1
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Morfino P, Aimo A, Franzini M, Vergaro G, Castiglione V, Panichella G, Limongelli G, Emdin M. Pathophysiology of Cardiac Amyloidosis. Heart Fail Clin 2024; 20:261-270. [PMID: 38844297 DOI: 10.1016/j.hfc.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Amyloidosis refers to a heterogeneous group of disorders sharing common pathophysiological mechanisms characterized by the extracellular accumulation of fibrillar deposits consisting of the aggregation of misfolded proteins. Cardiac amyloidosis (CA), usually caused by deposition of misfolded transthyretin or immunoglobulin light chains, is an increasingly recognized cause of heart failure burdened by a poor prognosis. CA manifests with a restrictive cardiomyopathy which progressively leads to biventricular thickening, diastolic and then systolic dysfunction, arrhythmias, and valvular disease. The pathophysiology of CA is multifactorial and includes increased oxidative stress, mitochondrial damage, apoptosis, impaired metabolism, and modifications of intracellular calcium balance.
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Affiliation(s)
| | - Alberto Aimo
- Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy; Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Maria Franzini
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Giuseppe Vergaro
- Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy; Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Vincenzo Castiglione
- Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy; Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Giorgia Panichella
- Department of Clinical and Experimental Medicine, Careggi University Hospital, Florence, Italy
| | - Giuseppe Limongelli
- Inherited and Rare Cardiovascular Disease Unit, Department of Translational Medical Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Michele Emdin
- Scuola Superiore Sant'Anna, Pisa, Italy; Fondazione Toscana Gabriele Monasterio, via G. Moruzzi 1, 56124, Pisa, Italy.
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2
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Lane BJ, Ma Y, Yan N, Wang B, Ackermann K, Karamanos TK, Bode BE, Pliotas C. Monitoring the conformational ensemble and lipid environment of a mechanosensitive channel under cyclodextrin-induced membrane tension. Structure 2024; 32:739-750.e4. [PMID: 38521071 DOI: 10.1016/j.str.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/29/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Membrane forces shift the equilibria of mechanosensitive channels enabling them to convert mechanical cues into electrical signals. Molecular tools to stabilize and methods to capture their highly dynamic states are lacking. Cyclodextrins can mimic tension through the sequestering of lipids from membranes. Here we probe the conformational ensemble of MscS by EPR spectroscopy, the lipid environment with NMR, and function with electrophysiology under cyclodextrin-induced tension. We show the extent of MscS activation depends on the cyclodextrin-to-lipid ratio, and that lipids are depleted slower when MscS is present. This has implications in MscS' activation kinetics when distinct membrane scaffolds such as nanodiscs or liposomes are used. We find MscS transits from closed to sub-conducting state(s) before it desensitizes, due to the lack of lipid availability in its vicinity required for closure. Our approach allows for monitoring tension-sensitive states in membrane proteins and screening molecules capable of inducing molecular tension in bilayers.
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Affiliation(s)
- Benjamin J Lane
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yue Ma
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Nana Yan
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Bolin Wang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Theodoros K Karamanos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK; Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
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3
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Florio D, Luciano P, Di Natale C, Marasco D. The effects of histidine substitution of aromatic residues on the amyloidogenic properties of the fragment 264-277 of nucleophosmin 1. Bioorg Chem 2024; 147:107404. [PMID: 38678777 DOI: 10.1016/j.bioorg.2024.107404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Histidine (His) plays a key role in mediating protein interactions and its unique side chain determines pH responsive self-assembling processes and thus in the formation of nanostructures. In this study, To identify novel self-assembling bioinspired sequences, we analyzed a series of peptide sequences obtained through the point mutation of aromatic residues of 264-277 fragment of nucleophosmin 1 (NPM1) with single and double histidines. Through several orthogonal biophysical techniques and under different pH and ionic strength conditions we evaluated the effects of these substitutions in the amyloidogenic features of derived peptides. The results clearly indicate that both the type of aromatic mutated residue and its position can have different effect on amyloid-like behaviors. They corroborate the crucial role exerted by Tyr271 in the self-assembling process of CTD of NPM1 in AML mutated form and add novel insights in the accurate investigation of how side chain orientations can determine successful design of innovative bioinspired materials.
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Affiliation(s)
- Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Paolo Luciano
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Concetta Di Natale
- Department of Ingegneria Chimica, dei Materiali e della Produzione Industriale (DICMAPI), Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy.
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4
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Dolui S, Roy A, Pal U, Kundu S, Pandit E, N Ratha B, Pariary R, Saha A, Bhunia A, Maiti NC. Raman Spectroscopic Insights of Phase-Separated Insulin Aggregates. ACS PHYSICAL CHEMISTRY AU 2024; 4:268-280. [PMID: 38800728 PMCID: PMC11117687 DOI: 10.1021/acsphyschemau.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/29/2024]
Abstract
Phase-separated protein accumulation through the formation of several aggregate species is linked to the pathology of several human disorders and diseases. Our current investigation envisaged detailed Raman signature and structural intricacy of bovine insulin in its various forms of aggregates produced in situ at an elevated temperature (60 °C). The amide I band in the Raman spectrum of the protein in its native-like conformation appeared at 1655 cm-1 and indicated the presence of a high content of α-helical structure as prepared freshly in acidic pH. The disorder content (turn and coils) also was predominately present in both the monomeric and oligomeric states and was confirmed by the presence shoulder amide I maker band at ∼1680 cm-1. However, the band shifted to ∼1671 cm-1 upon the transformation of the protein solution into fibrillar aggregates as produced for a longer time of incubation. The protein, however, maintained most of its helical conformation in the oligomeric phase; the low-frequency backbone α-helical conformation signal at ∼935 cm-1 was similar to that of freshly prepared aqueous protein solution enriched in helical conformation. The peak intensity was significantly weak in the fibrillar aggregates, and it appeared as a good Raman signature to follow the phase separation and the aggregation behavior of insulin and similar other proteins. Tyrosine phenoxy moieties in the protein may maintained its H-bond donor-acceptor integrity throughout the course of fibril formation; however, it entered in more hydrophobic environment in its journey of fibril formation. In addition, it was noticed that oligomeric bovine insulin maintained the orientation/conformation of the disulfide bonds. However, in the fibrillar state, the disulfide linkages became more strained and preferred to maintain a single conformation state.
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Affiliation(s)
- Sandip Dolui
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anupam Roy
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Uttam Pal
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Shubham Kundu
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Esha Pandit
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Bhisma N Ratha
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Ranit Pariary
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Achintya Saha
- Department
of Chemical Technology, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009, India
| | - Anirban Bhunia
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Nakul C. Maiti
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
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5
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Palmioli A, Airoldi C. An NMR Toolkit to Probe Amyloid Oligomer Inhibition in Neurodegenerative Diseases: From Ligand Screening to Dissecting Binding Topology and Mechanisms of Action. Chempluschem 2024:e202400243. [PMID: 38712695 DOI: 10.1002/cplu.202400243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
The aggregation of amyloid peptides and proteins into toxic oligomers is a hallmark of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Machado-Joseph's disease, and transmissible spongiform encephalopathies. Inhibition of amyloid oligomers formation and interactions with biological counterparts, as well as the triggering of non-toxic amorphous aggregates, are strategies towards preventive interventions against these pathologies. NMR spectroscopy addresses the need for structural characterization of amyloid proteins and their aggregates, their binding to inhibitors, and rapid screening of compound libraries for ligand identification. Here we briefly discuss the solution experiments constituting the NMR spectroscopist's toolkit and provide examples of their application.
