1
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Holfeld A, Schuster D, Sesterhenn F, Gillingham AK, Stalder P, Haenseler W, Barrio-Hernandez I, Ghosh D, Vowles J, Cowley SA, Nagel L, Khanppnavar B, Serdiuk T, Beltrao P, Korkhov VM, Munro S, Riek R, de Souza N, Picotti P. Systematic identification of structure-specific protein-protein interactions. Mol Syst Biol 2024:10.1038/s44320-024-00037-6. [PMID: 38702390 DOI: 10.1038/s44320-024-00037-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis-mass spectrometry (LiP-MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP-MS detects well-characterized PPIs, including antibody-target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states.
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Affiliation(s)
- Aleš Holfeld
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dina Schuster
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Fabian Sesterhenn
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Patrick Stalder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Walther Haenseler
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- University Research Priority Program AdaBD (Adaptive Brain Circuits in Development and Learning), University of Zurich, Zurich, Switzerland
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Jane Vowles
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sally A Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Luise Nagel
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Basavraj Khanppnavar
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Volodymyr M Korkhov
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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2
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Kwiatkowski W, Greenwald J, Murzakhmetov L, Robinson RC, Riek R. Short Peptide Amyloids Are a Potential Sequence Pool for the Emergence of Proteins. J Mol Biol 2024; 436:168495. [PMID: 38360090 DOI: 10.1016/j.jmb.2024.168495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/15/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
Under prebiotic conditions, peptides are capable of self-replication through a structure-based template-assisted mechanism when they form amyloids. Furthermore, peptide amyloids can spontaneously form inside fatty acid vesicles creating membrane enclosed complex structures of variable morphologies. This is possible because fatty acid vesicle membranes act as filters allowing passage of activated amino acids while some amino acids derived from the activated species become non-permeable and trapped in the vesicles. Similarly, nascent peptides derived from the condensation of the activated amino acids are also trapped in the vesicles. It is hypothesized that such preselected peptide amyloids become a sequence pool for the emergence of proteins in life and that after billions of years of cellular evolution, the sequences in the current proteome have diverged significantly from these original seed peptides. If this hypothesis is correct, it could be possible to detect the traces of these seed sequences in current proteomes. Here, we show for all possible 3, 6, 7, 8 or 9 residue sequence motifs that those motifs that are most amyloidogenic/aggregation prone are over-represented in extant proteomes compared to a sequence-randomized proteome. Furthermore, we find that there is a greater proportion of amyloidogenic sequence motifs in archaea proteomes than in the larger primate proteomes. This suggests that the evolution towards larger proteomes leads to smaller proportion of amyloidogenic sequences.
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Affiliation(s)
| | | | | | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand; Research Institute for Interdisciplinary Science, Okayama University, Japan
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3
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Gampp O, Kadavath H, Riek R. NMR tools to detect protein allostery. Curr Opin Struct Biol 2024; 86:102792. [PMID: 38428364 DOI: 10.1016/j.sbi.2024.102792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Allostery is a fundamental mechanism of cellular homeostasis by intra-protein communication between distinct functional sites. It is an internal process of proteins to steer interactions not only with each other but also with other biomolecules such as ligands, lipids, and nucleic acids. In addition, allosteric regulation is particularly important in enzymatic activities. A major challenge in structural and molecular biology today is unraveling allosteric sites in proteins, to elucidate the detailed mechanism of allostery and the development of allosteric drugs. Here we summarize the recently developed tools and approaches which enable the elucidation of regulatory hotspots and correlated motion in biomolecules, focusing primarily on solution-state nuclear magnetic resonance spectroscopy (NMR). These tools open an avenue towards a rational understanding of the mechanism of allostery and provide essential information for the design of allosteric drugs.
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Affiliation(s)
- Olivia Gampp
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Harindranath Kadavath
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland; St. Jude Children's Research Hospital, 262 Danny Thomas Place, 38105 Memphis, Tennessee, USA. https://twitter.com/harijik
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland.
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4
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Prymaczok NC, De Francesco PN, Mazzetti S, Humbert-Claude M, Tenenbaum L, Cappelletti G, Masliah E, Perello M, Riek R, Gerez JA. Cell-to-cell transmitted alpha-synuclein recapitulates experimental Parkinson's disease. NPJ Parkinsons Dis 2024; 10:10. [PMID: 38184623 PMCID: PMC10771530 DOI: 10.1038/s41531-023-00618-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/08/2023] [Indexed: 01/08/2024] Open
Abstract
Parkinson's disease is characterized by a progressive accumulation of alpha-Synuclein (αSyn) neuronal inclusions called Lewy bodies in the nervous system. Lewy bodies can arise from the cell-to-cell propagation of αSyn, which can occur via sequential steps of secretion and uptake. Here, by fusing a removable short signal peptide to the N-terminus of αSyn, we developed a novel mouse model with enhanced αSyn secretion and cell-to-cell transmission. Expression of the secreted αSyn in the mouse brain was under the control of a novel hybrid promoter in combination with adeno-associated virus serotype 9 (AAV9). This combination of promoter and viral vector induced a robust expression in neurons but not in the glia of injected mice. Biochemical characterization of the secreted αSyn revealed that, in cultured cells, this protein is released to the extracellular milieu via conventional secretion. The released αSyn is then internalized and processed by acceptor cells via the endosome-lysosome pathway indicating that the secreted αSyn is cell-to-cell transmitted. The secreted αSyn is aggregation-prone and amyloidogenic, and when expressed in the brain of wild-type non-transgenic mice, it induces a Parkinson's disease-like phenotype that includes a robust αSyn pathology in the substantia nigra, neuronal loss, neuroinflammation, and motor deficits, all the key features of experimental animal models of Parkinson's disease. In summary, a novel animal model of Parkinson's disease based on enhanced cell-to-cell transmission of αSyn was developed. The neuron-produced cell-to-cell transmitted αSyn triggers all phenotypic features of experimental Parkinson's disease in mice.
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Affiliation(s)
- Natalia Cecilia Prymaczok
- Institute of Molecular Physical Science, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Pablo Nicolas De Francesco
- Laboratory of Neurophysiology of the Multidisciplinary Institute of Cell Biology (IMBICE), dependent of the Argentine Research Council (CONICET), Scientific Research Commission and University of La Plata Buenos Aires, La Plata, Argentina
| | - Samanta Mazzetti
- Department of Biosciences, Università degli Studi di Milano, Milano, Italy
- Fondazione Grigioni per il Morbo di Parkinson, Milano, Italy
| | - Marie Humbert-Claude
- Laboratory of Neurotherapies and NeuroModulation, Clinical Neuroscience Department, Center for Neuroscience Research, Lausanne University Hospital, Lausanne, Switzerland
| | - Liliane Tenenbaum
- Laboratory of Neurotherapies and NeuroModulation, Clinical Neuroscience Department, Center for Neuroscience Research, Lausanne University Hospital, Lausanne, Switzerland
| | - Graziella Cappelletti
- Department of Biosciences, Università degli Studi di Milano, Milano, Italy
- Fondazione Grigioni per il Morbo di Parkinson, Milano, Italy
| | - Eliezer Masliah
- Division of Neurosciences, National Institute on Aging/NIH, 7201, Wisconsin Ave, Bethesda, MD, USA
| | - Mario Perello
- Laboratory of Neurophysiology of the Multidisciplinary Institute of Cell Biology (IMBICE), dependent of the Argentine Research Council (CONICET), Scientific Research Commission and University of La Plata Buenos Aires, La Plata, Argentina
| | - Roland Riek
- Institute of Molecular Physical Science, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Juan Atilio Gerez
- Institute of Molecular Physical Science, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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5
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Klukowski P, Damberger FF, Allain FHT, Iwai H, Kadavath H, Ramelot TA, Montelione GT, Riek R, Güntert P. The 100-protein NMR spectra dataset: A resource for biomolecular NMR data analysis. Sci Data 2024; 11:30. [PMID: 38177162 PMCID: PMC10767026 DOI: 10.1038/s41597-023-02879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024] Open
Abstract
Multidimensional NMR spectra are the basis for studying proteins by NMR spectroscopy and crucial for the development and evaluation of methods for biomolecular NMR data analysis. Nevertheless, in contrast to derived data such as chemical shift assignments in the BMRB and protein structures in the PDB databases, this primary data is in general not publicly archived. To change this unsatisfactory situation, we present a standardized set of solution NMR data comprising 1329 2-4-dimensional NMR spectra and associated reference (chemical shift assignments, structures) and derived (peak lists, restraints for structure calculation, etc.) annotations. With the 100-protein NMR spectra dataset that was originally compiled for the development of the ARTINA deep learning-based spectra analysis method, 100 protein structures can be reproduced from their original experimental data. The 100-protein NMR spectra dataset is expected to help the development of computational methods for NMR spectroscopy, in particular machine learning approaches, and enable consistent and objective comparisons of these methods.
