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Shi D, Zhu X, Zhang H, Yan J, Bai C. Catalytic mechanism study of ATP-citrate lyase during citryl-CoA synthesis process. iScience 2024; 27:110605. [PMID: 39220258 PMCID: PMC11365397 DOI: 10.1016/j.isci.2024.110605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 06/03/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
ATP-citrate lyase (ACLY) is a critical metabolic enzyme and promising target for drug development. The structure determinations of ACLY have revealed its homotetramer states with various subunit symmetries, but catalytic mechanism of ACLY tetramer and the importance of subunit symmetry have not been clarified. Here, we constructed the free energy landscape of ACLY tetramer with arbitrary subunit symmetries and investigated energetic and conformational coupling of subunits during citryl-CoA synthesis process. The optimal conformational pathway indicates that ACLY tetramer encounters three critical conformational barriers and undergoes a loss of rigid-D2 symmetry to gain an energetic advantage. Energetic coupling of conformational changes and biochemical reactions suggests that these biological events are not independent but rather coupled with each other, showing a comparable energy barrier to the experimental data for the rate-limiting step. These findings could contribute to further research on catalytic mechanism, functional modulation, and inhibitor design of ACLY.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, Guangdong, People's Republic of China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Xuzhou College of Industrial Technology, Xuzhou 221140, China
| | - Xiaohong Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, Guangdong, People's Republic of China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Honghui Zhang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, Guangdong, People's Republic of China
| | - Junfang Yan
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, Guangdong, People's Republic of China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, Guangdong, People's Republic of China
- Chenzhu Biotechnology Co., Ltd, Hangzhou 310005, China
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2
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Qi X, Meng J, Li C, Cheng W, Fan A, Huang J, Lin W. Praelolide alleviates collagen-induced arthritis through increasing catalase activity and activating Nrf2 pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 135:156040. [PMID: 39299092 DOI: 10.1016/j.phymed.2024.156040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/13/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024]
Abstract
BACKGROUND Marine diterpenes represent a promising reservoir for identifying potential anti-rheumatoid arthritis (RA) candidates. Praelolide is a gorgonian-derived briarane-type diterpenoid with antioxidative and anti-osteoclastogenetic properties. OBJECTIVE This study aims to evaluate the therapeutic efficacy of praelolide against RA and investigate its underlying mechanisms both in vivo and in vitro. METHOD Collagen-induced arthritis (CIA) mice and human RA fibroblast-like synoviocyte MH7A cells were employed for bioassays. The VisuGait system was utilized to assess gait dysfunction resulting from joint pain. Histopathological changes in ankle and synovial tissues were evaluated using micro-computed tomography, hematoxylin and eosin staining, Safranin-O/Fast Green staining, tartrate resistant acid phosphatase staining, and immunohistochemistry. Fluorescence spectroscopy, circular dichroism, and surface plasmon resonance were employed to investigate interactions between praelolide and catalase. The production of inflammatory cytokines and expression levels of proteins were assessed using ELISA and Western blotting, respectively. RESULT Praelolide significantly reduced paw swelling and arthritis scores, improved gait deficits, and restored synovial histopathological alterations and bone erosion in CIA mice. In vivo and in vitro, praelolide effectively decreased the expression and production of inflammatory cytokines such as interleukin (IL)-1β and IL-6. Additionally, praelolide inhibited osteoclastogenesis on bone surface of the ankle joints and in a tumor necrosis factor-α (TNF-α)-induced MH7A/bone marrow-derived macrophages (BMMs) co-culture system, and it strongly suppressed reactive oxygen species (ROS) production. Mechanistically, praelolide modulated catalase through non-covalent interactions, inducing conformational alterations that enhanced catalase activity and stability against time- and temperature-induced degradation. Further investigation revealed that praelolide significantly upregulated the expression of Nrf2, subsequently activating downstream antioxidant enzymes. CONCLUSION Praelolide markedly alleviated synovial inflammation and bone destruction in CIA mice by enhancing catalase activity and activating the Nrf2 pathway to reduce disease-related ROS accumulation, highlighting praelolide as a promising candidate for multitarget treatment of RA.
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Affiliation(s)
- Xinyi Qi
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, PR China
| | - Junjun Meng
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, PR China
| | - Changhong Li
- Department of Rheumatology and Immunology, Peking University Third Hospital, Beijing 100191, PR China
| | - Wei Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, PR China
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, PR China
| | - Jian Huang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, PR China.
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, PR China; Institute of Ocean Research, Ningbo Institute of Marine Medicine, Peking University, Beijing, 100191, PR China.
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3
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Tamarín S, Galaz-Davison P, Ramírez-Sarmiento CA, Babul J, Medina E. Dissecting the structural and functional consequences of the evolutionary proline-glycine deletion in the wing 1 region of the forkhead domain of human FoxP1. FEBS Lett 2024; 598:2281-2291. [PMID: 38946055 DOI: 10.1002/1873-3468.14972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024]
Abstract
The human FoxP transcription factors dimerize via three-dimensional domain swapping, a unique feature among the human Fox family, as result of evolutionary sequence adaptations in the forkhead domain. This is the case for the conserved glycine and proline residues in the wing 1 region, which are absent in FoxP proteins but present in most of the Fox family. In this work, we engineered both glycine (G) and proline-glycine (PG) insertion mutants to evaluate the deletion events in FoxP proteins in their dimerization, stability, flexibility, and DNA-binding ability. We show that the PG insertion only increases protein stability, whereas the single glycine insertion decreases the association rate and protein stability and promotes affinity to the DNA ligand.
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Affiliation(s)
- Stephanie Tamarín
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, Talca, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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4
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Yagi S, Tagami S. An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins. Nat Commun 2024; 15:5938. [PMID: 39025855 PMCID: PMC11258233 DOI: 10.1038/s41467-024-50013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/25/2024] [Indexed: 07/20/2024] Open
Abstract
Numerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which these numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by double-psi β-barrels (DPBBs) conserved in DNA and RNA polymerases, and similar but topologically distinct six-stranded β-barrel RIFT or five-stranded β-barrel folds such as OB and SH3 in ribosomal proteins. Here, we discover that the previously reconstructed ancient DPBB sequence could also adopt a β-barrel fold named Double-Zeta β-barrel (DZBB), as a metamorphic protein. The DZBB fold is not found in any modern protein, although its structure shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be further converted into SH3 by circular-permutation as previously predicted. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution.
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Affiliation(s)
- Sota Yagi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Faculty of Human Sciences, Waseda University, 2-579-15, Mikajima, Tokorozawa, Saitama, 359-1192, Japan.
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Medicine, Science and Technology, Shinshu University, 3-1-1 Asahi, Matsumoto City, Nagano, 390-8621, Japan.
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM²), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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5
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Goto Y, Miyafusa T, Honda S. Designing monomeric IFNγ: The significance of domain-swapped dimer structure in IFNγ immune responses. J Biol Chem 2024; 300:107464. [PMID: 38879015 DOI: 10.1016/j.jbc.2024.107464] [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: 02/22/2024] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Interferon (IFN) γ can initiate immune responses by inducing the expression of major histocompatibility complex molecules, suggesting its potential for cancer immunotherapy. However, it also has an immunosuppressive function that limits its application as a therapeutic agent. IFNγ has a characteristic domain-swapped dimer structure with two of the six α-helices exchanged with each other. As we hypothesized that the contrasting functions of IFNγ could be attributed to its unique domain-swapped structure, we designed monomeric IFNγ by transforming the domain-swapped dimer structure of WT IFNγ. We conjectured the evolution of this domain-swapped dimer and hypothesized that the current IFNγ structure emerged through shortening of the loop structure at the base of the swapped domain and the accumulation of hydrophobic amino acids at the newly generated interface during domain-swapping. We then designed and generated a stable monomeric IFNγ by retracing this evolutionary process, complementing the lost loop structure with a linker, and replacing the accumulated hydrophobic amino acids with hydrophilic ones. We determined that the designed variant was a monomer based on molecular size and number of epitopes and exhibited activity in cell-based assays. Notably, the monomeric IFNγ showed a qualitatively similar balance between immunostimulatory and immunosuppressive gene expression as WT IFNγ. This study demonstrates that the structural format of IFNγ affects the strength of its activity rather than regulating the fate of downstream gene expression.
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Affiliation(s)
- Yota Goto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takamitsu Miyafusa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Shinya Honda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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Simpson GA, Rezende IF, da Silva Peixoto A, de Oliveira Soares IB, Barbosa JARG, de Freitas SM, Valadares NF. Crystal structure and interconversion of monomers and domain-swapped dimers of the walnut tree phytocystatin. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140975. [PMID: 38056804 DOI: 10.1016/j.bbapap.2023.140975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Biotechnological applications of phytocystatins have garnered significant interest due to their potential applications in crop protection and improve crop resistance to abiotic stress factors. Cof1 and Wal1 are phytocystatins derived from Coffea arabica and Juglans regia, respectively. These plants hold significant economic value due to coffee's global demand and the walnut tree's production of valuable timber and widely consumed walnuts with culinary and nutritional benefits. The study involved the heterologous expression in E. coli Lemo 21(DE3), purification by immobilized metal ion affinity and size exclusion chromatography, and biophysical characterization of both phytocystatins, focusing on isolating and interconverting their monomers and dimers. The crystal structure of the domain-swapped dimer of Wal1 was determined revealing two domain-swapped dimers in the asymmetric unit, an arrangement reminiscent of the human cystatin C structure. Alphafold models of monomers and Alphafold-Multimer models of domain-swapped dimers of Cof1 and Wal1 were analyzed in the context of the crystal structure. The methodology and data presented here contribute to a deeper understanding of the oligomerization mechanisms of phytocystatins and their potential biotechnological applications in agriculture.
