1
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Aubrey LD, Ninkina N, Ulamec SM, Abramycheva NY, Vasili E, Devine OM, Wilkinson M, Mackinnon E, Limorenko G, Walko M, Muwanga S, Amadio L, Peters OM, Illarioshkin SN, Outeiro TF, Ranson NA, Brockwell DJ, Buchman VL, Radford SE. Substitution of Met-38 to Ile in γ-synuclein found in two patients with amyotrophic lateral sclerosis induces aggregation into amyloid. Proc Natl Acad Sci U S A 2024; 121:e2309700120. [PMID: 38170745 PMCID: PMC10786281 DOI: 10.1073/pnas.2309700120] [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: 06/08/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
α-, β-, and γ-Synuclein are intrinsically disordered proteins implicated in physiological processes in the nervous system of vertebrates. α-synuclein (αSyn) is the amyloidogenic protein associated with Parkinson's disease and certain other neurodegenerative disorders. Intensive research has focused on the mechanisms that cause αSyn to form amyloid structures, identifying its NAC region as being necessary and sufficient for amyloid assembly. Recent work has shown that a 7-residue sequence (P1) is necessary for αSyn amyloid formation. Although γ-synuclein (γSyn) is 55% identical in sequence to αSyn and its pathological deposits are also observed in association with neurodegenerative conditions, γSyn is resilient to amyloid formation in vitro. Here, we report a rare single nucleotide polymorphism (SNP) in the SNCG gene encoding γSyn, found in two patients with amyotrophic lateral sclerosis (ALS). The SNP results in the substitution of Met38 with Ile in the P1 region of the protein. These individuals also had a second, common and nonpathological, SNP in SNCG resulting in the substitution of Glu110 with Val. In vitro studies demonstrate that the Ile38 variant accelerates amyloid fibril assembly. Contrastingly, Val110 retards fibril assembly and mitigates the effect of Ile38. Substitution of residue 38 with Leu had little effect, while Val retards, and Ala increases the rate of amyloid formation. Ile38 γSyn also results in the formation of γSyn-containing inclusions in cells. The results show how a single point substitution can enhance amyloid formation of γSyn and highlight the P1 region in driving amyloid formation in another synuclein family member.
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Affiliation(s)
- Liam D. Aubrey
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Ninkina
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sabine M. Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Y. Abramycheva
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Eftychia Vasili
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Oliver M. Devine
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Eilish Mackinnon
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Galina Limorenko
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Sarah Muwanga
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Leonardo Amadio
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Owen M. Peters
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Sergey N. Illarioshkin
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Tiago F. Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen37075, Germany
- Max Planck Institute for Multidisciplinary Sciences, Goettingen37075, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon TyneNE2 4HH, United Kingdom
- Scientific employee with a honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen, Göttingen37075, Germany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Vladimir L. Buchman
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
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2
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Saccuzzo EG, Mebrat MD, Scelsi HF, Kim M, Ma MT, Su X, Hill SE, Rheaume E, Li R, Torres MP, Gumbart JC, Van Horn WD, Lieberman RL. Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller. Nat Commun 2024; 15:155. [PMID: 38168102 PMCID: PMC10762032 DOI: 10.1038/s41467-023-44479-2] [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: 02/14/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Studies of folded-to-misfolded transitions using model protein systems reveal a range of unfolding needed for exposure of amyloid-prone regions for subsequent fibrillization. Here, we probe the relationship between unfolding and aggregation for glaucoma-associated myocilin. Mutations within the olfactomedin domain of myocilin (OLF) cause a gain-of-function, namely cytotoxic intracellular aggregation, which hastens disease progression. Aggregation by wild-type OLF (OLFWT) competes with its chemical unfolding, but only below the threshold where OLF loses tertiary structure. Representative moderate (OLFD380A) and severe (OLFI499F) disease variants aggregate differently, with rates comparable to OLFWT in initial stages of unfolding, and variants adopt distinct partially folded structures seen along the OLFWT urea-unfolding pathway. Whether initiated with mutation or chemical perturbation, unfolding propagates outward to the propeller surface. In sum, for this large protein prone to amyloid formation, the requirement for a conformational change to promote amyloid fibrillization leads to direct competition between unfolding and aggregation.