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Affiliation(s)
- Piotr Klukowski
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Fred F Damberger
- Institute of Biochemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Hideo Iwai
- Institute of Biotechnology, University of Helsinki, 00100, Helsinki, Finland
| | | | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
| | - Peter Güntert
- Institute of Molecular Physical Science, ETH Zurich, 8093, Zurich, Switzerland.
- Institute of Biophysical Chemistry, Goethe University, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, 192-0397, Tokyo, Japan.
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6
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Klukowski P, Riek R, Güntert P. Time-optimized protein NMR assignment with an integrative deep learning approach using AlphaFold and chemical shift prediction. Sci Adv 2023; 9:eadi9323. [PMID: 37992167 PMCID: PMC10664993 DOI: 10.1126/sciadv.adi9323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Chemical shift assignment is vital for nuclear magnetic resonance (NMR)-based studies of protein structures, dynamics, and interactions, providing crucial atomic-level insight. However, obtaining chemical shift assignments is labor intensive and requires extensive measurement time. To address this limitation, we previously proposed ARTINA, a deep learning method for automatic assignment of two-dimensional (2D)-4D NMR spectra. Here, we present an integrative approach that combines ARTINA with AlphaFold and UCBShift, enabling chemical shift assignment with reduced experimental data, increased accuracy, and enhanced robustness for larger systems, as presented in a comprehensive study with more than 5000 automated assignment calculations on 89 proteins. We demonstrate that five 3D spectra yield more accurate assignments (92.59%) than pure ARTINA runs using all experimentally available NMR data (on average 10 3D spectra per protein, 91.37%), considerably reducing the required measurement time. We also showcase automated assignments of only 15N-labeled samples, and report improved assignment accuracy in larger synthetic systems of up to 500 residues.
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Affiliation(s)
- Piotr Klukowski
- Institute of Molecular Physical Science, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Peter Güntert
- Institute of Molecular Physical Science, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, 192-0397 Tokyo, Japan
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7
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Rout S, Cadalbert R, Schröder N, Wang J, Zehnder J, Gampp O, Wiegand T, Güntert P, Klingler D, Kreutz C, Knörlein A, Hall J, Greenwald J, Riek R. An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA. J Am Chem Soc 2023; 145:21915-21924. [PMID: 37782045 PMCID: PMC10571083 DOI: 10.1021/jacs.3c06287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 10/03/2023]
Abstract
Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.
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Affiliation(s)
- Saroj
K. Rout
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Nina Schröder
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Julia Wang
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Johannes Zehnder
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Olivia Gampp
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
- Max
Planck Institute for Chemical Energy Conversion, 45470 Mülheim/Ruhr, Germany
| | - Peter Güntert
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
- Institute
of Biophysical Chemistry, Goethe University, 60438 Frankfurt
am Main, Germany
- Department
of Chemistry, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - David Klingler
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute
of Organic Chemistry and Center for Molecular Biosciences Innsbruck
(CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Anna Knörlein
- Institute
of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Institute
of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland
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8
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Wetton H, Klukowski P, Riek R, Güntert P. Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA. Front Mol Biosci 2023; 10:1244029. [PMID: 37854037 PMCID: PMC10581199 DOI: 10.3389/fmolb.2023.1244029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023] Open
Abstract
Chemical shift transfer (CST) is a well-established technique in NMR spectroscopy that utilizes the chemical shift assignment of one protein (source) to identify chemical shifts of another (target). Given similarity between source and target systems (e.g., using homologs), CST allows the chemical shifts of the target system to be assigned using a limited amount of experimental data. In this study, we propose a deep-learning based workflow, ARTINA-CST, that automates this procedure, allowing CST to be carried out within minutes or hours of computational time and strictly without any human supervision. We characterize the efficacy of our method using three distinct synthetic and experimental datasets, demonstrating its effectiveness and robustness even when substantial differences exist between the source and target proteins. With its potential applications spanning a wide range of NMR projects, including drug discovery and protein interaction studies, ARTINA-CST is anticipated to be a valuable method that facilitates research in the field.
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Affiliation(s)
- Henry Wetton
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
| | - Piotr Klukowski
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
| | - Peter Güntert
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
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9
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Stadler GR, Segawa TF, Bütikofer M, Decker V, Loss S, Czarniecki B, Torres F, Riek R. Fragment Screening and Fast Micromolar Detection on a Benchtop NMR Spectrometer Boosted by Photoinduced Hyperpolarization. Angew Chem Int Ed Engl 2023; 62:e202308692. [PMID: 37524651 DOI: 10.1002/anie.202308692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023]
Abstract
Fragment-based drug design is a well-established strategy for rational drug design, with nuclear magnetic resonance (NMR) on high-field spectrometers as the method of reference for screening and hit validation. However, high-field NMR spectrometers are not only expensive, but require specialized maintenance, dedicated space, and depend on liquid helium cooling which became critical over the recurring global helium shortages. We propose an alternative to high-field NMR screening by applying the recently developed approach of fragment screening by photoinduced hyperpolarized NMR on a cryogen-free 80 MHz benchtop NMR spectrometer yielding signal enhancements of up to three orders in magnitude. It is demonstrated that it is possible to discover new hits and kick-off drug design using a benchtop NMR spectrometer at low micromolar concentrations of both protein and ligand. The approach presented performs at higher speed than state-of-the-art high-field NMR approaches while exhibiting a limit of detection in the nanomolar range. Photoinduced hyperpolarization is known to be inexpensive and simple to be implemented, which aligns greatly with the philosophy of benchtop NMR spectrometers. These findings open the way for the use of benchtop NMR in near-physiological conditions for drug design and further life science applications.
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Affiliation(s)
- Gabriela R Stadler
- ETH Zürich, Swiss Federal Institute of Technology, Institute for Molecular Physical Science, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Takuya F Segawa
- ETH Zürich, Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Matthias Bütikofer
- ETH Zürich, Swiss Federal Institute of Technology, Institute for Molecular Physical Science, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Venita Decker
- Bruker BioSpin GmbH, Rudolf-Plank-Strasse 23, 76275, Ettlingen, Germany
| | - Sandra Loss
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Barbara Czarniecki
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Felix Torres
- ETH Zürich, Swiss Federal Institute of Technology, Institute for Molecular Physical Science, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
- NexMR GmbH, Wiesenstrasse 10 A, 8952, Schlieren, Switzerland
| | - Roland Riek
- ETH Zürich, Swiss Federal Institute of Technology, Institute for Molecular Physical Science, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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10
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Sofińska K, Batys P, Cernescu A, Ghosh D, Skirlińska-Nosek K, Barbasz J, Seweryn S, Wilkosz N, Riek R, Szymoński M, Lipiec E. Nanoscale insights into the local structural rearrangements of amyloid-β induced by bexarotene. Nanoscale 2023; 15:14606-14614. [PMID: 37614107 DOI: 10.1039/d3nr01608k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
A better understanding of the abnormal protein aggregation and the effect of anti-aggregation agents on the fibrillation pathways and the secondary structure of aggregates can determine strategies for the early treatment of dementia. Herein, we present a combination of experimental and theoretical studies providing new insights into the influence of the anti-aggregation drug bexarotene on the secondary structure of individual amyloid-β aggregates and its primary aggregation. The molecular rearrangements and the spatial distribution of β-sheets within individual aggregates were monitored at the nanoscale with infrared nanospectroscopy. We observed that bexarotene limits the parallel β-sheets formation, known to be highly abundant in fibrils at later phases of the amyloid-β aggregation composed of in-register cross-β structure. Moreover, we applied molecular dynamics to provide molecular-level insights into the investigated system. Both theoretical and experimental results revealed that bexarotene slows down the protein aggregation process via steric effects, largely prohibiting the antiparallel to parallel β-sheet rearrangement. We also found that bexarotene interacts not only via the single hydrogen bond formation with the peptide backbone but also with the amino acid side residue via a hydrophobic effect. The studied model of the drug-amyloid-β interaction contributes to a better understanding of the inhibition mechanism of the amyloid-β aggregation by the small molecule drugs. However, our nanoscale findings need to meet in vivo research requiring different analytical approaches.