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Affiliation(s)
- Gisele Alvarenga Simpson
- Laboratory of Molecular Biophysics, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Isabela Fernandes Rezende
- Laboratory of Molecular Biophysics, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Alencar da Silva Peixoto
- Laboratory of Molecular Biophysics, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | | | | | - Sônia Maria de Freitas
- Laboratory of Molecular Biophysics, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Napoleão Fonseca Valadares
- Laboratory of Molecular Biophysics, Department of Cellular Biology, University of Brasília, Brasília, Brazil..
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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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8
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Noro I, Bettin I, Fasoli S, Smania M, Lunardi L, Giannini M, Andreoni L, Montioli R, Gotte G. Human RNase 1 can extensively oligomerize through 3D domain swapping thanks to the crucial contribution of its C-terminus. Int J Biol Macromol 2023; 249:126110. [PMID: 37536419 DOI: 10.1016/j.ijbiomac.2023.126110] [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: 04/24/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Human ribonuclease (RNase) 1 and bovine RNase A are the proto-types of the secretory "pancreatic-type" (pt)-RNase super-family. RNase A can oligomerize through the 3D domain swapping (DS) mechanism upon acetic acid (HAc) lyophilisation, producing enzymatically active oligomeric conformers by swapping both N- and C-termini. Also some RNase 1 mutants were found to self-associate through 3D-DS, however forming only N-swapped dimers. Notably, enzymatically active dimers and larger oligomers of wt-RNase 1 were collected here, in higher amount than RNase A, from HAc lyophilisation. In particular, RNase 1 self-associates through the 3D-DS of its N-terminus and, at a higher extent, of the C-terminus. Since RNase 1 is four-residues longer than RNase A, we further analyzed its oligomerization tendency in a mutant lacking the last four residues. The C-terminus role has been investigated also in amphibian onconase (ONC®), a pt-RNase that can form only a N-swapped dimer, since its C-terminus, that is three-residues longer than RNase A, is locked by a disulfide bond. While ONC mutants designed to unlock or cut this constraint were almost unable to dimerize, the RNase 1 mutant self-associated at a higher extent than the wt, suggesting a specific role of the C-terminus in the oligomerization of different RNases. Overall, RNase 1 reaches here the highest ability, among pt-RNases, to extensively self-associate through 3D-DS, paving the way for new investigations on the structural and biological properties of its oligomers.
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Affiliation(s)
- Irene Noro
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Ilaria Bettin
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Sabrina Fasoli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Marcello Smania
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Luca Lunardi
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Michele Giannini
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Leonardo Andreoni
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Riccardo Montioli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
| | - Giovanni Gotte
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
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Stańczykiewicz B, Łuc M, Banach M, Zabłocka A. Cystatins: unravelling the biological implications for neuroprotection. Arch Med Sci 2023; 20:157-166. [PMID: 38414464 PMCID: PMC10895963 DOI: 10.5114/aoms/171706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/31/2023] [Indexed: 02/29/2024] Open
Abstract
Cystatins, a family of proteins known for their inhibitory role against cysteine proteases, have garnered significant attention in the field of neurodegeneration. Numerous genetic, experimental, and clinical studies concerning cystatin C suggest it plays an important role in the course of neurodegenerative diseases. Its beneficial effects are associated with cysteine protease inhibition, impact on β-amyloid aggregation, as well as regulation of cell proliferation, autophagy, and apoptosis. Cystatin isolated from chicken egg white, called ovocystatin, has been widely used in medical and pharmaceutical research due to its structural and biological similarities to human cystatin C. This article focuses on the potential use of cystatins, with special emphasis on easily obtained ovocystatin, in the treatment of neurodegenerative diseases, such as dementia. The current evidence on cystatin use has shed light on its mechanisms of action and therapeutic implications for neuroprotection and maintenance of cognitive functions.
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Affiliation(s)
- Bartłomiej Stańczykiewicz
- Division of Consultation Psychiatry and Neuroscience, Department of Psychiatry, Wroclaw Medical University, Wroclaw, Poland
| | - Mateusz Łuc
- Division of Consultation Psychiatry and Neuroscience, Department of Psychiatry, Wroclaw Medical University, Wroclaw, Poland
| | - Maciej Banach
- Department of Preventive Cardiology and Lipidology, Medical University of Lodz, Lodz, Poland
| | - Agnieszka Zabłocka
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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Coñuecar R, Asela I, Rivera M, Galaz-Davison P, González-Higueras J, Hamilton GL, Engelberger F, Ramírez-Sarmiento CA, Babul J, Sanabria H, Medina E. DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 2023; 26:107228. [PMID: 37485372 PMCID: PMC10362293 DOI: 10.1016/j.isci.2023.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
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Affiliation(s)
- Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - George L. Hamilton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Felipe Engelberger
- Institute for Drug Discovery, Leipzig University Medical School, 04107 Leipzig, Germany
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
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11
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Villalobos P, Carvajal AI, Castro-Fernández V, Babul J, Ramírez-Sarmiento CA, Medina E. Unraveling the folding and dimerization properties of the human FoxP subfamily of transcription factors. FEBS Lett 2023; 597:1894-1905. [PMID: 37199668 DOI: 10.1002/1873-3468.14665] [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: 03/29/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Human FoxP proteins share a highly conserved DNA-binding domain that dimerizes via three-dimensional domain swapping, although showing varying oligomerization propensities among its members. Here, we present an experimental and computational characterization of all human FoxP proteins to unravel how their amino acid substitutions impact their folding and dimerization mechanism. We solved the crystal structure of the forkhead domain of FoxP4 to then perform a comparison across all members, finding that their sequence changes impact not only the structural heterogeneity of their forkhead domains but also the protein-protein association energy barrier. Lastly, we demonstrate that the accumulation of a monomeric intermediate is an oligomerization-dependent feature rather than a common aspect of monomers and dimers in this protein subfamily.
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Affiliation(s)
- Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alonso I Carvajal
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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12
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Kim D, Na Y, Chang H, Boo J, Kang S, Jin C, Kang S, Lee SY, Lee B. Domain swapping of the C-terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis. Protein Sci 2023; 32:e4644. [PMID: 37070717 PMCID: PMC10182728 DOI: 10.1002/pro.4644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/22/2023] [Accepted: 04/16/2023] [Indexed: 04/19/2023]
Abstract
Polyketide metabolism-associated proteins in Mycobacterium tuberculosis play an essential role in the survival of the bacterium, which makes them potential drug targets for the treatment of tuberculosis (TB). The novel ribonuclease protein Rv1546 is predicted to be a member of the steroidogenic acute regulatory protein-related lipid-transfer (START) domain superfamily, which comprises bacterial polyketide aromatase/cyclases (ARO/CYCs). Here, we determined the crystal structure of Rv1546 in a V-shaped dimer. The Rv1546 monomer consists of four α-helices and seven antiparallel β-strands. Interestingly, in the dimeric state, Rv1546 forms a helix-grip fold, which is present in START domain proteins, via three-dimensional domain swapping. Structural analysis revealed that the conformational change of the C-terminal α-helix of Rv1546 might contribute to the unique dimer structure. Site-directed mutagenesis followed by in vitro ribonuclease activity assays was performed to identify catalytic sites of the protein. This experiment suggested that surface residues R63, K84, K88, and R113 are important in the ribonuclease function of Rv1546. In summary, this study presents the structural and functional characterization of Rv1546 and supplies new perspectives for exploiting Rv1546 as a novel drug target for TB treatment.
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Affiliation(s)
- Do‐Hee Kim
- Jeju Research Institute of Pharmaceutical SciencesCollege of Pharmacy, Jeju National UniversityJejuKorea
- Interdisciplinary Graduate Program in Advanced Convergence Technology and ScienceJeju National UniversityJejuKorea
| | - Youngseo Na
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Heesun Chang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Jun‐Hyuk Boo
- Jeju Research Institute of Pharmaceutical SciencesCollege of Pharmacy, Jeju National UniversityJejuKorea
| | - Sung‐Min Kang
- College of Pharmacy, Duksung Women's UniversitySeoulKorea
| | - Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Su‐Jin Kang
- College of Pharmacy, Dongduk Women's UniversitySeoulKorea
| | - Su Yeon Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Bong‐Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
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13
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Guffy SL, Pulavarti SVSRK, Harrison J, Fleming D, Szyperski T, Kuhlman B. Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry 2023; 62:770-781. [PMID: 36634348 PMCID: PMC9939277 DOI: 10.1021/acs.biochem.2c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The de novo design of functional proteins requires specification of tertiary structure and incorporation of molecular binding sites. Here, we develop an inside-out design strategy in the molecular modeling program Rosetta that begins with amino acid side chains from one or two α-helices making well-defined contacts with a ligand. A full-sized protein is then built around the ligand by adding additional helices that promote the formation of a protein core and allow additional contacts with the ligand. The protocol was tested by designing 12 zinc-binding proteins, each with 4-5 helices. Four of the designs were folded and bound to zinc with equilibrium dissociation constants varying between 95 nM and 1.1 μM. The design with the tightest affinity for zinc, N12, adopts a unique conformation in the folded state as assessed with nuclear magnetic resonance (NMR) and the design model closely matches (backbone root-mean-square deviation (RMSD) < 1 Å) an AlphaFold model of the sequence. Retrospective analysis with AlphaFold suggests that the sequences of many of the failed designs did not encode the desired tertiary packing.
