1
|
Cereghetti G, Kissling VM, Koch LM, Arm A, Schmidt CC, Thüringer Y, Zamboni N, Afanasyev P, Linsenmeier M, Eichmann C, Kroschwald S, Zhou J, Cao Y, Pfizenmaier DM, Wiegand T, Cadalbert R, Gupta G, Boehringer D, Knowles TPJ, Mezzenga R, Arosio P, Riek R, Peter M. An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions. Dev Cell 2024; 59:1876-1891.e7. [PMID: 38788715 DOI: 10.1016/j.devcel.2024.04.018] [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: 06/01/2022] [Revised: 10/15/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024]
Abstract
Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.
Collapse
Affiliation(s)
- Gea Cereghetti
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK.
| | - Vera M Kissling
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | - Lisa M Koch
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Alexandra Arm
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Claudia C Schmidt
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yannik Thüringer
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, 8093 Zürich, Switzerland
| | - Miriam Linsenmeier
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Sonja Kroschwald
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiangtao Zhou
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Yiping Cao
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Dorota M Pfizenmaier
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland; Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Govind Gupta
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | | | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
2
|
Xie F, Wu D, Huang J, Liu X, Shen Y, Huang J, Su Z, Li J. ZBP1 condensate formation synergizes Z-NAs recognition and signal transduction. Cell Death Dis 2024; 15:487. [PMID: 38982083 PMCID: PMC11233663 DOI: 10.1038/s41419-024-06889-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
Z-DNA binding protein 1 (ZBP1) is a crucial player in the intracellular recognition of Z-form nucleic acids (Z-NAs) through its Zαβ domain, initiating downstream interactions with RIPK1 and RIPK3 via RHIM domains. This engagement leads to the assembly of PANoptosomes, ultimately inducing programmed cell death to curb pathogen dissemination. How Zαβ and RHIM domain cooperate to trigger Z-NAs recognition and signal transduction remains unclear. Here, we show that ZBP1 condensate formation facilitates Z-NAs binding and antiviral signal transduction. The ZBP1 Zαβ dimerizes in a concentration-dependent manner, forming characteristic condensates in solutions evidenced by DLS and SAXS methods. ZBP1 exhibits a binding preference for 10-bp length CG (10CG) DNA and Z-RNA ligand, which in turn enhanced Zαβ dimerization, expediting the formation of droplet condensates in vitro and amyloid-like puncta in cells. Subsequent investigations reveal that Zαβ could form condensates with liquid-liquid phase separation property upon HSV and IAV infections, while full-length ZBP1 forms amyloid-like puncta with or without infections. Furthermore, ZBP1 RHIM domains show typical amyloidal fibril characterizations and cross-polymerize with RIPK1 depending on the core motif of 206IQIG209, while mutated ZBP1 could impede necroptosis and antiviral immunity in HT-29 cells. Thus, ZBP1 condensate formation facilitates the recognition of viral Z-NAs and activation of downstream signal transduction via synergic action of different domains, revealing its elaborated mechanism in innate immunity.
Collapse
Affiliation(s)
- Feiyan Xie
- Department of Neurology, Huashan Hospital and School of Life Sciences, State Key Laboratory of Genetic Engineering, Fudan University, 200438, Shanghai, China
| | - Di Wu
- Department of Neurology, Huashan Hospital and School of Life Sciences, State Key Laboratory of Genetic Engineering, Fudan University, 200438, Shanghai, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, 410083, Hunan, China
| | - Xuehe Liu
- Department of Neurology, Huashan Hospital and School of Life Sciences, State Key Laboratory of Genetic Engineering, Fudan University, 200438, Shanghai, China
| | - Yanfang Shen
- Department of Neurology, Huashan Hospital and School of Life Sciences, State Key Laboratory of Genetic Engineering, Fudan University, 200438, Shanghai, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhipeng Su
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Jixi Li
- Department of Neurology, Huashan Hospital and School of Life Sciences, State Key Laboratory of Genetic Engineering, Fudan University, 200438, Shanghai, China.
| |
Collapse
|
3
|
Miura Y, Namioka S, Iwai A, Yoshida N, Konno H, Sohma Y, Kanai M, Makabe K. Redesign of a thioflavin-T-binding protein with a flat β-sheet to evaluate a thioflavin-T-derived photocatalyst with enhanced affinity. Int J Biol Macromol 2024; 269:131992. [PMID: 38697433 DOI: 10.1016/j.ijbiomac.2024.131992] [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: 02/26/2024] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
Amyloids, proteinous aggregates with β-sheet-rich fibrils, are involved in several neurodegenerative diseases such as Alzheimer's disease; thus, their detection is critically important. The most common fluorescent dye for amyloid detection is thioflavin-T (ThT), which shows on/off fluorescence upon amyloid binding. We previously reported that an engineered globular protein with a flat β-sheet, peptide self-assembly mimic (PSAM), can be used as an amyloid binding model. In this study, we further explored the residue-specific properties of ThT-binding to the flat β-sheet by introducing systematic mutations. We found that site-specific mutations at the ThT-binding channel enhanced affinity. We also evaluated the binding of a ThT-based photocatalyst, which showed the photooxygenation activity on the amyloid fibril upon light radiation. Upon binding of the photocatalyst to the PSAM variant, singlet oxygen-generating activity was observed. The results of this study expand our understanding of the detailed binding mechanism of amyloid-specific molecules.
Collapse
Affiliation(s)
- Yuina Miura
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Sae Namioka
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Atsushi Iwai
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Norio Yoshida
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-Ward, Nagoya 464-8601, Japan
| | - Hiroyuki Konno
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Youhei Sohma
- Graduate School of Medical and Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shichiban-cho, Wakayama 640-8156, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan.
| |
Collapse
|
4
|
Baghel D, de Oliveira AP, Satyarthy S, Chase WE, Banerjee S, Ghosh A. Structural characterization of amyloid aggregates with spatially resolved infrared spectroscopy. Methods Enzymol 2024; 697:113-150. [PMID: 38816120 PMCID: PMC11147165 DOI: 10.1016/bs.mie.2024.02.013] [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: 06/01/2024]
Abstract
The self-assembly of proteins and peptides into ordered structures called amyloid fibrils is a hallmark of numerous diseases, impacting the brain, heart, and other organs. The structure of amyloid aggregates is central to their function and thus has been extensively studied. However, the structural heterogeneities between aggregates as they evolve throughout the aggregation pathway are still not well understood. Conventional biophysical spectroscopic methods are bulk techniques and only report on the average structural parameters. Understanding the structure of individual aggregate species in a heterogeneous ensemble necessitates spatial resolution on the length scale of the aggregates. Recent technological advances have led to augmentation of infrared (IR) spectroscopy with imaging modalities, wherein the photothermal response of the sample upon vibrational excitation is leveraged to provide spatial resolution beyond the diffraction limit. These combined approaches are ideally suited to map out the structural heterogeneity of amyloid ensembles. AFM-IR, which integrates IR spectroscopy with atomic force microscopy enables identification of the structural facets the oligomers and fibrils at individual aggregate level with nanoscale resolution. These capabilities can be extended to chemical mapping in diseased tissue specimens with submicron resolution using optical photothermal microscopy, which combines IR spectroscopy with optical imaging. This book chapter provides the basic premise of these novel techniques and provides the typical methodology for using these approaches for amyloid structure determination. Detailed procedures pertaining to sample preparation and data acquisition and analysis are discussed and the aggregation of the amyloid β peptide is provided as a case study to provide the reader the experimental parameters necessary to use these techniques to complement their research efforts.