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Affiliation(s)
- Emily G Saccuzzo
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Mubark D Mebrat
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA
- School of Molecular Sciences, Arizona State University, Tempe, USA
| | - Hailee F Scelsi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Minjoo Kim
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA
- School of Molecular Sciences, Arizona State University, Tempe, USA
| | - Minh Thu Ma
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Xinya Su
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Shannon E Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Elisa Rheaume
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, USA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, USA
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - James C Gumbart
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
- School of Physics, Georgia Institute of Technology, Atlanta, USA
| | - Wade D Van Horn
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA.
- School of Molecular Sciences, Arizona State University, Tempe, USA.
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA.
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3
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Ghorbani M, Brooks BR, Klauda JB. Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics. J Phys Chem B 2023; 127:6887-6895. [PMID: 37527428 DOI: 10.1021/acs.jpcb.3c02473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Conformational dynamics in proteins can give rise to aggregation prone states during folding, and these kinetically stable states could form oligomers and aggregates. In this study, we investigate the intermediate states and near-folded states of β2-microglobulin and their physico-chemical properties using molecular dynamics and Markov state modeling. Analysis of hundreds of microseconds simulation show the importance of the edge strands in the misfolded states that give rise to a high exposure of hydrophobic residues in the core of the protein that could initiate oligomerization and aggregate formation. Our study sheds light on the first step of aggregation of β2m monomers and gave a better picture of the landscape of protein misfolding and aggregation.
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Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
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4
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Miller JE, Castells-Graells R, Arbing MA, Munoz A, Jiang YX, Espinoza CT, Nguyen B, Moroz P, Yeates TO. Design of Beta-2 Microglobulin Adsorbent Protein Nanoparticles. Biomolecules 2023; 13:1122. [PMID: 37509158 PMCID: PMC10377675 DOI: 10.3390/biom13071122] [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: 06/04/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Beta-2 microglobulin (B2M) is an immune system protein that is found on the surface of all nucleated human cells. B2M is naturally shed from cell surfaces into the plasma, followed by renal excretion. In patients with impaired renal function, B2M will accumulate in organs and tissues leading to significantly reduced life expectancy and quality of life. While current hemodialysis methods have been successful in managing electrolyte as well as small and large molecule disturbances arising in chronic renal failure, they have shown only modest success in managing plasma levels of B2M and similar sized proteins, while sparing important proteins such as albumin. We describe a systematic protein design effort aimed at adding the ability to selectively remove specific, undesired waste proteins such as B2M from the plasma of chronic renal failure patients. A novel nanoparticle built using a tetrahedral protein assembly as a scaffold that presents 12 copies of a B2M-binding nanobody is described. The designed nanoparticle binds specifically to B2M through protein-protein interactions with nanomolar binding affinity (~4.2 nM). Notably, binding to the nanoparticle increases the effective size of B2M by over 50-fold, offering a potential selective avenue for separation based on size. We present data to support the potential utility of such a nanoparticle for removing B2M from plasma by either size-based filtration or by polyvalent binding to a stationary matrix under blood flow conditions. Such applications could address current shortcomings in the management of problematic mid-sized proteins in chronic renal failure patients.
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Affiliation(s)
- Justin E. Miller
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | | | - Mark A. Arbing
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Aldo Munoz
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yi-Xiao Jiang
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Charlize T. Espinoza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Brian Nguyen
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Paul Moroz
- School of Medicine, Curtin University, Perth, WA 6845, Australia
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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5
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Zhao Y, Zheng Q, Hong Y, Gao Y, Hu J, Lang M, Zhang H, Zhou Y, Luo H, Zhang X, Sun H, Yan XX, Huang TY, Wang YJ, Xu H, Liu C, Wang X. β 2-Microglobulin coaggregates with Aβ and contributes to amyloid pathology and cognitive deficits in Alzheimer's disease model mice. Nat Neurosci 2023:10.1038/s41593-023-01352-1. [PMID: 37264159 DOI: 10.1038/s41593-023-01352-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/03/2023] [Indexed: 06/03/2023]
Abstract
Extensive studies indicate that β-amyloid (Aβ) aggregation is pivotal for Alzheimer's disease (AD) progression; however, cumulative evidence suggests that Aβ itself is not sufficient to trigger AD-associated degeneration, and whether other additional pathological factors drive AD pathogenesis remains unclear. Here, we characterize pathogenic aggregates composed of β2-microglobulin (β2M) and Aβ that trigger neurodegeneration in AD. β2M, a component of major histocompatibility complex class I (MHC class I), is upregulated in the brains of individuals with AD and constitutes the amyloid plaque core. Elevation of β2M aggravates amyloid pathology independent of MHC class I, and coaggregation with β2M is essential for Aβ neurotoxicity. B2m genetic ablation abrogates amyloid spreading and cognitive deficits in AD mice. Antisense oligonucleotide- or monoclonal antibody-mediated β2M depletion mitigates AD-associated neuropathology, and inhibition of β2M-Aβ coaggregation with a β2M-based blocking peptide ameliorates amyloid pathology and cognitive deficits in AD mice. Our findings identify β2M as an essential factor for Aβ neurotoxicity and a potential target for treating AD.