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Affiliation(s)
- Sharon L. Guffy
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Joseph Harrison
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Drew Fleming
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Thomas Szyperski
- Department of Chemistry, State University of New York, Buffalo, NY, 14260, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
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14
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Michel F, Shanmugaratnam S, Romero-Romero S, Höcker B. Structures of permuted halves of a modern ribose-binding protein. Acta Crystallogr D Struct Biol 2023; 79:40-49. [PMID: 36601806 PMCID: PMC9815098 DOI: 10.1107/s205979832201186x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer-dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold type I conformations with structural deviations from modern RBPs. One of the half variants forms a dimer via segment swapping, suggesting a high degree of malleability. The structural findings on these permuted halves support the evolutionary hypothesis that PBPs arose via a duplication event of a flavodoxin-like protein and further support a domain-swapping step that might have occurred during the evolution of the PBP-like fold, a process that is necessary to generate the characteristic motion of PBPs essential to perform their functions.
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Affiliation(s)
- Florian Michel
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | | | | | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany,Correspondence e-mail:
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15
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Zhu X, Wang J, Jia Z, Feng J, Wang B, Wang Z, Liu Q, Wu K, Huang W, Zhao X, Dang H, Zou J. Novel Dimeric Architecture of an IFN-γ-Related Cytokine Provides Insights into Subfunctionalization of Type II IFNs in Teleost Fish. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2203-2214. [PMID: 36426983 DOI: 10.4049/jimmunol.2200334] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/06/2022] [Indexed: 01/04/2023]
Abstract
Gene duplication leads to subfunctionalization of paralogs. In mammals, IFN-γ is the sole member of the type II IFN family and binds to a receptor complex consisting of IFN-γR1 and IFN-γR2. In teleost fish, IFN-γ and its receptors have been duplicated due to the teleost-specific whole-genome duplication event. In this study, the functions of an IFN-γ-related (IFN-γrel) cytokine were found to be partially retained relative to IFN-γ in grass carp (Ctenopharyngodon idella [CiIFN-γrel]). CiIFN-γrel upregulated the expression of proinflammatory genes but had lost the ability to activate genes involved in Th1 response. The results suggest that CiIFN-γrel could have been subfunctionalized from CiIFN-γ. Moreover, CiIFN-γrel induced STAT1 phosphorylation via interaction with duplicated homologs of IFN-γR1 (cytokine receptor family B [CRFB] 17 and CRFB13). Strikingly, CiIFN-γrel did not bind to the IFN-γR2 homolog (CRFB6). To gain insight into the subfunctionalization, the crystal structure of CiIFN-γrel was solved at 2.26 Å, revealing that it forms a homodimer that is connected by two pairs of disulfide bonds. Due to the spatial positions of helix A, loop AB, and helix B, CiIFN-γrel displays a unique topology that requires elements from two identical monomers to form a unit that is similar to IFN-γ. Further, mutagenesis analyses identified key residues interacting with CiIFN-γrel receptors and those required for the biological functions. Our study can help understand the subfunctionalization of duplicated IFN-γ paralogs in fish.
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Affiliation(s)
- Xiaozhen Zhu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Junya Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Zhao Jia
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Jianhua Feng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Bangjie Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Zixuan Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Qin Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Kaizheng Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Wenji Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xin Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Huifeng Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China; and.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Schutt CE, Karlén M, Karlsson R. A structural model of the profilin-formin pacemaker system for actin filament elongation. Sci Rep 2022; 12:20515. [PMID: 36443454 PMCID: PMC9705415 DOI: 10.1038/s41598-022-25011-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The formins constitute a large class of multi-domain polymerases that catalyze the localization and growth of unbranched actin filaments in cells from yeast to mammals. The conserved FH2 domains form dimers that bind actin at the barbed end of growing filaments and remain attached as new subunits are added. Profilin-actin is recruited and delivered to the barbed end by formin FH1 domains via the binding of profilin to interspersed tracts of poly-L-proline. We present a structural model showing that profilin-actin can bind the FH2 dimer at the barbed end stabilizing a state where profilin prevents its associated actin subunit from directly joining the barbed end. It is only with the dissociation of profilin from the polymerase that an actin subunit rotates and docks into its helical position, consistent with observations that under physiological conditions optimal elongation rates depend on the dissociation rate of profilin, independently of cellular concentrations of actin subunits.
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Affiliation(s)
- Clarence E. Schutt
- grid.16750.350000 0001 2097 5006Department of Chemistry, Princeton University, Princeton, NJ USA
| | | | - Roger Karlsson
- Department of Molecular Biosciences, WGI, Stockholm University, Stockholm, Sweden.
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17
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Slow Evolution toward “Super-Aggregation” of the Oligomers Formed through the Swapping of RNase A N-Termini: A Wish for Amyloidosis? Int J Mol Sci 2022; 23:ijms231911192. [PMID: 36232496 PMCID: PMC9569824 DOI: 10.3390/ijms231911192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Natively monomeric RNase A can oligomerize upon lyophilization from 40% acetic acid solutions or when it is heated at high concentrations in various solvents. In this way, it produces many dimeric or oligomeric conformers through the three-dimensional domain swapping (3D-DS) mechanism involving both RNase A N- or/and C-termini. Here, we found many of these oligomers evolving toward not negligible amounts of large derivatives after being stored for up to 15 months at 4 °C in phosphate buffer. We call these species super-aggregates (SAs). Notably, SAs do not originate from native RNase A monomer or from oligomers characterized by the exclusive presence of the C-terminus swapping of the enzyme subunits as well. Instead, the swapping of at least two subunits’ N-termini is mandatory to produce them. Through immunoblotting, SAs are confirmed to derive from RNase A even if they retain only low ribonucleolytic activity. Then, their interaction registered with Thioflavin-T (ThT), in addition to TEM analyses, indicate SAs are large and circular but not “amyloid-like” derivatives. This confirms that RNase A acts as an “auto-chaperone”, although it displays many amyloid-prone short segments, including the 16–22 loop included in its N-terminus. Therefore, we hypothesize the opening of RNase A N-terminus, and hence its oligomerization through 3D-DS, may represent a preliminary step favoring massive RNase A aggregation. Interestingly, this process is slow and requires low temperatures to limit the concomitant oligomers’ dissociation to the native monomer. These data and the hypothesis proposed are discussed in the light of protein aggregation in general, and of possible future applications to contrast amyloidosis.
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18
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Sievers K, Ficner R. Structure of angiogenin dimer bound to double-stranded RNA. Acta Crystallogr F Struct Biol Commun 2022; 78:330-337. [PMID: 36048083 PMCID: PMC9435672 DOI: 10.1107/s2053230x22008317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/20/2022] [Indexed: 11/23/2022] Open
Abstract
Angiogenin is an unusual member of the RNase A family and is of great interest in multiple pathological contexts. Although it has been assigned various regulatory roles, its core catalytic function is that of an RNA endonuclease. However, its catalytic efficiency is comparatively low and this has been linked to a unique C-terminal helix which partially blocks its RNA-binding site. Assuming that binding to its RNA substrate could trigger a conformational rearrangement, much speculation has arisen on the topic of the interaction of angiogenin with RNA. To date, no structural data on angiogenin-RNA interactions have been available. Here, the structure of angiogenin bound to a double-stranded RNA duplex is reported. The RNA does not reach the active site of angiogenin and no structural arrangement of the C-terminal domain is observed. However, angiogenin forms a previously unobserved crystallographic dimer that makes several backbone interactions with the major and minor grooves of the RNA double helix.
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Affiliation(s)
- Katharina Sievers
- Department for Molecular Structural Biology, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department for Molecular Structural Biology, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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19
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Ch'ng ACW, Schepergerdes L, Choong YS, Hust M, Lim TS. Antimicrobial antibodies by phage display: Identification of antibody-based inhibitor against mycobacterium tuberculosis isocitrate lyase. Mol Immunol 2022; 150:47-57. [PMID: 35987135 DOI: 10.1016/j.molimm.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/23/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
The increasing incidence reports of antibiotic resistance highlights the need for alternative approaches to deal with bacterial infections. This brought about the idea of utilizing monoclonal antibodies as an alternative antibacterial treatment. Majority of the studies are focused on developing antibodies to bacterial surface antigens, with little emphasis on antibodies that inhibit the growth mechanisms of a bacteria host. Isocitrate lyase (ICL) is an important enzyme for the growth and survival of Mycobacterium tuberculosis (MTB) during latent infection as a result of its involvement in the mycobacterial glyoxylate and methylisocitrate cycles. It is postulated that the inhibition of ICL can disrupt the life cycle of MTB. To this extent, we utilized antibody phage display to identify a single chain fragment variable (scFv) antibody against the recombinant ICL protein from MTB. The soluble a-ICL-C6 scFv clone exhibited good binding characteristics with high specificity against ICL. More importantly, the clone exhibited in vitro inhibitory effect with an enzymatic assay resulting in a decrease of ICL enzymatic activity. In silico analysis showed that the scFv-ICL interactions are driven by 23 hydrogen bonds and 13 salt bridges that might disrupt the formation of ICL subunits for the tertiary structure or the formation of active site β domain. However, further validation is necessary to confirm if the isolated clone is indeed a good inhibitor against ICL for application against MTB.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Lena Schepergerdes
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, 38106 Braunschweig
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, 38106 Braunschweig
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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20
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Medved L, Weisel JW. The Story of the Fibrin(ogen) αC-Domains: Evolution of Our View on Their Structure and Interactions. Thromb Haemost 2022; 122:1265-1278. [PMID: 34902868 PMCID: PMC10658776 DOI: 10.1055/a-1719-5584] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Although much has been established concerning the overall structure and function of fibrinogen, much less has been known about its two αC regions, each consisting of an αC-connector and an αC-domain, but new information has been accumulating. This review summarizes the state of our current knowledge of the structure and interactions of fibrinogen's αC regions. A series of studies with isolated αC regions and their fragments demonstrated that the αC-domain forms compact ordered structures consisting of N- and C-terminal subdomains including β sheets and suggested that the αC-connector has a poly(L-proline) type II structure. Functionally, the αC-domains interact intramolecularly with each other and with the central region of the molecule, first demonstrated by electron microscopy and then quantified by optical trap force spectroscopy. Upon conversion of fibrinogen into fibrin, the αC-domains switch from intra- to intermolecular interactions to form ordered αC polymers. The formation of αC polymers occurs mainly through the homophilic interaction between the N-terminal subdomains; interaction between the C-terminal subdomains and the αC-connectors also contributes to this process. Considerable evidence supports the idea that the αC-regions accelerate fibrin polymerization and affect the final structure of fibrin clots. The interactions between αC-regions are important for the mechanical properties of clots, increasing their stiffness and extensibility. Conversion of fibrinogen into fibrin results in exposure of multiple binding sites in its αC regions, providing interaction of fibrin with different proteins and cell types during hemostasis and wound healing. This heretofore mysterious part of the fibrinogen molecule is finally giving up its secrets.
