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Tsekrekou M, Giannakou M, Papanikolopoulou K, Skretas G. Protein aggregation and therapeutic strategies in SOD1- and TDP-43- linked ALS. Front Mol Biosci 2024; 11:1383453. [PMID: 38855322 PMCID: PMC11157337 DOI: 10.3389/fmolb.2024.1383453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with severe socio-economic impact. A hallmark of ALS pathology is the presence of aberrant cytoplasmic inclusions composed of misfolded and aggregated proteins, including both wild-type and mutant forms. This review highlights the critical role of misfolded protein species in ALS pathogenesis, particularly focusing on Cu/Zn superoxide dismutase (SOD1) and TAR DNA-binding protein 43 (TDP-43), and emphasizes the urgent need for innovative therapeutic strategies targeting these misfolded proteins directly. Despite significant advancements in understanding ALS mechanisms, the disease remains incurable, with current treatments offering limited clinical benefits. Through a comprehensive analysis, the review focuses on the direct modulation of the misfolded proteins and presents recent discoveries in small molecules and peptides that inhibit SOD1 and TDP-43 aggregation, underscoring their potential as effective treatments to modify disease progression and improve clinical outcomes.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Giannakou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
- Institute for Bio-innovation, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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2
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Fernández Ramírez MDC, Afrin S, Saelices L. Conformational inhibitors of protein aggregation. Curr Opin Struct Biol 2023; 83:102700. [PMID: 37717490 DOI: 10.1016/j.sbi.2023.102700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023]
Abstract
Amyloidoses are fatal conditions associated with the aggregation of proteins into amyloid fibrils that deposit systemically and/or locally. Possibly because the causal mechanism of protein aggregation and deposition is not fully understood, this group of diseases remains uncurable. Advances in structural biology, such as the use of nuclear magnetic resonance and cryo-electron microscopy, have enabled the study of the structures and the conformational nature of the proteins whose aggregation is associated with the underlying pathogenesis of amyloidosis. As a result, the last years of research have translated into the development of directed therapeutic strategies that target the specific conformations of precursors, fibrils, and intermediary species. Current efforts include the use of small molecules, peptides, and antibodies. This review summarizes the recent progress in developing strategies that target specific protein conformations for the treatment of amyloidoses.
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Affiliation(s)
- María Del Carmen Fernández Ramírez
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA. https://twitter.com/FernandezR_MC
| | - Shumaila Afrin
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA. https://twitter.com/Shumyla44
| | - Lorena Saelices
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
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3
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Cheung DL. Aggregation of an Amyloidogenic Peptide on Gold Surfaces. Biomolecules 2023; 13:1261. [PMID: 37627326 PMCID: PMC10452923 DOI: 10.3390/biom13081261] [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: 07/06/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Solid surfaces have been shown to affect the aggregation and assembly of many biomolecular systems. One important example is the formation of protein fibrils, which can occur on a range of biological and synthetic surfaces. The rate of fibrillation depends on both the protein structure and the surface chemistry, with the different molecular and oligomer structures adopted by proteins on surfaces likely to be crucial. In this paper, the aggregation of the model amyloidogenic peptide, Aβ(16-22), corresponding to a hydrophobic segment of the amyloid beta protein on a gold surface is studied using molecular dynamics simulation. Previous simulations of this peptide on gold surfaces have shown that it adopts conformations on surfaces that are quite different from those in bulk solution. These simulations show that this then leads to significant differences in the oligomer structures formed in solution and on gold surfaces. In particular, oligomers formed on the surface are low in beta-strands so are unlike the structures formed in bulk solution. When oligomers formed in solution adsorb onto gold surfaces they can then restructure themselves. This can then help explain the inhibition of Aβ(16-22) fibrillation by gold surfaces and nanoparticles seen experimentally.
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Affiliation(s)
- David L Cheung
- School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
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4
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Fernández-Ramírez MDC, Ng KKS, Menéndez M, Laurents DV, Hervás R, Carrión-Vázquez M. Expanded Conformations of Monomeric Tau Initiate Its Amyloidogenesis. Angew Chem Int Ed Engl 2022; 62:e202209252. [PMID: 36542681 DOI: 10.1002/anie.202209252] [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: 06/26/2022] [Revised: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Understanding early amyloidogenesis is key to rationally develop therapeutic strategies. Tau protein forms well-characterized pathological deposits but its aggregation mechanism is still poorly understood. Using single-molecule force spectroscopy based on a mechanical protection strategy, we studied the conformational landscape of the monomeric tau repeat domain (tau-RD244-368 ). We found two sets of conformational states, whose frequency is influenced by mutations and the chemical context. While pathological mutations Δ280K and P301L and a pro-amyloidogenic milieu favored expanded conformations and destabilized local structures, an anti-amyloidogenic environment promoted a compact ensemble, including a conformer whose topology might mask two amyloidogenic segments. Our results reveal that to initiate aggregation, monomeric tau-RD244-368 decreases its polymorphism adopting expanded conformations. This could account for the distinct structures found in vitro and across tauopathies.
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Affiliation(s)
- María Del Carmen Fernández-Ramírez
- Instituto Cajal, IC-CSIC, Avda. Doctor Arce 37, 28002, Madrid, Spain.,Current address: Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kevin Kan-Shing Ng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, 28006, Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), Spain
| | - Douglas V Laurents
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, 28006, Madrid, Spain
| | - Rubén Hervás
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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5
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Li J, Li H. New insights into the folding–unfolding mechanism and conformations of cytochrome C. Chem Sci 2022; 13:7498-7508. [PMID: 35872809 PMCID: PMC9241957 DOI: 10.1039/d2sc01126c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
Optical trapping experiments offer new insights into the folding and unfolding of cytochrome C.
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Affiliation(s)
- Jiayu Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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6
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González LF, Bevilacqua LE, Naves R. Nanotechnology-Based Drug Delivery Strategies to Repair the Mitochondrial Function in Neuroinflammatory and Neurodegenerative Diseases. Pharmaceutics 2021; 13:2055. [PMID: 34959337 PMCID: PMC8707316 DOI: 10.3390/pharmaceutics13122055] [Citation(s) in RCA: 9] [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: 10/25/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are vital organelles in eukaryotic cells that control diverse physiological processes related to energy production, calcium homeostasis, the generation of reactive oxygen species, and cell death. Several studies have demonstrated that structural and functional mitochondrial disturbances are involved in the development of different neuroinflammatory (NI) and neurodegenerative (ND) diseases (NI&NDDs) such as multiple sclerosis, Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Remarkably, counteracting mitochondrial impairment by genetic or pharmacologic treatment ameliorates neurodegeneration and clinical disability in animal models of these diseases. Therefore, the development of nanosystems enabling the sustained and selective delivery of mitochondria-targeted drugs is a novel and effective strategy to tackle NI&NDDs. In this review, we outline the impact of mitochondrial dysfunction associated with unbalanced mitochondrial dynamics, altered mitophagy, oxidative stress, energy deficit, and proteinopathies in NI&NDDs. In addition, we review different strategies for selective mitochondria-specific ligand targeting and discuss novel nanomaterials, nanozymes, and drug-loaded nanosystems developed to repair mitochondrial function and their therapeutic benefits protecting against oxidative stress, restoring cell energy production, preventing cell death, inhibiting protein aggregates, and improving motor and cognitive disability in cellular and animal models of different NI&NDDs.
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Affiliation(s)
| | | | - Rodrigo Naves
- Immunology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile; (L.F.G.); (L.E.B.)
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7
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Petrosyan R, Narayan A, Woodside MT. Single-Molecule Force Spectroscopy of Protein Folding. J Mol Biol 2021; 433:167207. [PMID: 34418422 DOI: 10.1016/j.jmb.2021.167207] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
The use of force probes to induce unfolding and refolding of single molecules through the application of mechanical tension, known as single-molecule force spectroscopy (SMFS), has proven to be a powerful tool for studying the dynamics of protein folding. Here we provide an overview of what has been learned about protein folding using SMFS, from small, single-domain proteins to large, multi-domain proteins. We highlight the ability of SMFS to measure the energy landscapes underlying folding, to map complex pathways for native and non-native folding, to probe the mechanisms of chaperones that assist with native folding, to elucidate the effects of the ribosome on co-translational folding, and to monitor the folding of membrane proteins.