Collapse
Affiliation(s)
- Divya Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Ana Pacheco de Oliveira
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Saumya Satyarthy
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - William E Chase
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, United States.
| |
Collapse
|
5
|
Chisholm TS, Hunter CA. A closer look at amyloid ligands, and what they tell us about protein aggregates. Chem Soc Rev 2024; 53:1354-1374. [PMID: 38116736 DOI: 10.1039/d3cs00518f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The accumulation of amyloid fibrils is characteristic of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease. Detecting these fibrils with fluorescent or radiolabelled ligands is one strategy for diagnosing and better understanding these diseases. A vast number of amyloid-binding ligands have been reported in the literature as a result. To obtain a better understanding of how amyloid ligands bind, we have compiled a database of 3457 experimental dissociation constants for 2076 unique amyloid-binding ligands. These ligands target Aβ, tau, or αSyn fibrils, as well as relevant biological samples including AD brain homogenates. From this database significant variation in the reported dissociation constants of ligands was found, possibly due to differences in the morphology of the fibrils being studied. Ligands were also found to bind to Aβ(1-40) and Aβ(1-42) fibrils with similar affinities, whereas a greater difference was found for binding to Aβ and tau or αSyn fibrils. Next, the binding of ligands to fibrils was shown to be largely limited by the hydrophobic effect. Some Aβ ligands do not fit into this hydrophobicity-limited model, suggesting that polar interactions can play an important role when binding to this target. Finally several binding site models were outlined for amyloid fibrils that describe what ligands target what binding sites. These models provide a foundation for interpreting and designing site-specific binding assays.
Collapse
Affiliation(s)
- Timothy S Chisholm
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1 EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1 EW, UK.
| |
Collapse
|
6
|
Ragonis-Bachar P, Axel G, Blau S, Ben-Tal N, Kolodny R, Landau M. What can AlphaFold do for antimicrobial amyloids? Proteins 2024; 92:265-281. [PMID: 37855235 DOI: 10.1002/prot.26618] [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: 07/13/2023] [Revised: 09/05/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023]
Abstract
Amyloids, protein, and peptide assemblies in various organisms are crucial in physiological and pathological processes. Their intricate structures, however, present significant challenges, limiting our understanding of their functions, regulatory mechanisms, and potential applications in biomedicine and technology. This study evaluated the AlphaFold2 ColabFold method's structure predictions for antimicrobial amyloids, using eight antimicrobial peptides (AMPs), including those with experimentally determined structures and AMPs known for their distinct amyloidogenic morphological features. Additionally, two well-known human amyloids, amyloid-β and islet amyloid polypeptide, were included in the analysis due to their disease relevance, short sequences, and antimicrobial properties. Amyloids typically exhibit tightly mated β-strand sheets forming a cross-β configuration. However, certain amphipathic α-helical subunits can also form amyloid fibrils adopting a cross-α structure. Some AMPs in the study exhibited a combination of cross-α and cross-β amyloid fibrils, adding complexity to structure prediction. The results showed that the AlphaFold2 ColabFold models favored α-helical structures in the tested amyloids, successfully predicting the presence of α-helical mated sheets and a hydrophobic core resembling the cross-α configuration. This implies that the AI-based algorithms prefer assemblies of the monomeric state, which was frequently predicted as helical, or capture an α-helical membrane-active form of toxic peptides, which is triggered upon interaction with lipid membranes.
Collapse
Affiliation(s)
| | - Gabriel Axel
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Blau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nir Ben-Tal
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- The Center for Experimental Medicine, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| |
Collapse
|
7
|
Nishiyama A, Shimizu M, Narita T, Kodera N, Ozeki Y, Yokoyama A, Mayanagi K, Yamaguchi T, Hakamata M, Shaban A, Tateishi Y, Ito K, Matsumoto S. Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy. Nucleic Acids Res 2024; 52:816-830. [PMID: 38048321 PMCID: PMC10810275 DOI: 10.1093/nar/gkad1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
Mycobacteria are the major human pathogens with the capacity to become dormant persisters. Mycobacterial DNA-binding protein 1 (MDP1), an abundant histone-like protein in dormant mycobacteria, induces dormancy phenotypes, e.g. chromosome compaction and growth suppression. For these functions, the polycationic intrinsically disordered region (IDR) is essential. However, the disordered property of IDR stands in the way of clarifying the molecular mechanism. Here we clarified the molecular and structural mechanism of DNA compaction by MDP1. Using high-speed atomic force microscopy, we observed that monomeric MDP1 bundles two adjacent DNA duplexes side-by-side via IDR. Combined with coarse-grained molecular dynamics simulation, we revealed the novel dynamic DNA cross-linking model of MDP1 in which a stretched IDR cross-links two DNA duplexes like double-sided tape. IDR is able to hijack HU function, resulting in the induction of strong mycobacterial growth arrest. This IDR-mediated reversible DNA cross-linking is a reasonable model for MDP1 suppression of the genomic function in the resuscitable non-replicating dormant mycobacteria.