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Affiliation(s)
- Leonid Medved
- Center for Vascular and Inflammatory Diseases and the Department of Biochemistry, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - John W. Weisel
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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21
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Scalone E, Broggini L, Visentin C, Erba D, Bačić Toplek F, Peqini K, Pellegrino S, Ricagno S, Paissoni C, Camilloni C. Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution. Proc Natl Acad Sci U S A 2022; 119:e2203181119. [PMID: 35737839 PMCID: PMC9245614 DOI: 10.1073/pnas.2203181119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/17/2022] [Indexed: 12/25/2022] Open
Abstract
Protein aggregation into amyloid fibrils is the archetype of aberrant biomolecular self-assembly processes, with more than 50 associated diseases that are mostly uncurable. Understanding aggregation mechanisms is thus of fundamental importance and goes in parallel with the structural characterization of the transient oligomers formed during the process. Oligomers have been proven elusive to high-resolution structural techniques, while the large sizes and long time scales, typical of aggregation processes, have limited the use of computational methods to date. To surmount these limitations, we here present multi-eGO, an atomistic, hybrid structure-based model which, leveraging the knowledge of monomers conformational dynamics and of fibril structures, efficiently captures the essential structural and kinetics aspects of protein aggregation. Multi-eGO molecular dynamics simulations can describe the aggregation kinetics of thousands of monomers. The concentration dependence of the simulated kinetics, as well as the structural features of the resulting fibrils, are in qualitative agreement with in vitro experiments carried out on an amyloidogenic peptide from Transthyretin, a protein responsible for one of the most common cardiac amyloidoses. Multi-eGO simulations allow the formation of primary nuclei in a sea of transient lower-order oligomers to be observed over time and at atomic resolution, following their growth and the subsequent secondary nucleation events, until the maturation of multiple fibrils is achieved. Multi-eGO, combined with the many experimental techniques deployed to study protein aggregation, can provide the structural basis needed to advance the design of molecules targeting amyloidogenic diseases.
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Affiliation(s)
- Emanuele Scalone
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Luca Broggini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
| | - Cristina Visentin
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
| | - Davide Erba
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Fran Bačić Toplek
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Kaliroi Peqini
- Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Sara Pellegrino
- Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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22
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Role of the Ribonuclease ONCONASE in miRNA Biogenesis and tRNA Processing: Focus on Cancer and Viral Infections. Int J Mol Sci 2022; 23:ijms23126556. [PMID: 35742999 PMCID: PMC9223570 DOI: 10.3390/ijms23126556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 12/23/2022] Open
Abstract
The majority of transcribed RNAs do not codify for proteins, nevertheless they display crucial regulatory functions by affecting the cellular protein expression profile. MicroRNAs (miRNAs) and transfer RNA-derived small RNAs (tsRNAs) are effectors of interfering mechanisms, so that their biogenesis is a tightly regulated process. Onconase (ONC) is an amphibian ribonuclease known for cytotoxicity against tumors and antiviral activity. Additionally, ONC administration in patients resulted in clinical effectiveness and in a well-tolerated feature, at least for lung carcinoma and malignant mesothelioma. Moreover, the ONC therapeutic effects are actually potentiated by cotreatment with many conventional antitumor drugs. This review not only aims to describe the ONC activity occurring either in different tumors or in viral infections but also to analyze the molecular mechanisms underlying ONC pleiotropic and cellular-specific effects. In cancer, data suggest that ONC affects malignant phenotypes by generating tRNA fragments and miRNAs able to downregulate oncogenes expression and upregulate tumor-suppressor proteins. In cells infected by viruses, ONC hampers viral spread by digesting the primer tRNAs necessary for viral DNA replication. In this scenario, new therapeutic tools might be developed by exploiting the action of ONC-elicited RNA derivatives.
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23
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Identification of a Steric Zipper Motif in the Amyloidogenic Core of Human Cystatin C and Its Use for the Design of Self-Assembling Peptides. Int J Mol Sci 2022; 23:ijms23105800. [PMID: 35628610 PMCID: PMC9147961 DOI: 10.3390/ijms23105800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/14/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
Amyloid fibrils have been known for many years. Unfortunately, their fame stems from negative aspects related to amyloid diseases. Nevertheless, due to their properties, they can be used as interesting nanomaterials. Apart from their remarkable stability, amyloid fibrils may be regarded as a kind of a storage medium and as a source of active peptides. In many cases, their structure may guarantee a controlled and slow release of peptides in their active form; therefore, they can be used as a potential nanomaterial in drug delivery systems. In addition, amyloid fibrils display controllable stiffness, flexibility, and satisfactory mechanical strength. In addition, they can be modified and functionalized very easily. Understanding the structure and genesis of amyloid assemblies derived from a broad range of amyloidogenic proteins could help to better understand and use this unique material. One of the factors responsible for amyloid aggregation is the steric zipper. Here, we report the discovery of steric zipper-forming peptides in the sequence of the amyloidogenic protein, human cystatin C (HCC). The ability of short peptides derived from this fragment of HCC to form fibrillar structures with defined self-association characteristics and the factors influencing this aggregation are also presented in this paper.
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24
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Tenorio CA, Parker JB, Blaber M. Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways. Protein Sci 2022; 31:e4301. [PMID: 35481645 PMCID: PMC8996475 DOI: 10.1002/pro.4301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/02/2023]
Abstract
Successful de novo protein design ideally targets specific folding kinetics, stability thermodynamics, and biochemical functionality, and the simultaneous achievement of all these criteria in a single step design is challenging. Protein design is potentially simplified by separating the problem into two steps: (a) an initial design of a protein "scaffold" having appropriate folding kinetics and stability thermodynamics, followed by (b) appropriate functional mutation-possibly involving insertion of a peptide functional "cassette." This stepwise approach can also separate the orthogonal effects of the "stability/function" and "foldability/function" tradeoffs commonly observed in protein design. If the scaffold is a protein architecture having an exact rotational symmetry, then there is the potential for redundant folding nuclei and multiple equivalent sites of functionalization; thereby enabling broader functional adaptation. We describe such a "scaffold" and functional "cassette" design strategy applied to a β-trefoil threefold symmetric architecture and a heparin ligand functionality. The results support the availability of redundant folding nuclei within this symmetric architecture, and also identify a minimal peptide cassette conferring heparin affinity. The results also identify an energy barrier of destabilization that switches the protein folding pathway from monomeric to trimeric, thereby identifying another potential advantage of symmetric protein architecture in de novo design.
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Affiliation(s)
- Connie A. Tenorio
- Department of Biomedical SciencesFlorida State UniversityTallahasseeFloridaUSA
| | - Joseph B. Parker
- Department of Biomedical SciencesFlorida State UniversityTallahasseeFloridaUSA
| | - Michael Blaber
- Department of Biomedical SciencesFlorida State UniversityTallahasseeFloridaUSA
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25
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Sagar V, Wistow G. Acquired disorder and asymmetry in a domain-swapped model for γ-crystallin aggregation. J Mol Biol 2022; 434:167559. [PMID: 35341744 PMCID: PMC9050881 DOI: 10.1016/j.jmb.2022.167559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/19/2022]
Abstract
Misfolding and aggregation of proteins occur in many pathological states. Because of the inherent disorder involved, these processes are difficult to study. We attempted to capture aggregation intermediates of γ S-crystallin, a highly stable, internally symmetrical monomeric protein, by crystallization under mildly acidic and oxidizing conditions. Here we describe novel oligomerization through strained domain-swapping and partial intermolecular disulfide formation. This forms an octamer built from asymmetric tetramers, each of which comprises an asymmetric pair of twisted, domain-swapped dimers. Each tetramer shows patterns of acquired disorder among subunits, ranging from local loss of secondary structure to regions of intrinsic disorder. The octamer ring is tied together by partial intermolecular disulfide bonds, which may contribute to strain and disorder in the octamer. Oligomerization in this structure is self-limited by the distorted octamer ring. In a more heterogeneous environment, the disordered regions could serve as seeds for cascading interactions with other proteins. Indeed, solubilized protein from crystals retain many features observed in the crystal and are prone to further oligomerization and precipitation. This structure illustrates modes of loss of organized structure and aggregation that are relevant for cataract and for other disorders involving deposition of formerly well-folded proteins.
