709643 DOI: 10.1038/s41467-023-43443-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Overexpression of antibody light chains in small plasma cell clones can lead to misfolding and aggregation. On the other hand, the formation of amyloid fibrils from antibody light chains is related to amyloidosis. Although aggregation of antibody light chain is an important issue, atomic-level structural examinations of antibody light chain aggregates are sparse. In this study, we present an antibody light chain that maintains an equilibrium between its monomeric and tetrameric states. According to data from X-ray crystallography, thermodynamic and kinetic measurements, as well as theoretical studies, this antibody light chain engages in 3D domain swapping within its variable region. Here, a pair of domain-swapped dimers creates a tetramer through hydrophobic interactions, facilitating the revelation of the domain-swapped structure. The negative cotton effect linked to the β-sheet structure, observed around 215 nm in the circular dichroism (CD) spectrum of the tetrameric variable region, is more pronounced than that of the monomer. This suggests that the monomer contains less β-sheet structures and exhibits greater flexibility than the tetramer in solution. These findings not only clarify the domain-swapped structure of the antibody light chain but also contribute to controlling antibody quality and advancing the development of future molecular recognition agents and drugs.
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Affiliation(s)
- Takahiro Sakai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Tsuyoshi Mashima
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Naoya Kobayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Hideaki Ogata
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Lian Duan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Ryo Fujiki
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Taizo Uda
- Nanotechnology Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT), 4‑1 Kyudai‑Shinmachi, Fukuoka, 879‑5593, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Emi Hifumi
- Institute for Research Management, Oita University, 700 Dannoharu, Oita-shi, Oita, 870‑1192, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
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2
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Martínez-Rodríguez S, Cámara-Artigas A, Gavira JA. First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family. Biochem Biophys Res Commun 2023; 682:85-90. [PMID: 37804591 DOI: 10.1016/j.bbrc.2023.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Acylphosphatase (AcP, EC 3.6.1.7) is a small model protein conformed by a ferredoxin-like fold, profoundly studied to get insights into protein folding and aggregation processes. Numerous studies focused on the aggregation and/or amyloidogenic properties of AcPs suggest the importance of edge-β-strands in the process. In this work, we present the first crystallographic structure of Escherichia coli AcP (EcoAcP), showing notable differences with the only available NMR structure for this enzyme. EcoAcP is crystalised as an intertwined dimer formed by replacing a single C-terminal β-strand between two protomers, suggesting a flexible character of the C-terminal edge of EcoAcP. Despite numerous works where AcP from different sources have been used as a model system for protein aggregation, our domain-swapped EcoAcP structure is the first 3-D structural evidence of native-like aggregated species for any AcP reported to date, providing clues on molecular determinants unleashing aggregation.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Avenida de La Investigación 11, Granada, 18071, Spain; Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain.
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Centro de Investigación en Agrosistemas Intensivos Mediterráneos y Biotecnología Agroalimentaria (CIAMBITAL), Carretera de Sacramento S/n, Almería, 04120, Spain
| | - Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain
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Dionne U, Percival LJ, Chartier FJM, Landry CR, Bisson N. SRC homology 3 domains: multifaceted binding modules. Trends Biochem Sci 2022; 47:772-784. [PMID: 35562294 DOI: 10.1016/j.tibs.2022.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
The assembly of complexes following the detection of extracellular signals is often controlled by signaling proteins comprising multiple peptide binding modules. The SRC homology (SH)3 family represents the archetypical modular protein interaction module, with ~300 annotated SH3 domains in humans that regulate an impressive array of signaling processes. We review recent findings regarding the allosteric contributions of SH3 domains host protein context, their phosphoregulation, and their roles in phase separation that challenge the simple model in which SH3s are considered to be portable domains binding to specific proline-rich peptide motifs.
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Affiliation(s)
- Ugo Dionne
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Lily J Percival
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Manchester, UK
| | - François J M Chartier
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Christian R Landry
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Institute of Integrative and Systems Biology, Université Laval, Quebec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC, Canada; Department of Biology, Université Laval, Quebec, QC, Canada.
| | - Nicolas Bisson
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, QC, Canada.
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4
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Salinas-Garcia MC, Plaza-Garrido M, Camara-Artigas A. The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain. Acta Crystallogr D Struct Biol 2021; 77:854-866. [PMID: 34076598 PMCID: PMC8171063 DOI: 10.1107/s2059798321004344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 03/26/2023] Open
Abstract
Src kinase belongs to the family of Src-related nonreceptor tyrosine kinases. Because of its physiological role in cell growth and proliferation, its activity is strictly controlled by several mechanisms. Nevertheless, in viral Src kinase (v-Src) some of these mechanisms fail, and its uncontrolled activity is responsible for the occurrence of cancer. Here, the crystal structures of three SH3-domain mutants of v-Src were determined to unveil the effects of these oncogenic mutations in this regulatory domain. Mutations in the n-Src and distal loops have a low impact on the overall structure of the domain and its capacity to form intertwined dimers. However, mutations in the RT loop compromise the stability of the domain and make the protein very prone to aggregation. Additionally, these mutations prevent the formation of intertwined dimers. The results show a synergistic effect between mutations in the RT loop and those in the n-Src and distal loops. Analysis of the structures of the v-Src SH3-domain mutants and the closed inactive conformation of cellular Src kinase (c-Src) point to a loss of the interactions that are required to establish the compact inactive form of the kinase. Nevertheless, an analysis of structures of the c-Src SH3 domain complexed with class I and II peptides points to minor changes in the interactions between the v-Src SH3 domain and these peptides. In this way, the structures reported here indicate that mutations in the RT loop might impair the kinase regulation mechanism without affecting the recognition of short proline-rich motifs in the target proteins of the kinase, thus explaining the oncogenic behaviour of the protein.