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Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
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Byeon CH, Hansen KH, Jeffrey J, Saricayir H, Andreasen M, Akbey Ü. Intrinsically disordered Pseudomonas chaperone FapA slows down the fibrillation of major biofilm-forming functional amyloid FapC. FEBS J 2024; 291:1925-1943. [PMID: 38349812 DOI: 10.1111/febs.17084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024]
Abstract
Functional bacterial amyloids play a crucial role in the formation of biofilms, which mediate chronic infections and contribute to antimicrobial resistance. This study focuses on the FapC amyloid fibrillar protein from Pseudomonas, a major contributor to biofilm formation. We investigate the initial steps of FapC amyloid formation and the impact of the chaperone-like protein FapA on this process. Using solution nuclear magnetic resonance (NMR), we recently showed that both FapC and FapA are intrinsically disordered proteins (IDPs). Here, the secondary structure propensities (SSPs) are compared to alphafold (DeepMind, protein structure prediction tool/algorithm: https://alphafold.ebi.ac.uk/) models. We further demonstrate that the FapA chaperone interacts with FapC and significantly slows down the formation of FapC fibrils. Our NMR titrations reveal ~ 18% of the resonances show FapA-induced chemical shift perturbations (CSPs), which has not been previously observed, the largest being for A82, N201, C237, C240, A241, and G245. These sites may suggest a specific interaction site and/or hotspots of fibrillation inhibition/control interface at the repeat-1 (R1)/loop-2 (L2) and L2/R3 transition areas and at the C-terminus of FapC. Remarkably, ~ 90% of FapA NMR signals exhibit substantial CSPs upon titration with FapC, the largest being for S63, A69, A80, and I92. A temperature-dependent effect of FapA was observed on FapC by thioflavin T (ThT) and NMR experiments. This study provides a detailed understanding of the interaction between the FapA and FapC, shedding light on the regulation and slowing down of amyloid formation, and has important implications for the development of therapeutic strategies targeting biofilms and associated infections.
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Affiliation(s)
- Chang-Hyeock Byeon
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kasper Holst Hansen
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jasper Jeffrey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hakan Saricayir
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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7
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Meyer N, Torrent J, Balme S. Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches. SMALL METHODS 2024:e2400058. [PMID: 38644684 DOI: 10.1002/smtd.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/10/2024] [Indexed: 04/23/2024]
Abstract
Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
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8
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Oliyantakath Hassan MS, Abdul Vahid A, Sahayaraj AE, Viswanathan R, Vijayan V. NMR Relaxation Experiments Probe Monomer-Fibril Interaction and Identify Critical Interacting Residues Responsible for Distinct Tau Fibril Morphologies. J Phys Chem Lett 2023; 14:6583-6591. [PMID: 37458827 DOI: 10.1021/acs.jpclett.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Tau aggregation is governed by secondary processes, a major pathological pathway for tau protein fibril propagation, yet its molecular mechanism remains unknown. This work uses saturation transfer and lifetime line-broadening experiments to identify the critical residues involved in these secondary processes. Distinct residue-specific NMR relaxation parameters were obtained for the truncated three repeat tau construct (K19) in equilibrium with structurally different, self-aggregated (saK19) or heparin-induced (hK19) fibrils. The interacting residues are restricted to R3 repeat for hK19 and to R3, R4, and R' repeats for saK19 fibrils. Furthermore, the relaxation profiles of tau monomers in equilibrium with the structurally comparable, in vitro pathological fibrils (tauAD and tauCTE) were similar but distinct from hK19 or saK19 fibrils. Thus, residue-specific relaxation identifies the important residues involved in the binding of monomers to the fibrils. The relaxation profile of the monomers in equilibrium with the NMR invisible fibril seeds potentially distinguishes the distinct structures of tau fibrils.
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Affiliation(s)
| | - Arshad Abdul Vahid
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Allwin Ebenezer Sahayaraj
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Renjith Viswanathan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Vinesh Vijayan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala PO, Vithura, Thiruvananthapuram, Kerala 695551, India
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9
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Falgarone T, Villain E, Richard F, Osmanli Z, Kajava AV. Census of exposed aggregation-prone regions in proteomes. Brief Bioinform 2023; 24:bbad183. [PMID: 37200152 DOI: 10.1093/bib/bbad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
Loss of solubility usually leads to the detrimental elimination of protein function. In some cases, the protein aggregation is also required for beneficial functions. Given the duality of this phenomenon, it remains a fundamental question how natural selection controls the aggregation. The exponential growth of genomic sequence data and recent progress with in silico predictors of the aggregation allows approaching this problem by a large-scale bioinformatics analysis. Most of the aggregation-prone regions are hidden within the 3D structure, rendering them inaccessible for the intermolecular interactions responsible for aggregation. Thus, the most realistic census of the aggregation-prone regions requires crossing aggregation prediction with information about the location of the natively unfolded regions. This allows us to detect so-called 'exposed aggregation-prone regions' (EARs). Here, we analyzed the occurrence and distribution of the EARs in 76 reference proteomes from the three kingdoms of life. For this purpose, we used a bioinformatics pipeline, which provides a consensual result based on several predictors of aggregation. Our analysis revealed a number of new statistically significant correlations about the presence of EARs in different organisms, their dependence on protein length, cellular localizations, co-occurrence with short linear motifs and the level of protein expression. We also obtained a list of proteins with the conserved aggregation-prone sequences for further experimental tests. Insights gained from this work led to a deeper understanding of the relationship between protein evolution and aggregation.
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Affiliation(s)
- Théo Falgarone
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Francois Richard
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Zarifa Osmanli
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
- Biophysics Institute, Ministry of Science and Education of Azerbaijan Republic, Az1141, Baku, Azerbaijan
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
- Institut de Biologie Computationnelle, Université Montpellier, 34095 Montpellier, France
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10
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Alonso-Moreno P, Rodriguez I, Izquierdo-Garcia JL. Benchtop NMR-Based Metabolomics: First Steps for Biomedical Application. Metabolites 2023; 13:metabo13050614. [PMID: 37233655 DOI: 10.3390/metabo13050614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics is a valuable tool for identifying biomarkers and understanding the underlying metabolic changes associated with various diseases. However, the translation of metabolomics analysis to clinical practice has been limited by the high cost and large size of traditional high-resolution NMR spectrometers. Benchtop NMR, a compact and low-cost alternative, offers the potential to overcome these limitations and facilitate the wider use of NMR-based metabolomics in clinical settings. This review summarizes the current state of benchtop NMR for clinical applications where benchtop NMR has demonstrated the ability to reproducibly detect changes in metabolite levels associated with diseases such as type 2 diabetes and tuberculosis. Benchtop NMR has been used to identify metabolic biomarkers in a range of biofluids, including urine, blood plasma and saliva. However, further research is needed to optimize the use of benchtop NMR for clinical applications and to identify additional biomarkers that can be used to monitor and manage a range of diseases. Overall, benchtop NMR has the potential to revolutionize the way metabolomics is used in clinical practice, providing a more accessible and cost-effective way to study metabolism and identify biomarkers for disease diagnosis, prognosis, and treatment.
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Affiliation(s)
- Pilar Alonso-Moreno
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ignacio Rodriguez
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Chemistry in Pharmaceutical Sciences, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jose Luis Izquierdo-Garcia
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Chemistry in Pharmaceutical Sciences, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
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11
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Maity D. Recent advances in the modulation of amyloid protein aggregation using the supramolecular host-guest approaches. Biophys Chem 2023; 297:107022. [PMID: 37058879 DOI: 10.1016/j.bpc.2023.107022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Misfolding of proteins is associated with many incurable diseases in human beings. Understanding the process of aggregation from monomers to fibrils, the characterization of all intermediate species, and the origin of toxicity is very challenging. Extensive research including computational and experimental shed some light on these tricky phenomena. Non-covalent interactions between amyloidogenic domains of proteins play a major role in their self-assembly which can be disrupted by designed chemical tools. This will lead to the development of inhibitors of detrimental amyloid formations. In supramolecular host-guest chemistry approaches, different macrocycles function as hosts for encapsulating hydrophobic guests, i.e. phenylalanine residues of proteins, in their hydrophobic cavities via non-covalent interactions. In this way, they can disrupt the interactions between adjacent amyloidogenic proteins and prevent their self-aggregation. This supramolecular approach has also emerged as a prospective tool to modify the aggregation of several amyloidogenic proteins. In this review, we discussed recent supramolecular host-guest chemistry-based strategies for the inhibition of amyloid protein aggregation.