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Affiliation(s)
- Kamila Sofińska
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | | | - Dhiman Ghosh
- ETH Zürich, Laboratory of Physical Chemistry, 8093 Zürich, Switzerland
| | - Katarzyna Skirlińska-Nosek
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Jakub Barbasz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Sara Seweryn
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Natalia Wilkosz
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Reymonta 19, 30-059 Krakow, Poland
| | - Roland Riek
- ETH Zürich, Laboratory of Physical Chemistry, 8093 Zürich, Switzerland
| | - Marek Szymoński
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
| | - Ewelina Lipiec
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
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11
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Torres F, Bütikofer M, Stadler GR, Renn A, Kadavath H, Bobrovs R, Jaudzems K, Riek R. Ultrafast Fragment Screening Using Photo-Hyperpolarized (CIDNP) NMR. J Am Chem Soc 2023. [PMID: 37227050 DOI: 10.1021/jacs.3c01392] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
While nuclear magnetic resonance (NMR) is regarded as a reference in fragment-based drug design, its implementation in a high-throughput manner is limited by its lack of sensitivity resulting in long acquisition times and high micromolar sample concentrations. Several hyperpolarization approaches could, in principle, improve the sensitivity of NMR also in drug research. However, photochemically induced dynamic nuclear polarization (photo-CIDNP) is the only method that is directly applicable in aqueous solution and agile for scalable implementation using off-the-shelf hardware. With the use of photo-CIDNP, this work demonstrates the detection of weak binders in the millimolar affinity range using low micromolar concentrations down to 5 μM of ligand and 2 μM of target, thereby exploiting the photo-CIDNP-induced polarization twice: (i) increasing the signal-to-noise by one to two orders in magnitude and (ii) polarization-only of the free non-bound molecule allowing identification of binding by polarization quenching, yielding another factor of hundred in time when compared with standard techniques. The interaction detection was performed with single-scan NMR experiments of a duration of 2 to 5 s. Taking advantage of the readiness of photo-CIDNP setup implementation, an automated flow-through platform was designed to screen samples at a screening rate of 1500 samples per day. Furthermore, a 212 compounds photo-CIDNP fragment library is presented, opening an avenue toward a comprehensive fragment-based screening method.
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Affiliation(s)
- Felix Torres
- ETH, Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
- NexMR GmbH, Wiesenstrasse 10A, 8952 Schlieren, Switzerland
| | - Matthias Bütikofer
- ETH, Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Gabriela R Stadler
- ETH, Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Alois Renn
- ETH, Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Harindranath Kadavath
- ETH, Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
- St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105-3678 United States
| | - Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles street 21, LV-1006 Riga, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles street 21, LV-1006 Riga, Latvia
| | - Roland Riek
- ETH, Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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12
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Klukowski P, Riek R, Güntert P. NMRtist: an online platform for automated biomolecular NMR spectra analysis. Bioinformatics 2023; 39:7019933. [PMID: 36723167 PMCID: PMC9913044 DOI: 10.1093/bioinformatics/btad066] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/01/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023] Open
Abstract
SUMMARY We present NMRtist, an online platform that combines deep learning, large-scale optimization and cloud computing to automate protein NMR spectra analysis. Our website provides virtual storage for NMR spectra deposition together with a set of applications designed for automated peak picking, chemical shift assignment and protein structure determination. The system can be used by non-experts and allows protein assignments and structures to be determined within hours after the measurements, strictly without any human intervention. AVAILABILITY AND IMPLEMENTATION NMRtist is freely available to non-commercial users at https://nmrtist.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Piotr Klukowski
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.,Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.,Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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13
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Kadavath H, Cecilia Prymaczok N, Eichmann C, Riek R, Gerez JA. Multi-Dimensional Structure and Dynamics Landscape of Proteins in Mammalian Cells Revealed by In-Cell NMR. Angew Chem Int Ed Engl 2023; 62:e202213976. [PMID: 36379877 PMCID: PMC10107511 DOI: 10.1002/anie.202213976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Governing function, half-life and subcellular localization, the 3D structure and dynamics of proteins are in nature constantly changing in a tightly regulated manner to fulfill the physiological and adaptive requirements of the cells. To find evidence for this hypothesis, we applied in-cell NMR to three folded model proteins and propose that the splitting of cross peaks constitutes an atomic fingerprint of distinct structural states that arise from multiple target binding co-existing inside mammalian cells. These structural states change upon protein loss of function or subcellular localisation into distinct cell compartments. In addition to peak splitting, we observed NMR signal intensity attenuations indicative of transient interactions with other molecules and dynamics on the microsecond to millisecond time scale.
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Affiliation(s)
| | | | - Cédric Eichmann
- ETH Zurich, Vladimir-Prelog-weg 2, 8093, Zurich, Switzerland
| | - Roland Riek
- ETH Zurich, Vladimir-Prelog-weg 2, 8093, Zurich, Switzerland
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14
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Ghosh D, Wälti MA, Riek R. An Efficient Method of Expression and Purification of Amyloid-Beta (Aβ 1-42) Peptide from E. coli. Methods Mol Biol 2023; 2551:41-51. [PMID: 36310195 DOI: 10.1007/978-1-0716-2597-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Amyloid-beta (Aβ) aggregation into soluble oligomers and fibril formation are associated with Alzheimer's disease (AD) pathogenesis. Aβ1-42 is the major form of the Aβ peptide present in neuritic plaques and shown to be neurotoxic both in vivo and in vitro. However, understanding the mechanism of its toxicity, aggregation, and other biochemical properties is limited because of its difficult production (recombinant or synthetic) and irreproducibility issues attributed to batch-to-batch preparation differences. Chemically synthetic Aβ1-42 is now well established, but it always introduces up to 5% D-isomers along with its L-isomeric form, and thus it is not fruitful for biochemical/structural studies. Here, we optimized an efficient published method for expression and purification of Aβ1-42 upon overexpression in Escherichia coli (E. coli) that provides a satisfactory yield as well as minimizes the variability between batch preparations. With the present protocol, ~7-8 mg/liter of unlabeled peptide and ~3.5-4 mg/liter for 13C,15N-labeled (double-labeled) Aβ1-42 were obtained.
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Affiliation(s)
- Dhiman Ghosh
- Laboratory for Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Roland Riek
- Laboratory for Physical Chemistry, ETH Zurich, Zurich, Switzerland.