Collapse
Affiliation(s)
- Akihito Nishiyama
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Masahiro Shimizu
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
- Division of Quantum Beam Material Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Tomoyuki Narita
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Akira Yokoyama
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan
| | - Mariko Hakamata
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Respiratory Medicine and Infectious Disease, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Amina Kaboso Shaban
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Kosuke Ito
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, East Java 60115, Indonesia
- Division of Research Aids, Hokkaido University Institute for Vaccine Research & Development, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| |
Collapse
|
8
|
de Raffele D, Ilie IM. Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning. Chem Commun (Camb) 2024; 60:632-645. [PMID: 38131333 DOI: 10.1039/d3cc04630c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address only their symptoms and do not prevent disease onset. Common therapeutic agents, such as small molecules and antibodies struggle with insufficient selectivity, stability and bioavailability, leading to poor performance in clinical trials. Peptide-based therapeutics are emerging as promising candidates, with successful applications for cardiovascular diseases and cancers due to their high bioavailability, good efficacy and specificity. In particular, cyclic peptides have a long in vivo stability, while maintaining a robust antibody-like binding affinity. However, the de novo design of cyclic peptides is challenging due to the lack of long-lived druggable pockets of the target polypeptide, absence of exhaustive conformational distributions of the target and/or the binder, unknown binding site, methodological limitations, associated constraints (failed trials, time, money) and the vast combinatorial sequence space. Hence, efficient alignment and cooperation between disciplines, and synergies between experiments and simulations complemented by popular techniques like machine-learning can significantly speed up the therapeutic cyclic-peptide development for neurodegenerative diseases. We review the latest advancements in cyclic peptide design against amyloidogenic targets from a computational perspective in light of recent advancements and potential of machine learning to optimize the design process. We discuss the difficulties encountered when designing novel peptide-based inhibitors and we propose new strategies incorporating experiments, simulations and machine learning to design cyclic peptides to inhibit the toxic propagation of amyloidogenic polypeptides. Importantly, these strategies extend beyond the mere design of cyclic peptides and serve as template for the de novo generation of (bio)materials with programmable properties.
Collapse
Affiliation(s)
- Daria de Raffele
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Ioana M Ilie
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| |
Collapse
|
9
|
Yang L, Wang Y, Zhang W, Ma G. New Insight into the Structural Nature of Diphenylalanine Nanotube through Comparison with Amyloid Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1046-1057. [PMID: 38153333 DOI: 10.1021/acs.langmuir.3c03270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Diphenylalanine (FF) nanotubes are a star material in the field of peptide self-assembly and have demonstrated numerous intriguing applications. Due to its resemblance to amyloid assembly, the FF nanotube is widely regarded as a simplified mimic of amyloids. Yet, whether FF nanotube truly possesses amyloid structure remains an open question. To better understand the structural nature of FF nanotube, we herein performed a comparative structural investigation between FF nanotube and typical amyloid systems by Aβ1-40, Aβ1-42, Aβ16-22, Aβ13-23, α-synuclein, and lysozyme using Fourier transform infrared spectroscopy. Through this comparative investigation, we obtained clear evidence to support that the FF nanotube does not possess a β-sheet structure, a key structural characteristic of amyloid assembly, thus revealing the non-amyloid structural nature of the FF nanotube. At last, in light of our new finding, we further discussed the unique self-assembly behaviors of FF during nanotube formation and the implications of our work for FF nanotube related applications.
Collapse
Affiliation(s)
- Lujuan Yang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Yao Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Wenkai Zhang
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Gang Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| |
Collapse
|
10
|
Ohno S, Manabe N, Yamaguchi Y. Prediction of protein structure and AI. J Hum Genet 2024:10.1038/s10038-023-01215-4. [PMID: 38177398 DOI: 10.1038/s10038-023-01215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/10/2023] [Indexed: 01/06/2024]
Abstract
AlphaFold, an artificial intelligence (AI)-based tool for predicting the 3D structure of proteins, is now widely recognized for its high accuracy and versatility in the folding of human proteins. AlphaFold is useful for understanding structure-function relationships from protein 3D structure models and can serve as a template or a reference for experimental structural analysis including X-ray crystallography, NMR and cryo-EM analysis. Its use is expanding among researchers, not only in structural biology but also in other research fields. Researchers are currently exploring the full potential of AlphaFold-generated protein models. Predicting disease severity caused by missense mutations is one such application. This article provides an overview of the 3D structural modeling of AlphaFold based on deep learning techniques and highlights the challenges in predicting the pathogenicity of missense mutations.
Collapse
Affiliation(s)
- Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan.
| |
Collapse
|
11
|
Wilkinson M, Xu Y, Thacker D, Taylor AIP, Fisher DG, Gallardo RU, Radford SE, Ranson NA. Structural evolution of fibril polymorphs during amyloid assembly. Cell 2023; 186:5798-5811.e26. [PMID: 38134875 DOI: 10.1016/j.cell.2023.11.025] [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: 10/29/2022] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Cryoelectron microscopy (cryo-EM) has provided unprecedented insights into amyloid fibril structures, including those associated with disease. However, these structures represent the endpoints of long assembly processes, and their relationship to fibrils formed early in assembly is unknown. Consequently, whether different fibril architectures, with potentially different pathological properties, form during assembly remains unknown. Here, we used cryo-EM to determine structures of amyloid fibrils at different times during in vitro fibrillation of a disease-related variant of human islet amyloid polypeptide (IAPP-S20G). Strikingly, the fibrils formed in the lag, growth, and plateau phases have different structures, with new forms appearing and others disappearing as fibrillation proceeds. A time course with wild-type hIAPP also shows fibrils changing with time, suggesting that this is a general property of IAPP amyloid assembly. The observation of transiently populated fibril structures has implications for understanding amyloid assembly mechanisms with potential new insights into amyloid progression in disease.
Collapse
Affiliation(s)
- Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Dev Thacker
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alexander I P Taylor
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Declan G Fisher
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
12
|
Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
Collapse
Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| |
Collapse
|
13
|
Gnilitskyi I, Rymar S, Iungin O, Vyshnevskyy O, Parisse P, Potters G, Zayats AV, Moshynets O. Femtosecond laser modified metal surfaces alter biofilm architecture and reduce bacterial biofilm formation. NANOSCALE ADVANCES 2023; 5:6659-6669. [PMID: 38024323 PMCID: PMC10662203 DOI: 10.1039/d3na00599b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Biofilm formation, or microfouling, is a basic strategy of bacteria to colonise a surface and may happen on surfaces of any nature whenever bacteria are present. Biofilms are hard to eradicate due to the matrix in which the bacteria reside, consisting of strong, adhesive and adaptive self-produced polymers such as eDNA and functional amyloids. Targeting a biofilm matrix may be a promising strategy to prevent biofilm formation. Here, femtosecond laser irradiation was used to modify the stainless steel surface in order to introduce either conical spike or conical groove textures. The resulting topography consists of hierarchical nano-microstructures which substantially increase roughness. The biofilms of two model bacterial strains, P. aeruginosa PA01 and S. aureus ATCC29423, formed on such nanotextured metal surfaces, were considerably modified due to a substantial reduction in amyloid production and due to changes in eDNA surface adhesion, leading to significant reduction in biofilm biomass. Altering the topography of the metal surface, therefore, radically diminishes biofilm development solely by altering biofilm architecture. At the same time, growth and colonisation of the surface by eukaryotic adipose tissue-derived stem cells were apparently enhanced, leading to possible further advantages in controlling eukaryotic growth while suppressing prokaryotic contamination. The obtained results are important for developing anti-bacterial surfaces for numerous applications.