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Affiliation(s)
- Debabrata Maity
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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12
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Oxidative Damages on the Alzheimer's Related-Aβ Peptide Alters Its Ability to Assemble. Antioxidants (Basel) 2023; 12:antiox12020472. [PMID: 36830030 PMCID: PMC9951946 DOI: 10.3390/antiox12020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Oxidative stress that can lead to oxidation of the amyloid-β (Aβ) peptide is considered a key feature in Alzheimer's disease (AD), influencing the ability of Aβ to assemble into β-sheet rich fibrils that are commonly found in senile plaques of AD patients. The present study aims at investigating the fallouts of Aβ oxidation on the assembly properties of the Aβ peptide. To accomplish this, we performed kinetics and analysis on an oxidized Aβ (oxAβ) peptide, resulting from the attack of reactive oxygen species (ROS) that are formed by the biologically relevant Cu/Aβ/dioxygen/ascorbate system. oxAβ was still able to assemble but displayed ill-defined and small oligomeric assemblies compared to the long and thick β-sheet rich fibrils from the non-oxidized counterpart. In addition, oxAβ does affect the assembly of the parent Aβ peptide. In a mixture of the two peptides, oxAβ has a mainly kinetic effect on the assembly of the Aβ peptide and was able to slow down the formation of Aβ fibril in a wide pH range [6.0-7.4]. However, oxAβ does not change the quantity and morphology of the Aβ fibrils formed to a significant extent. In the presence of copper or zinc di-cations, oxAβ assembled into weakly-structured aggregates rather than short, untangled Cu-Aβ fibrils and long untangled Zn-Aβ fibrils. The delaying effect of oxAβ on metal altered Aβ assembly was also observed. Hence, our results obtained here bring new insights regarding the tight interconnection between (i) ROS production leading to Aβ oxidation and (ii) Aβ assembly, in particular via the modulation of the Aβ assembly by oxAβ. It is the first time that co-assembly of oxAβ and Aβ under various environmental conditions (pH, metal ions …) are reported.
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13
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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14
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Wishart DS, Rout M, Lee BL, Berjanskii M, LeVatte M, Lipfert M. Practical Aspects of NMR-Based Metabolomics. Handb Exp Pharmacol 2023; 277:1-41. [PMID: 36271165 DOI: 10.1007/164_2022_613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for >40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5-10 years.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada.
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Mark Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcia LeVatte
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Matthias Lipfert
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Reference Standard Management & NMR QC, Lonza Group AG, Visp, Switzerland
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15
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Tibble RW, Gross JD. A call to order: Examining structured domains in biomolecular condensates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107318. [PMID: 36657879 PMCID: PMC10878105 DOI: 10.1016/j.jmr.2022.107318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Diverse cellular processes have been observed or predicted to occur in biomolecular condensates, which are comprised of proteins and nucleic acids that undergo liquid-liquid phase separation (LLPS). Protein-driven LLPS often involves weak, multivalent interactions between intrinsically disordered regions (IDRs). Due to their inherent lack of defined tertiary structures, NMR has been a powerful resource for studying the behavior and interactions of IDRs in condensates. While IDRs in proteins are necessary for phase separation, core proteins enriched in condensates often contain structured domains that are essential for their function and contribute to phase separation. How phase separation can affect the structure and conformational dynamics of structured domains is critical for understanding how biochemical reactions can be effectively regulated in cellular condensates. In this perspective, we discuss the consequences phase separation can have on structured domains and outline NMR observables we believe are useful for assessing protein structure and dynamics in condensates.
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Affiliation(s)
- Ryan W Tibble
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
| | - John D Gross
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States.
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16
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Alraawi Z, Banerjee N, Mohanty S, Kumar TKS. Amyloidogenesis: What Do We Know So Far? Int J Mol Sci 2022; 23:ijms232213970. [PMID: 36430450 PMCID: PMC9695042 DOI: 10.3390/ijms232213970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.
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Affiliation(s)
- Zeina Alraawi
- Department of Chemistry and Biochemistry, Fulbright College of Art and Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Nayan Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Srujana Mohanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
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17
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Chalapathi D, Kumar A, Behera P, Sathi SN, Swaminathan R, Narayana C. Insights on Aggregation of Hen Egg-White Lysozyme from Raman Spectroscopy and MD Simulations. Molecules 2022; 27:molecules27207122. [PMID: 36296716 PMCID: PMC9609503 DOI: 10.3390/molecules27207122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/07/2022] Open
Abstract
Protein misfolding and aggregation play a significant role in several neurodegenerative diseases. In the present work, the spontaneous aggregation of hen egg-white lysozyme (HEWL) in an alkaline pH 12.2 at an ambient temperature was studied to obtain molecular insights. The time-dependent changes in spectral peaks indicated the formation of β sheets and their effects on the backbone and amino acids during the aggregation process. Introducing iodoacetamide revealed the crucial role of intermolecular disulphide bonds amidst monomers in the aggregation process. These findings were corroborated by Molecular Dynamics (MD) simulations and protein-docking studies. MD simulations helped establish and visualize the unfolding of the proteins when exposed to an alkaline pH. Protein docking revealed a preferential dimer formation between the HEWL monomers at pH 12.2 compared with the neutral pH. The combination of Raman spectroscopy and MD simulations is a powerful tool to study protein aggregation mechanisms.
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Affiliation(s)
- Divya Chalapathi
- Chemistry and Physics of Materials Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Amrendra Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Guwahati, North Amingaon, Guwahati 781039, India
| | - Pratik Behera
- Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojapura, Thiruvananthapuram 695014, India
| | - Shijulal Nelson Sathi
- Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojapura, Thiruvananthapuram 695014, India
| | - Rajaram Swaminathan
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Guwahati, North Amingaon, Guwahati 781039, India
- Correspondence: (R.S.); or (C.N.); Tel.: +91-471-2347-973 (R.S. & C.N.)
| | - Chandrabhas Narayana
- Chemistry and Physics of Materials Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
- Correspondence: (R.S.); or (C.N.); Tel.: +91-471-2347-973 (R.S. & C.N.)
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18
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Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196448. [PMID: 36234985 PMCID: PMC9573641 DOI: 10.3390/molecules27196448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.
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19
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Paschold A, Voigt B, Hause G, Kohlmann T, Rothemund S, Binder WH. Modulating the Fibrillization of Parathyroid-Hormone (PTH) Peptides: Azo-Switches as Reversible and Catalytic Entities. Biomedicines 2022; 10:biomedicines10071512. [PMID: 35884817 PMCID: PMC9313110 DOI: 10.3390/biomedicines10071512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
We here report a novel strategy to control the bioavailability of the fibrillizing parathyroid hormone (PTH)-derived peptides, where the concentration of the bioactive form is controlled by an reversible, photoswitchable peptide. PTH1–84, a human hormone secreted by the parathyroid glands, is important for the maintenance of extracellular fluid calcium and phosphorus homeostasis. Controlling fibrillization of PTH1–84 represents an important approach for in vivo applications, in view of the pharmaceutical applications for this protein. We embed the azobenzene derivate 3-{[(4-aminomethyl)phenyl]diazenyl}benzoic acid (3,4′-AMPB) into the PTH-derived peptide PTH25–37 to generate the artificial peptide AzoPTH25–37 via solid-phase synthesis. AzoPTH25–37 shows excellent photostability (more than 20 h in the dark) and can be reversibly photoswitched between its cis/trans forms. As investigated by ThT-monitored fibrillization assays, the trans-form of AzoPTH25–37 fibrillizes similar to PTH25–37, while the cis-form of AzoPTH25–37 generates only amorphous aggregates. Additionally, cis-AzoPTH25–37 catalytically inhibits the fibrillization of PTH25–37 in ratios of up to one-fifth. The approach reported here is designed to control the concentration of PTH-peptides, where the bioactive form can be catalytically controlled by an added photoswitchable peptide.