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Affiliation(s)
- Yini Zhao
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Qiuyang Zheng
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Yujuan Hong
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yue Gao
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Maoju Lang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hongfeng Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Ying Zhou
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Hong Luo
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xian Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hao Sun
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xiao-Xin Yan
- Department of Anatomy and Neurobiology, Central South University Xiangya Medical School, Changsha, China
| | - Timothy Y Huang
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Yan-Jiang Wang
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Huaxi Xu
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Xiamen University, Xiamen, China
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Xin Wang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
- Shenzhen Research Institute of Xiamen University, Shenzhen, China.
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6
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β2-Microglobulin boosts β-amyloid aggregation and neurotoxicity in an Alzheimer's disease model. Nat Neurosci 2023:10.1038/s41593-023-01354-z. [PMID: 37264162 DOI: 10.1038/s41593-023-01354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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7
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Tomiyama R, So M, Yamaguchi K, Miyanoiri Y, Sakurai K. The residual structure of acid-denatured β 2 -microglobulin is relevant to an ordered fibril morphology. Protein Sci 2023; 32:e4487. [PMID: 36321362 PMCID: PMC9793977 DOI: 10.1002/pro.4487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
β2 -Microglobulin (β2m) forms amyloid fibrils in vitro under acidic conditions. Under these conditions, the residual structure of acid-denatured β2m is relevant to seeding and fibril extension processes. Disulfide (SS) bond-oxidized β2m has been shown to form rigid, ordered fibrils, whereas SS bond-reduced β2m forms curvy, less-ordered fibrils. These findings suggest that the presence of an SS bond affects the residual structure of the monomer, which subsequently influences the fibril morphology. To clarify this process, we herein performed NMR experiments. The results obtained revealed that oxidized β2m contained a residual structure throughout the molecule, including the N- and C-termini, whereas the residual structure of the reduced form was localized and other regions had a random coil structure. The range of the residual structure in the oxidized form was wider than that of the fibril core. These results indicate that acid-denatured β2m has variable conformations. Most conformations in the ensemble cannot participate in fibril formation because their core residues are hidden by residual structures. However, when hydrophobic residues are exposed, polypeptides competently form an ordered fibril. This conformational selection phase may be needed for the ordered assembly of amyloid fibrils.
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Affiliation(s)
- Ryosuke Tomiyama
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan
| | - Masatomo So
- Institute for Protein ResearchOsaka UniversityOsakaJapan,Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and InformaticsOsaka UniversitySuitaJapan
| | | | - Kazumasa Sakurai
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan,High Pressure Protein Research Center, Institute of Advanced TechnologyKindai UniversityWakayamaJapan
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8
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Maya-Martinez R, Xu Y, Guthertz N, Walko M, Karamanos TK, Sobott F, Breeze AL, Radford SE. Dimers of D76N-β 2-microglobulin display potent antiamyloid aggregation activity. J Biol Chem 2022; 298:102659. [PMID: 36328246 PMCID: PMC9712992 DOI: 10.1016/j.jbc.2022.102659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022] Open
Abstract
Self-association of WT β2-microglobulin (WT-β2m) into amyloid fibrils is associated with the disorder dialysis related amyloidosis. In the familial variant D76N-β2m, the single amino acid substitution enhances the aggregation propensity of the protein dramatically and gives rise to a disorder that is independent of renal dysfunction. Numerous biophysical and structural studies on WT- and D76N-β2m have been performed in order to better understand the structure and dynamics of the native proteins and their different potentials to aggregate into amyloid. However, the structural properties of transient D76N-β2m oligomers and their role(s) in assembly remained uncharted. Here, we have utilized NMR methods, combined with photo-induced crosslinking, to detect, trap, and structurally characterize transient dimers of D76N-β2m. We show that the crosslinked D76N-β2m dimers have different structures from those previously characterized for the on-pathway dimers of ΔN6-β2m and are unable to assemble into amyloid. Instead, the crosslinked D76N-β2m dimers are potent inhibitors of amyloid formation, preventing primary nucleation and elongation/secondary nucleation when added in substoichiometric amounts with D76N-β2m monomers. The results highlight the specificity of early protein-protein interactions in amyloid formation and show how mapping these interfaces can inform new strategies to inhibit amyloid assembly.