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Affiliation(s)
- Vatsala Sagar
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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26
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Natural Receptor- and Ligand-Based Chimeric Antigen Receptors: Strategies Using Natural Ligands and Receptors for Targeted Cell Killing. Cells 2021; 11:cells11010021. [PMID: 35011583 PMCID: PMC8750724 DOI: 10.3390/cells11010021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/29/2021] [Accepted: 12/04/2021] [Indexed: 12/29/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has been widely successful in the treatment of B-cell malignancies, including B-cell lymphoma, mantle cell lymphoma, and multiple myeloma; and three generations of CAR designs have led to effective FDA approved therapeutics. Traditionally, CAR antigen specificity is derived from a monoclonal antibody where the variable heavy (VH) and variable light (VL) chains are connected by a peptide linker to form a single-chain variable fragment (scFv). While this provides a level of antigen specificity parallel to that of an antibody and has shown great success in the clinic, this design is not universally successful. For instance, issues of stability, immunogenicity, and antigen escape hinder the translational application of some CARs. As an alternative, natural receptor- or ligand-based designs may prove advantageous in some circumstances compared to scFv-based designs. Herein, the advantages and disadvantages of scFv-based and natural receptor- or ligand-based CAR designs are discussed. In addition, several translational aspects of natural receptor- and ligand-based CAR approaches that are being investigated in preclinical and clinical studies will be examined.
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27
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Yuan Z, Qu Z, Duan B, Wang T, Xu J, Xia B. Is amyloid fibrillation related to 3D domain swapping for the C-terminal domain of SARS-CoV main protease? Int J Biol Macromol 2021; 197:68-76. [PMID: 34953805 PMCID: PMC8694786 DOI: 10.1016/j.ijbiomac.2021.12.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/02/2021] [Accepted: 12/12/2021] [Indexed: 12/02/2022]
Abstract
The C-terminal domain of SARS-CoV main protease (Mpro-C) can form 3D domain-swapped dimer by exchanging the α1-helices fully buried inside the protein hydrophobic core, under non-denaturing conditions. Here, we report that Mpro-C can also form amyloid fibrils under the 3D domain-swappable conditions in vitro, and the fibrils are not formed through runaway/propagated domain swapping. It is found that there are positive correlations between the rates of domain swapping dimerization and amyloid fibrillation at different temperatures, and for different mutants. However, some Mpro-C mutants incapable of 3D domain swapping can still form amyloid fibrils, indicating that 3D domain swapping is not essential for amyloid fibrillation. Furthermore, NMR H/D exchange data and molecular dynamics simulation results suggest that the protofibril core region tends to unpack at the early stage of 3D domain swapping, so that the amyloid fibrillation can proceed during the 3D domain swapping process. We propose that 3D domain swapping makes it possible for the unpacking of the amyloidogenic fragment of the protein and thus accelerates the amyloid fibrillation process kinetically, which explains the well-documented correlations between amyloid fibrillation and 3D domain swapping observed in many proteins.
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Affiliation(s)
- Zhiliang Yuan
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhi Qu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bo Duan
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tianyi Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiajun Xu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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28
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Gotte G, Campagnari R, Loreto D, Bettin I, Calzetti F, Menegazzi M, Merlino A. The crystal structure of the domain-swapped dimer of onconase highlights some catalytic and antitumor activity features of the enzyme. Int J Biol Macromol 2021; 191:560-571. [PMID: 34563576 DOI: 10.1016/j.ijbiomac.2021.09.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Onconase (ONC) is a monomeric amphibian "pancreatic-type" RNase endowed with remarkable anticancer activity. ONC spontaneously forms traces of a dimer (ONC-D) in solution, while larger amounts can be formed when ONC is lyophilized from mildly acidic solutions. Here, we report the crystal structure of ONC-D and analyze its catalytic and antitumor activities in comparison to ONC. ONC-D forms via the three-dimensional swapping of the N-terminal α-helix between two monomers, but it displays a significantly different quaternary structure from that previously modeled [Fagagnini A et al., 2017, Biochem J 474, 3767-81], and based on the crystal structure of the RNase A N-terminal swapped dimer. ONC-D presents a variable quaternary assembly deriving from a variable open interface, while it retains a catalytic activity that is similar to that of ONC. Notably, ONC-D displays antitumor activity against two human melanoma cell lines, although it exerts a slightly lower cytostatic effect than the monomer. The inhibition of melanoma cell proliferation by ONC or ONC-D is associated with the reduction of the expression of the anti-apoptotic B cell lymphoma 2 (Bcl2), as well as of the total expression and phosphorylation of the Signal Transducer and Activator of Transcription (STAT)-3. Phosphorylation is inhibited in both STAT3 Tyr705 and Ser727 key-residues, as well as in its upstream tyrosine-kinase Src. Consequently, both ONC species should exert their anti-cancer action by inhibiting the pro-tumor pleiotropic STAT3 effects deriving either by its phospho-tyrosine activation or by its non-canonical signaling pathways. Both ONC species, indeed, increase the portion of A375 cells undergoing apoptotic cell death. This study expands the variety of RNase domain-swapped dimeric structures, underlining the unpredictability of the open interface arrangement upon domain swapping. Structural data also offer valuable insights to analyze the differences in the measured ONC or ONC-D biological activities.
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Affiliation(s)
- Giovanni Gotte
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
| | - Rachele Campagnari
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Domenico Loreto
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy
| | - Ilaria Bettin
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Federica Calzetti
- Department of Medicine, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Marta Menegazzi
- Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy.
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29
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Bustamante A, Rivera R, Floor M, Babul J, Baez M. Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein. Biophys J 2021; 120:4809-4818. [PMID: 34555362 PMCID: PMC8595740 DOI: 10.1016/j.bpj.2021.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/15/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Domain swapping is a mechanism of protein oligomerization by which two or more subunits exchange structural elements to generate an intertwined complex. Numerous studies support a diversity of swapping mechanisms in which structural elements can be exchanged at different stages of the folding pathway of a subunit. Here, we used single-molecule optical tweezers technique to analyze the swapping mechanism of the forkhead DNA-binding domain of human transcription factor FoxP1. FoxP1 populates folded monomers in equilibrium with a swapped dimer. We generated a fusion protein linking two FoxP1 domains in tandem to obtain repetitive mechanical folding and unfolding trajectories. Thus, by stretching the same molecule several times, we detected either the independent folding of each domain or the elusive swapping step between domains. We found that a swapped dimer can be formed directly from fully or mostly folded monomer. In this situation, the interaction between the monomers in route to the domain-swapped dimer is the rate-limiting step. This approach is a useful strategy to test the different proposed domain swapping mechanisms for proteins with relevant physiological functions.
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Affiliation(s)
- Andres Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Rodrigo Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Martin Floor
- Bioinformatics and Medical Statistics Group, Faculty of Science and Technology, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain; Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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30
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Chen TR, Lin YC, Huang YW, Chen CC, Lo WC. CirPred, the first structure modeling and linker design system for circularly permuted proteins. BMC Bioinformatics 2021; 22:494. [PMID: 34641789 PMCID: PMC8513176 DOI: 10.1186/s12859-021-04403-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Background This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors.
Results Here we present CirPred, a structure modeling and termini linker design method for circularly permuted proteins. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling. CirPred performs well when the permutant shares low sequence identity with the native protein and even when the permutant adopts a different conformation from the native protein because of three-dimensional (3D) domain swapping. Linker redesign experiments demonstrated that the linker design algorithm of CirPred achieved subangstrom accuracy. Conclusions The CirPred system is capable of (1) predicting the structure of circular permutants, (2) designing termini linkers, (3) performing traditional co-linear protein structure modeling, and (4) identifying the CP-induced occurrence of 3D domain swapping. This method is supposed helpful for broadening the application of CP, and its web server is available at http://10.life.nctu.edu.tw/CirPred/ and http://lo.life.nctu.edu.tw/CirPred/. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04403-1.
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Affiliation(s)
- Teng-Ruei Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yen-Cheng Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Wei Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wei-Cheng Lo
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan. .,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan. .,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan. .,The Center for Bioinformatics Research, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
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31
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Markova K, Kunka A, Chmelova K, Havlasek M, Babkova P, Marques SM, Vasina M, Planas-Iglesias J, Chaloupkova R, Bednar D, Prokop Z, Damborsky J, Marek M. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Klara Markova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Klaudia Chmelova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Martin Havlasek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petra Babkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sérgio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Enantis Ltd., Kamenice 771/34, 625 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping. Int J Mol Sci 2021; 22:ijms221910296. [PMID: 34638644 PMCID: PMC8508939 DOI: 10.3390/ijms221910296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/18/2023] Open
Abstract
The association of two or more proteins to adopt a quaternary complex is one of the most widespread mechanisms by which protein function is modulated. In this scenario, three-dimensional domain swapping (3D-DS) constitutes one plausible pathway for the evolution of protein oligomerization that exploits readily available intramolecular contacts to be established in an intermolecular fashion. However, analysis of the oligomerization kinetics and thermodynamics of most extant 3D-DS proteins shows its dependence on protein unfolding, obscuring the elucidation of the emergence of 3D-DS during evolution, its occurrence under physiological conditions, and its biological relevance. Here, we describe the human FoxP subfamily of transcription factors as a feasible model to study the evolution of 3D-DS, due to their significantly faster dissociation and dimerization kinetics and lower dissociation constants in comparison to most 3D-DS models. Through the biophysical and functional characterization of FoxP proteins, relevant structural aspects highlighting the evolutionary adaptations of these proteins to enable efficient 3D-DS have been ascertained. Most biophysical studies on FoxP suggest that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling its fast oligomerization under physiological conditions. Moreover, comparison of biophysical parameters between human FoxP proteins in the context of their minute sequence differences suggests differential evolutionary strategies to favor homoassociation and presages the possibility of heteroassociations, with direct impacts in their gene regulation function.