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Affiliation(s)
- André Paschold
- Department of Chemistry, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (A.P.); (T.K.)
| | - Bruno Voigt
- Department of Physics, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Gerd Hause
- Biozentrum, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Tim Kohlmann
- Department of Chemistry, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (A.P.); (T.K.)
| | - Sven Rothemund
- Core Unit Peptide—Technologies, University Leipzig, 04103 Leipzig, Germany;
| | - Wolfgang H. Binder
- Department of Chemistry, Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (A.P.); (T.K.)
- Correspondence:
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20
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Lysozyme Amyloid Fibril Structural Variability Dependence on Initial Protein Folding State. Int J Mol Sci 2022; 23:ijms23105421. [PMID: 35628230 PMCID: PMC9141980 DOI: 10.3390/ijms23105421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 02/05/2023] Open
Abstract
Amyloid fibril formation is associated with several amyloidoses, including neurodegenerative Alzheimer's or Parkinson's diseases. The process of such fibrillar structure formation is still not fully understood, with new mechanistic insights appearing on a regular basis. This, in turn, has limited the development of potential anti-amyloid compounds, with only a handful of effective cures or treatment modalities available. One of the multiple amyloid aggregation factors that requires further examination is the ability of proteins to form multiple, structurally distinct aggregates, based on the environmental conditions. In this work, we examine how the initial folding state affects the fibrilization of lysozyme-an amyloidogenic protein, often used in protein aggregation studies. We show that there is a correlation between the initial state of the protein and the aggregate formation lag time, rate of elongation, resulting aggregate structural variability and dye-binding properties, as well as formation lag time and rate of elongation.
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21
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Karamanos TK, Kalverda AP, Radford SE. Generating Ensembles of Dynamic Misfolding Proteins. Front Neurosci 2022; 16:881534. [PMID: 35431773 PMCID: PMC9008329 DOI: 10.3389/fnins.2022.881534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 01/09/2023] Open
Abstract
The early stages of protein misfolding and aggregation involve disordered and partially folded protein conformers that contain a high degree of dynamic disorder. These dynamic species may undergo large-scale intra-molecular motions of intrinsically disordered protein (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization of the interconverting species that captures the conformations explored and their physico-chemical properties remains hugely challenging. How specific sub-ensembles of conformers that are on-pathway to aggregation into amyloid can be identified from their aggregation-resilient counterparts within these large heterogenous pools of rapidly moving molecules represents an additional level of complexity. Here, we describe current experimental and computational approaches designed to capture the dynamic nature of the early stages of protein misfolding and aggregation, and discuss potential challenges in describing these species because of the ensemble averaging of experimental restraints that arise from motions on the millisecond timescale. We give a perspective of how machine learning methods can be used to extract aggregation-relevant sub-ensembles and provide two examples of such an approach in which specific interactions of defined species within the dynamic ensembles of α-synuclein (αSyn) and β2-microgloblulin (β2m) can be captured and investigated.
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Affiliation(s)
- Theodoros K. Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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22
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Trusova V, Tarabara U, Zhytniakivska O, Vus K, Gorbenko G. Fӧrster resonance energy transfer analysis of amyloid state of proteins. BBA ADVANCES 2022; 2:100059. [PMID: 37082586 PMCID: PMC10074846 DOI: 10.1016/j.bbadva.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
The Förster resonance energy transfer (FRET) is a well-established and versatile spectroscopic technique extensively used for exploring a variety of biomolecular interactions and processes. The present review is intended to cover the main results of our FRET studies focused on amyloid fibrils, a particular type of disease-associated protein aggregates. Based on the examples of several fibril-forming proteins including insulin, lysozyme and amyloidogenic variants of N-terminal fragment of apolipoprotein A-I, it was demonstrated that: (i) the two- and three-step FRET with the classical amyloid marker Thioflavin T as an input donor has a high amyloid-sensing potential and can be used to refine the amyloid detection assays; (ii) the intermolecular time-resolved and single-molecule pulse interleaved excitation FRET can give quantitative information on the nucleation of amyloid fibrils; (iii) FRET between the membrane fluorescent probes and protein-associated intrinsic or extrinsic fluorophores is suitable for monitoring the membrane binding of fibrillar proteins, exploring their location relative to lipid-water interface and restructuring on a lipid matrix; (iv) the FRET-based distance estimation between fibril-bound donor and acceptor fluorophores can serve as one of the verification criteria upon structural modeling of amyloid fibrils.
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23
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Abstract
Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.
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Affiliation(s)
| | - Natalia Szulc
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland
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24
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Ranjan R, Tiwari N, Kayastha AM, Sinha N. Biophysical Investigation of the Interplay between the Conformational Species of Domain-Swapped GB1 Amyloid Mutant through Real-Time Monitoring of Amyloid Fibrillation. ACS OMEGA 2021; 6:34359-34366. [PMID: 34963921 PMCID: PMC8697013 DOI: 10.1021/acsomega.1c04223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Mutant polypeptide GB1HS#124F26A, which is known to aggregate into amyloid-like fibrils, has been utilized as a model in this study for gaining insights into the mechanism of domain-swapped aggregation through real-time monitoring. Size exclusion with UV monitoring at 280 nm and dynamic light scattering (DLS) profiles through different time points of fibrillation reveal that the dimer transitions into monomeric intermediates during the aggregation, which could further facilitate domain swapping to form amyloid fibrils. The 1D 1H and 2D 1H-13C HSQC nuclear magnetic resonance (NMR) spectra profiling through different time points of fibrillation reveal that there may be some other species present along with the dimer during aggregation which contribute to different trends for the intensity of protons in the spectral peaks. Diffusion NMR reveals changes in the mobility of the dimeric species during the process of aggregation, indicating that the dimer gives rise to other lower molecular weight species midway during aggregation, which further add up to form the oligomers and amyloid fibrils successively. The present work is a preliminary study which explores the possibility of utilizing biophysical methods to gain atomistic level insights into the different stages of aggregation.
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Affiliation(s)
- Renuka Ranjan
- Centre
of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar
Pradesh
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Nidhi Tiwari
- Centre
of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar
Pradesh
- Department
of Chemistry, Institute of Science, Banaras
Hindu University, Varanasi 221005, Uttar Pradesh
| | - Arvind M. Kayastha
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Neeraj Sinha
- Centre
of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar
Pradesh
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25
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Posey N, Ma Y, Lueckheide M, Danischewski J, Fagan JA, Prabhu VM. Tuning Net Charge in Aliphatic Polycarbonates Alters Solubility and Protein Complexation Behavior. ACS OMEGA 2021; 6:22589-22602. [PMID: 34514231 PMCID: PMC8427630 DOI: 10.1021/acsomega.1c02523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
A synthetic strategy yielded polyelectrolytes and polyampholytes with tunable net charge for complexation and protein binding. Organocatalytic ring-opening polymerizations yielded aliphatic polycarbonates that were functionalized with both carboxylate and ammonium side chains in a post-polymerization, radical-mediated thiol-ene reaction. Incorporating net charge into the polymer architecture altered the chain dimensions in phosphate buffered solution in a manner consistent with self-complexation and complexation behavior with model proteins. A net cationic polyampholyte with 5% of carboxylate side chains formed large clusters rather than small complexes with bovine serum albumin, while 50% carboxylate polyampholyte was insoluble. Overall, the aliphatic polycarbonates with varying net charge exhibited different macrophase solution behaviors when mixed with protein, where self-complexation appears to compete with protein binding and larger-scale complexation.