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15
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Gerez JA, Prymaczok NC, Kadavath H, Ghosh D, Bütikofer M, Fleischmann Y, Güntert P, Riek R. Protein structure determination in human cells by in-cell NMR and a reporter system to optimize protein delivery or transexpression. Commun Biol 2022; 5:1322. [PMID: 36460747 PMCID: PMC9718737 DOI: 10.1038/s42003-022-04251-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Most experimental methods for structural biology proceed in vitro and therefore the contribution of the intracellular environment on protein structure and dynamics is absent. Studying proteins at atomic resolution in living mammalian cells has been elusive due to the lack of methodologies. In-cell nuclear magnetic resonance spectroscopy (in-cell NMR) is an emerging technique with the power to do so. Here, we improved current methods of in-cell NMR by the development of a reporter system that allows monitoring the delivery of exogenous proteins into mammalian cells, a process that we called here "transexpression". The reporter system was used to develop an efficient protocol for in-cell NMR which enables spectral acquisition with higher quality for both disordered and folded proteins. With this method, the 3D atomic resolution structure of the model protein GB1 in human cells was determined with a backbone root-mean-square deviation (RMSD) of 1.1 Å.
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Affiliation(s)
- Juan A Gerez
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
| | | | | | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | | | | | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, 192-0397, Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
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16
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Kadavath H, Prymaczok NC, Eichmann C, Riek R, Gerez JA. Multi‐Dimensional Structure and Dynamics Landscape of Proteins in Mammalian Cells Revealed by In‐Cell NMR. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202213976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Harindranath Kadavath
- Swiss Federal Institute of Technology: Eidgenossische Technische Hochschule Zurich DCHAB Vladimir-Prelog-Weg 2 CH-8093 Zürich SWITZERLAND
| | - Natalia Cecilia Prymaczok
- Swiss Federal Institute of Technology: Eidgenossische Technische Hochschule Zurich D-CHAB Vladimir-Prelog-Weg 2 CH-8093 Zurich SWITZERLAND
| | - Cédric Eichmann
- Swiss Federal Institute of Technology: Eidgenossische Technische Hochschule Zurich D-CHAB Vladimir-Prelog-Weg 2 CH-8093 Zurich SWITZERLAND
| | - Roland Riek
- Swiss Federal Institute of Technology: Eidgenossische Technische Hochschule Zurich D-CHAB Vladimir-Prelog-Weg 2 CH-8093 Zurich SWITZERLAND
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology: Eidgenossische Technische Hochschule Zurich Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 2 CH-8093 Zurich SWITZERLAND
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17
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Ashkinadze D, Kadavath H, Pokharna A, Chi CN, Friedmann M, Strotz D, Kumari P, Minges M, Cadalbert R, Königl S, Güntert P, Vögeli B, Riek R. Atomic resolution protein allostery from the multi-state structure of a PDZ domain. Nat Commun 2022; 13:6232. [PMID: 36266302 PMCID: PMC9584909 DOI: 10.1038/s41467-022-33687-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/28/2022] [Indexed: 12/25/2022] Open
Abstract
Recent methodological advances in solution NMR allow the determination of multi-state protein structures and provide insights into structurally and dynamically correlated protein sites at atomic resolution. This is demonstrated in the present work for the well-studied PDZ2 domain of protein human tyrosine phosphatase 1E for which protein allostery had been predicted. Two-state protein structures were calculated for both the free form and in complex with the RA-GEF2 peptide using the exact nuclear Overhauser effect (eNOE) method. In the apo protein, an allosteric conformational selection step comprising almost 60% of the domain was detected with an "open" ligand welcoming state and a "closed" state that obstructs the binding site by changing the distance between the β-sheet 2, α-helix 2, and sidechains of residues Lys38 and Lys72. The observed induced fit-type apo-holo structural rearrangements are in line with the previously published evolution-based analysis covering ~25% of the domain with only a partial overlap with the protein allostery of the open form. These presented structural studies highlight the presence of a dedicated highly optimized and complex dynamic interplay of the PDZ2 domain owed by the structure-dynamics landscape.
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Affiliation(s)
- Dzmitry Ashkinadze
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Harindranath Kadavath
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Aditya Pokharna
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Celestine N. Chi
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75121 Uppsala, Sweden
| | - Michael Friedmann
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Dean Strotz
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Pratibha Kumari
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Martina Minges
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Stefan Königl
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Güntert
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland ,grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany ,grid.265074.20000 0001 1090 2030Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 1920397 Japan
| | - Beat Vögeli
- grid.266190.a0000000096214564Biochemistry and Molecular Genetics Department, University of Colorado School of Medicine, Colorado, CO USA
| | - Roland Riek
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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18
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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19
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022; 61:e202205858. [PMID: 36115062 PMCID: PMC9539013 DOI: 10.1002/anie.202205858] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/17/2022]
Abstract
SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80% of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome.
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Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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20
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Pokharna A, Torres F, Kadavath H, Orts J, Riek R. An improved, time-efficient approach to extract accurate distance restraints for NMR 2 structure calculation. Magn Reson (Gott) 2022; 3:137-144. [PMID: 37904864 PMCID: PMC10539809 DOI: 10.5194/mr-3-137-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/14/2022] [Indexed: 11/01/2023]
Abstract
Exact nuclear Overhauser enhancement (eNOE) yields highly accurate, ensemble averaged 1 H-1 H distance restraints with an accuracy of up to 0.1 Å for the multi-state structure determination of proteins as well as for nuclear magnetic resonance molecular replacement (N MR2 ) to determine the structure of the protein-ligand interaction site in a time-efficient manner. However, in the latter application, the acquired eNOEs lack the obtainable precision of 0.1 Å because of the asymmetrical nature of the filtered nuclear Overhauser enhancement spectroscopy (NOESY) experiment used in N MR2 . This error is further propagated to the eNOE equations used to fit and extract the distance restraints. In this work, a new analysis method is proposed to obtain inter-molecular distance restraints from the filtered NOESY spectrum more accurately and intuitively by dividing the NOE cross peak by the corresponding diagonal peak of the ligand. The method termed diagonal-normalised eNOEs was tested on the data acquired by on the complex of PIN1 and a small, weak-binding phenylimidazole fragment. N MR2 calculations performed using the distances derived from diagonal-normalised eNOEs yielded the right orientation of the fragment in the binding pocket and produced a structure that more closely resembles the benchmark X-ray structure (2XP6) with an average heavy-atom root-mean-square deviation (RMSD) of 1.681 Å with respect to it, when compared to the one produced with traditional N MR2 with an average heavy atom RMSD of 3.628 Å. This is attributed to the higher precision of the evaluated distance restraints.
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Affiliation(s)
- Aditya Pokharna
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Felix Torres
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 2F 353, 1090 Vienna, Austria
| | - Julien Orts
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 2F 353, 1090 Vienna, Austria
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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21
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Lutomski CA, El-Baba TJ, Robinson CV, Riek R, Scheres SHW, Yan N, AlQuraishi M, Gan L. The next decade of protein structure. Cell 2022; 185:2617-2620. [PMID: 35868264 DOI: 10.1016/j.cell.2022.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022]
Abstract
With recent dramatic advances in various techniques used for protein structure research, we asked researchers to comment on the next exciting questions for the field and about how these techniques will advance our knowledge not only about proteins but also about human health and diseases.
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22
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Ashkinadze D, Kadavath H, Riek R, Güntert P. Optimization and validation of multi-state NMR protein structures using structural correlations. J Biomol NMR 2022; 76:39-47. [PMID: 35305195 PMCID: PMC9018667 DOI: 10.1007/s10858-022-00392-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Recent advances in the field of protein structure determination using liquid-state NMR enable the elucidation of multi-state protein conformations that can provide insight into correlated and non-correlated protein dynamics at atomic resolution. So far, NMR-derived multi-state structures were typically evaluated by means of visual inspection of structure superpositions, target function values that quantify the violation of experimented restraints and root-mean-square deviations that quantify similarity between conformers. As an alternative or complementary approach, we present here the use of a recently introduced structural correlation measure, PDBcor, that quantifies the clustering of protein states as an additional measure for multi-state protein structure analysis. It can be used for various assays including the validation of experimental distance restraints, optimization of the number of protein states, estimation of protein state populations, identification of key distance restraints, NOE network analysis and semiquantitative analysis of the protein correlation network. We present applications for the final quality analysis stages of typical multi-state protein structure calculations.