Collapse
Affiliation(s)
- Iaroslav Gnilitskyi
- Department of Physics and London Centre for Nanotechnology, King's College London Strand London WC2R 2LS UK
- NoviNano Lab LLC Lviv Ukraine
- Lviv Polytechnic National University Ukraine
| | - Svitlana Rymar
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine Kyiv Ukraine
| | - Olga Iungin
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine Kyiv Ukraine
- Kyiv National University of Technologies and Design Kyiv Ukraine
| | - Olexiy Vyshnevskyy
- M. P. Semenenko Institute of Geochemistry, Mineralogy and Ore Formation of National Academy of Sciences of Ukraine Kyiv Ukraine
| | - Pietro Parisse
- Istituto Officina dei Materiali (IOM)-CNR, Laboratorio TASC I-34149 Trieste Italy
| | - Geert Potters
- Antwerp Maritime Academy Antwerp Belgium
- Department of Bioscience Engineering, University of Antwerp Antwerp Belgium
| | - Anatoly V Zayats
- Department of Physics and London Centre for Nanotechnology, King's College London Strand London WC2R 2LS UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine Kyiv Ukraine
| |
Collapse
|
14
|
Nowakowska AW, Wojciechowski JW, Szulc N, Kotulska M. The role of tandem repeats in bacterial functional amyloids. J Struct Biol 2023; 215:108002. [PMID: 37482232 DOI: 10.1016/j.jsb.2023.108002] [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: 03/24/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration. However, recent discoveries showed that amyloid structure of a protein could also be beneficial and desired, e.g., to promote cell adhesion. Functional amyloids are proteins which differ in their characteristics from pathological amyloids, so that the fibril formation could be more under control of an organism. We propose that repeats in the sequence could regulate the aggregation propensity of these proteins. The inclusion of multiple symmetric interactions, due to the presence of the repeats, could be supporting and strengthening the desirable structural properties of functional amyloids. Our results show that tandem repeats in bacterial functional amyloids have a distinct characteristic. The pattern of repeats supports the appropriate level of fibril formation and better controllability of fibril stability. The repeats tend to be more imperfect, which attenuates excessive aggregation propensity. Their desired structure and function are also reinforced by their amino acid profile. Although in the study we focused on bacterial functional amyloids, due to their importance in biofilm formation, we propose that similar mechanisms could be employed in other functional amyloids which are designed by evolution to aggregate in a desirable manner, but not necessarily in pathological amyloids.
Collapse
Affiliation(s)
- Alicja W Nowakowska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
| | - Jakub W Wojciechowski
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland
| | - Natalia Szulc
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland; Wrocław University of Environmental and Life Sciences, Department of Physics and Biophysics, Poland; LPCT, CNRS, Universite de Lorraine, F-54000 Nancy, France
| | - Malgorzata Kotulska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
| |
Collapse
|
15
|
Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
Collapse
Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| |
Collapse
|
16
|
Indig RY, Landau M. Designed inhibitors to reduce amyloid virulence and cytotoxicity and combat neurodegenerative and infectious diseases. Curr Opin Chem Biol 2023; 75:102318. [PMID: 37196450 DOI: 10.1016/j.cbpa.2023.102318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
The review highlights the role of amyloids in various diseases and the challenges associated with targeting human amyloids in therapeutic development. However, due to the better understanding of microbial amyloids' role as virulence factors, there is a growing interest in repurposing and designing anti-amyloid compounds for antivirulence therapy. The identification of amyloid inhibitors has not only significant clinical implications but also provides valuable insights into the structure and function of amyloids. The review showcases small molecules and peptides that specifically target amyloids in both humans and microbes, reducing cytotoxicity and biofilm formation, respectively. The review emphasizes the importance of further research on amyloid structures, mechanisms, and interactions across all life forms to yield new drug targets and improve the design of selective treatments. Overall, the review highlights the potential for amyloid inhibitors in therapeutic development for both human diseases and microbial infections.
Collapse
Affiliation(s)
- Rinat Yona Indig
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; Centre for Structural Systems Biology (CSSB) and Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany; Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg, Germany.
| |
Collapse
|
17
|
Shenoy J, Lends A, Berbon M, Bilal M, El Mammeri N, Bertoni M, Saad A, Morvan E, Grélard A, Lecomte S, Theillet FX, Buell AK, Kauffmann B, Habenstein B, Loquet A. Structural polymorphism of the low-complexity C-terminal domain of TDP-43 amyloid aggregates revealed by solid-state NMR. Front Mol Biosci 2023; 10:1148302. [PMID: 37065450 PMCID: PMC10095165 DOI: 10.3389/fmolb.2023.1148302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Aberrant aggregation of the transactive response DNA-binding protein (TDP-43) is associated with several lethal neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Cytoplasmic neuronal inclusions of TDP-43 are enriched in various fragments of the low-complexity C-terminal domain and are associated with different neurotoxicity. Here we dissect the structural basis of TDP-43 polymorphism using magic-angle spinning solid-state NMR spectroscopy in combination with electron microscopy and Fourier-transform infrared spectroscopy. We demonstrate that various low-complexity C-terminal fragments, namely TDP-13 (TDP-43300–414), TDP-11 (TDP-43300–399), and TDP-10 (TDP-43314–414), adopt distinct polymorphic structures in their amyloid fibrillar state. Our work demonstrates that the removal of less than 10% of the low-complexity sequence at N- and C-termini generates amyloid fibrils with comparable macroscopic features but different local structural arrangement. It highlights that the assembly mechanism of TDP-43, in addition to the aggregation of the hydrophobic region, is also driven by complex interactions involving low-complexity aggregation-prone segments that are a potential source of structural polymorphism.