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Affiliation(s)
| | - Yuanchi Ma
- Materials Science and Engineering Division,
Material Measurement Laboratory, National
Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Michael Lueckheide
- Materials Science and Engineering Division,
Material Measurement Laboratory, National
Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Julia Danischewski
- Materials Science and Engineering Division,
Material Measurement Laboratory, National
Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Jeffrey A. Fagan
- Materials Science and Engineering Division,
Material Measurement Laboratory, National
Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Vivek M. Prabhu
- Materials Science and Engineering Division,
Material Measurement Laboratory, National
Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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26
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Iwakawa N, Morimoto D, Walinda E, Shirakawa M, Sugase K. Multiple-State Monitoring of SOD1 Amyloid Formation at Single-Residue Resolution by Rheo-NMR Spectroscopy. J Am Chem Soc 2021; 143:10604-10613. [PMID: 34232041 DOI: 10.1021/jacs.1c02974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formation of protein aggregates or fibrils entails the conversion of soluble native protein monomers via multiple molecular states. No spectroscopic techniques have succeeded in capturing the transient molecular-scale events of fibrillation in situ. Here we report residue- and state-specific real-time monitoring of the fibrillation of amyotrophic lateral sclerosis-related SOD1 by rheology NMR (Rheo-NMR) spectroscopy. Under moderately denaturing conditions, where NMR signals of folded and unfolded monomeric SOD1 are simultaneously observable, the cross-peak intensities of folded monomeric SOD1 decreased faster than those of the unfolded species, and a 310-helix in folded SOD1 was deformed prior to global unfolding. Furthermore, real-time protein dynamics analysis identified residues involved in the core structure formation of SOD1 oligomers. Our findings provide insight into local and global unfolding events in SOD1 and fibril formation. This Rheo-NMR analysis will be applicable not only to atomic-level monitoring of other amyloidogenic proteins but also to quantification of shear-induced structural changes of non-amyloidogenic proteins and elucidation of shear-enhanced chemical phenomena such as viscosity increase and crystallization of various solution-state compounds.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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27
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Toward the equilibrium and kinetics of amyloid peptide self-assembly. Curr Opin Struct Biol 2021; 70:87-98. [PMID: 34153659 DOI: 10.1016/j.sbi.2021.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/09/2021] [Accepted: 05/09/2021] [Indexed: 01/28/2023]
Abstract
Several devastating human diseases are linked to peptide self-assembly, but our understanding their onset and progression is not settled. This is a sign of the complexity of the aggregation process, which is prevented, catalyzed, or retarded by numerous factors in body fluids and cells, varying in time and space. Biophysical studies of pure peptide solutions contribute insights into the underlying steps in the process and quantitative parameters relating to rate constants (energy barriers) and equilibrium constants (population distributions). This requires methods to quantify the concentration of at least one species in the process. Translation to an in vivo situation poses an enormous challenge, and the effects of selected components (bottom up) or entire body fluids (top down) need to be quantified.
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Tangrodchanapong T, Sornkaew N, Yurasakpong L, Niamnont N, Nantasenamat C, Sobhon P, Meemon K. Beneficial Effects of Cyclic Ether 2-Butoxytetrahydrofuran from Sea Cucumber Holothuria scabra against Aβ Aggregate Toxicity in Transgenic Caenorhabditis elegans and Potential Chemical Interaction. Molecules 2021; 26:molecules26082195. [PMID: 33920352 PMCID: PMC8070609 DOI: 10.3390/molecules26082195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
The pathological finding of amyloid-β (Aβ) aggregates is thought to be a leading cause of untreated Alzheimer’s disease (AD). In this study, we isolated 2-butoxytetrahydrofuran (2-BTHF), a small cyclic ether, from Holothuria scabra and demonstrated its therapeutic potential against AD through the attenuation of Aβ aggregation in a transgenic Caenorhabditis elegans model. Our results revealed that amongst the five H. scabra isolated compounds, 2-BTHF was shown to be the most effective in suppressing worm paralysis caused by Aβ toxicity and in expressing strong neuroprotection in CL4176 and CL2355 strains, respectively. An immunoblot analysis showed that CL4176 and CL2006 treated with 2-BTHF showed no effect on the level of Aβ monomers but significantly reduced the toxic oligomeric form and the amount of 1,4-bis(3-carboxy-hydroxy-phenylethenyl)-benzene (X-34)-positive fibril deposits. This concurrently occurred with a reduction of reactive oxygen species (ROS) in the treated CL4176 worms. Mechanistically, heat shock factor 1 (HSF-1) (at residues histidine 63 (HIS63) and glutamine 72 (GLN72)) was shown to be 2-BTHF’s potential target that might contribute to an increased expression of autophagy-related genes required for the breakdown of the Aβ aggregate, thus attenuating its toxicity. In conclusion, 2-BTHF from H. scabra could protect C. elegans from Aβ toxicity by suppressing its aggregation via an HSF-1-regulated autophagic pathway and has been implicated as a potential drug for AD.
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Affiliation(s)
- Taweesak Tangrodchanapong
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
| | - Nilubon Sornkaew
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand; (N.S.); (N.N.)
| | - Laphatrada Yurasakpong
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
| | - Nakorn Niamnont
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand; (N.S.); (N.N.)
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand;
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
| | - Krai Meemon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
- Correspondence: or ; Tel.: +66-22-015-407
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Gao Y, Saccuzzo EG, Hill SE, Huard DJE, Robang AS, Lieberman RL, Paravastu AK. Structural Arrangement within a Peptide Fibril Derived from the Glaucoma-Associated Myocilin Olfactomedin Domain. J Phys Chem B 2021; 125:2886-2897. [PMID: 33683890 DOI: 10.1021/acs.jpcb.0c11460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myocilin-associated glaucoma is a new addition to the list of diseases linked to protein misfolding and amyloid formation. Single point variants of the ∼257-residue myocilin olfactomedin domain (mOLF) lead to mutant myocilin aggregation. Here, we analyze the 12-residue peptide P1 (GAVVYSGSLYFQ), corresponding to residues 326-337 of mOLF, previously shown to form amyloid fibrils in vitro and in silico. We applied solid-state NMR structural measurements to test the hypothesis that P1 fibrils adopt one of three predicted structures. Our data are consistent with a U-shaped fibril arrangement for P1, one that is related to the U-shape predicted previously in silico. Our data are also consistent with an antiparallel fibril arrangement, likely driven by terminal electrostatics. Our proposed structural model is reminiscent of fibrils formed by the Aβ(1-40) Iowa mutant peptide, but with a different arrangement of molecular turn regions. Taken together, our results strengthen the connection between mOLF fibrils and the broader amylome and contribute to our understanding of the fundamental molecular interactions governing fibril architecture and stability.
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Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
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Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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31
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Chang Z, Deng J, Zhao W, Yang J. Exploring interactions between lipids and amyloid-forming proteins: A review on applying fluorescence and NMR techniques. Chem Phys Lipids 2021; 236:105062. [PMID: 33600803 DOI: 10.1016/j.chemphyslip.2021.105062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/27/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
A hallmark of Alzheimer's, Parkinson's, and other amyloid diseases is the assembly of amyloid proteins into amyloid aggregates or fibrils. In many cases, the formation and cytotoxicity of amyloid assemblies are associated with their interaction with cell membranes. Despite studied for many years, the characterization of the interaction is challenged for reasons on the multiple aggregation states of amyloid-forming proteins, transient and weak interactions in the complex system. Although several strategies such as computation biology, spectroscopy, and imaging methods have been performed, there is an urgent need to detail the molecular mechanism in different time scales and high resolutions. This review highlighted the recent applications of fluorescence, solution and solid-state NMR in exploring the interactions between amyloid protein and membranes attributing to their advantages of high sensitivity and atomic resolution.
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Affiliation(s)
- Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, PR China.
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Patil SM, Qin B, Wang Y, Ahmed S, Yilmaz H, Jiang X, Keire DA, Chen K. A Real-Time NMR Method for Measurement of In Vitro Aggregation Kinetics Of Degarelix Drug Products. AAPS PharmSciTech 2021; 22:73. [PMID: 33586081 DOI: 10.1208/s12249-021-01948-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/26/2021] [Indexed: 11/30/2022] Open
Abstract
Degarelix is a gonadotropin-releasing hormone (GnRH) receptor antagonist. Upon contact with physiological fluid, degarelix undergoes quick gelation and forms a depot at the site of injection providing sustained release. The molecular gelling kinetics is a critical physiochemical quality attribute of degarelix products that may impact drug delivery. However, high-resolution and drug substance (DS)-specific analytical methods for characterizing gelling kinetics of degarelix are still lacking. Accordingly, the current study focused on developing NMR-based methods to characterize in vitro initial aggregation of degarelix in Firmagon® drug product (DP). The high-precision real-time NMR method was demonstrated to quickly differentiate lot to lot differences in degarelix aggregation kinetics, and to reveal the effects of degarelix concentration, pH, salt, and temperature on the kinetics. The results could be useful for quality assurance of degarelix products and facilitate complex generic drug development. The real-time NMR method developed here could also be adopted to other complex DPs that have varied aggregation and release properties.