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Affiliation(s)
- Rafayel Petrosyan
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Abhishek Narayan
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
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8
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Unfolded and intermediate states of PrP play a key role in the mechanism of action of an antiprion chaperone. Proc Natl Acad Sci U S A 2021; 118:2010213118. [PMID: 33619087 DOI: 10.1073/pnas.2010213118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prion and prion-like diseases involve the propagation of misfolded protein conformers. Small-molecule pharmacological chaperones can inhibit propagated misfolding, but how they interact with disease-related proteins to prevent misfolding is often unclear. We investigated how pentosan polysulfate (PPS), a polyanion with antiprion activity in vitro and in vivo, interacts with mammalian prion protein (PrP) to alter its folding. Calorimetry showed that PPS binds two sites on natively folded PrP, but one PPS molecule can bind multiple PrP molecules. Force spectroscopy measurements of single PrP molecules showed PPS stabilizes not only the native fold of PrP but also many different partially folded intermediates that are not observed in the absence of PPS. PPS also bound tightly to unfolded segments of PrP, delaying refolding. These observations imply that PPS can act through multiple possible modes, inhibiting misfolding not only by stabilizing the native fold or sequestering natively folded PrP into aggregates, as proposed previously, but also by binding to partially or fully unfolded states that play key roles in mediating misfolding. These results underline the likely importance of unfolded states as critical intermediates on the prion conversion pathway.
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9
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Hervás R, Del Carmen Fernández-Ramírez M, Galera-Prat A, Suzuki M, Nagai Y, Bruix M, Menéndez M, Laurents DV, Carrión-Vázquez M. Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold. BMC Biol 2021; 19:43. [PMID: 33706787 PMCID: PMC7953810 DOI: 10.1186/s12915-021-00967-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Amyloids are ordered, insoluble protein aggregates, characterized by a cross-β sheet quaternary structure in which molecules in a β-strand conformation are stacked along the filament axis via intermolecular interactions. While amyloids are typically associated with pathological conditions, functional amyloids have also been identified and are present in a wide variety of organisms ranging from bacteria to humans. The cytoplasmic polyadenylation element-binding (CPEB) prion-like protein is an mRNA-binding translation regulator, whose neuronal isoforms undergo activity-dependent aggregation, a process that has emerged as a plausible biochemical substrate for memory maintenance. CPEB aggregation is driven by prion-like domains (PLD) that are divergent in sequence across species, and it remains unknown whether such divergent PLDs follow a similar aggregating assembly pathway. Here, we describe the amyloid-like features of the neuronal Aplysia CPEB (ApCPEB) PLD and compare them to those of the Drosophila ortholog, Orb2 PLD. RESULTS Using in vitro single-molecule and bulk biophysical methods, we find transient oligomers and mature amyloid-like filaments that suggest similarities in the late stages of the assembly pathway for both ApCPEB and Orb2 PLDs. However, while prior to aggregation the Orb2 PLD monomer remains mainly as a random coil in solution, ApCPEB PLD adopts a diversity of conformations comprising α-helical structures that evolve to coiled-coil species, indicating structural differences at the beginning of their amyloid assembly pathways. CONCLUSION Our results indicate that divergent PLDs of CPEB proteins from different species retain the ability to form a generic amyloid-like fold through different assembly mechanisms.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC, Avda. Doctor Arce 37, E-28002, Madrid, Spain. .,Present address: School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | | | | | - Mari Suzuki
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Diabetic Neuropathy Project, Department of Sensory and Motor Systems, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Department of Neurology, Faculty of Medicine, Kindai University, Osaka-Sayama, Osaka, Japan
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), C/ Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
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10
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Hervás R, Oroz J. Mechanistic Insights into the Role of Molecular Chaperones in Protein Misfolding Diseases: From Molecular Recognition to Amyloid Disassembly. Int J Mol Sci 2020; 21:ijms21239186. [PMID: 33276458 PMCID: PMC7730194 DOI: 10.3390/ijms21239186] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 12/14/2022] Open
Abstract
Age-dependent alterations in the proteostasis network are crucial in the progress of prevalent neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, or amyotrophic lateral sclerosis, which are characterized by the presence of insoluble protein deposits in degenerating neurons. Because molecular chaperones deter misfolded protein aggregation, regulate functional phase separation, and even dissolve noxious aggregates, they are considered major sentinels impeding the molecular processes that lead to cell damage in the course of these diseases. Indeed, members of the chaperome, such as molecular chaperones and co-chaperones, are increasingly recognized as therapeutic targets for the development of treatments against degenerative proteinopathies. Chaperones must recognize diverse toxic clients of different orders (soluble proteins, biomolecular condensates, organized protein aggregates). It is therefore critical to understand the basis of the selective chaperone recognition to discern the mechanisms of action of chaperones in protein conformational diseases. This review aimed to define the selective interplay between chaperones and toxic client proteins and the basis for the protective role of these interactions. The presence and availability of chaperone recognition motifs in soluble proteins and in insoluble aggregates, both functional and pathogenic, are discussed. Finally, the formation of aberrant (pro-toxic) chaperone complexes will also be disclosed.
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Affiliation(s)
- Rubén Hervás
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA;
| | - Javier Oroz
- Rocasolano Institute for Physical Chemistry, Spanish National Research Council (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain
- Correspondence: ; Tel.: +34-915619400
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11
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Depicting Conformational Ensembles of α-Synuclein by Single Molecule Force Spectroscopy and Native Mass Spectroscopy. Int J Mol Sci 2019; 20:ijms20205181. [PMID: 31635031 PMCID: PMC6829300 DOI: 10.3390/ijms20205181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022] Open
Abstract
Description of heterogeneous molecular ensembles, such as intrinsically disordered proteins, represents a challenge in structural biology and an urgent question posed by biochemistry to interpret many physiologically important, regulatory mechanisms. Single-molecule techniques can provide a unique contribution to this field. This work applies single molecule force spectroscopy to probe conformational properties of α-synuclein in solution and its conformational changes induced by ligand binding. The goal is to compare data from such an approach with those obtained by native mass spectrometry. These two orthogonal, biophysical methods are found to deliver a complex picture, in which monomeric α-synuclein in solution spontaneously populates compact and partially compacted states, which are differently stabilized by binding to aggregation inhibitors, such as dopamine and epigallocatechin-3-gallate. Analyses by circular dichroism and Fourier-transform infrared spectroscopy show that these transitions do not involve formation of secondary structure. This comparative analysis provides support to structural interpretation of charge-state distributions obtained by native mass spectrometry and helps, in turn, defining the conformational components detected by single molecule force spectroscopy.
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12
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Mompeán M, Ramírez de Mingo D, Hervás R, Fernández-Ramírez MDC, Carrión-Vázquez M, Laurents DV. Molecular mechanism of the inhibition of TDP-43 amyloidogenesis by QBP1. Arch Biochem Biophys 2019; 675:108113. [PMID: 31568752 DOI: 10.1016/j.abb.2019.108113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/18/2019] [Accepted: 09/22/2019] [Indexed: 12/14/2022]
Abstract
Transactive Response DNA-Binding Protein of 43 kDa (TDP-43) is an essential human protein implicated in Amyotrophic Lateral Sclerosis (ALS) and common dementias. Its C-terminal disordered region, composed of residues 264-414 includes a hydrophobic segment (residues 320-340), which drives physiological liquid/liquid phase separation and a Q/N-rich segment (residues 341-357), which is essential for pathological amyloid formation. Due to TDP-43's relevance for pathology, identifying inhibitors and characterizing their mechanism of action are important pharmacological goals. The Polyglutamine Binding Peptide 1 (QBP1), whose minimal active core is the octapeptide WGWWPGIF, strongly inhibits the aggregation of polyQ-containing amyloidogenic proteins such as Huntingtin. Rather promiscuous, this inhibitor also blocks the aggregation of other glutamine containing amyloidogenic proteins, but not Aβ, and its mechanism of action remains unknown. Using a series of spectroscopic assays and biochemical tests, we establish that QBP1 binds and inhibits amyloid formation by TDP-43's Q/N-rich region. NMR spectroscopic data evince that the aromatic rings of QBP1 accept hydrogen bonds from the HN groups of the Asn and Gln to block amyloidogenesis. This mechanism of blockage may be general to polyphenol amyloid inhibitors.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, Madrid, 28006, Spain
| | | | - Rubén Hervás
- Instituto Cajal, CSIC, Avda. Doctor Arce 37, Madrid, 28002, Spain
| | | | | | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, Madrid, 28006, Spain.