Collapse
Affiliation(s)
- Jayakrishna Shenoy
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Alons Lends
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Muhammed Bilal
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Nadia El Mammeri
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mathilde Bertoni
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Ahmad Saad
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Estelle Morvan
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Axelle Grélard
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Sophie Lecomte
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - François-Xavier Theillet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-surYvette Cedex, France
| | - Alexander K. Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Brice Kauffmann
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Birgit Habenstein
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
| | - Antoine Loquet
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
| |
Collapse
|
18
|
Obstarczyk P, Pniakowska A, Nonappa, Grzelczak MP, Olesiak-Bańska J. Crown Ether-Capped Gold Nanoclusters as a Multimodal Platform for Bioimaging. ACS OMEGA 2023; 8:11503-11511. [PMID: 37008092 PMCID: PMC10061685 DOI: 10.1021/acsomega.3c00426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 12/01/2023]
Abstract
The distinct polarity of biomolecule surfaces plays a pivotal role in their biochemistry and functions as it is involved in numerous processes, such as folding, aggregation, or denaturation. Therefore, there is a need to image both hydrophilic and hydrophobic bio-interfaces with markers of distinct responses to hydrophobic and hydrophilic environments. In this work, we present a synthesis, characterization, and application of ultrasmall gold nanoclusters capped with a 12-crown-4 ligand. The nanoclusters present an amphiphilic character and can be successfully transferred between aqueous and organic solvents and have their physicochemical integrity retained. They can serve as probes for multimodal bioimaging with light (as they emit near-infrared luminescence) and electron microscopy (due to the high electron density of gold). In this work, we used protein superstructures, namely, amyloid spherulites, as a hydrophobic surface model and individual amyloid fibrils with a mixed hydrophobicity profile. Our nanoclusters spontaneously stained densely packed amyloid spherulites as observed under fluorescence microscopy, which is limited for hydrophilic markers. Moreover, our clusters revealed structural features of individual amyloid fibrils at a nanoscale as observed under a transmission electron microscope. We show the potential of crown ether-capped gold nanoclusters in multimodal structural characterization of bio-interfaces where the amphiphilic character of the supramolecular ligand is required.
Collapse
Affiliation(s)
- Patryk Obstarczyk
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Anna Pniakowska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Nonappa
- Faculty
of Engineering and Natural Sciences, Tampere
University, FI-33720 Tampere, Finland
| | - Marcin P. Grzelczak
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, 50-370 Wrocław, Poland
| |
Collapse
|
19
|
Peptide Inhibitors of Insulin Fibrillation: Current and Future Challenges. Int J Mol Sci 2023; 24:ijms24021306. [PMID: 36674821 PMCID: PMC9863703 DOI: 10.3390/ijms24021306] [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: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Amyloidoses include a large variety of local and systemic diseases that share the common feature of protein unfolding or refolding into amyloid fibrils. The most studied amyloids are those directly involved in neurodegenerative diseases, while others, such as those formed by insulin, are surprisingly far less studied. Insulin is a very important polypeptide that plays a variety of biological roles and, first and foremost, is at the basis of the therapy of diabetic patients. It is well-known that it can form fibrils at the site of injection, leading to inflammation and immune response, in addition to other side effects. In this concise review, we analyze the current knowledge on insulin fibrillation, with a focus on the development of peptide-based inhibitors, which are promising candidates for their biocompatibility but still pose challenges to their effective use in therapy.
Collapse
|
20
|
Cell-free synthesis of amyloid fibrils with infectious properties and amenable to sub-milligram magic-angle spinning NMR analysis. Commun Biol 2022; 5:1202. [DOI: 10.1038/s42003-022-04175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractStructural investigations of amyloid fibrils often rely on heterologous bacterial overexpression of the protein of interest. Due to their inherent hydrophobicity and tendency to aggregate as inclusion bodies, many amyloid proteins are challenging to express in bacterial systems. Cell-free protein expression is a promising alternative to classical bacterial expression to produce hydrophobic proteins and introduce NMR-active isotopes that can improve and speed up the NMR analysis. Here we implement the cell-free synthesis of the functional amyloid prion HET-s(218-289). We present an interesting case where HET-s(218-289) directly assembles into infectious fibril in the cell-free expression mixture without the requirement of denaturation procedures and purification. By introducing tailored 13C and 15N isotopes or CF3 and 13CH2F labels at strategic amino-acid positions, we demonstrate that cell-free synthesized amyloid fibrils are readily amenable to high-resolution magic-angle spinning NMR at sub-milligram quantity.
Collapse
|
21
|
Ibáñez de Opakua A, Geraets JA, Frieg B, Dienemann C, Savastano A, Rankovic M, Cima-Omori MS, Schröder GF, Zweckstetter M. Molecular interactions of FG nucleoporin repeats at high resolution. Nat Chem 2022; 14:1278-1285. [PMID: 36138110 PMCID: PMC9630130 DOI: 10.1038/s41557-022-01035-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/02/2022] [Indexed: 12/01/2022]
Abstract
Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG–FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities. ![]()
Proteins rich in phenylalanine-glycine (FG) repeats can phase separate through FG–FG interactions. The molecular interactions of an important FG-repeat protein, nucleoporin 98, have now been studied in liquid-like transient and amyloid-like cohesive states. These interactions underlie the behaviour of FG-repeat proteins and their function in physiological and pathological cell activities.
Collapse
Affiliation(s)
| | - James A Geraets
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Benedikt Frieg
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | | | - Marija Rankovic
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany
| | | | - Gunnar F Schröder
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases, Göttingen, Germany. .,Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany.
| |
Collapse
|
22
|
Wang Y, Liu Y, Zhang Y, Wei G, Ding F, Sun Y. Molecular insights into the oligomerization dynamics and conformations of amyloidogenic and non-amyloidogenic amylin from discrete molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:21773-21785. [PMID: 36098068 PMCID: PMC9623603 DOI: 10.1039/d2cp02851d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The amyloid aggregation of human islet amyloid polypeptide (hIAPP) is associated with pancreatic β-cell death in type 2 diabetes. The S20G substitution of hIAPP (hIAPP(S20G)), found in Japanese and Chinese people, is more amyloidogenic and cytotoxic than wild-type hIAPP. Rat amylin (rIAPP) does not have aggregation propensity or cytotoxicity. Mounting evidence suggests that soluble low-molecular-weight amyloid oligomers formed during early aggregation are more cytotoxic than mature fibrils. The self-assembly dynamics and oligomeric conformations remain unknown because the oligomers are heterogeneous and transient. The molecular mechanism of sequence-variation rendering dramatically different aggregation propensity and cytotoxicity is also elusive. Here, we investigate the oligomerization dynamics and conformations of amyloidogenic hIAPP, hIAPP(S20G), and non-amyloidogenic rIAPP using atomistic discrete molecular dynamics (DMD) simulations. Our simulation results demonstrated that all three monomeric amylin peptides mainly adopted an unstructured formation with partial dynamical helices near the N-terminus. Relatively transient β-hairpins were more abundant in hIAPP and hIAPP(S20G) than in rIAPP. The S20G-substituting mutant of hIAPP altered the turn region of the β-hairpin motif, resulting in more hydrophobic residue-pairwise contacts within the β-hairpin. Oligomerization dynamic investigation revealed that all three peptides spontaneously accumulated into helix-populated oligomers. The conformational conversion to form β-sheet-rich oligomers was only observed in hIAPP and hIAPP(S20G). The population of high-β-sheet-content oligomers was enhanced by S20G substitution. Interestingly, both hIAPP and hIAPP(S20G) could form β-barrel formations, and the β-barrel propensity of hIAPP(S20G) was three times larger than that of hIAPP. No β-sheet-rich or β-barrel formations were observed in rIAPP. Our direct observation of the correlation between β-barrel oligomer formation and cytotoxicity suggests that β-barrels might play a critically important role in the cytotoxicity of amyloidosis.