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Fatafta H, Samantray S, Sayyed-Ahmad A, Coskuner-Weber O, Strodel B. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:135-185. [PMID: 34656328 DOI: 10.1016/bs.pmbts.2021.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce metadynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Suman Samantray
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; AICES Graduate School, RWTH Aachen University, Aachen, Germany
| | | | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, Istanbul, Turkey
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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34
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2020; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease. Methods to study structure, toxicity, and kinetics of transient amyloid oligomers. NMR and single particle methods can characterize lowly-populated oligomers. Chemical tools/antibodies stabilize oligomers for structural and toxicity studies A combination of methods is needed to fully characterize amyloid assembly pathways.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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35
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Ghosh R, Kishore N. Physicochemical Insights into the Role of Drug Functionality in Fibrillation Inhibition of Bovine Serum Albumin. J Phys Chem B 2020; 124:8989-9008. [DOI: 10.1021/acs.jpcb.0c06167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ritutama Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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36
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Tangrodchanapong T, Sobhon P, Meemon K. Frondoside A Attenuates Amyloid-β Proteotoxicity in Transgenic Caenorhabditis elegans by Suppressing Its Formation. Front Pharmacol 2020; 11:553579. [PMID: 33013392 PMCID: PMC7513805 DOI: 10.3389/fphar.2020.553579] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/24/2020] [Indexed: 11/16/2022] Open
Abstract
Oligomeric assembly of Amyloid-β (Aβ) is the main toxic species that contribute to early cognitive impairment in Alzheimer’s patients. Therefore, drugs that reduce the formation of Aβ oligomers could halt the disease progression. In this study, by using transgenic Caenorhabditis elegans model of Alzheimer’s disease, we investigated the effects of frondoside A, a well-known sea cucumber Cucumaria frondosa saponin with anti-cancer activity, on Aβ aggregation and proteotoxicity. The results showed that frondoside A at a low concentration of 1 µM significantly delayed the worm paralysis caused by Aβ aggregation as compared with control group. In addition, the number of Aβ plaque deposits in transgenic worm tissues was significantly decreased. Frondoside A was more effective in these activities than ginsenoside-Rg3, a comparable ginseng saponin. Immunoblot analysis revealed that the level of small oligomers as well as various high molecular weights of Aβ species in the transgenic C. elegans were significantly reduced upon treatment with frondoside A, whereas the level of Aβ monomers was not altered. This suggested that frondoside A may primarily reduce the level of small oligomeric forms, the most toxic species of Aβ. Frondoside A also protected the worms from oxidative stress and rescued chemotaxis dysfunction in a transgenic strain whose neurons express Aβ. Taken together, these data suggested that low dose of frondoside A could protect against Aβ-induced toxicity by primarily suppressing the formation of Aβ oligomers. Thus, the molecular mechanism of how frondoside A exerts its anti-Aβ aggregation should be studied and elucidated in the future.
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Affiliation(s)
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Krai Meemon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
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37
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Kaur A, New EJ, Sunde M. Strategies for the Molecular Imaging of Amyloid and the Value of a Multimodal Approach. ACS Sens 2020; 5:2268-2282. [PMID: 32627533 DOI: 10.1021/acssensors.0c01101] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein aggregation has been widely implicated in neurodegenerative diseases such as Alzheimer's disease, frontotemporal dementia, Parkinson's disease, and Huntington disease, as well as in systemic amyloidoses and conditions associated with localized amyloid deposits, such as type-II diabetes. The pressing need for a better understanding of the factors governing protein assembly has driven research for the development of molecular sensors for amyloidogenic proteins. To date, a number of sensors have been developed that report on the presence of protein aggregates utilizing various modalities, and their utility demonstrated for imaging protein aggregation in vitro and in vivo. Analysis of these sensors highlights the various advantages and disadvantages of the different imaging modalities and makes clear that multimodal sensors with properties amenable to more than one imaging technique need to be developed. This critical review highlights the key molecular scaffolds reported for molecular imaging modalities such as fluorescence, positron emission tomography, single photon emission computed tomography, and magnetic resonance imaging and includes discussion of the advantages and disadvantages of each modality, and future directions for the design of amyloid sensors. We also discuss the recent efforts focused on the design and development of multimodal sensors and the value of cross-validation across multiple modalities.
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Affiliation(s)
- Amandeep Kaur
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, New South Wales 2006, Australia
- The University of Sydney, Nano Institute (Sydney Nano), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elizabeth J. New
- The University of Sydney, Nano Institute (Sydney Nano), The University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney, School of Chemistry, Faculty of Science, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Margaret Sunde
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, New South Wales 2006, Australia
- The University of Sydney, Nano Institute (Sydney Nano), The University of Sydney, Sydney, New South Wales 2006, Australia
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Kaur A, Kaur A, Goyal D, Goyal B. How Does the Mono-Triazole Derivative Modulate Aβ 42 Aggregation and Disrupt a Protofibril Structure: Insights from Molecular Dynamics Simulations. ACS OMEGA 2020; 5:15606-15619. [PMID: 32637837 PMCID: PMC7331201 DOI: 10.1021/acsomega.0c01825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/08/2020] [Indexed: 05/31/2023]
Abstract
Clinical studies have identified that abnormal self-assembly of amyloid-β (Aβ) peptide into toxic fibrillar aggregates is associated with the pathology of Alzheimer's disease (AD). The most acceptable therapeutic approach to stop the progression of AD is to inhibit the formation of β-sheet-rich structures. Recently, we designed and evaluated a series of novel mono-triazole derivatives 4(a-x), where compound 4v was identified as the most potent inhibitor of Aβ42 aggregation and disaggregates preformed Aβ42 fibrils significantly. Moreover, 4v strongly averts the Cu2+-induced Aβ42 aggregation and disaggregates the preformed Cu2+-induced Aβ42 fibrils, halts the generation of reactive oxygen species, and shows neuroprotective effects in SH-SY5Y cells. However, the underlying molecular mechanism of inhibition of Aβ42 aggregation by 4v and disaggregation of preformed Aβ42 fibrils remains obscure. In this work, molecular dynamics (MD) simulations have been performed to explore the conformational ensemble of the Aβ42 monomer and a pentameric protofibril structure of Aβ42 in the presence of 4v. The MD simulations highlighted that 4v binds preferentially at the central hydrophobic core region of the Aβ42 monomer and chains D and E of the Aβ42 protofibril. The dictionary of secondary structure of proteins analysis indicated that 4v retards the conformational conversion of the helix-rich structure of the Aβ42 monomer into the aggregation-prone β-sheet conformation. The binding free energy calculated by the molecular mechanics Poisson-Boltzmann surface area method revealed an energetically favorable process with ΔG binding = -44.9 ± 3.3 kcal/mol for the Aβ42 monomer-4v complex. The free energy landscape analysis highlighted that the Aβ42 monomer-4v complex sampled conformations with significantly higher helical contents (35 and 49%) as compared to the Aβ42 monomer alone (17%). Compound 4v displayed hydrogen bonding with Gly37 (chain E) and π-π interactions with Phe19 (chain D) of the Aβ42 protofibril. Further, the per-residue binding free energy analysis also highlighted that Phe19 (chain D) and Gly37 (chain E) of the Aβ42 protofibril showed the maximum contribution in the binding free energy. The decreased binding affinity and residue-residue contacts between chains D and E of the Aβ42 protofibril in the presence of 4v indicate destabilization of the Aβ42 protofibril structure. Overall, the structural information obtained through MD simulations indicated that 4v stabilizes the native helical conformation of the Aβ42 monomer and persuades a destabilization in the protofibril structure of Aβ42. The results of the study will be useful in the rational design of potent inhibitors against amyloid aggregation.