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13
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Churchill CDM, Healey MA, Preto J, Tuszynski JA, Woodside MT. Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments. Biophys J 2019; 117:1125-1135. [PMID: 31477241 DOI: 10.1016/j.bpj.2019.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/21/2019] [Accepted: 08/12/2019] [Indexed: 11/29/2022] Open
Abstract
Intrinsically disordered proteins often play an important role in protein aggregation. However, it is challenging to determine the structures and interactions that drive the early stages of aggregation because they are transient and obscured in a heterogeneous mixture of disordered states. Even computational methods are limited because the lack of ordered structure makes it difficult to ensure that the relevant conformations are sampled. We address these challenges by integrating atomistic simulations with high-resolution single-molecule measurements reported previously, using the measurements to help discern which parts of the disordered ensemble of structures in the simulations are most probable while using the simulations to identify residues and interactions that are important for oligomer stability. This approach was applied to α-synuclein, an intrinsically disordered protein that aggregates in the context of Parkinson's disease. We simulated single-molecule pulling experiments on dimers, the minimal oligomer, and compared them to force spectroscopy measurements. Force-extension curves were simulated starting from a set of 66 structures with substantial structured content selected from the ensemble of dimer structures generated at zero force via Monte Carlo simulations. The pattern of contour length changes as the structures unfolded through intermediate states was compared to the results from optical trapping measurements on the same dimer to discern likely structures occurring in the measurements. Simulated pulling curves were generally consistent with experimental data but with a larger number of transient intermediates. We identified an ensemble of β-rich dimer structures consistent with the experimental data from which dimer interfaces could be deduced. These results suggest specific druggable targets in the structural motifs of α-synuclein that may help prevent the earliest steps of oligomerization.
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Affiliation(s)
| | - Mark A Healey
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Jordane Preto
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada; Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada.
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da S. Hage-Melim LI, Ferreira JV, de Oliveira NK, Correia LC, Almeida MR, Poiani JG, Taft CA, de Paula da Silva CH. The Impact of Natural Compounds on the Treatment of Neurodegenerative Diseases. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190327100418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neurodegenerative diseases (NDDs) are characterized by a progressive deterioration of the motor and/or cognitive function, that are often accompanied by psychiatric disorders, caused by a selective loss of neurons in the central nervous system. Among the NDDs we can mention Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia 3 (SCA3), spinal and bulbar muscular atrophy (SBMA) and Creutzfeldt-Jakob disease (CJD). AD and HD are characterized mainly by massive neuronal loss. PD, ALS, SCA3 and SBMA are agerelated diseases which have characteristic motor symptoms. CJD is an NDD caused by prion proteins. With increasing life expectancy, elderly populations tend to have more health problems, such as chronic diseases related to age and disability. Therefore, the development of therapeutic strategies to treat or prevent multiple pathophysiological conditions in the elderly can improve the expectation and quality of life. The attention of researchers has been focused on bioactive natural compounds that represent important resources in the discovery and development of drug candidates against NDDs. In this review, we discuss the pathogenesis, symptoms, potential targets, treatment and natural compounds effective in the treatment of AD, PD, HD, ALS, SCA3, SBMA and CJD.
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Affiliation(s)
- Lorane I. da S. Hage-Melim
- Laboratorio de Quimica Farmaceutica e Medicinal (PharMedChem), Universidade Federal do Amapa, Macapa, Brazil
| | - Jaderson V. Ferreira
- Laboratorio de Quimica Farmaceutica e Medicinal (PharMedChem), Universidade Federal do Amapa, Macapa, Brazil
| | - Nayana K.S. de Oliveira
- Laboratorio de Quimica Farmaceutica e Medicinal (PharMedChem), Universidade Federal do Amapa, Macapa, Brazil
| | - Lenir C. Correia
- Laboratorio de Quimica Farmaceutica e Medicinal (PharMedChem), Universidade Federal do Amapa, Macapa, Brazil
| | - Marcos R.S. Almeida
- Laboratorio de Quimica Farmaceutica e Medicinal (PharMedChem), Universidade Federal do Amapa, Macapa, Brazil
| | - João G.C. Poiani
- Laboratorio Computacional de Química Farmaceutica, Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Carlton A. Taft
- Centro Brasileiro de Pesquisas Fisicas, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos H.T. de Paula da Silva
- Laboratorio Computacional de Química Farmaceutica, Departamento de Ciencias Farmaceuticas, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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15
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Ruggeri FS, Šneideris T, Vendruscolo M, Knowles TPJ. Atomic force microscopy for single molecule characterisation of protein aggregation. Arch Biochem Biophys 2019; 664:134-148. [PMID: 30742801 PMCID: PMC6420408 DOI: 10.1016/j.abb.2019.02.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The development of atomic force microscopy (AFM) has opened up a wide range of novel opportunities in nanoscience and new modalities of observation in complex biological systems. AFM imaging has been widely employed to resolve the complex and heterogeneous conformational states involved in protein aggregation at the single molecule scale and shed light onto the molecular basis of a variety of human pathologies, including neurodegenerative disorders. The study of individual macromolecules at nanoscale, however, remains challenging, especially when fully quantitative information is required. In this review, we first discuss the principles of AFM with a special emphasis on the fundamental factors defining its sensitivity and accuracy. We then review the fundamental parameters and approaches to work at the limit of AFM resolution in order to perform single molecule statistical analysis of biomolecules and nanoscale protein aggregates. This single molecule statistical approach has proved to be powerful to unravel the molecular and hierarchical assembly of the misfolded species present transiently during protein aggregation, to visualise their dynamics at the nanoscale, as well to study the structural properties of amyloid-inspired functional nanomaterials.
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Affiliation(s)
- Francesco Simone Ruggeri
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom.
| | - Tomas Šneideris
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Michele Vendruscolo
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom; Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, United Kingdom.
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16
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Hussain R, Zubair H, Pursell S, Shahab M. Neurodegenerative Diseases: Regenerative Mechanisms and Novel Therapeutic Approaches. Brain Sci 2018; 8:E177. [PMID: 30223579 PMCID: PMC6162719 DOI: 10.3390/brainsci8090177] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/03/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022] Open
Abstract
Regeneration refers to regrowth of tissue in the central nervous system. It includes generation of new neurons, glia, myelin, and synapses, as well as the regaining of essential functions: sensory, motor, emotional and cognitive abilities. Unfortunately, regeneration within the nervous system is very slow compared to other body systems. This relative slowness is attributed to increased vulnerability to irreversible cellular insults and the loss of function due to the very long lifespan of neurons, the stretch of cells and cytoplasm over several dozens of inches throughout the body, insufficiency of the tissue-level waste removal system, and minimal neural cell proliferation/self-renewal capacity. In this context, the current review summarized the most common features of major neurodegenerative disorders; their causes and consequences and proposed novel therapeutic approaches.
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Affiliation(s)
- Rashad Hussain
- Center for Translational Neuromedicine, University of Rochester, NY 14642, USA.
| | - Hira Zubair
- Department of Animal Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
| | - Sarah Pursell
- Center for Translational Neuromedicine, University of Rochester, NY 14642, USA.
| | - Muhammad Shahab
- Department of Animal Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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17
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Fernández-Ramírez MDC, Hervás R, Galera-Prat A, Laurents DV, Carrión-Vázquez M. Efficient and simplified nanomechanical analysis of intrinsically disordered proteins. NANOSCALE 2018; 10:16857-16867. [PMID: 30168565 DOI: 10.1039/c8nr02785d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a tertiary structure. Amyloidogenic IDPs (aIDPs) in particular have attracted great interest due to their implication in several devastating diseases as well as in critical biological functions. However, the conformational changes that trigger amyloid formation in aIDPs are largely unknown. aIDPs' conformational polymorphism at the monomer level encumbers their study using bulk techniques. Single-molecule techniques like atomic force microscopy-based single-molecule force spectroscopy represent a promising approach and a "carrier-guest" strategy, in which the protein of interest is mechanically protected, was developed to overcome the spurious signals from the noisy proximal region. However, since the carrier and single-molecule markers have similar mechanostabilities, their signals can intermingle in the force-extension recordings, making peak selection and analysis very laborious, cumbersome and prone to error for the non-expert. Here we have developed a new carrier, the c8C module from the CipC scaffoldin, with a higher mechanostability so that the signals from the protected protein will appear at the end of the recordings. This assures an accurate, more efficient and expert-independent analysis, simplifying both the selection and analysis of the single-molecule data. Furthermore, this modular design can be integrated into any SMFS polyprotein-based vector, thus constituting a useful utensil in the growing toolbox of protein nanomechanics.