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33
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Tran LH, Urbanowicz A, Jasiński M, Jaskolski M, Ruszkowski M. 3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:756341. [PMID: 34630499 PMCID: PMC8498639 DOI: 10.3389/fpls.2021.756341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Cytokinins are phytohormones regulating many biological processes that are vital to plants. CYTOKININ RESPONSE1 (CRE1), the main cytokinin receptor, has a modular architecture composed of a cytokinin-binding CHASE (Cyclases/Histidine kinases Associated Sensory Extracellular) domain, followed by a transmembrane fragment, an intracellular histidine kinase (HK) domain, and a receiver domain (REC). Perception of cytokinin signaling involves (i) a hormone molecule binding to the CHASE domain, (ii) CRE1 autophosphorylation at a conserved His residue in the HK domain, followed by a phosphorelay to (iii) a conserved Asp residue in the REC domain, (iv) a histidine-containing phosphotransfer protein (HPt), and (v) a response regulator (RR). This work focuses on the crystal structures of the REC domain of CRE1 from the model plant Arabidopsis thaliana and from the model legume Medicago truncatula. Both REC domains form tight 3D-domain-swapped dimers. Dimerization of the REC domain agrees with the quaternary assembly of the entire CRE1 but is incompatible with a model of its complex with HPt, suggesting that a considerable conformational change should occur to enable the signal transduction. Indeed, phosphorylation of the REC domain can change the HPt-binding properties of CRE1, as shown by functional studies.
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Affiliation(s)
- Linh H. Tran
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michał Jasiński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań, Poland
| | - Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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34
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Dimerization of Human Angiogenin and of Variants Involved in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms221810068. [PMID: 34576228 PMCID: PMC8468037 DOI: 10.3390/ijms221810068] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/25/2022] Open
Abstract
Human Angiogenin (hANG, or ANG, 14.1 kDa) promotes vessel formation and is also called RNase 5 because it is included in the pancreatic-type ribonuclease (pt-RNase) super-family. Although low, its ribonucleolytic activity is crucial for angiogenesis in tumor tissues but also in the physiological development of the Central Nervous System (CNS) neuronal progenitors. Nevertheless, some ANG variants are involved in both neurodegenerative Parkinson disease (PD) and Amyotrophic Lateral Sclerosis (ALS). Notably, some pt-RNases acquire new biological functions upon oligomerization. Considering neurodegenerative diseases correlation with massive protein aggregation, we analyzed the aggregation propensity of ANG and of three of its pathogenic variants, namely H13A, S28N, and R121C. We found no massive aggregation, but wt-ANG, as well as S28N and R121C variants, can form an enzymatically active dimer, which is called ANG-D. By contrast, the enzymatically inactive H13A-ANG does not dimerize. Corroborated by a specific cross-linking analysis and by the behavior of H13A-ANG that in turn lacks one of the two His active site residues necessary for pt-RNases to self-associate through the three-dimensional domain swapping (3D-DS), we demonstrate that ANG actually dimerizes through 3D-DS. Then, we deduce by size exclusion chromatography (SEC) and modeling that ANG-D forms through the swapping of ANG N-termini. In light of these novelties, we can expect future investigations to unveil other ANG determinants possibly related with the onset and/or development of neurodegenerative pathologies.
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35
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Parisi G, Palopoli N, Tosatto SC, Fornasari MS, Tompa P. "Protein" no longer means what it used to. Curr Res Struct Biol 2021; 3:146-152. [PMID: 34308370 PMCID: PMC8283027 DOI: 10.1016/j.crstbi.2021.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 01/02/2023] Open
Abstract
Every biologist knows that the word protein describes a group of macromolecules essential to sustain life on Earth. As biologists, we are invariably trained under a protein paradigm established since the early twentieth century. However, in recent years, the term protein unveiled itself as an euphemism to describe the overwhelming heterogeneity of these compounds. Most of our current studies are targeted on carefully selected subsets of proteins, but we tend to think and write about these as representative of the whole population. Here we discuss how seeking for universal definitions and general rules in any arbitrarily segmented study would be misleading about the conclusions. Of course, it is not our purpose to discourage the use of the word protein. Instead, we suggest to embrace the extended universe of proteins to reach a deeper understanding of their full potential, realizing that the term encompasses a group of molecules very heterogeneous in terms of size, shape, chemistry and functions, i.e. the term protein no longer means what it used to.
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Affiliation(s)
- Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | | | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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36
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Beitia GJ, Rutherford TJ, Freund SMV, Pelham HR, Bienz M, Gammons MV. Regulation of Dishevelled DEP domain swapping by conserved phosphorylation sites. Proc Natl Acad Sci U S A 2021; 118:e2103258118. [PMID: 34155117 PMCID: PMC8256032 DOI: 10.1073/pnas.2103258118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Wnt signals bind to Frizzled receptors to trigger canonical and noncanonical signaling responses that control cell fates during animal development and tissue homeostasis. All Wnt signals are relayed by the hub protein Dishevelled. During canonical (β-catenin-dependent) signaling, Dishevelled assembles signalosomes via dynamic head-to-tail polymerization of its Dishevelled and Axin (DIX) domain, which are cross-linked by its Dishevelled, Egl-10, and Pleckstrin (DEP) domain through a conformational switch from monomer to domain-swapped dimer. The domain-swapped conformation of DEP masks the site through which Dishevelled binds to Frizzled, implying that DEP domain swapping results in the detachment of Dishevelled from Frizzled. This would be incompatible with noncanonical Wnt signaling, which relies on long-term association between Dishevelled and Frizzled. It is therefore likely that DEP domain swapping is differentially regulated during canonical and noncanonical Wnt signaling. Here, we use NMR spectroscopy and cell-based assays to uncover intermolecular contacts in the DEP dimer that are essential for its stability and for Dishevelled function in relaying canonical Wnt signals. These contacts are mediated by an intrinsically structured sequence spanning a conserved phosphorylation site upstream of the DEP domain that serves to clamp down the swapped N-terminal α-helix onto the structural core of a reciprocal DEP molecule in the domain-swapped configuration. Mutations of this phosphorylation site and its cognate surface on the reciprocal DEP core attenuate DEP-dependent dimerization of Dishevelled and its canonical signaling activity in cells without impeding its binding to Frizzled. We propose that phosphorylation of this crucial residue could be employed to switch off canonical Wnt signaling.
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Affiliation(s)
- Gonzalo J Beitia
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Trevor J Rutherford
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Stefan M V Freund
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Hugh R Pelham
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Mariann Bienz
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Melissa V Gammons
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
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37
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Tetter S, Terasaka N, Steinauer A, Bingham RJ, Clark S, Scott AJP, Patel N, Leibundgut M, Wroblewski E, Ban N, Stockley PG, Twarock R, Hilvert D. Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein. Science 2021; 372:1220-1224. [PMID: 34112695 DOI: 10.1126/science.abg2822] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/29/2021] [Indexed: 12/14/2022]
Abstract
Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme that lacks affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding messenger RNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid that is impermeable to nucleases, and emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity. In addition to evincing a plausible evolutionary pathway for primordial viruses, these findings highlight practical strategies for developing nonviral carriers for diverse vaccine and delivery applications.
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Affiliation(s)
- Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Naohiro Terasaka
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Richard J Bingham
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Sam Clark
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Andrew J P Scott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Marc Leibundgut
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Reidun Twarock
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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38
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Kumari P, Bhavesh NS. Human DND1-RRM2 forms a non-canonical domain swapped dimer. Protein Sci 2021; 30:1184-1195. [PMID: 33860980 PMCID: PMC8138521 DOI: 10.1002/pro.4083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/09/2022]
Abstract
RNA recognition motif (RRM) being the most abundant RNA binding domain in eukaryotes, is a major player in cellular regulation. Several variations in the canonical βαββαβ topology have been observed. We have determined the 2.3 Å crystal structure of the human DND1-RRM2 domain. The structure revealed an interesting non-canonical RRM fold, which is maintained by the formation of a 3D domain swapped dimer between β1 and β4 strands across protomers. We have delineated the structural basis of the stable domain swapped dimer formation using the residue level dynamics of protein explored by NMR spectroscopy and MD simulations. Our structural and dynamics studies substantiate major determinants and molecular basis for domain swapped dimerization observed in the RRM domain.