Collapse
Affiliation(s)
- Ying Wang
- Department of Physics, Ningbo University, Ningbo 315211, China.
| | - Yuying Liu
- Department of Physics, Ningbo University, Ningbo 315211, China.
| | - Yu Zhang
- Department of Physics, Ningbo University, Ningbo 315211, China.
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China.
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
23
|
Siemer AB. What makes functional amyloids work? Crit Rev Biochem Mol Biol 2022; 57:399-411. [PMID: 35997712 PMCID: PMC9588633 DOI: 10.1080/10409238.2022.2113030] [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: 01/25/2022] [Revised: 06/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-β fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-β fibrils that show how function is usually achieved by leveraging many of these properties.
Collapse
Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
24
|
Bücker R, Seuring C, Cazey C, Veith K, García-Alai M, Grünewald K, Landau M. The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Nat Commun 2022; 13:4356. [PMID: 35896552 PMCID: PMC9329304 DOI: 10.1038/s41467-022-32039-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids. In this work the authors provide high-resolution structural support for the amyloid-antimicrobial link via functional amyloids displaying propeller-like and kinked cross-β fibrils.
Collapse
Affiliation(s)
- Robert Bücker
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Rigaku Europe SE, Neu-Isenburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Cornelia Cazey
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Maria García-Alai
- Centre for Structural Systems Biology, Hamburg, Germany.,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Hamburg, Germany. .,Department of Chemistry, University of Hamburg, Hamburg, Germany. .,Leibniz Institute of Virology, Hamburg, Germany. .,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Meytal Landau
- Centre for Structural Systems Biology, Hamburg, Germany. .,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany. .,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
| |
Collapse
|
25
|
Golan N, Engelberg Y, Landau M. Structural Mimicry in Microbial and Antimicrobial Amyloids. Annu Rev Biochem 2022; 91:403-422. [PMID: 35729071 DOI: 10.1146/annurev-biochem-032620-105157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The remarkable variety of microbial species of human pathogens and microbiomes generates significant quantities of secreted amyloids, which are structured protein fibrils that serve diverse functions related to virulence and interactions with the host. Human amyloids are associated largely with fatal neurodegenerative and systemic aggregation diseases, and current research has put forward the hypothesis that the interspecies amyloid interactome has physiological and pathological significance. Moreover, functional and molecular-level connections between antimicrobial activity and amyloid structures suggest a neuroimmune role for amyloids that are otherwise known to be pathological. Compared to the extensive structural information that has been accumulated for human amyloids, high-resolution structures of microbial and antimicrobial amyloids are only emerging. These recent structures reveal both similarities and surprising departures from the typical amyloid motif, in accordance with their diverse activities, and advance the discovery of novel antivirulence and antimicrobial agents. In addition, the structural information has led researchers to postulate that amyloidogenic sequences are natural targets for structural mimicry, for instance in host-microbe interactions. Microbial amyloid research could ultimately be used to fight aggressive infections and possibly processes leading to autoimmune and neurodegenerative diseases.
Collapse
Affiliation(s)
- Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Yizhaq Engelberg
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel; .,European Molecular Biology Laboratory (EMBL) and Center for Structural Systems Biology (CSSB), Hamburg, Germany
| |
Collapse
|
26
|
Akbey Ü, Andreasen M. Functional amyloids from bacterial biofilms - structural properties and interaction partners. Chem Sci 2022; 13:6457-6477. [PMID: 35756505 PMCID: PMC9172111 DOI: 10.1039/d2sc00645f] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/05/2022] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation and amyloid formation have historically been linked with various diseases such as Alzheimer's and Parkinson's disease, but recently functional amyloids have gained a great deal of interest in not causing a disease and having a distinct function in vivo. Functional bacterial amyloids form the structural scaffold in bacterial biofilms and provide a survival strategy for the bacteria along with antibiotic resistance. The formation of functional amyloids happens extracellularly which differs from most disease related amyloids. Studies of functional amyloids have revealed several distinctions compared to disease related amyloids including primary structures designed to optimize amyloid formation while still retaining a controlled assembly of the individual subunits into classical cross-β-sheet structures, along with a unique cross-α-sheet amyloid fold. Studies have revealed that functional amyloids interact with components found in the extracellular matrix space such as lipids from membranes and polymers from the biofilm. Intriguingly, a level of complexity is added as functional amyloids also interact with several disease related amyloids and a causative link has even been established between functional amyloids and neurodegenerative diseases. It is hence becoming increasingly clear that functional amyloids are not inert protein structures found in bacterial biofilms but interact with many different components including human proteins related to pathology. Gaining a clear understanding of the factors governing the interactions will lead to improved strategies to combat biofilm associated infections and the correlated antibiotic resistance. In the current review we summarize the current state of the art knowledge on this exciting and fast growing research field of biofilm forming bacterial functional amyloids, their structural features and interaction partners.
Collapse
Affiliation(s)
- Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University Wilhelm Meyers Allé 3 8000 Aarhus Denmark
| |
Collapse
|
27
|
Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
Collapse
|
28
|
Adhesion as a Focus in Trichoderma–Root Interactions. J Fungi (Basel) 2022; 8:jof8040372. [PMID: 35448603 PMCID: PMC9026816 DOI: 10.3390/jof8040372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 02/06/2023] Open
Abstract
Fungal spores, germlings, and mycelia adhere to substrates, including host tissues. The adhesive forces depend on the substrate and on the adhesins, the fungal cell surface proteins. Attachment is often a prerequisite for the invasion of the host, hence its importance. Adhesion visibly precedes colonization of root surfaces and outer cortex layers, but little is known about the molecular details. We propose that by starting from what is already known from other fungi, including yeast and other filamentous pathogens and symbionts, the mechanism and function of Trichoderma adhesion will become accessible. There is a sequence, and perhaps functional, homology to other rhizosphere-competent Sordariomycetes. Specifically, Verticillium dahliae is a soil-borne pathogen that establishes itself in the xylem and causes destructive wilt disease. Metarhizium species are best-known as insect pathogens with biocontrol potential, but they also colonize roots. Verticillium orthologs of the yeast Flo8 transcription factor, Som1, and several other relevant genes are already under study for their roles in adhesion. Metarhizium encodes relevant adhesins. Trichoderma virens encodes homologs of Som1, as well as adhesin candidates. These genes should provide exciting leads toward the first step in the establishment of beneficial interactions with roots in the rhizosphere.