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18
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Galera-Prat A, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. The cohesin module is a major determinant of cellulosome mechanical stability. J Biol Chem 2018; 293:7139-7147. [PMID: 29567834 PMCID: PMC5950008 DOI: 10.1074/jbc.ra117.000644] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Indexed: 01/20/2023] Open
Abstract
Cellulosomes are bacterial protein complexes that bind and efficiently degrade lignocellulosic substrates. These are formed by multimodular scaffolding proteins known as scaffoldins, which comprise cohesin modules capable of binding dockerin-bearing enzymes and usually a carbohydrate-binding module that anchors the system to a substrate. It has been suggested that cellulosomes bound to the bacterial cell surface might be exposed to significant mechanical forces. Accordingly, the mechanical properties of these anchored cellulosomes may be important to understand and improve cellulosome function. Here we used single-molecule force spectroscopy to study the mechanical properties of selected cohesin modules from scaffoldins of different cellulosomes. We found that cohesins located in the region connecting the cell and the substrate are more robust than those located outside these two anchoring points. This observation applies to cohesins from primary scaffoldins (i.e. those that directly bind dockerin-bearing enzymes) from different cellulosomes despite their sequence differences. Furthermore, we also found that cohesin nanomechanics (specifically, mechanostability and the position of the mechanical clamp of cohesin) are not significantly affected by other cellulosomal components, including linkers between cohesins, multiple cohesin repeats, and dockerin binding. Finally, we also found that cohesins (from both the connecting and external regions) have poor refolding efficiency but similar refolding rates, suggesting that the high mechanostability of connecting cohesins may be an evolutionarily conserved trait selected to minimize the occurrence of cohesin unfolding, which could irreversibly damage the cellulosome. We conclude that cohesin mechanostability is a major determinant of the overall mechanical stability of the cellulosome.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
| | - Sarah Moraïs
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Vazana
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain.
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19
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Doherty CPA, Young LM, Karamanos TK, Smith HI, Jackson MP, Radford SE, Brockwell DJ. A peptide-display protein scaffold to facilitate single molecule force studies of aggregation-prone peptides. Protein Sci 2018; 27:1205-1217. [PMID: 29417650 PMCID: PMC6032367 DOI: 10.1002/pro.3386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/05/2018] [Accepted: 02/05/2018] [Indexed: 01/12/2023]
Abstract
Protein aggregation is linked with the onset of several neurodegenerative disorders, including Parkinson's disease (PD), which is associated with the aggregation of α‐synuclein (αSyn). The structural mechanistic details of protein aggregation, including the nature of the earliest protein–protein interactions, remain elusive. In this study, we have used single molecule force spectroscopy (SMFS) to probe the first dimerization events of the central aggregation‐prone region of αSyn (residues 71–82) that may initiate aggregation. This region has been shown to be necessary for the aggregation of full length αSyn and is capable of forming amyloid fibrils in isolation. We demonstrate that the interaction of αSyn71‐82 peptides can be studied using SMFS when inserted into a loop of protein L, a mechanically strong and soluble scaffold protein that acts as a display system for SMFS studies. The corresponding fragment of the homolog protein γ‐synuclein (γSyn), which has a lower aggregation propensity, has also been studied here. The results from SMFS, together with native mass spectrometry and aggregation assays, demonstrate that the dimerization propensity of γSyn71‐82 is lower than that of αSyn71‐82, but that a mixed αSyn71‐82: γSyn71‐82 dimer forms with a similar propensity to the αSyn71‐82 homodimer, slowing amyloid formation. This work demonstrates the utility of a novel display method for SMFS studies of aggregation‐prone peptides, which would otherwise be difficult to study.
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Affiliation(s)
- Ciaran P A Doherty
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Lydia M Young
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Hugh I Smith
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
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20
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Bhattacharya S, Xu L, Thompson D. Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Liang Xu
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Damien Thompson
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
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21
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Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories. Nat Commun 2017; 8:1881. [PMID: 29192167 PMCID: PMC5709426 DOI: 10.1038/s41467-017-01996-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023] Open
Abstract
Prion-like misfolding of superoxide dismutase 1 (SOD1) is associated with the disease ALS, but the mechanism of misfolding remains unclear, partly because misfolding is difficult to observe directly. Here we study the most misfolding-prone form of SOD1, reduced un-metallated monomers, using optical tweezers to measure unfolding and refolding of single molecules. We find that the folding is more complex than suspected, resolving numerous previously undetected intermediate states consistent with the formation of individual β-strands in the native structure. We identify a stable core of the protein that unfolds last and refolds first, and directly observe several distinct misfolded states that branch off from the native folding pathways at specific points after the formation of the stable core. Partially folded intermediates thus play a crucial role mediating between native and non-native folding. These results suggest an explanation for SOD1's propensity for prion-like misfolding and point to possible targets for therapeutic intervention.
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22
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Yen CF, Harischandra DS, Kanthasamy A, Sivasankar S. Copper-induced structural conversion templates prion protein oligomerization and neurotoxicity. SCIENCE ADVANCES 2016; 2:e1600014. [PMID: 27419232 PMCID: PMC4942324 DOI: 10.1126/sciadv.1600014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/27/2016] [Indexed: 05/26/2023]
Abstract
Prion protein (PrP) misfolding and oligomerization are key pathogenic events in prion disease. Copper exposure has been linked to prion pathogenesis; however, its mechanistic basis is unknown. We resolve, with single-molecule precision, the molecular mechanism of Cu(2+)-induced misfolding of PrP under physiological conditions. We also demonstrate that misfolded PrPs serve as seeds for templated formation of aggregates, which mediate inflammation and degeneration of neuronal tissue. Using a single-molecule fluorescence assay, we demonstrate that Cu(2+) induces PrP monomers to misfold before oligomer assembly; the disordered amino-terminal region mediates this structural change. Single-molecule force spectroscopy measurements show that the misfolded monomers have a 900-fold higher binding affinity compared to the native isoform, which promotes their oligomerization. Real-time quaking-induced conversion demonstrates that misfolded PrPs serve as seeds that template amyloid formation. Finally, organotypic slice cultures show that misfolded PrPs mediate inflammation and degeneration of neuronal tissue. Our study establishes a direct link, at the molecular level, between copper exposure and PrP neurotoxicity.
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Affiliation(s)
- Chi-Fu Yen
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
| | - Dilshan S. Harischandra
- Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Anumantha Kanthasamy
- Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Sanjeevi Sivasankar
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA
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23
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Oroz J, Bruix M, Laurents D, Galera-Prat A, Schönfelder J, Cañada F, Carrión-Vázquez M. The Y9P Variant of the Titin I27 Module: Structural Determinants of Its Revisited Nanomechanics. Structure 2016; 24:606-616. [DOI: 10.1016/j.str.2016.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/30/2015] [Accepted: 02/22/2016] [Indexed: 11/28/2022]
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24
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Zhang Q, Tsoi H, Peng S, Li PP, Lau KF, Rudnicki DD, Ngo JCK, Chan HYE. Assessing a peptidylic inhibitor-based therapeutic approach that simultaneously suppresses polyglutamine RNA- and protein-mediated toxicities in patient cells and Drosophila. Dis Model Mech 2016; 9:321-34. [PMID: 26839389 PMCID: PMC4833327 DOI: 10.1242/dmm.022350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/27/2016] [Indexed: 02/03/2023] Open
Abstract
Polyglutamine (polyQ) diseases represent a group of progressive neurodegenerative disorders that are caused by abnormal expansion of CAG triplet nucleotides in disease genes. Recent evidence indicates that not only mutant polyQ proteins, but also their corresponding mutant RNAs, contribute to the pathogenesis of polyQ diseases. Here, we describe the identification of a 13-amino-acid peptide, P3, which binds directly and preferentially to long-CAG RNA within the pathogenic range. When administered to cell and Drosophila disease models, as well as to patient-derived fibroblasts, P3 inhibited expanded-CAG-RNA-induced nucleolar stress and suppressed neurotoxicity. We further examined the combined therapeutic effect of P3 and polyQ-binding peptide 1 (QBP1), a well-characterized polyQ protein toxicity inhibitor, on neurodegeneration. When P3 and QBP1 were co-administered to disease models, both RNA and protein toxicities were effectively mitigated, resulting in a notable improvement of neurotoxicity suppression compared with the P3 and QBP1 single-treatment controls. Our findings indicate that targeting toxic RNAs and/or simultaneous targeting of toxic RNAs and their corresponding proteins could open up a new therapeutic strategy for treating polyQ degeneration.