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Affiliation(s)
| | | | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
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23
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Rout SK, Rhyner D, Riek R, Greenwald J. Cover Feature: Prebiotically Plausible Autocatalytic Peptide Amyloids (Chem. Eur. J. 3/2022). Chemistry 2022. [DOI: 10.1002/chem.202104546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Saroj K. Rout
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH Hönggerberg Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - David Rhyner
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH Hönggerberg Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH Hönggerberg Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH Hönggerberg Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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24
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Ashkinadze D, Klukowski P, Kadavath H, Güntert P, Riek R. PDBcor: An automated correlation extraction calculator for multi-state protein structures. Structure 2021; 30:646-652.e2. [PMID: 34963060 DOI: 10.1016/j.str.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/15/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022]
Abstract
Allostery and correlated motion are key elements linking protein dynamics with the mechanisms of action of proteins. Here, we present PDBCor, an automated and unbiased method for the detection and analysis of correlated motions from experimental multi-state protein structures. It uses torsion angle and distance statistics and does not require any structure superposition. Clustering of protein conformers allows us to extract correlations in the form of mutual information based on information theory. With PDBcor, we elucidated correlated motion in the WW domain of PIN1, the protein GB3, and the enzyme cyclophilin, in line with reported findings. Correlations extracted with PDBcor can be utilized in subsequent assays including nuclear magnetic resonance (NMR) multi-state structure optimization and validation. As a guide for the interpretation of PDBcor results, we provide a series of protein structure ensembles that exhibit different levels of correlation, including non-correlated, locally correlated, and globally correlated ensembles.
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Affiliation(s)
- Dzmitry Ashkinadze
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Piotr Klukowski
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 1920397, Japan.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
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25
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Morawska MM, Moreira CG, Ginde VR, Valko PO, Weiss T, Büchele F, Imbach LL, Masneuf S, Kollarik S, Prymaczok N, Gerez JA, Riek R, Baumann CR, Noain D. Slow-wave sleep affects synucleinopathy and regulates proteostatic processes in mouse models of Parkinson's disease. Sci Transl Med 2021; 13:eabe7099. [PMID: 34878820 DOI: 10.1126/scitranslmed.abe7099] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Marta M Morawska
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland.,University of Zurich (UZH), Neuroscience Center Zurich (ZNZ), Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Carlos G Moreira
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland.,ETH Zurich, Neuroscience Center Zurich (ZNZ), Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Varun R Ginde
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Philipp O Valko
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Tobias Weiss
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Fabian Büchele
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Lukas L Imbach
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Sophie Masneuf
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Sedef Kollarik
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland.,University of Zurich (UZH), Neuroscience Center Zurich (ZNZ), Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Natalia Prymaczok
- ETH Zurich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Juan A Gerez
- ETH Zurich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Roland Riek
- ETH Zurich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Christian R Baumann
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland.,University of Zurich (UZH), Neuroscience Center Zurich (ZNZ), Winterthurerstrasse 190, Zurich 8057, Switzerland.,Center of Competence Sleep and Health Zurich, University of Zurich, Frauenklinikstrasse 26, Zurich 8091, Switzerland
| | - Daniela Noain
- Department of Neurology, University Hospital Zurich (USZ), Frauenklinikstrasse 26, Zurich 8091, Switzerland.,University of Zurich (UZH), Neuroscience Center Zurich (ZNZ), Winterthurerstrasse 190, Zurich 8057, Switzerland.,Center of Competence Sleep and Health Zurich, University of Zurich, Frauenklinikstrasse 26, Zurich 8091, Switzerland
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26
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Sawner AS, Ray S, Yadav P, Mukherjee S, Panigrahi R, Poudyal M, Patel K, Ghosh D, Kummerant E, Kumar A, Riek R, Maji SK. Modulating α-Synuclein Liquid-Liquid Phase Separation. Biochemistry 2021; 60:3676-3696. [PMID: 34431665 DOI: 10.1021/acs.biochem.1c00434] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Liquid-liquid phase separation (LLPS) is a crucial phenomenon for the formation of functional membraneless organelles. However, LLPS is also responsible for protein aggregation in various neurodegenerative diseases such as amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease (PD). Recently, several reports, including ours, have shown that α-synuclein (α-Syn) undergoes LLPS and a subsequent liquid-to-solid phase transition, which leads to amyloid fibril formation. However, how the environmental (and experimental) parameters modulate the α-Syn LLPS remains elusive. Here, we show that in vitro α-Syn LLPS is strongly dependent on the presence of salts, which allows charge neutralization at both terminal segments of protein and therefore promotes hydrophobic interactions supportive for LLPS. Using various purification methods and experimental conditions, we showed, depending upon conditions, α-Syn undergoes either spontaneous (instantaneous) or delayed LLPS. Furthermore, we delineate that the kinetics of liquid droplet formation (i.e., the critical concentration and critical time) is relative and can be modulated by the salt/counterion concentration, pH, presence of surface, PD-associated multivalent cations, and N-terminal acetylation, which are all known to regulate α-Syn aggregation in vitro. Together, our observations suggest that α-Syn LLPS and subsequent liquid-to-solid phase transition could be pathological, which can be triggered only under disease-associated conditions (high critical concentration and/or conditions promoting α-Syn self-assembly). This study will significantly improve our understanding of the molecular mechanisms of α-Syn LLPS and the liquid-to-solid transition.
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Affiliation(s)
- Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Preeti Yadav
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Rajlaxmi Panigrahi
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Dhiman Ghosh
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Eric Kummerant
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Roland Riek
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
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27
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Vagenknecht P, Dean‐Ben XL, Gerez JA, Mu L, Ji B, Riek R, Razansky D, Klohs J, Nitsch RM, Ni R. High‐resolution non‐invasive whole brain imaging of tauopathy in a tauopathy mouse model. Alzheimers Dement 2021. [DOI: 10.1002/alz.049083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | | | - Bin Ji
- National Institutes for Quantum and Radiological Science and Technology Chiba Japan
| | | | | | - Jan Klohs
- ETH Zurich & University of Zurich Zurich Switzerland
| | | | - Ruiqing Ni
- ETH Zurich & University of Zurich Zurich Switzerland
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Abstract
The prebiotic emergence of molecules capable both of self-replication and of storing information was a defining event at the dawn of life. Still, no plausible prebiotic self-replication of biologically relevant molecules has been demonstrated. Building upon the known templating nature of amyloids, we present two systems in which the products of a peptide-bond-forming reaction act as self-replicators to enhance the yield and stereoselectivity of their formation. This first report of an amino acid condensation that can undergo autocatalysis further supports the potential role of amyloids in prebiotic molecular evolution as an environment-responsive and information-coding system capable of self-replication.
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Affiliation(s)
- Saroj K Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - David Rhyner
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis. Cell 2021; 184:4857-4873. [PMID: 34534463 PMCID: PMC8772536 DOI: 10.1016/j.cell.2021.08.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 02/05/2023]
Abstract
The hidden world of amyloid biology has suddenly snapped into atomic-level focus, revealing over 80 amyloid protein fibrils, both pathogenic and functional. Unlike globular proteins, amyloid proteins flatten and stack into unbranched fibrils. Stranger still, a single protein sequence can adopt wildly different two-dimensional conformations, yielding distinct fibril polymorphs. Thus, an amyloid protein may define distinct diseases depending on its conformation. At the heart of this conformational variability lies structural frustrations. In functional amyloids, evolution tunes frustration levels to achieve either stability or sensitivity according to the fibril's biological function, accounting for the vast versatility of the amyloid fibril scaffold.