Collapse
|
29
|
Tempra C, Scollo F, Pannuzzo M, Lolicato F, La Rosa C. A unifying framework for amyloid-mediated membrane damage: The lipid-chaperone hypothesis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140767. [PMID: 35144022 DOI: 10.1016/j.bbapap.2022.140767] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Aβ peptide, which is known to form senile plaques in Alzheimer's disease; ii) α-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) functional conformations and accumulate as amyloid aggregates upon interaction with other cytosolic partners such as proteins or lipid membranes. In addition, an increasing number of reports link the toxicity of amyloid proteins to their harmful effects on membrane integrity. Still, the molecular mechanism underlying the amyloidogenic proteins transfer from the aqueous environment to the hydrocarbon core of the membrane is poorly understood. This review starts with a historical overview of the toxicity models of amyloidogenic proteins to contextualize the more recent lipid-chaperone hypothesis. Then, we report the early molecular-level events in the aggregation and ion-channel pore formation of Aβ, IAPP, and α-synuclein interacting with model membranes, emphasizing the complexity of these processes due to their different spatial-temporal resolutions. Next, we underline the need for a combined experimental and computational approach, focusing on the strengths and weaknesses of the most commonly used techniques. Finally, the last two chapters highlight the crucial role of lipid-protein complexes as molecular switches among ion-channel-like formation, detergent-like, and fibril formation mechanisms and their implication in fighting amyloidogenic diseases.
Collapse
Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
| | - Federica Scollo
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
| |
Collapse
|
30
|
Computational methods to predict protein aggregation. Curr Opin Struct Biol 2022; 73:102343. [PMID: 35240456 DOI: 10.1016/j.sbi.2022.102343] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 01/13/2023]
Abstract
In most cases, protein aggregation stems from the establishment of non-native intermolecular contacts. The formation of insoluble protein aggregates is associated with many human diseases and is a major bottleneck for the industrial production of protein-based therapeutics. Strikingly, fibrillar aggregates are naturally exploited for structural scaffolding or to generate molecular switches and can be artificially engineered to build up multi-functional nanomaterials. Thus, there is a high interest in rationalizing and forecasting protein aggregation. Here, we review the available computational toolbox to predict protein aggregation propensities, identify sequential or structural aggregation-prone regions, evaluate the impact of mutations on aggregation or recognize prion-like domains. We discuss the strengths and limitations of these algorithms and how they can evolve in the next future.
Collapse
|
31
|
Sexton DL, Burgold S, Schertel A, Tocheva EI. Super-resolution confocal cryo-CLEM with cryo-FIB milling for in situ imaging of Deinococcus radiodurans. Curr Res Struct Biol 2022; 4:1-9. [PMID: 34977598 PMCID: PMC8688812 DOI: 10.1016/j.crstbi.2021.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022] Open
Abstract
Studying bacterial cell envelope architecture with electron microscopy is challenging due to the poor preservation of microbial ultrastructure with traditional methods. Here, we established and validated a super-resolution cryo-correlative light and electron microscopy (cryo-CLEM) method, and combined it with cryo-focused ion beam (cryo-FIB) milling and scanning electron microscopy (SEM) volume imaging to structurally characterize the bacterium Deinococcus radiodurans. Subsequent cryo-electron tomography (cryo-ET) revealed an unusual diderm cell envelope architecture with a thick layer of peptidoglycan (PG) between the inner and outer membranes, an additional periplasmic layer, and a proteinaceous surface S-layer. Cells grew in tetrads, and division septa were formed by invagination of the inner membrane (IM), followed by a thick layer of PG. Cytoskeletal filaments, FtsA and FtsZ, were observed at the leading edges of constricting septa. Numerous macromolecular complexes were found associated with the cytoplasmic side of the IM. Altogether, our study revealed several unique ultrastructural features of D. radiodurans cells, opening new lines of investigation into the physiology and evolution of the bacterium. User-friendly, commercially available method for correlative cryo-super resolution light microscopy (LM) and cryo-FIB-milling. Cryo-super resolution LM, cryo-FIB milling, cryo-SEM volume imaging, and cryo-electron tomography (cryo-ET) to study Deinococcus radiodurans. Unique D. radiodurans cell envelope is composed of two membranes, thick peptidoglycan, an additional layer, and an S-layer. Cytoskeletal filaments FtsA and FtsZ were observed at the leading edges of division septa.
Collapse
Affiliation(s)
- Danielle L Sexton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | | | | | - Elitza I Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| |
Collapse
|
32
|
Lendel C, Solin N. Protein nanofibrils and their use as building blocks of sustainable materials. RSC Adv 2021; 11:39188-39215. [PMID: 35492452 PMCID: PMC9044473 DOI: 10.1039/d1ra06878d] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022] Open
Abstract
The development towards a sustainable society requires a radical change of many of the materials we currently use. Besides the replacement of plastics, derived from petrochemical sources, with renewable alternatives, we will also need functional materials for applications in areas ranging from green energy and environmental remediation to smart foods. Proteins could, with their intriguing ability of self-assembly into various forms, play important roles in all these fields. To achieve that, the code for how to assemble hierarchically ordered structures similar to the protein materials found in nature must be cracked. During the last decade it has been demonstrated that amyloid-like protein nanofibrils (PNFs) could be a steppingstone for this task. PNFs are formed by self-assembly in water from a range of proteins, including plant resources and industrial side streams. The nanofibrils display distinct functional features and can be further assembled into larger structures. PNFs thus provide a framework for creating ordered, functional structures from the atomic level up to the macroscale. This review address how industrial scale protein resources could be transformed into PNFs and further assembled into materials with specific mechanical and functional properties. We describe what is required from a protein to form PNFs and how the structural properties at different length scales determine the material properties. We also discuss potential chemical routes to modify the properties of the fibrils and to assemble them into macroscopic structures.