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Affiliation(s)
- Qian Zhang
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ho Tsoi
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Shaohong Peng
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Pan P Li
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kwok-Fai Lau
- Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Cell and Molecular Biology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Dobrila D Rudnicki
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jacky Chi-Ki Ngo
- Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Cell and Molecular Biology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ho Yin Edwin Chan
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Cell and Molecular Biology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
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25
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Direct Detection of α-Synuclein Dimerization Dynamics: Single-Molecule Fluorescence Analysis. Biophys J 2016; 108:2038-47. [PMID: 25902443 DOI: 10.1016/j.bpj.2015.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/30/2015] [Accepted: 03/09/2015] [Indexed: 11/20/2022] Open
Abstract
The aggregation of α-synuclein (α-Syn) is linked to Parkinson's disease. The mechanism of early aggregation steps and the effect of pathogenic single-point mutations remain elusive. We report here a single-molecule fluorescence study of α-Syn dimerization and the effect of mutations. Specific interactions between tethered fluorophore-free α-Syn monomers on a substrate and fluorophore-labeled monomers diffusing freely in solution were observed using total internal reflection fluorescence microscopy. The results showed that wild-type (WT) α-Syn dimers adopt two types of dimers. The lifetimes of type 1 and type 2 dimers were determined to be 197 ± 3 ms and 3334 ± 145 ms, respectively. All three of the mutations used, A30P, E46K, and A53T, increased the lifetime of type 1 dimer and enhanced the relative population of type 2 dimer, with type 1 dimer constituting the major fraction. The kinetic stability of type 1 dimers (expressed in terms of lifetime) followed the order A30P (693 ± 14 ms) > E46K (292 ± 5 ms) > A53T (226 ± 6 ms) > WT (197 ± 3 ms). Type 2 dimers, which are more stable, had lifetimes in the range of several seconds. The strongest effect, observed for the A30P mutant, resulted in a lifetime 3.5 times higher than observed for the WT type 1 dimer. This mutation also doubled the relative fraction of type 2 dimer. These data show that single-point mutations promote dimerization, and they suggest that the structural heterogeneity of α-Syn dimers could lead to different aggregation pathways.
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26
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Wojciechowski M, Gómez-Sicilia À, Carrión-Vázquez M, Cieplak M. Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins. MOLECULAR BIOSYSTEMS 2016; 12:2700-12. [DOI: 10.1039/c6mb00214e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Knots in proteins have been proposed to resist proteasomal degradation, thought in turn to be related to neurodegenerative diseases such as Huntington.
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Affiliation(s)
| | - Àngel Gómez-Sicilia
- Instituto Cajal
- Consejo Superior de Investigaciones Científicas
- (CSIC)
- 28002 Madrid
- Spain
| | | | - Marek Cieplak
- Institute of Physics
- Polish Academy of Sciences
- PL-02668 Warsaw
- Poland
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27
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Hervás R, Li L, Majumdar A, Fernández-Ramírez MDC, Unruh JR, Slaughter BD, Galera-Prat A, Santana E, Suzuki M, Nagai Y, Bruix M, Casas-Tintó S, Menéndez M, Laurents DV, Si K, Carrión-Vázquez M. Molecular Basis of Orb2 Amyloidogenesis and Blockade of Memory Consolidation. PLoS Biol 2016; 14:e1002361. [PMID: 26812143 PMCID: PMC4727891 DOI: 10.1371/journal.pbio.1002361] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 12/16/2015] [Indexed: 12/03/2022] Open
Abstract
Amyloids are ordered protein aggregates that are typically associated with neurodegenerative diseases and cognitive impairment. By contrast, the amyloid-like state of the neuronal RNA binding protein Orb2 in Drosophila was recently implicated in memory consolidation, but it remains unclear what features of this functional amyloid-like protein give rise to such diametrically opposed behaviour. Here, using an array of biophysical, cell biological and behavioural assays we have characterized the structural features of Orb2 from the monomer to the amyloid state. Surprisingly, we find that Orb2 shares many structural traits with pathological amyloids, including the intermediate toxic oligomeric species, which can be sequestered in vivo in hetero-oligomers by pathological amyloids. However, unlike pathological amyloids, Orb2 rapidly forms amyloids and its toxic intermediates are extremely transient, indicating that kinetic parameters differentiate this functional amyloid from pathological amyloids. We also observed that a well-known anti-amyloidogenic peptide interferes with long-term memory in Drosophila. These results provide structural insights into how the amyloid-like state of the Orb2 protein can stabilize memory and be nontoxic. They also provide insight into how amyloid-based diseases may affect memory processes.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Liying Li
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Amitabha Majumdar
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- National Brain Research Centre, Manesar, Guragon, Haryana, India
| | | | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Albert Galera-Prat
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | | | - Mari Suzuki
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Japan
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | | | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias, Madrid, Spain
| | | | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
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28
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Yu H, Han W, Ma W, Schulten K. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. J Chem Phys 2015; 143:243142. [PMID: 26723627 PMCID: PMC4684271 DOI: 10.1063/1.4936910] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/18/2015] [Indexed: 12/18/2022] Open
Abstract
Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and (3)J(HNHCα )-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.
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Affiliation(s)
- Hang Yu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wei Han
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wen Ma
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Gómez-Sicilia À, Sikora M, Cieplak M, Carrión-Vázquez M. An Exploration of the Universe of Polyglutamine Structures. PLoS Comput Biol 2015; 11:e1004541. [PMID: 26495838 PMCID: PMC4619799 DOI: 10.1371/journal.pcbi.1004541] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/08/2015] [Indexed: 12/02/2022] Open
Abstract
Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease. Misfolding and aggregation of several proteins are known to be related to neurodegenerative diseases. Among them, polyglutamine expansions are known to be responsible for at least 9 diseases, including Huntington. Nonetheless, the structural properties of these intrinsically disordered proteins are difficult to study using classical techniques because of their rapid fluctuations that result in high conformational polymorphism. Here, we use molecular dynamics simulations to study polyglutamines of different chain lengths, starting with short non-pathogenic ones, and study the independent structures they are able to form. We characterize all structures by their geometrical properties, connectivity, putative mechanical stability and residence time (life span). Similar to the findings of a previous study with polyvalines, only some of the conformers are similar to those found in natural globular proteins. Moreover, we find structures that contain knots in both polyglutamine and polyvaline 60-mers, although the former contains many more knotted conformers than the latter. We suggest that these knotted conformers may impair the cell machinery for degradation and eventually lead to toxicity.