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Affiliation(s)
- M. Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
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Richter K, Rufer AC, Muller M, Burger D, Casagrande F, Grossenbacher T, Huber S, Hug MN, Koldewey P, D'Osualdo A, Schlatter D, Stoll T, Rudolph MG. Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain. J Biol Chem 2020; 295:7849-7864. [PMID: 32317279 PMCID: PMC7278359 DOI: 10.1074/jbc.ra120.012788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3ϵ that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3.1). Inhibition of this protein/protein interaction ameliorated inflammatory symptoms in mouse models of multiple sclerosis, psoriasis, and asthma. A small molecule, AX-024, was reported to inhibit the Nck/CD3ϵ interaction by physically binding to the Nck1-SH3.1 domain, suggesting a route to develop an inhibitor of the Nck1/CD3ϵ interaction for modulating TCR activity in autoimmune and inflammatory diseases. We show here that AX-024 reduces T cell proliferation upon weak TCR stimulation but does not significantly affect phosphorylation of Zap70 (ζ chain of T cell receptor–associated protein kinase 70). We also find that AX-024 is likely not involved in modulating the Nck/TCR interaction but probably has other targets in T cells. An array of biophysical techniques did not detect a direct interaction between AX-024 and Nck-SH3.1 in vitro. Crystal structures of the Nck-SH3.1 domain revealed its binding mode to the PRS in CD3ϵ. The SH3 domain tends to generate homodimers through a domain swap. Domain swaps observed previously in other SH3 domains indicate a general propensity of this protein fold to exchange structural elements. The swapped form of Nck-SH3.1 is unable to bind CD3ϵ, possibly representing an inactive form of Nck in cells.
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Affiliation(s)
- Kirsten Richter
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Arne C Rufer
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Magali Muller
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Dominique Burger
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Fabio Casagrande
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tabea Grossenbacher
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sylwia Huber
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melanie N Hug
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Philipp Koldewey
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andrea D'Osualdo
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Daniel Schlatter
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Theodor Stoll
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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6
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Youkharibache P, Veretnik S, Li Q, Stanek KA, Mura C, Bourne PE. The Small β-Barrel Domain: A Survey-Based Structural Analysis. Structure 2018; 27:6-26. [PMID: 30393050 DOI: 10.1016/j.str.2018.09.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 11/27/2022]
Abstract
The small β-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an "urfold." To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure ↔ function versatility of the SBB.
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Affiliation(s)
- Philippe Youkharibache
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Stella Veretnik
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
| | - Qingliang Li
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Philip E Bourne
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
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Mathiharan YK, Murthy M. Molecular dynamics studies on the domain swapped Salmonella typhimurium survival protein SurE: insights on the possible reasons for catalytic cooperativity. J Biomol Struct Dyn 2018; 36:2303-2311. [DOI: 10.1080/07391102.2017.1351400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - M.R.N. Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
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Bonjack-Shterengartz M, Avnir D. The enigma of the near-symmetry of proteins: Domain swapping. PLoS One 2017; 12:e0180030. [PMID: 28708874 PMCID: PMC5510828 DOI: 10.1371/journal.pone.0180030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/08/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of proteins form oligomers which have rotational symmetry. Literature has suggested many functional advantages that the symmetric packing offers. Yet, despite these advantages, the vast majority of protein oligomers are only nearly symmetric. A key question in the field of proteins structure is therefore, if symmetry is so advantageous, why do oligomers settle for aggregates that do not maximize that structural property? The answer to that question is apparently multi-parametric, and involves distortions at the interaction zones of the monomer units of the oligomer in order to minimize the free energy, the dynamics of the protein, the effects of surroundings parameters, and the mechanism of oligomerization. The study of this problem is in its infancy: Only the first parameter has been explored so far. Here we focus on the last parameter-the mechanism of formation. To test this effect we have selected to focus on the domain swapping mechanism of oligomerization, by which oligomers form in a mechanism that swaps identical portions of monomeric units, resulting in an interwoven oligomer. We are using continuous symmetry measures to analyze in detail the oligomer formed by this mechanism, and found, that without exception, in all analyzed cases, perfect symmetry is given away, and we are able to identify that the main burden of distortion lies in the hinge regions that connect the swapped portions. We show that the continuous symmetry analysis method clearly identifies the hinge region of swapped domain proteins-considered to be a non-trivial task. We corroborate our conclusion about the central role of the hinge region in affecting the symmetry of the oligomers, by a special probability analysis developed particularly for that purpose.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Avnir
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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