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Affiliation(s)
- Pooja Kumari
- Transcription Regulation GroupInternational Centre for Genetic Engineering and Biotechnology (ICGEB)New DelhiIndia
| | - Neel Sarovar Bhavesh
- Transcription Regulation GroupInternational Centre for Genetic Engineering and Biotechnology (ICGEB)New DelhiIndia
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39
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Virion structure and in vitro genome release mechanism of dicistrovirus Kashmir bee virus. J Virol 2021; 95:JVI.01950-20. [PMID: 33658338 PMCID: PMC8139710 DOI: 10.1128/jvi.01950-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Infections of Kashmir bee virus (KBV) are lethal for honeybees and have been associated with colony collapse disorder. KBV and closely related viruses contribute to the ongoing decline in the number of honeybee colonies in North America, Europe, Australia, and other parts of the world. Despite the economic and ecological impact of KBV, its structure and infection process remain unknown. Here we present the structure of the virion of KBV determined to a resolution of 2.8 Å. We show that the exposure of KBV to acidic pH induces a reduction in inter-pentamer contacts within capsids and the reorganization of its RNA genome from a uniform distribution to regions of high and low density. Capsids of KBV crack into pieces at acidic pH, resulting in the formation of open particles lacking pentamers of capsid proteins. The large openings of capsids enable the rapid release of genomes and thus limit the probability of their degradation by RNases. The opening of capsids may be a shared mechanism for the genome release of viruses from the family Dicistroviridae ImportanceThe western honeybee (Apis mellifera) is indispensable for maintaining agricultural productivity as well as the abundance and diversity of wild flowering plants. However, bees suffer from environmental pollution, parasites, and pathogens, including viruses. Outbreaks of virus infections cause the deaths of individual honeybees as well as collapses of whole colonies. Kashmir bee virus has been associated with colony collapse disorder in the US, and no cure of the disease is currently available. Here we report the structure of an infectious particle of Kashmir bee virus and show how its protein capsid opens to release the genome. Our structural characterization of the infection process determined that therapeutic compounds stabilizing contacts between pentamers of capsid proteins could prevent the genome release of the virus.
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40
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Rocha MA, Sprague-Piercy MA, Kwok AO, Roskamp KW, Martin RW. Chemical Properties Determine Solubility and Stability in βγ-Crystallins of the Eye Lens. Chembiochem 2021; 22:1329-1346. [PMID: 33569867 PMCID: PMC8052307 DOI: 10.1002/cbic.202000739] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/17/2020] [Indexed: 11/10/2022]
Abstract
βγ-Crystallins are the primary structural and refractive proteins found in the vertebrate eye lens. Because crystallins are not replaced after early eye development, their solubility and stability must be maintained for a lifetime, which is even more remarkable given the high protein concentration in the lens. Aggregation of crystallins caused by mutations or post-translational modifications can reduce crystallin protein stability and alter intermolecular interactions. Common post-translational modifications that can cause age-related cataracts include deamidation, oxidation, and tryptophan derivatization. Metal ion binding can also trigger reduced crystallin solubility through a variety of mechanisms. Interprotein interactions are critical to maintaining lens transparency: crystallins can undergo domain swapping, disulfide bonding, and liquid-liquid phase separation, all of which can cause opacity depending on the context. Important experimental techniques for assessing crystallin conformation in the absence of a high-resolution structure include dye-binding assays, circular dichroism, fluorescence, light scattering, and transition metal FRET.
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Affiliation(s)
- Megan A. Rocha
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
| | - Ashley O. Kwok
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
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41
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Mangiagalli M, Barbiroli A, Santambrogio C, Ferrari C, Nardini M, Lotti M, Brocca S. The activity and stability of a cold-active acylaminoacyl peptidase rely on its dimerization by domain swapping. Int J Biol Macromol 2021; 181:263-274. [PMID: 33775759 DOI: 10.1016/j.ijbiomac.2021.03.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023]
Abstract
The study of enzymes from extremophiles arouses interest in Protein Science because of the amazing solutions these proteins adopt to cope with extreme conditions. Recently solved, the structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) pinpoints a mechanism of dimerization unusual for this class of enzymes. The quaternary structure of SpAAP relies on a domain-swapping mechanism involving the N-terminal A1 helix. The A1 helix is conserved among homologous mesophilic and psychrophilic proteins and its deletion causes the formation of a monomeric enzyme, which is inactive and prone to aggregate. Here, we investigate the dimerization mechanism of SpAAP through the analysis of chimeric heterodimers where a protomer lacking the A1 helix combines with a protomer carrying the inactivated catalytic site. Our results indicate that the two active sites are independent, and that a single A1 helix is sufficient to partially recover the quaternary structure and the activity of chimeric heterodimers. Since catalytically competent protomers are unstable and inactive unless they dimerize, SpAAP reveals as an "obligomer" for both structural and functional reasons.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Cristian Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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42
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Kaplan AR, Olson R, Alexandrescu AT. Protein yoga: Conformational versatility of the Hemolysin II C-terminal domain detailed by NMR structures for multiple states. Protein Sci 2021; 30:990-1005. [PMID: 33733504 DOI: 10.1002/pro.4066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 11/05/2022]
Abstract
The C-terminal domain of Bacillus cereus hemolysin II (HlyIIC), stabilizes the trans-membrane-pore formed by the HlyII toxin and may aid in target cell recognition. Initial efforts to determine the NMR structure of HlyIIC were hampered by cis/trans isomerization about the single proline at position 405 that leads to doubling of NMR resonances. We used the mutant P405M-HlyIIC that eliminates the cis proline to determine the NMR structure of the domain, which revealed a novel fold. Here, we extend earlier studies to the NMR structure determination of the cis and trans states of WT-HlyIIC that exist simultaneously in solution. The primary structural differences between the cis and trans states are in the loop that contains P405, and structurally adjacent loops. Thermodynamic linkage analysis shows that at 25 C the cis proline, which already has a large fraction of 20% in the unfolded protein, increases to 50% in the folded state due to coupling with the global stability of the domain. The P405M or P405A substitutions eliminate heterogeneity due to proline isomerization but lead to the formation of a new dimeric species. The NMR structure of the dimer shows that it is formed through domain-swapping of strand β5, the last segment of secondary structure following P405. The presence of P405 in WT-HlyIIC strongly disfavors the dimer compared to the P405M-HlyIIC or P405A-HlyIIC mutants. The WT proline may thus act as a "gatekeeper," warding off aggregative misfolding.
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Affiliation(s)
- Anne R Kaplan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, USA
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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43
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In Silico Therapeutic Peptide Design Against Pathogenic Domain Swapped Human Cystatin C Dimer. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10191-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Mondal B, Nagesh J, Reddy G. Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation. J Phys Chem B 2021; 125:1705-1715. [PMID: 33566611 DOI: 10.1021/acs.jpcb.0c07833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human γD (HγD) and γC (HγC) are two-domain crystallin (Crys) proteins expressed in the nucleus of the eye lens. Structural perturbations in the protein often trigger aggregation, which eventually leads to cataract. To decipher the underlying molecular mechanism, it is important to characterize the partially unfolded conformations, which are aggregation-prone. Using a coarse grained protein model and molecular dynamics simulations, we studied the role of on-pathway folding intermediates in the early stages of aggregation. The multidimensional free energy surface revealed at least three different folding pathways with the population of partially structured intermediates. The two dominant pathways confirm sequential folding of the N-terminal [Ntd] and the C-terminal domains [Ctd], while the third, least favored, pathway involves intermediates where both the domains are partially folded. A native-like intermediate (I*), featuring the folded domains and disrupted interdomain contacts, gets populated in all three pathways. I* forms domain swapped dimers by swapping the entire Ntds and Ctds with other monomers. Population of such oligomers can explain the increased resistance to unfolding resulting in hysteresis observed in the folding experiments of HγD Crys. An ensemble of double domain swapped dimers are also formed during refolding, where intermediates consisting of partially folded Ntds and Ctds swap secondary structures with other monomers. The double domain swapping model presented in our study provides structural insights into the early events of aggregation in Crys proteins and identifies the key secondary structural swapping elements, where introducing mutations will aid in regulating the overall aggregation propensity.
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Affiliation(s)
- Balaka Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
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45
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Montioli R, Campagnari R, Fasoli S, Fagagnini A, Caloiu A, Smania M, Menegazzi M, Gotte G. RNase A Domain-Swapped Dimers Produced Through Different Methods: Structure-Catalytic Properties and Antitumor Activity. Life (Basel) 2021; 11:life11020168. [PMID: 33669993 PMCID: PMC7926746 DOI: 10.3390/life11020168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022] Open
Abstract
Upon oligomerization, RNase A can acquire important properties, such as cytotoxicity against leukemic cells. When lyophilized from 40% acetic acid solutions, the enzyme self-associates through the so-called three-dimensional domain swapping (3D-DS) mechanism involving both N- and/or C-terminals. The same species are formed if the enzyme is subjected to thermal incubation in various solvents, especially in 40% ethanol. We evaluated here if significant structural modifications might occur in RNase A N- or C-swapped dimers and/or in the residual monomer(s), as a function of the oligomerization protocol applied. We detected that the monomer activity vs. ss-RNA was partly affected by both protocols, although the protein does not suffer spectroscopic alterations. Instead, the two N-swapped dimers showed differences in the fluorescence emission spectra but almost identical enzymatic activities, while the C-swapped dimers displayed slightly different activities vs. both ss- or ds-RNA substrates together with not negligible fluorescence emission alterations within each other. Besides these results, we also discuss the reasons justifying the different relative enzymatic activities displayed by the N-dimers and C-dimers. Last, similarly with data previously registered in a mouse model, we found that both dimeric species significantly decrease human melanoma A375 cell viability, while only N-dimers reduce human melanoma MeWo cell growth.