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Affiliation(s)
- Àngel Gómez-Sicilia
- Intituto Cajal/CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia),Madrid, Spain
| | - Mateusz Sikora
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Mariano Carrión-Vázquez
- Intituto Cajal/CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia),Madrid, Spain
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30
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Mompeán M, Hervás R, Xu Y, Tran TH, Guarnaccia C, Buratti E, Baralle F, Tong L, Carrión-Vázquez M, McDermott AE, Laurents DV. Structural Evidence of Amyloid Fibril Formation in the Putative Aggregation Domain of TDP-43. J Phys Chem Lett 2015; 6:2608-15. [PMID: 26266742 PMCID: PMC5568655 DOI: 10.1021/acs.jpclett.5b00918] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
TDP-43 can form pathological proteinaceous aggregates linked to ALS and FTLD. Within the putative aggregation domain, engineered repeats of residues 341-366 can recruit endogenous TDP-43 into aggregates inside cells; however, the nature of these aggregates is a debatable issue. Recently, we showed that a coil to β-hairpin transition in a short peptide corresponding to TDP-43 residues 341-357 enables oligomerization. Here we provide definitive structural evidence for amyloid formation upon extensive characterization of TDP-43(341-357) via chromophore and antibody binding, electron microscopy (EM), solid-state NMR, and X-ray diffraction. On the basis of these findings, structural models for TDP-43(341-357) oligomers were constructed, refined, verified, and analyzed using docking, molecular dynamics, and semiempirical quantum mechanics methods. Interestingly, TDP-43(341-357) β-hairpins assemble into a novel parallel β-turn configuration showing cross-β spine, cooperative H-bonding, and tight side-chain packing. These results expand the amyloid foldome and could guide the development of future therapeutics to prevent this structural conversion.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física Rocasolano, CSIC Serrano 119, 28006 Madrid, Spain
- Corresponding Authors: (M.M.) Tel: +34 91-745-9543. Fax: +34 91-564-2431. . (D.V.L.)
| | - Rubén Hervás
- Instituto Cajal, CSIC Avda, Doctor Arce 37, E-28002 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Crta. de Cantoblanco no. 8, E-28049 Cantoblanco, Madrid, Spain
| | - Yunyao Xu
- Department of Chemistry, Columbia University, 344 Havemeyer Hall, New York, New York 10027, United States
| | - Timothy H. Tran
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Francisco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Mariano Carrión-Vázquez
- Instituto Cajal, CSIC Avda, Doctor Arce 37, E-28002 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Crta. de Cantoblanco no. 8, E-28049 Cantoblanco, Madrid, Spain
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, 344 Havemeyer Hall, New York, New York 10027, United States
| | - Douglas V. Laurents
- Instituto de Química Física Rocasolano, CSIC Serrano 119, 28006 Madrid, Spain
- Corresponding Authors: (M.M.) Tel: +34 91-745-9543. Fax: +34 91-564-2431. . (D.V.L.)
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Jembrek MJ, Šimić G, Hof PR, Šegota S. Atomic force microscopy as an advanced tool in neuroscience. Transl Neurosci 2015; 6:117-130. [PMID: 28123795 PMCID: PMC4936619 DOI: 10.1515/tnsci-2015-0011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/05/2015] [Indexed: 12/16/2022] Open
Abstract
This review highlights relevant issues about applications and improvements of atomic force microscopy (AFM) toward a better understanding of neurodegenerative changes at the molecular level with the hope of contributing to the development of effective therapeutic strategies for neurodegenerative illnesses. The basic principles of AFM are briefly discussed in terms of evaluation of experimental data, including the newest PeakForce Quantitative Nanomechanical Mapping (QNM) and the evaluation of Young’s modulus as the crucial elasticity parameter. AFM topography, revealed in imaging mode, can be used to monitor changes in live neurons over time, representing a valuable tool for high-resolution detection and monitoring of neuronal morphology. The mechanical properties of living cells can be quantified by force spectroscopy as well as by new AFM. A variety of applications are described, and their relevance for specific research areas discussed. In addition, imaging as well as non-imaging modes can provide specific information, not only about the structural and mechanical properties of neuronal membranes, but also on the cytoplasm, cell nucleus, and particularly cytoskeletal components. Moreover, new AFM is able to provide detailed insight into physical structure and biochemical interactions in both physiological and pathophysiological conditions.
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Affiliation(s)
| | - Goran Šimić
- Department for Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, Zagreb, Croatia
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 New York, USA
| | - Suzana Šegota
- Division for Marine and Environmental Research, Ruđer Bošković Institute, POB 180, Zagreb, Croatia
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32
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Lee T, Moran-Gutierrez CR, Deniz AA. Probing protein disorder and complexity at single-molecule resolution. Semin Cell Dev Biol 2014; 37:26-34. [PMID: 25305580 DOI: 10.1016/j.semcdb.2014.09.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 09/15/2014] [Accepted: 09/30/2014] [Indexed: 12/16/2022]
Abstract
A substantial fraction of the human proteome encodes disordered proteins. Protein disorder is associated with a variety of cellular functions and misfunction, and is therefore of clear import to biological systems. However, disorder lends itself to conformational flexibility and heterogeneity, rendering proteins which feature prominent disorder difficult to study using conventional structural biology methods. Here we discuss a few examples of how single-molecule methods are providing new insight into the biophysics and complexity of these proteins by avoiding ensemble averaging, thereby providing direct information about the complex distributions and dynamics of this important class of proteins. Examples of note include characterization of isolated IDPs in solution as collapsed and dynamic species, detailed insight into complex IDP folding landscapes, and new information about how tunable regulation of structure-mediated binding cooperativity and consequent function can be achieved through protein disorder. With these exciting advances in view, we conclude with a discussion of a few complementary and emerging single-molecule efforts of particular promise, including complementary and enhanced methodologies for studying disorder in proteins, and experiments to investigate the potential role for IDP-induced phase separation as a critical functional element in biological systems.
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Affiliation(s)
- Taehyung Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Crystal R Moran-Gutierrez
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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Petrlova J, Bhattacherjee A, Boomsma W, Wallin S, Lagerstedt JO, Irbäck A. Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I. Protein Sci 2014; 23:1559-71. [PMID: 25131953 DOI: 10.1002/pro.2534] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/11/2014] [Accepted: 08/04/2014] [Indexed: 11/12/2022]
Abstract
Several disease-linked mutations of apolipoprotein A-I, the major protein in high-density lipoprotein (HDL), are known to be amyloidogenic, and the fibrils often contain N-terminal fragments of the protein. Here, we present a combined computational and experimental study of the fibril-associated disordered 1-93 fragment of this protein, in wild-type and mutated (G26R, S36A, K40L, W50R) forms. In atomic-level Monte Carlo simulations of the free monomer, validated by circular dichroism spectroscopy, we observe changes in the position-dependent β-strand probability induced by mutations. We find that these conformational shifts match well with the effects of these mutations in thioflavin T fluorescence and transmission electron microscopy experiments. Together, our results point to molecular mechanisms that may have a key role in disease-linked aggregation of apolipoprotein A-I.
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Affiliation(s)
- Jitka Petrlova
- Department of Experimental Medical Science, Lund University, BMC Floor C12, SE-221 84, Lund, Sweden
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35
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Ramos-Martín F, Hervás R, Carrión-Vázquez M, Laurents DV. NMR spectroscopy reveals a preferred conformation with a defined hydrophobic cluster for polyglutamine binding peptide 1. Arch Biochem Biophys 2014; 558:104-10. [PMID: 25009140 DOI: 10.1016/j.abb.2014.06.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/20/2014] [Accepted: 06/21/2014] [Indexed: 11/16/2022]
Abstract
Several important human inherited neurodegenerative diseases are caused by "polyQ expansions", which are aberrant long repeats of glutamine residues in proteins. PolyQ binding peptide 1 (QBP1), whose minimal active core sequence is Trp-Lys-Trp-Trp-Pro-Gly-Ile-Phe, binds to expanded polyQs and blocks their β-structure transition, aggregation and in vivo neurodegeneration. Whereas QBP1 is a widely used, commercially available product, its structure is unknown. Here, we have characterized the conformations of QBP1 and a scrambled peptide (Trp-Pro-Ile-Trp-Lys-Gly-Trp-Phe) in aqueous solution by CD, fluorescence and NMR spectroscopies. A CD maximum at 227 nm suggests the presence of rigid Trp side chains in QBP1. Based on 41 NOE-derived distance constraints, the 3D structure of QBP1 was determined. The side chains of Trp 4 and Ile 7, and to a lesser extent, those of Lys 2, Trp 3 and Phe 8, form a small hydrophobic cluster. Pro 5 and Gly 6 adopt a type II tight turn and Lys 2's ζ-NH3(+) is positioned to form a favorable cation-π interaction with Trp 4's indole ring. In contrast, the scrambled QBP1 peptide, which lacks inhibitory activity, does not adopt a preferred structure. These results provide a basis for future structure-based design approaches to further optimize QBP1 for therapy.