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Affiliation(s)
- Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jose A Rodriguez
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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30
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Riek R, Chatterjee A. Causality in Discrete Time Physics Derived from Maupertuis Reduced Action Principle. Entropy (Basel) 2021; 23:e23091212. [PMID: 34573836 PMCID: PMC8472125 DOI: 10.3390/e23091212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/17/2022]
Abstract
Causality describes the process and consequences from an action: a cause has an effect. Causality is preserved in classical physics as well as in special and general theories of relativity. Surprisingly, causality as a relationship between the cause and its effect is in neither of these theories considered a law or a principle. Its existence in physics has even been challenged by prominent opponents in part due to the time symmetric nature of the physical laws. With the use of the reduced action and the least action principle of Maupertuis along with a discrete dynamical time physics yielding an arrow of time, causality is defined as the partial spatial derivative of the reduced action and as such is position- and momentum-dependent and requests the presence of space. With this definition the system evolves from one step to the next without the need of time, while (discrete) time can be reconstructed.
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Affiliation(s)
- Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, CH 8093 Zurich, Switzerland
- Correspondence:
| | - Atanu Chatterjee
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel;
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Sobol A, Güntert P, Riek R. On the Entropy of a One-Dimensional Gas with and without Mixing Using Sinai Billiard. Entropy (Basel) 2021; 23:e23091188. [PMID: 34573813 PMCID: PMC8467902 DOI: 10.3390/e23091188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022]
Abstract
A one-dimensional gas comprising N point particles undergoing elastic collisions within a finite space described by a Sinai billiard generating identical dynamical trajectories are calculated and analyzed with regard to strict extensivity of the entropy definitions of Boltzmann–Gibbs. Due to the collisions, trajectories of gas particles are strongly correlated and exhibit both chaotic and periodic properties. Probability distributions for the position of each particle in the one-dimensional gas can be obtained analytically, elucidating that the entropy in this special case is extensive at any given number N. Furthermore, the entropy obtained can be interpreted as a measure of the extent of interactions between molecules. The results obtained for the non-mixable one-dimensional system are generalized to mixable one- and two-dimensional systems, the latter by a simple example only providing similar findings.
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32
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Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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33
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Torres F, Sobol A, Greenwald J, Renn A, Morozova O, Yurkovskaya A, Riek R. Molecular features toward high photo-CIDNP hyperpolariztion explored through the oxidocyclization of tryptophan. Phys Chem Chem Phys 2021; 23:6641-6650. [PMID: 33710192 DOI: 10.1039/d0cp06068b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Photo-chemically induced dynamic nuclear polarization (photo-CIDNP) is a promising solution to the inherent lack of sensitivity in NMR spectroscopy. It is particularly interesting in biological systems since it operates in water, at room temperature, and it can be repeated if the bleaching of the system can be controlled. However, the photo-CIDNP signal enhancement is well below those of other hyperpolarization techniques. While DNP, PHIP, and SABRE reach polarization enhancements of 103 to 104-fold, photo-CIDNP enhancement is typically only one order of magnitude for 1H and two orders of magnitude for 13C in the amino-acids tryptophan and tyrosine. Here we report on a photo-oxidation product of tryptophan that is strongly photo-CIDNP active under continuous wave light irradiation. In conjunction with the dye Atto Thio 12, a 1H signal enhancement of 120-fold was observed on a 600 MHz spectrometer, while at 200 MHz the enhancement was 380-fold. These enhancements in signal to noise correspond to a reduction in measurement time of 14 400-fold and 144 400-fold, respectively. The enhancement for 13C is estimated to be over 1200-fold at 600 MHz which corresponds to an impressive measurement time reduction of 1 440 000-fold. This photo-CIDNP active oxidation product of tryptophan has been identified to be 3α-hydroxypyrroloindole. The reasons for its improved signal enhancement compared to tryptophan have been further investigated.
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Affiliation(s)
- Felix Torres
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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34
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Kwiatkowski W, Bomba R, Afanasyev P, Boehringer D, Riek R, Greenwald J. Präbiotische Peptid‐Synthese und spontane Amyloid‐Bildung im Inneren eines protozellulären Kompartiments. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Witek Kwiatkowski
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Radoslaw Bomba
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Pavel Afanasyev
- Wissenschaftliches Zentrum für optische und Elektronenmikroskopie Eidgenössische Technische Hochschule, ETH-Hönggerberg Otto-Stern-Weg 3 CH-8093 Zürich Schweiz
| | - Daniel Boehringer
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule, ETH-Hönggerberg Otto-Stern-Weg 5 CH-8093 Zürich Schweiz
| | - Roland Riek
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
| | - Jason Greenwald
- Laboratorium für Physikalische Chemie Eidgenössische Technische Hochschule, ETH-Hönggerberg Vladimir-Prelog-Weg 2 CH-8093 Zürich Schweiz
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35
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Kwiatkowski W, Bomba R, Afanasyev P, Boehringer D, Riek R, Greenwald J. Prebiotic Peptide Synthesis and Spontaneous Amyloid Formation Inside a Proto-Cellular Compartment. Angew Chem Int Ed Engl 2021; 60:5561-5568. [PMID: 33325627 DOI: 10.1002/anie.202015352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Cellular life requires a high degree of molecular complexity and self-organization, some of which must have originated in a prebiotic context. Here, we demonstrate how both of these features can emerge in a plausibly prebiotic system. We found that chemical gradients in simple mixtures of activated amino acids and fatty acids can lead to the formation of amyloid-like peptide fibrils that are localized inside of a proto-cellular compartment. In this process, the fatty acid or lipid vesicles act both as a filter, allowing the selective passage of activated amino acids, and as a barrier, blocking the diffusion of the amyloidogenic peptides that form spontaneously inside the vesicles. This synergy between two distinct building blocks of life induces a significant increase in molecular complexity and spatial order thereby providing a route for the early molecular evolution that could give rise to a living cell.
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Affiliation(s)
- Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Pavel Afanasyev
- Scientific Center for Optical and Electron Microscopy, Swiss Federal Institute of Technology, ETH-Hönggerberg, Otto-Stern-Weg 3, CH-8093, Zürich, Switzerland
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, ETH-Hönggerberg, Otto-Stern-Weg 5, CH-8093, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
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36
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Seuring C, Verasdonck J, Ringler P, Cadalbert R, Stahlberg H, Böckmann A, Meier BH, Riek R. Correction to "Amyloid Fibril Polymorphism: Almost Identical on the Atomic Level, Mesoscopically Very Different". J Phys Chem B 2021; 125:484. [PMID: 33373227 DOI: 10.1021/acs.jpcb.0c10858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Olerinyova A, Sonn-Segev A, Gault J, Eichmann C, Schimpf J, Kopf AH, Rudden LSP, Ashkinadze D, Bomba R, Frey L, Greenwald J, Degiacomi MT, Steinhilper R, Killian JA, Friedrich T, Riek R, Struwe WB, Kukura P. Mass Photometry of Membrane Proteins. Chem 2021; 7:224-236. [PMID: 33511302 PMCID: PMC7815066 DOI: 10.1016/j.chempr.2020.11.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/20/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane-mimetic systems at the single-particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterizing the particle size, sample purity, and heterogeneity. Using methods established for cryogenic electron microscopy, we eliminate detergent background, enabling high-resolution studies of membrane-protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene-maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers—in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non-functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation. We introduce a label-free, single molecule approach for membrane-protein characterization Mass photometry quantifies membrane proteins in different membrane-mimetic systems MP reveals carrier and protein heterogeneity It helps distinguish different functional states of membrane proteins
Membrane proteins are some of the most important biological molecules, carrying out vital functions and being frequent drug targets. Yet, preferring lipid environments and so requiring solubilization, they are challenging to study. Here, we show that mass photometry can characterize the heterogeneity of membrane proteins and the carriers in which they are solubilized. It can also distinguish different functional states of membrane proteins. Our approach thus opens the door to more comprehensive studies of function, structure, and interaction of these critical proteins in their native membrane environment at the single-molecule level.