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Affiliation(s)
- Riccardo Montioli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Rachele Campagnari
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Sabrina Fasoli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Andrea Fagagnini
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Andra Caloiu
- Department of Microbiology and Virology, Wexham Park Hospital, Wexham Road, Slough SL24HL, Berkshire, UK;
| | - Marcello Smania
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Marta Menegazzi
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
- Correspondence: (M.M.); (G.G.); Tel.: +39-045-8027168 (M.M.); +39-045-8027694 (G.G.)
| | - Giovanni Gotte
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
- Correspondence: (M.M.); (G.G.); Tel.: +39-045-8027168 (M.M.); +39-045-8027694 (G.G.)
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46
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Fagagnini A, Garavís M, Gómez-Pinto I, Fasoli S, Gotte G, Laurents DV. NMR Characterization of Angiogenin Variants and tRNA Ala Products Impacting Aberrant Protein Oligomerization. Int J Mol Sci 2021; 22:1439. [PMID: 33535464 PMCID: PMC7867098 DOI: 10.3390/ijms22031439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Protein oligomerization is key to countless physiological processes, but also to abnormal amyloid conformations implicated in over 25 mortal human diseases. Human Angiogenin (h-ANG), a ribonuclease A family member, produces RNA fragments that regulate ribosome formation, the creation of new blood vessels and stress granule function. Too little h-ANG activity leads to abnormal protein oligomerization, resulting in Amyotrophic Lateral Sclerosis (ALS) or Parkinson's disease. While a score of disease linked h-ANG mutants has been studied by X-ray diffraction, some elude crystallization. There is also a debate regarding the structure that RNA fragments adopt after cleavage by h-ANG. Here, to better understand the beginning of the process that leads to aberrant protein oligomerization, the solution secondary structure and residue-level dynamics of WT h-ANG and two mutants i.e., H13A and R121C, are characterized by multidimensional heteronuclear NMR spectroscopy under near-physiological conditions. All three variants are found to adopt well folded and highly rigid structures in the solution, although the elements of secondary structure are somewhat shorter than those observed in crystallography studies. R121C alters the environment of nearby residues only. By contrast, the mutation H13A affects local residues as well as nearby active site residues K40 and H114. The conformation characterization by CD and 1D 1H NMR spectroscopies of tRNAAla before and after h-ANG cleavage reveals a retention of the duplex structure and little or no G-quadruplex formation.
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Affiliation(s)
- Andrea Fagagnini
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, Strada Le Grazie 8, I-37134 Verona, Italy; (A.F.); (S.F.)
| | - Miguel Garavís
- Instituto de Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, c/Serrano 119, E-28006 Madrid, Spain; (M.G.); (I.G.-P.)
| | - Irene Gómez-Pinto
- Instituto de Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, c/Serrano 119, E-28006 Madrid, Spain; (M.G.); (I.G.-P.)
| | - Sabrina Fasoli
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, Strada Le Grazie 8, I-37134 Verona, Italy; (A.F.); (S.F.)
| | - Giovanni Gotte
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, Strada Le Grazie 8, I-37134 Verona, Italy; (A.F.); (S.F.)
| | - Douglas V. Laurents
- Instituto de Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, c/Serrano 119, E-28006 Madrid, Spain; (M.G.); (I.G.-P.)
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47
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Christiansen A, Weiel M, Winkler A, Schug A, Reinstein J. The Trimeric Major Capsid Protein of Mavirus is stabilized by its Interlocked N-termini Enabling Core Flexibility for Capsid Assembly. J Mol Biol 2021; 433:166859. [PMID: 33539884 DOI: 10.1016/j.jmb.2021.166859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Icosahedral viral capsids assemble with high fidelity from a large number of identical buildings blocks. The mechanisms that enable individual capsid proteins to form stable oligomeric units (capsomers) while affording structural adaptability required for further assembly into capsids are mostly unknown. Understanding these mechanisms requires knowledge of the capsomers' dynamics, especially for viruses where no additional helper proteins are needed during capsid assembly like for the Mavirus virophage that despite its complexity (triangulation number T = 27) can assemble from its major capsid protein (MCP) alone. This protein forms the basic building block of the capsid namely a trimer (MCP3) of double-jelly roll protomers with highly intertwined N-terminal arms of each protomer wrapping around the other two at the base of the capsomer, secured by a clasp that is formed by part of the C-terminus. Probing the dynamics of the capsomer with HDX mass spectrometry we observed differences in conformational flexibility between functional elements of the MCP trimer. While the N-terminal arm and clasp regions show above average deuterium incorporation, the two jelly-roll units in each protomer also differ in their structural plasticity, which might be needed for efficient assembly. Assessing the role of the N-terminal arm in maintaining capsomer stability showed that its detachment is required for capsomer dissociation, constituting a barrier towards capsomer monomerisation. Surprisingly, capsomer dissociation was irreversible since it was followed by a global structural rearrangement of the protomers as indicated by computational studies showing a rearrangement of the N-terminus blocking part of the capsomer forming interface.
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Affiliation(s)
- Alexander Christiansen
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanismsm Heidelberg, Germany
| | - Marie Weiel
- Karlsruhe Institute of Technology, Steinbuch Centre for Computing and Department of Physics, Eggenstein-Leopoldshafen, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology. Graz, Austria
| | - Alexander Schug
- Institute for Advanced Simulation, Jülich Supercomputing Center, Jülich, Germany
| | - Jochen Reinstein
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanismsm Heidelberg, Germany.
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48
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Hirota S, Nagao S. New Aspects of Cytochromec: 3D Domain Swapping, Membrane Interaction, Peroxidase Activity, and Met80 Sulfoxide Modification. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200272] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
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49
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Liang R, Wang G, Zhang D, Ye G, Li M, Shi Y, Shi J, Chen H, Peng G. Structural comparisons of host and African swine fever virus dUTPases reveal new clues for inhibitor development. J Biol Chem 2021; 296:100015. [PMID: 33139328 PMCID: PMC7948977 DOI: 10.1074/jbc.ra120.014005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 11/06/2022] Open
Abstract
African swine fever, caused by the African swine fever virus (ASFV), is among the most significant swine diseases. There are currently no effective treatments against ASFV. ASFV contains a gene encoding a dUTPase (E165R), which is required for viral replication in swine macrophages, making it an attractive target for inhibitor development. However, the full structural details of the ASFV dUTPase and those of the comparable swine enzyme are not available, limiting further insights. Herein, we determine the crystal structures of ASFV dUTPase and swine dUTPase in both their ligand-free and ligand-bound forms. We observe that the swine enzyme employs a classical dUTPase architecture made up of three-subunit active sites, whereas the ASFV enzyme employs a novel two-subunit active site. We then performed a comparative analysis of all dUTPase structures uploaded in the Protein Data Bank (PDB), which showed classical and non-classical types were mainly determined by the C-terminal β-strand orientation, and the difference was mainly related to the four amino acids behind motif IV. Thus, our study not only explains the reason for the structural diversity of dUTPase but also reveals how to predict dUTPase type, which may have implications for the dUTPase family. Finally, we tested two dUTPase inhibitors developed for the Plasmodium falciparum dUTPase against the swine and ASFV enzymes. One of these compounds inhibited the ASFV dUTPase at low micromolar concentrations (Kd = 15.6 μM) and with some selectivity (∼2x) over swine dUTPase. In conclusion, our study expands our understanding of the dUTPase family and may aid in the development of specific ASFV inhibitors.
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Affiliation(s)
- Rui Liang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Gang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Ding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Gang Ye
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Mengxia Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jiale Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei Province, China.
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50
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Terse VL, Gosavi S. The Molecular Mechanism of Domain Swapping of the C-Terminal Domain of the SARS-Coronavirus Main Protease. Biophys J 2020; 120:504-516. [PMID: 33359834 PMCID: PMC7837137 DOI: 10.1016/j.bpj.2020.11.2277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022] Open
Abstract
In three-dimensional domain swapping, two protein monomers exchange a part of their structures to form an intertwined homodimer, whose subunits resemble the monomer. Several viral proteins domain swap to increase their structural complexity or functional avidity. The main protease (Mpro) of the severe acute respiratory syndrome (SARS) coronavirus proteolyzes viral polyproteins and has been a target for anti-SARS drug design. Domain swapping in the α-helical C-terminal domain of Mpro (MproC) locks Mpro into a hyperactive octameric form that is hypothesized to promote the early stages of viral replication. However, in the absence of a complete molecular understanding of the mechanism of domain swapping, investigations into the biological relevance of this octameric Mpro have stalled. Isolated MproC can exist as a monomer or a domain-swapped dimer. Here, we investigate the mechanism of domain swapping of MproC using coarse-grained structure-based models and molecular dynamics simulations. Our simulations recapitulate several experimental features of MproC folding. Further, we find that a contact between a tryptophan in the MproC domain-swapping hinge and an arginine elsewhere forms early during folding, modulates the folding route, and promotes domain swapping to the native structure. An examination of the sequence and the structure of the tryptophan containing hinge loop shows that it has a propensity to form multiple secondary structures and contacts, indicating that it could be stabilized into either the monomer- or dimer-promoting conformations by mutations or ligand binding. Finally, because all residues in the tryptophan loop are identical in SARS-CoV and SARS-CoV-2, mutations that modulate domain swapping may provide insights into the role of octameric Mpro in the early-stage viral replication of both viruses.
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Affiliation(s)
- Vishram L Terse
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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