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Affiliation(s)
- Francisco Ramos-Martín
- Instituto Cajal, IC-Consejo Superior de Investigaciones Científicas, Avda. Doctor Arce 37, E-28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), E-28049 Cantoblanco, Madrid, Spain
| | - Rubén Hervás
- Instituto Cajal, IC-Consejo Superior de Investigaciones Científicas, Avda. Doctor Arce 37, E-28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), E-28049 Cantoblanco, Madrid, Spain
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-Consejo Superior de Investigaciones Científicas, Avda. Doctor Arce 37, E-28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), E-28049 Cantoblanco, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid E-28006, Spain.
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36
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Li Y, Qin M, Li Y, Cao Y, Wang W. Single molecule evidence for the adaptive binding of DOPA to different wet surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4358-4366. [PMID: 24716607 DOI: 10.1021/la501189n] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
3,4-Dihydroxyphenylalanine (DOPA) is the noncanonical amino acid widely found in mussel holdfast proteins, which is proposed to be responsible for their strong wet adhesion. This feature has also inspired the successful development of a range of DOPA-containing synthetic polymers for wet adhesions and surface coating. Despite the increasing applications of DOPA in material science, the underlying mechanism of DOPA-wet surface interactions remains unclear. In this work, we studied DOPA-surface interactions one bond at a time using atomic force microscope (AFM) based single molecule force spectroscopy. With our recently developed "multiple fishhook" protocol, we were able to perform high-throughput quantification of the binding strength of DOPA to various types of surfaces for the first time. We found that the dissociation forces between DOPA and nine different types of organic and inorganic surfaces are all in the range of 60-90 pN at a pulling speed of 1000 nm s(-1), suggesting the strong and versatile binding capability of DOPA to different types of surfaces. Moreover, by constructing the free energy landscape for the rupture events, we revealed several distinct binding modes between DOPA and different surfaces, which are directly related to the chemistry nature of the surfaces. These results explain the molecular origin of the versatile binding ability of DOPA. Moreover, we could quantitatively predict the relationship between DOPA contents and the binding strength based on the measured rupture kinetics. These serve as the bases for the quantitative prediction of the relationship between DOPA contents and adhesion strength to different wet surfaces, which is important for the design of novel DOPA based materials.
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Affiliation(s)
- Yiran Li
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu, China 210093
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Solanki A, Neupane K, Woodside MT. Single-molecule force spectroscopy of rapidly fluctuating, marginally stable structures in the intrinsically disordered protein α-synuclein. PHYSICAL REVIEW LETTERS 2014; 112:158103. [PMID: 24785077 DOI: 10.1103/physrevlett.112.158103] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Indexed: 05/11/2023]
Abstract
Intrinsically disordered proteins form transient, fluctuating structures that are difficult to observe directly. We used optical tweezers to apply force to single α-synuclein molecules and measure their extension, characterizing the resulting conformational transitions. Force-extension curves revealed rapid fluctuations at low force, arising from the folding of two different classes of structure that were only marginally stable. The energy landscape for these transitions was characterized via the force-dependent kinetics derived from correlation analysis of the extension trajectories. The barriers were small, only a few kBT, but the diffusion was slow, revealing a landscape that is flat but rough.
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Affiliation(s)
- Allison Solanki
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Krishna Neupane
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada and National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta T6G 2M9, Canada
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Chwastyk M, Galera-Prat A, Sikora M, Gómez-Sicilia À, Carrión-Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins 2014; 82:717-26. [DOI: 10.1002/prot.24436] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/27/2013] [Accepted: 09/26/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Mateusz Chwastyk
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences; Aleja Lotników 32/46 02-668 Warsaw Poland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED; Av. Doctor Arce, 37 28002 Madrid Spain
| | - Mateusz Sikora
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences; Aleja Lotników 32/46 02-668 Warsaw Poland
- Institute of Science and Technology Austria; Klosterneuburg Austria
| | - Àngel Gómez-Sicilia
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED; Av. Doctor Arce, 37 28002 Madrid Spain
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED; Av. Doctor Arce, 37 28002 Madrid Spain
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences; Aleja Lotników 32/46 02-668 Warsaw Poland
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Neupane K, Solanki A, Sosova I, Belov M, Woodside MT. Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy. PLoS One 2014; 9:e86495. [PMID: 24475132 PMCID: PMC3901707 DOI: 10.1371/journal.pone.0086495] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 12/12/2013] [Indexed: 11/18/2022] Open
Abstract
Oligomeric aggregates are widely suspected as toxic agents in diseases caused by protein aggregation, yet they remain poorly characterized, partly because they are challenging to isolate from a heterogeneous mixture of species. We developed an assay for characterizing structure, stability, and kinetics of individual oligomers at high resolution and sensitivity using single-molecule force spectroscopy, and applied it to observe the formation of transient structured aggregates within single oligomers of α-synuclein, an intrinsically-disordered protein linked to Parkinson's disease. Measurements of the molecular extension as the proteins unfolded under tension in optical tweezers revealed that even small oligomers could form numerous metastable structures, with a surprisingly broad range of sizes. Comparing the structures formed in monomers, dimers and tetramers, we found that the average mechanical stability increased with oligomer size. Most structures formed within a minute, with size-dependent rates. These results provide a new window onto the complex α-synuclein aggregation landscape, characterizing the microscopic structural heterogeneity and kinetics of different pathways.
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Affiliation(s)
- Krishna Neupane
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Allison Solanki
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Iveta Sosova
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
| | - Miro Belov
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
| | - Michael T. Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
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40
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Biophysical groundwork as a hinge to unravel the biology of α-synuclein aggregation and toxicity. Q Rev Biophys 2014; 47:1-48. [PMID: 24443929 DOI: 10.1017/s0033583513000097] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Alpha-synuclein (aS) and its aggregation properties are central in the development and spread of Parkinson's disease. Point mutations and multiplications of the SNCA gene encoding aS cause autosomal dominant forms of the disorder. Moreover, protein inclusions found in the surviving neurons of parkinsonian brains consist mainly of a fibrillar form of aS. Aggregates of aS, which form a transient, complex and heterogeneous ensemble, participate in a wide variety of toxic mechanisms that may be amplified by aS spreading among neighbouring neurons. Recently, significant effort has been directed into the study of the aS aggregation process and the impact of aS aggregates on neuron survival. In this review, we present state-of-the-art biophysical studies on the aS aggregation process in vitro and in cellular models. We comprehensively review the new insights generated by the recent biophysical investigations, which could provide a solid basis from which to design future biomedical studies. The diverse cellular models of aS toxicity and their potential use in the biophysical investigation are also discussed.
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41
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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42
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Jónsson SÆ, Mitternacht S, Irbäck A. Mechanical resistance in unstructured proteins. Biophys J 2014; 104:2725-32. [PMID: 23790381 DOI: 10.1016/j.bpj.2013.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022] Open
Abstract
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force resistance, we perform pulling simulations of the amyloid β-peptide (Aβ) and α-synuclein (αS), starting from simulated conformational ensembles for the free monomers. For both proteins, the simulations yield a set of rupture events that agree well with the experimental data. By analyzing the conformations occurring shortly before rupture in each event, we find that the mechanically resistant structures share a common architecture, with similarities to the folds adopted by Aβ and αS in amyloid fibrils. The disease-linked Arctic mutation of Aβ is found to increase the occurrence of highly force-resistant structures. Our study suggests that the high rupture forces observed in Aβ and αS pulling experiments are caused by structures that might have a key role in amyloid formation.
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Affiliation(s)
- Sigurður Ægir Jónsson
- Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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43
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Cieplak M. Mechanostability of Virus Capsids and Their Proteins in Structure-Based Models. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [DOI: 10.1007/978-3-642-28554-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Popiel HA, Takeuchi T, Burke JR, Strittmatter WJ, Toda T, Wada K, Nagai Y. Inhibition of protein misfolding/aggregation using polyglutamine binding peptide QBP1 as a therapy for the polyglutamine diseases. Neurotherapeutics 2013; 10:440-6. [PMID: 23504628 PMCID: PMC3701761 DOI: 10.1007/s13311-013-0184-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Protein misfolding and aggregation in the brain have been recognized to be crucial in the pathogenesis of various neurodegenerative diseases, including Alzheimer's, Parkinson's, and the polyglutamine (polyQ) diseases, which are collectively called the "protein misfolding diseases". In the polyQ diseases, an abnormally expanded polyQ stretch in the responsible proteins causes the proteins to misfold and aggregate, eventually resulting in neurodegeneration. Hypothesizing that polyQ protein misfolding and aggregation could be inhibited by molecules specifically binding to the expanded polyQ stretch, we identified polyQ binding peptide 1 (QBP1). We show that QBP1 does, indeed, inhibit misfolding and aggregation of the expanded polyQ protein in vitro. Furthermore overexpression of QBP1 by the crossing of transgenic animals inhibits neurodegeneration in Drosophila models of the polyQ diseases. We also introduce our attempts to deliver QBP1 into the brain by administration using viral vectors and protein transduction domains. Interestingly, recent data suggest that QBP1 can also inhibit the misfolding/aggregation of proteins responsible for other protein misfolding diseases, highlighting the potential of QBP1 as a general therapeutic molecule for a wide range of neurodegenerative diseases. We hope that in the near future, aggregation inhibitor-based drugs will be developed and bring relief to patients suffering from these currently intractable protein misfolding diseases.