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Affiliation(s)
- Amandeep Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anupamjeet Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Bhupesh Goyal
- School
of Chemistry & Biochemistry, Thapar
Institute of Engineering & Technology, Patiala 147004, Punjab, India
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Kawasaki R, Tate SI. Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments. Int J Mol Sci 2020; 21:ijms21113920. [PMID: 32486218 PMCID: PMC7313075 DOI: 10.3390/ijms21113920] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/23/2022] Open
Abstract
Tau forms intracellular insoluble aggregates as a neuropathological hallmark of Alzheimer’s disease. Tau is largely unstructured, which complicates the characterization of the tau aggregation process. Recent studies have demonstrated that tau samples two distinct conformational ensembles, each of which contains the soluble and aggregation-prone states of tau. A shift to populate the aggregation-prone ensemble may promote tau fibrillization. However, the mechanism of this ensemble transition remains elusive. In this study, we explored the conformational dynamics of a tau fragment by using paramagnetic relaxation enhancement (PRE) and interference (PRI) NMR experiments. The PRE correlation map showed that tau is composed of segments consisting of residues in correlated motions. Intriguingly, residues forming the β-structures in the heparin-induced tau filament coincide with residues in these segments, suggesting that each segment behaves as a structural unit in fibrillization. PRI data demonstrated that the P301L mutation exclusively alters the transiently formed tau structures by changing the short- and long-range correlated motions among residues. The transient conformations of P301L tau expose the amyloid motif PHF6 to promote tau self-aggregation. We propose the correlated motions among residues within tau determine the population sizes of the conformational ensembles, and perturbing the correlated motions populates the aggregation-prone form.
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Affiliation(s)
- Ryosuke Kawasaki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
| | - Shin-ichi Tate
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Department of Mathematical and Life Sciences, Graduate School of the Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: ; Tel.: +81-82-424-7387
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40
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Sahoo BR, Cox SJ, Ramamoorthy A. High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease. Chem Commun (Camb) 2020; 56:4627-4639. [PMID: 32300761 PMCID: PMC7254607 DOI: 10.1039/d0cc01551b] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna in establishing the structure to function relationship for Aβ oligomers prevents the development of an effective treatment for AD. While the transient and heterogeneous properties of Aβ oligomers impose many challenges for structural investigation, an effective use of a combination of NMR techniques has successfully identified and characterized them at atomic-resolution. Here, we review the successful utilization of solution and solid-state NMR techniques to probe the aggregation and structures of small and large oligomers of Aβ. Biophysical studies utilizing the commonly used solution and 19F based NMR experiments to identify the formation of small size early intermediates and to obtain their structures, and dock-lock mechanism of fiber growth at atomic-resolution are discussed. In addition, the use of proton-detected magic angle spinning (MAS) solid-state NMR experiments to obtain high-resolution insights into the aggregation pathways and structures of large oligomers and other aggregates is also presented. We expect these NMR based studies to be valuable for real-time monitoring of the depletion of monomers and the formation of toxic oligomers and high-order aggregates under a variety of conditions, and to solve the high-resolution structures of small and large size oligomers for most amyloid proteins, and therefore to develop inhibitors and drugs.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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Munari F, D'Onofrio M, Assfalg M. Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins. Arch Biochem Biophys 2020; 683:108304. [PMID: 32097611 DOI: 10.1016/j.abb.2020.108304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
Abstract
The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.
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Affiliation(s)
- Francesca Munari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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Ebo JS, Guthertz N, Radford SE, Brockwell DJ. Using protein engineering to understand and modulate aggregation. Curr Opin Struct Biol 2020; 60:157-166. [PMID: 32087409 PMCID: PMC7132541 DOI: 10.1016/j.sbi.2020.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023]
Abstract
Protein aggregation occurs through a variety of mechanisms, initiated by the unfolded, non-native, or even the native state itself. Understanding the molecular mechanisms of protein aggregation is challenging, given the array of competing interactions that control solubility, stability, cooperativity and aggregation propensity. An array of methods have been developed to interrogate protein aggregation, spanning computational algorithms able to identify aggregation-prone regions, to deep mutational scanning to define the entire mutational landscape of a protein's sequence. Here, we review recent advances in this exciting and emerging field, focussing on protein engineering approaches that, together with improved computational methods, hold promise to predict and control protein aggregation linked to human disease, as well as facilitating the manufacture of protein-based therapeutics.
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Affiliation(s)
- Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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Gallardo R, Ranson NA, Radford SE. Amyloid structures: much more than just a cross-β fold. Curr Opin Struct Biol 2020; 60:7-16. [PMID: 31683043 DOI: 10.1016/j.sbi.2019.09.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/04/2019] [Indexed: 01/10/2023]
Abstract
In recent years our understanding of amyloid structure has been revolutionised by innovations in cryo-electron microscopy, electron diffraction and solid-state NMR. These techniques have yielded high-resolution structures of fibrils isolated from patients with neurodegenerative disease, as well as those formed from amyloidogenic proteins in vitro. The results not only show the expected cross-β amyloid structure, but also reveal that the amyloid fold is unexpectedly diverse and complex. Here, we discuss this diversity, highlighting dynamic regions, ligand binding motifs, cavities, non-protein components, and structural polymorphism. Collectively, these variations combine to allow the generic amyloid fold to be realised in three dimensions in different ways, and this diversity may be related to the roles of fibrils in disease.
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Affiliation(s)
- Rodrigo Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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44
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Alderson TR, Kay LE. Unveiling invisible protein states with NMR spectroscopy. Curr Opin Struct Biol 2020; 60:39-49. [DOI: 10.1016/j.sbi.2019.10.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
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45
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Zhao C, Somiya T, Takai S, Ueki S, Arata T. Structural Dynamics of the N-Extension of Cardiac Troponin I Complexed with Troponin C by Site-Directed Spin Labeling Electron Paramagnetic Resonance. Sci Rep 2019; 9:15259. [PMID: 31649274 PMCID: PMC6813352 DOI: 10.1038/s41598-019-51740-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/07/2019] [Indexed: 11/29/2022] Open
Abstract
The secondary structure of the N-extension of cardiac troponin I (cTnI) was determined by measuring the distance distribution between spin labels attached to the i and i + 4 residues: 15/19, 23/27, 27/31, 35/39, and 43/47. All of the EPR spectra of these regions in the monomeric state were broadened and had a amplitude that was reduced by two-thirds of that of the single spin-labeled spectra and was fit by two residual distance distributions, with a major distribution one spreading over the range from 1 to 2.5 nm and the other minor peak at 0.9 nm. Only slight or no obvious changes were observed when the extension was bound to cTnC in the cTnI-cTnC complex at 0.2 M KCl. However, at 0.1 M KCl, residues 43/47, located at the PKC phosphorylation sites Ser42/44 on the boundary of the extension, exclusively exhibited a 0.9 nm peak, as expected from α-helix in the crystal structure, in the complex. Furthermore, 23/27, which is located on the PKA phosphorylation sites Ser23/24, showed that the major distribution was markedly narrowed, centered at 1.4 nm and 0.5 nm wide, accompanying the spin label immobilization of residue 27. Residues 35 and 69 at site 1 and 2 of cTnC exhibited partial immobilization of the attached spin labels upon complex formation. The results show that the extension exhibited a primarily partially folded or unfolded structure equilibrated with a transiently formed α-helix-like short structure over the length. We hypothesize that the structure binds at least near sites 1 and 2 of cTnC and that the specific secondary structure of the extension on cTnC becomes uncovered when decreasing the ionic strength demonstrating that only the phosphorylation regions of cTnI interact stereospecifically with cTnC.
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Affiliation(s)
- Chenchao Zhao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043, Japan
| | - Takayasu Somiya
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043, Japan
| | - Shinji Takai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043, Japan
| | - Shoji Ueki
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Shido 1314-1, Samuki, Kagawa, 769-2193, Japan
| | - Toshiaki Arata
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043, Japan. .,Center for Advanced High Magnetic Field Science, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043, Japan. .,Department of Biology, Graduate School of Science, Osaka City University, Sugimoto 3-3-138, Osaka, Osaka, 558-8585, Japan.