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Affiliation(s)
- Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Adar Sonn-Segev
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Adrian H Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Lucas S P Rudden
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Dzmitry Ashkinadze
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Matteo T Degiacomi
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Ralf Steinhilper
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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38
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Lipiec E, Kaderli J, Kobierski J, Riek R, Skirlińska-Nosek K, Sofińska K, Szymoński M, Zenobi R. Nanoscale Hyperspectral Imaging of Amyloid Secondary Structures in Liquid. Angew Chem Int Ed Engl 2021; 60:4545-4550. [PMID: 32964527 DOI: 10.1002/anie.202010331] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 12/27/2022]
Abstract
Abnormal aggregation of amyloid-β is a very complex and heterogeneous process. Owing to methodological limitations, the aggregation pathway is still not fully understood. Herein a new approach is presented in which the secondary structure of single amyloid-β aggregates is investigated with tip-enhanced Raman spectroscopy (TERS) in a liquid environment. Clearly resolved TERS signatures of the amide I and amide III bands enabled a detailed analysis of the molecular structure of single aggregates at each phase of the primary aggregation of amyloid-β and also of small species on the surface of fibrils attributed to secondary nucleation. Notably, a β-sheet rearrangement from antiparallel in protofibrils to parallel in fibrils is observed. This study allows better understanding of Alzheimer's disease etiology and the methodology can be applied in studies of other neurodegenerative disorders.
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Affiliation(s)
- Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland.,Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.,The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Krakow, Poland
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Jan Kobierski
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy, Jagiellonian University Medical College, 31-007, Kraków, Poland
| | - Roland Riek
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Kamila Sofińska
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Marek Szymoński
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
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39
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Lipiec E, Kaderli J, Kobierski J, Riek R, Skirlińska‐Nosek K, Sofińska K, Szymoński M, Zenobi R. Nanoscale Hyperspectral Imaging of Amyloid Secondary Structures in Liquid. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ewelina Lipiec
- M. Smoluchowski Institute of Physics Jagiellonian University Łojasiewicza 11 30-348 Kraków Poland
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics Polish Academy of Sciences 31-342 Krakow Poland
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Jan Kobierski
- Department of Pharmaceutical Biophysics Faculty of Pharmacy Jagiellonian University Medical College 31-007 Kraków Poland
| | - Roland Riek
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | | | - Kamila Sofińska
- M. Smoluchowski Institute of Physics Jagiellonian University Łojasiewicza 11 30-348 Kraków Poland
| | - Marek Szymoński
- M. Smoluchowski Institute of Physics Jagiellonian University Łojasiewicza 11 30-348 Kraków Poland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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40
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Ni R, Chen Z, Gerez JA, Shi G, Zhou Q, Riek R, Nilsson KPR, Razansky D, Klohs J. Transcranial detection of tauopathy
in vivo
in P301L mice with high‐resolution large‐field multifocal illumination fluorescence microscopy. Alzheimers Dement 2020. [DOI: 10.1002/alz.047238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ruiqing Ni
- ETH Zurich & University of Zurich Zurich Switzerland
| | - Zhenyue Chen
- ETH Zurich & University of Zurich Zurich Switzerland
| | | | - Gloria Shi
- ETH Zurich & University of Zurich Zurich Switzerland
| | - Quanyu Zhou
- ETH Zurich & University of Zurich Zurich Switzerland
| | | | - K Peter R Nilsson
- Department of Physics Chemistry and Biology Linköping University Linköping Sweden
| | | | - Jan Klohs
- ETH Zurich & University of Zurich Zurich Switzerland
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41
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Strotz D, Orts J, Kadavath H, Friedmann M, Ghosh D, Olsson S, Chi CN, Güntert P, Vögeli B, Riek R. Protein Allostery at Atomic Resolution. Angew Chem Int Ed Engl 2020; 59:22132-22139. [PMID: 32797659 PMCID: PMC9202374 DOI: 10.1002/anie.202008734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/23/2020] [Indexed: 08/15/2023]
Abstract
Protein allostery is a phenomenon involving the long range coupling between two distal sites in a protein. In order to elucidate allostery at atomic resoluion on the ligand-binding WW domain of the enzyme Pin1, multistate structures were calculated from exact nuclear Overhauser effect (eNOE). In its free form, the protein undergoes a microsecond exchange between two states, one of which is predisposed to interact with its parent catalytic domain. In presence of the positive allosteric ligand, the equilibrium between the two states is shifted towards domain-domain interaction, suggesting a population shift model. In contrast, the allostery-suppressing ligand decouples the side-chain arrangement at the inter-domain interface thereby reducing the inter-domain interaction. As such, this mechanism is an example of dynamic allostery. The presented distinct modes of action highlight the power of the interplay between dynamics and function in the biological activity of proteins.
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Affiliation(s)
- Dean Strotz
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Julien Orts
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Michael Friedmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Simon Olsson
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Peter Güntert
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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42
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Strotz D, Orts J, Kadavath H, Friedmann M, Ghosh D, Olsson S, Chi CN, Pokharna A, Güntert P, Vögeli B, Riek R. Protein Allostery at Atomic Resolution. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dean Strotz
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Julien Orts
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Harindranath Kadavath
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Michael Friedmann
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Simon Olsson
- Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 6 14195 Berlin Germany
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology Uppsala Biomedical Center Uppsala University 751 23 Uppsala Sweden
| | - Aditya Pokharna
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies J.W. Goethe-Universität Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
- Graduate School of Science Tokyo Metropolitan University, Hachioji Tokyo 192-0397 Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics University of Colorado at Denver 12801 East 17th Avenue Aurora CO 80045 USA
| | - Roland Riek
- Laboratory of Physical Chemistry Swiss Federal Institute of Technology ETH-Hönggerberg 8093 Zürich Switzerland
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43
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Orts J, Riek R. Protein-ligand structure determination with the NMR molecular replacement tool, NMR 2. J Biomol NMR 2020; 74:633-642. [PMID: 32621003 DOI: 10.1007/s10858-020-00324-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.
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Affiliation(s)
- Julien Orts
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
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44
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Seuring C, Verasdonck J, Gath J, Ghosh D, Nespovitaya N, Wälti MA, Maji SK, Cadalbert R, Güntert P, Meier BH, Riek R. The three-dimensional structure of human β-endorphin amyloid fibrils. Nat Struct Mol Biol 2020; 27:1178-1184. [PMID: 33046908 DOI: 10.1038/s41594-020-00515-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022]
Abstract
In the pituitary gland, hormones are stored in a functional amyloid state within acidic secretory granules before they are released into the blood. To gain a detailed understanding of the structure-function relationship of amyloids in hormone secretion, the three-dimensional (3D) structure of the amyloid fibril of the human hormone β-endorphin was determined by solid-state NMR. We find that β-endorphin fibrils are in a β-solenoid conformation with a protonated glutamate residue in their fibrillar core. During exocytosis of the hormone amyloid the pH increases from acidic in the secretory granule to neutral level in the blood, thus it is suggested-and supported with mutagenesis data-that the pH change in the cellular milieu acts through the deprotonation of glutamate 8 to release the hormone from the amyloid. For amyloid disassembly in the blood, it is proposed that the pH change acts together with a buffer composition change and hormone dilution. In the pituitary gland, peptide hormones can be stored as amyloid fibrils within acidic secretory granules before release into the blood stream. Here, we use solid-state NMR to determine the 3D structure of the amyloid fiber formed by the human hormone β-endorphin. We find that β-endorphin fibrils are in a β-solenoid conformation that is generally reminiscent of other functional amyloids. In the β-endorphin amyloid, every layer of the β-solenoid is composed of a single peptide and protonated Glu8 is located in the fibrillar core. The secretory granule has an acidic pH but, on exocytosis, the β-endorphin fibril would encounter neutral pH conditions (pH 7.4) in the blood; this pH change would result in deprotonation of Glu8 to release the hormone peptide from the amyloid. Analyses of β-endorphin variants carrying mutations in Glu8 support the role of the protonation state of this residue in fibril disassembly, among other environmental changes.