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Affiliation(s)
- H. Akiko Popiel
- />Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa Higashi, Kodaira, Tokyo 187-8502 Japan
| | - Toshihide Takeuchi
- />Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa Higashi, Kodaira, Tokyo 187-8502 Japan
| | - James R. Burke
- />Department of Medicine (Neurology) and Deane Laboratory, Duke University Medical Center, Durham, NC 27710 USA
| | - Warren J. Strittmatter
- />Department of Medicine (Neurology) and Deane Laboratory, Duke University Medical Center, Durham, NC 27710 USA
| | - Tatsushi Toda
- />Division of Neurology/Molecular Brain Science, Kobe University Graduate School of Medicine, Kobe, 650-0017 Japan
| | - Keiji Wada
- />Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa Higashi, Kodaira, Tokyo 187-8502 Japan
| | - Yoshitaka Nagai
- />Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa Higashi, Kodaira, Tokyo 187-8502 Japan
- />Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, 332-0012 Japan
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Analysis of the REJ Module of Polycystin-1 Using Molecular Modeling and Force-Spectroscopy Techniques. JOURNAL OF BIOPHYSICS 2013; 2013:525231. [PMID: 23762046 PMCID: PMC3677617 DOI: 10.1155/2013/525231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/07/2013] [Indexed: 11/18/2022]
Abstract
Polycystin-1 is a large transmembrane protein, which, when mutated, causes autosomal dominant polycystic kidney disease, one of the most common life-threatening genetic diseases that is a leading cause of kidney failure. The REJ (receptor for egg lelly) module is a major component of PC1 ectodomain that extends to about 1000 amino acids. Many missense disease-causing mutations map to this module; however, very little is known about the structure or function of this region. We used a combination of homology molecular modeling, protein engineering, steered molecular dynamics (SMD) simulations, and single-molecule force spectroscopy (SMFS) to analyze the conformation and mechanical stability of the first ~420 amino acids of REJ. Homology molecular modeling analysis revealed that this region may contain structural elements that have an FNIII-like structure, which we named REJd1, REJd2, REJd3, and REJd4. We found that REJd1 has a higher mechanical stability than REJd2 (~190 pN and 60 pN, resp.). Our data suggest that the putative domains REJd3 and REJd4 likely do not form mechanically stable folds. Our experimental approach opens a new way to systematically study the effects of disease-causing mutations on the structure and mechanical properties of the REJ module of PC1.
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Nasal inoculation with α-synuclein aggregates evokes rigidity, locomotor deficits and immunity to such misfolded species as well as dopamine. Behav Brain Res 2013; 243:205-12. [DOI: 10.1016/j.bbr.2013.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/06/2013] [Accepted: 01/10/2013] [Indexed: 12/26/2022]
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Larini L, Gessel MM, LaPointe NE, Do TD, Bowers MT, Feinstein SC, Shea JE. Initiation of assembly of tau(273-284) and its ΔK280 mutant: an experimental and computational study. Phys Chem Chem Phys 2013; 15:8916-28. [PMID: 23515417 DOI: 10.1039/c3cp00063j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The microtubule associated protein tau is essential for the development and maintenance of the nervous system. Tau dysfunction is associated with a class of diseases called tauopathies, in which tau is found in an aggregated form. This paper focuses on a small aggregating fragment of tau, (273)GKVQIINKKLDL(284), encompassing the (PHF6*) region that plays a central role in tau aggregation. Using a combination of simulations and experiments, we probe the self-assembly of this peptide, with an emphasis on characterizing the early steps of aggregation. Ion-mobility mass spectrometry experiments provide a size distribution of early oligomers, TEM studies provide a time course of aggregation, and enhanced sampling molecular dynamics simulations provide atomistically detailed structural information about this intrinsically disordered peptide. Our studies indicate that a point mutation, as well the addition of heparin, lead to a shift in the conformations populated by the earliest oligomers, affecting the kinetics of subsequent fibril formation as well as the morphology of the resulting aggregates. In particular, a mutant associated with a K280 deletion (a mutation that causes a heritable form of neurodegeneration/dementia in the context of full length tau) is seen to aggregate more readily than its wild-type counterpart. Simulations and experiment reveal that the ΔK280 mutant peptide adopts extended conformations to a greater extent than the wild-type peptide, facilitating aggregation through the pre-structuring of the peptide into a fibril-competent structure.
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Affiliation(s)
- Luca Larini
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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Natalello A, Mattoo RUH, Priya S, Sharma SK, Goloubinoff P, Doglia SM. Biophysical characterization of two different stable misfolded monomeric polypeptides that are chaperone-amenable substrates. J Mol Biol 2013; 425:1158-71. [PMID: 23306033 DOI: 10.1016/j.jmb.2012.12.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 12/21/2012] [Accepted: 12/31/2012] [Indexed: 11/27/2022]
Abstract
Misfolded polypeptide monomers may be regarded as the initial species of many protein aggregation pathways, which could accordingly serve as primary targets for molecular chaperones. It is therefore of paramount importance to study the cellular mechanisms that can prevent misfolded monomers from entering the toxic aggregation pathway and moreover rehabilitate them into active proteins. Here, we produced two stable misfolded monomers of luciferase and rhodanese, which we found to be differently processed by the Hsp70 chaperone machinery and whose conformational properties were investigated by biophysical approaches. In spite of their monomeric nature, they displayed enhanced thioflavin T fluorescence, non-native β-sheets, and tertiary structures with surface-accessible hydrophobic patches, but differed in their conformational stability and aggregation propensity. Interestingly, minor structural differences between the two misfolded species could account for their markedly different behavior in chaperone-mediated unfolding/refolding assays. Indeed, only a single DnaK molecule was sufficient to unfold by direct clamping a misfolded luciferase monomer, while, by contrast, several DnaK molecules were necessary to unfold the more resistant misfolded rhodanese monomer by a combination of direct clamping and cooperative entropic pulling.
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Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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Oroz J, Hervás R, Carrión-Vázquez M. Unequivocal single-molecule force spectroscopy of proteins by AFM using pFS vectors. Biophys J 2012; 102:682-90. [PMID: 22325292 DOI: 10.1016/j.bpj.2011.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/28/2011] [Accepted: 12/12/2011] [Indexed: 11/28/2022] Open
Abstract
Nanomechanical analysis of proteins by single-molecule force spectroscopy based on atomic force microscopy is increasingly being used to investigate the inner workings of mechanical proteins and substrate proteins of unfoldase machines as well as to gain new insight into the process of protein folding. However, such studies are hindered by a number of technical problems, including the noise of the proximal region, ambiguous single-molecule identification, as well as difficulties in protein expression/folding and full-length purification. To overcome these major drawbacks in protein nanomechanics, we designed a family of cloning/expression vectors, termed pFS (plasmid for force spectroscopy), that essentially has an unstructured region to surmount the noisy proximal region, a homomeric polyprotein marker, a carrier to mechanically protect the protein of interest (only the pFS-2 version) that also acts as a reporter, and two purification tags. pFS-2 enables the unambiguous analysis of proteins with low mechanical stability or/and complex force spectra, such as the increasingly abundant class of intrinsically disordered proteins, which are hard to characterize by traditional bulk techniques and have important biological and clinical implications. The advantages, applications, and potential of this ready-to-go system are illustrated through the analysis of representative proteins.
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Affiliation(s)
- Javier Oroz
- Instituto Cajal/CSIC, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, IMDEA Nanociencia, Madrid, Spain
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