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46
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Dutta S, Patra P, Chakrabarti J. Self-assembly in amphiphilic macromolecules with solvent exposed hydrophobic moieties. Biopolymers 2019; 110:e23330. [PMID: 31498431 DOI: 10.1002/bip.23330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/03/2019] [Accepted: 08/19/2019] [Indexed: 11/12/2022]
Abstract
Self-assembly by amphiphilic molecules with solvent exposed hydrophobic groups are relevant in biomolecular systems as well as in technological applications. Here we study such self-assembly in these systems using a model system of spherical particles having charge at core but solvent repelling surface, using Monte-Carlo simulations and mean field treatment. We find that solvophobicity mediated attraction leads aggregation, while electrostatic repulsions control stability of finite clusters. The aggregation threshold relates the parameters of two interactions through an algebraic dependence. The study also qualitatively explains experimental observations on aggregation of misfolded proteins and can be useful guide to tune stability of nm sized self-assembly in systems with exposed hydrophobic groups.
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Affiliation(s)
- Sutapa Dutta
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, India
| | - Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, Nadia, West Bengal, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, India.,Unit of Nanoscience and Technology-II and The Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, India
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47
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Owen MC, Gnutt D, Gao M, Wärmländer SKTS, Jarvet J, Gräslund A, Winter R, Ebbinghaus S, Strodel B. Effects of in vivo conditions on amyloid aggregation. Chem Soc Rev 2019; 48:3946-3996. [PMID: 31192324 DOI: 10.1039/c8cs00034d] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One of the grand challenges of biophysical chemistry is to understand the principles that govern protein misfolding and aggregation, which is a highly complex process that is sensitive to initial conditions, operates on a huge range of length- and timescales, and has products that range from protein dimers to macroscopic amyloid fibrils. Aberrant aggregation is associated with more than 25 diseases, which include Alzheimer's, Parkinson's, Huntington's, and type II diabetes. Amyloid aggregation has been extensively studied in the test tube, therefore under conditions that are far from physiological relevance. Hence, there is dire need to extend these investigations to in vivo conditions where amyloid formation is affected by a myriad of biochemical interactions. As a hallmark of neurodegenerative diseases, these interactions need to be understood in detail to develop novel therapeutic interventions, as millions of people globally suffer from neurodegenerative disorders and type II diabetes. The aim of this review is to document the progress in the research on amyloid formation from a physicochemical perspective with a special focus on the physiological factors influencing the aggregation of the amyloid-β peptide, the islet amyloid polypeptide, α-synuclein, and the hungingtin protein.
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Affiliation(s)
- Michael C Owen
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany and Lead Discovery Wuppertal, Bayer AG, 42096 Wuppertal, Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany and Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 42525 Jülich, Germany. and Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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48
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Vugmeyster L, Au DF, Ostrovsky D, Fu R. Deuteron Solid-State NMR Relaxation Measurements Reveal Two Distinct Conformational Exchange Processes in the Disordered N-Terminal Domain of Amyloid-β Fibrils. Chemphyschem 2019; 20:1680-1689. [PMID: 31087613 PMCID: PMC6663588 DOI: 10.1002/cphc.201900363] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/12/2019] [Indexed: 12/26/2022]
Abstract
We employed deuterium solid-state NMR techniques under static conditions to discern the details of the μs-ms timescale motions in the flexible N-terminal subdomain of Aβ1-40 amyloid fibrils, which spans residues 1-16. In particular, we utilized a rotating frame (R1ρ ) and the newly developed time domain quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation measurements at the selectively deuterated side chains of A2, H6, and G9. The two experiments are complementary in terms of probing somewhat different timescales of motions, governed by the tensor parameters and the sampling window of the magnetization decay curves. The results indicated two mobile "free" states of the N-terminal domain undergoing global diffusive motions, with isotropic diffusion coefficients of 0.7-1 ⋅ 108 and 0.3-3 ⋅ 106 ad2 s-1 . The free states are also involved in the conformational exchange with a single bound state, in which the diffusive motions are quenched, likely due to transient interactions with the structured hydrophobic core. The conformational exchange rate constants are 2-3 ⋅ 105 s-1 and 2-3 ⋅ 104 s-1 for the fast and slow diffusion free states, respectively.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO, USA, 80204
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver CO, USA, 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO, USA, 80204
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL, 32310
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Chen D, Drombosky KW, Hou Z, Sari L, Kashmer OM, Ryder BD, Perez VA, Woodard DR, Lin MM, Diamond MI, Joachimiak LA. Tau local structure shields an amyloid-forming motif and controls aggregation propensity. Nat Commun 2019; 10:2493. [PMID: 31175300 PMCID: PMC6555816 DOI: 10.1038/s41467-019-10355-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Tauopathies are neurodegenerative diseases characterized by intracellular amyloid deposits of tau protein. Missense mutations in the tau gene (MAPT) correlate with aggregation propensity and cause dominantly inherited tauopathies, but their biophysical mechanism driving amyloid formation is poorly understood. Many disease-associated mutations localize within tau's repeat domain at inter-repeat interfaces proximal to amyloidogenic sequences, such as 306VQIVYK311. We use cross-linking mass spectrometry, recombinant protein and synthetic peptide systems, in silico modeling, and cell models to conclude that the aggregation-prone 306VQIVYK311 motif forms metastable compact structures with its upstream sequence that modulates aggregation propensity. We report that disease-associated mutations, isomerization of a critical proline, or alternative splicing are all sufficient to destabilize this local structure and trigger spontaneous aggregation. These findings provide a biophysical framework to explain the basis of early conformational changes that may underlie genetic and sporadic tau pathogenesis.
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Affiliation(s)
- Dailu Chen
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kenneth W Drombosky
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zhiqiang Hou
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Levent Sari
- Green Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Omar M Kashmer
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bryan D Ryder
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Valerie A Perez
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - DaNae R Woodard
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Milo M Lin
- Green Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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50
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Hong JY, Wang DD, Xue W, Yue HW, Yang H, Jiang LL, Wang WN, Hu HY. Structural and dynamic studies reveal that the Ala-rich region of ataxin-7 initiates α-helix formation of the polyQ tract but suppresses its aggregation. Sci Rep 2019; 9:7481. [PMID: 31097749 PMCID: PMC6522498 DOI: 10.1038/s41598-019-43926-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/04/2019] [Indexed: 11/26/2022] Open
Abstract
Ataxin-7 (Atx7) is a disease-related protein associated with the pathogenesis of spinocerebellar ataxia 7, while its polyglutamine (polyQ) tract in N-terminus is the causative source of aggregation and proteinopathy. We investigated the structure, dynamics and aggregation properties of the N-terminal 62-residue fragment of Atx7 (Atx7-N) by biochemical and biophysical approaches. The results showed that the normal Atx7-N with a tract of 10 glutamines (10Q) overall adopts a flexible and disordered structure, but it may contain a short or small population of helical structure in solution. PolyQ expansion increases the α-helical propensity of the polyQ tract and consequently enhances its transformation into β-sheet structures during amyloid aggregation. An alanine-rich region (ARR) just ahead of the polyQ tract forms a local and relatively stable α-helix. The ARR α-helix can initiate and stabilize helical formation of the following polyQ tract, but it may suppress aggregation of the polyQ-expanded Atx7-N both in vitro and in cell. Thus, the preceding ARR segment in Atx7-N may influence the dynamic structure and aggregation property of the polyQ tract and even determine the threshold of the pathogenic polyQ lengths. This study may gain structural and dynamic insights into amyloid aggregation of Atx7 and help us further understand the Atx7 proteinopathy based on polyQ expansion.
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Affiliation(s)
- Jun-Ye Hong
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Dong-Dong Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Wei Xue
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Hong-Wei Yue
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China
| | - Wen-Ning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.
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