Collapse
Affiliation(s)
- Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology Teknikringen 30 SE-100 44 Stockholm Sweden
| | - Niclas Solin
- Department of Physics, Chemistry, and Biology, Electronic and Photonic Materials, Biomolecular and Organic Electronics, Linköping University Linköping 581 83 Sweden
| |
Collapse
|
33
|
Siri M, Herrera M, Moyano AJ, Celej MS. Influence of the macromolecular crowder alginate in the fibrillar organization of the functional amyloid FapC from Pseudomonas aeruginosa. Arch Biochem Biophys 2021; 713:109062. [PMID: 34688606 DOI: 10.1016/j.abb.2021.109062] [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: 06/24/2021] [Revised: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Bacterial biofilms are an alternative lifestyle in which communities of bacteria are embedded in an extracellular matrix manly composed by polysaccharides, nucleic acids and proteins, being the hallmark of bacterial survival in a variety of ecological niches. Amyloid fibrils are one of the proteinaceous components of such extracellular crowded environments. FapC is the main component of the functional amyloid recently discovered in Pseudomonas species, including the opportunistic pathogen P. aeruginosa, which is a major cause of nosocomial infections and contamination of medical devices. Considering that several functional roles have been attributed to this bacterial amyloid, FapC emerged as a novel target to control Pseudomonas biofilm formation and to design new treatments against chronic infections. In this study, we used complementary biophysical techniques to evaluate conformational signatures of FapC amyloids formed in the presence of alginate, the major exopolysaccharide associated with the mucoid phenotype of P. aeruginosa strains isolated from cystic fibrosis patients. We found that the this naturally occurring macromolecular crowder leads to morphological similar yet polymorphic FapC fibrils, highlighting the importance of considering the complexity of the extracellular matrix in order to improve our understanding of microbial functional amyloids.
Collapse
Affiliation(s)
- Macarena Siri
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Melisa Herrera
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Alejandro J Moyano
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.
| |
Collapse
|
34
|
Turbant F, Wu P, Wien F, Arluison V. The Amyloid Region of Hfq Riboregulator Promotes DsrA: rpoS RNAs Annealing. BIOLOGY 2021; 10:biology10090900. [PMID: 34571778 PMCID: PMC8468756 DOI: 10.3390/biology10090900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 11/16/2022]
Abstract
Hfq is a bacterial RNA chaperone which promotes the pairing of small noncoding RNAs to target mRNAs, allowing post-transcriptional regulation. This RNA annealing activity has been attributed for years to the N-terminal region of the protein that forms a toroidal structure with a typical Sm-fold. Nevertheless, many Hfqs, including that of Escherichia coli, have a C-terminal region with unclear functions. Here we use a biophysical approach, Synchrotron Radiation Circular Dichroism (SRCD), to probe the interaction of the E. coli Hfq C-terminal amyloid region with RNA and its effect on RNA annealing. This C-terminal region of Hfq, which has been described to be dispensable for sRNA:mRNA annealing, has an unexpected and significant effect on this activity. The functional consequences of this novel property of the amyloid region of Hfq in relation to physiological stress are discussed.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Pengzhi Wu
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland;
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- UFR Sciences du Vivant, Université de Paris, 75006 Paris, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
| |
Collapse
|
35
|
Exploring amyloid oligomers with peptide model systems. Curr Opin Chem Biol 2021; 64:106-115. [PMID: 34229162 DOI: 10.1016/j.cbpa.2021.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/26/2021] [Accepted: 05/09/2021] [Indexed: 01/06/2023]
Abstract
The assembly of amyloidogenic peptides and proteins, such as the β-amyloid peptide, α-synuclein, huntingtin, tau, and islet amyloid polypeptide, into amyloid fibrils and oligomers is directly linked to amyloid diseases, such as Alzheimer's, Parkinson's, and Huntington's diseases, frontotemporal dementias, and type II diabetes. Although amyloid oligomers have emerged as especially important in amyloid diseases, high-resolution structures of the oligomers formed by full-length amyloidogenic peptides and proteins have remained elusive. Investigations of oligomers assembled from fragments or stabilized β-hairpin segments of amyloidogenic peptides and proteins have allowed investigators to illuminate some of the structural, biophysical, and biological properties of amyloid oligomers. Here, we summarize recent advances in the application of these peptide model systems to investigate and understand the structures, biological properties, and biophysical properties of amyloid oligomers.
Collapse
|
36
|
Masrati G, Landau M, Ben-Tal N, Lupas A, Kosloff M, Kosinski J. Integrative Structural Biology in the Era of Accurate Structure Prediction. J Mol Biol 2021; 433:167127. [PMID: 34224746 DOI: 10.1016/j.jmb.2021.167127] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
Characterizing the three-dimensional structure of macromolecules is central to understanding their function. Traditionally, structures of proteins and their complexes have been determined using experimental techniques such as X-ray crystallography, NMR, or cryo-electron microscopy-applied individually or in an integrative manner. Meanwhile, however, computational methods for protein structure prediction have been improving their accuracy, gradually, then suddenly, with the breakthrough advance by AlphaFold2, whose models of monomeric proteins are often as accurate as experimental structures. This breakthrough foreshadows a new era of computational methods that can build accurate models for most monomeric proteins. Here, we envision how such accurate modeling methods can combine with experimental structural biology techniques, enhancing integrative structural biology. We highlight the challenges that arise when considering multiple structural conformations, protein complexes, and polymorphic assemblies. These challenges will motivate further developments, both in modeling programs and in methods to solve experimental structures, towards better and quicker investigation of structure-function relationships.
Collapse
Affiliation(s)
- Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Andrei Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Mickey Kosloff
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838 Haifa, Israel.
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany; Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| |
Collapse
|
37
|
Turbant F, Hamoui OE, Partouche D, Sandt C, Busi F, Wien F, Arluison V. Identification and characterization of the Hfq bacterial amyloid region DNA interactions. BBA ADVANCES 2021; 1:100029. [PMID: 37082015 PMCID: PMC10074921 DOI: 10.1016/j.bbadva.2021.100029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Nucleic acid amyloid proteins interactions have been observed in the past few years. These interactions often promote protein aggregation. Nevertheless, molecular basis and physiological consequences of these interactions are still poorly understood. Additionally, it is unknown whether the nucleic acid promotes the formation of self-assembly due to direct interactions or indirectly via sequences surrounding the amyloid region. Here we focus our attention on a bacterial amyloid, Hfq. This protein is a pleiotropic bacterial regulator that mediates many aspects of nucleic acids metabolism. The protein notably mediates mRNA stability and translation efficiency by using stress-related small non coding regulatory RNA. In addition, Hfq, thanks to its amyloid C-terminal region, binds and compacts DNA. A combination of experimental methodologies, including synchrotron radiation circular dichroism (SRCD), gel shift assay and infrared (FTIR) spectroscopy have been used to probe the interaction of Hfq C-terminal region with DNA. We clearly identify important amino acids in this region involved in DNA binding and polymerization properties. This allows to understand better how this bacterial amyloid interacts with DNA. Possible functional consequence to answer to stresses are discussed.
Collapse
Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Omar El Hamoui
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - David Partouche
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Christophe Sandt
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florent Busi
- Université de Paris, UFR Sciences du vivant, 75006 Paris cedex, France
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
- Corresponding author.
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Université de Paris, UFR Sciences du vivant, 75006 Paris cedex, France
- Corresponding author.
| |
Collapse
|