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Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Joeri Verasdonck
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Julia Gath
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Dhimam Ghosh
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| | | | | | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| | | | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.,Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland. .,Structural Biology Laboratory, The Salk Institute, La Jolla, CA, USA.
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45
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Ni R, Chen Z, Gerez JA, Shi G, Zhou Q, Riek R, Nilsson KPR, Razansky D, Klohs J. Detection of cerebral tauopathy in P301L mice using high-resolution large-field multifocal illumination fluorescence microscopy. Biomed Opt Express 2020; 11:4989-5002. [PMID: 33014595 PMCID: PMC7510859 DOI: 10.1364/boe.395803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Current intravital microscopy techniques visualize tauopathy with high-resolution, but have a small field-of-view and depth-of-focus. Herein, we report a transcranial detection of tauopathy over the entire cortex of P301L tauopathy mice using large-field multifocal illumination (LMI) fluorescence microscopy technique and luminescent conjugated oligothiophenes. In vitro assays revealed that fluorescent ligand h-FTAA is optimal for in vivo tau imaging, which was confirmed by observing elevated probe retention in the cortex of P301L mice compared to non-transgenic littermates. Immunohistochemical staining further verified the specificity of h-FTAA to detect tauopathy in P301L mice. The new imaging platform can be leveraged in pre-clinical mechanistic studies of tau spreading and clearance as well as longitudinal monitoring of tau targeting therapeutics.
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Affiliation(s)
- Ruiqing Ni
- University of Zurich & ETH Zurich, Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, Wolfgang-Pauli-strasse 27 HIT E22.4, 8093, Zurich, Switzerland
- University of Zurich, Zurich Neuroscience Center, Zurich, Switzerland
| | - Zhenyue Chen
- University of Zurich & ETH Zurich, Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, Wolfgang-Pauli-strasse 27 HIT E22.4, 8093, Zurich, Switzerland
- University of Zurich, Faculty of Medicine and Institute of Pharmacology and Toxicology, Zurich, Switzerland
| | - Juan A. Gerez
- ETH Zurich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | - Gloria Shi
- University of Zurich & ETH Zurich, Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, Wolfgang-Pauli-strasse 27 HIT E22.4, 8093, Zurich, Switzerland
| | - Quanyu Zhou
- University of Zurich & ETH Zurich, Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, Wolfgang-Pauli-strasse 27 HIT E22.4, 8093, Zurich, Switzerland
- University of Zurich, Faculty of Medicine and Institute of Pharmacology and Toxicology, Zurich, Switzerland
| | - Roland Riek
- ETH Zurich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | - K. Peter R. Nilsson
- Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping, Sweden
| | - Daniel Razansky
- University of Zurich & ETH Zurich, Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, Wolfgang-Pauli-strasse 27 HIT E22.4, 8093, Zurich, Switzerland
- University of Zurich, Zurich Neuroscience Center, Zurich, Switzerland
- University of Zurich, Faculty of Medicine and Institute of Pharmacology and Toxicology, Zurich, Switzerland
| | - Jan Klohs
- University of Zurich & ETH Zurich, Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, Wolfgang-Pauli-strasse 27 HIT E22.4, 8093, Zurich, Switzerland
- University of Zurich, Zurich Neuroscience Center, Zurich, Switzerland
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Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future. Chem Soc Rev 2020; 49:5473-5509. [PMID: 32632432 PMCID: PMC7445747 DOI: 10.1039/c9cs00199a] [Citation(s) in RCA: 272] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.
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Affiliation(s)
- Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, CB3 0HE, Cambridge, UK
| | - Hilal A. Lashuel
- Laboratory of Molecular Neurobiology and Neuroproteomics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ian W. Hamley
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Daniel Erik Otzen
- Department of Molecular Biology, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, Centre for Microbial Research, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David S. Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Raffaele Mezzenga
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
- Department of Materials, ETH Zurich, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
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Abstract
The second law of thermodynamics, with its positive change of entropy for a system not in equilibrium, defines an arrow of time. Interestingly, also, causality, which is the connection between a cause and an effect, requests a direction of time by definition. It is noted that no other standard physical theories show this property. It is the attempt of this work to connect causality with entropy, which is possible by defining time as the metric of causality. Under this consideration that time appears only through a cause–effect relationship (“measured”, typically, in an apparatus called clock), it is demonstrated that time must be discrete in nature and cannot be continuous as assumed in all standard theories of physics including general and special relativity, and classical physics. The following lines of reasoning include: (i) (mechanical) causality requests that the cause must precede its effect (i.e., antecedence) requesting a discrete time interval >0. (ii) An infinitely small time step dt>0 is thereby not sufficient to distinguish between cause and effect as a mathematical relationship between the two (i.e., Poisson bracket) will commute at a time interval dt, while not evidently within discrete time steps Δt. As a consequence of a discrete time, entropy emerges (Riek, 2014) connecting causality and entropy to each other.
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Affiliation(s)
- Roland Riek
- Laboratory of Physical Chemistry, ETH Zuerich, Wolfgang-Pauli-Strasse 10, HCI F 225, CH-8093 Zurich, Switzerland
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48
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Ray S, Singh N, Kumar R, Patel K, Pandey S, Datta D, Mahato J, Panigrahi R, Navalkar A, Mehra S, Gadhe L, Chatterjee D, Sawner AS, Maiti S, Bhatia S, Gerez JA, Chowdhury A, Kumar A, Padinhateeri R, Riek R, Krishnamoorthy G, Maji SK. α-Synuclein aggregation nucleates through liquid-liquid phase separation. Nat Chem 2020; 12:705-716. [PMID: 32514159 DOI: 10.1038/s41557-020-0465-9] [Citation(s) in RCA: 333] [Impact Index Per Article: 83.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 04/07/2020] [Indexed: 12/22/2022]
Abstract
α-Synuclein (α-Syn) aggregation and amyloid formation is directly linked with Parkinson's disease pathogenesis. However, the early events involved in this process remain unclear. Here, using the in vitro reconstitution and cellular model, we show that liquid-liquid phase separation of α-Syn precedes its aggregation. In particular, in vitro generated α-Syn liquid-like droplets eventually undergo a liquid-to-solid transition and form an amyloid hydrogel that contains oligomers and fibrillar species. Factors known to aggravate α-Syn aggregation, such as low pH, phosphomimetic substitution and familial Parkinson's disease mutations, also promote α-Syn liquid-liquid phase separation and its subsequent maturation. We further demonstrate α-Syn liquid-droplet formation in cells. These cellular α-Syn droplets eventually transform into perinuclear aggresomes, the process regulated by microtubules. This work provides detailed insights into the phase-separation behaviour of natively unstructured α-Syn and its conversion to a disease-associated aggregated state, which is highly relevant in Parkinson's disease pathogenesis.
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Affiliation(s)
- Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Nitu Singh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | | | - Debalina Datta
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | | | | | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | | | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Siddhartha Maiti
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Sandhya Bhatia
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Juan Atilio Gerez
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | | | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | | | - Roland Riek
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | | | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India.
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Abstract
In-cell NMR enables structural insights at atomic resolution of proteins in their natural environment. To date, very few methods have been developed to study proteins by in-cell NMR in mammalian systems. Here we describe a detailed protocol to conduct in-cell NMR on the intrinsically disordered protein of alpha-Synuclein (αSyn) in mammalian cells. This chapter includes a simplified expression and purification protocol of recombinant αSyn and its delivery into mammalian cells. The chapter also describes how to assess the cell leakage that might occur to the cells, the setup of the instrument, and how to perform basic analyses with the obtained NMR data.
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Affiliation(s)
- Juan A Gerez
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Natalia C Prymaczok
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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50
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Affiliation(s)
- Alexander Sobol
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Felix Torres
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Anatol Aicher
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Alois Renn
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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