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Affiliation(s)
- Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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9
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Karamanos TK, Kalverda AP, Radford SE. Generating Ensembles of Dynamic Misfolding Proteins. Front Neurosci 2022; 16:881534. [PMID: 35431773 PMCID: PMC9008329 DOI: 10.3389/fnins.2022.881534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 01/09/2023] Open
Abstract
The early stages of protein misfolding and aggregation involve disordered and partially folded protein conformers that contain a high degree of dynamic disorder. These dynamic species may undergo large-scale intra-molecular motions of intrinsically disordered protein (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization of the interconverting species that captures the conformations explored and their physico-chemical properties remains hugely challenging. How specific sub-ensembles of conformers that are on-pathway to aggregation into amyloid can be identified from their aggregation-resilient counterparts within these large heterogenous pools of rapidly moving molecules represents an additional level of complexity. Here, we describe current experimental and computational approaches designed to capture the dynamic nature of the early stages of protein misfolding and aggregation, and discuss potential challenges in describing these species because of the ensemble averaging of experimental restraints that arise from motions on the millisecond timescale. We give a perspective of how machine learning methods can be used to extract aggregation-relevant sub-ensembles and provide two examples of such an approach in which specific interactions of defined species within the dynamic ensembles of α-synuclein (αSyn) and β2-microgloblulin (β2m) can be captured and investigated.
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Affiliation(s)
- Theodoros K. Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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10
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Sorokina SA, Shifrina ZB. Dendrimers as Antiamyloid Agents. Pharmaceutics 2022; 14:pharmaceutics14040760. [PMID: 35456594 PMCID: PMC9031116 DOI: 10.3390/pharmaceutics14040760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023] Open
Abstract
Dendrimer–protein conjugates have significant prospects for biological applications. The complexation changes the biophysical behavior of both proteins and dendrimers. The dendrimers could influence the secondary structure of proteins, zeta-potential, distribution of charged regions on the surface, the protein–protein interactions, etc. These changes offer significant possibilities for the application of these features in nanotheranostics and biomedicine. Based on the dendrimer–protein interactions, several therapeutic applications of dendrimers have emerged. Thus, the formation of stable complexes retains the disordered proteins on the aggregation, which is especially important in neurodegenerative diseases. To clarify the origin of these properties and assess the efficiency of action, the mechanism of protein–dendrimer interaction and the nature and driving force of binding are considered in this review. The review outlines the antiamyloid activity of dendrimers and discusses the effect of dendrimer structures and external factors on their antiamyloid properties.
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11
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Dang H, Chen Z, Chen W, Luo X, Liu P, Wang L, Chen J, Tang X, Wang Z, Liang Y. The residues 4 to 6 at the N-terminus in particular modulate fibril propagation of β-microglobulin. Acta Biochim Biophys Sin (Shanghai) 2021; 54:187-198. [PMID: 35130623 PMCID: PMC9909321 DOI: 10.3724/abbs.2021017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ΔN6 truncation is the main posttranslational modification of β-microglobulin (βM) found in dialysis-related amyloid. Investigation of the interaction of wild-type (WT) βM with N-terminally truncated variants is therefore of medical relevance. However, it is unclear which residues among the six residues at the N-terminus are crucial to the interactions and the modulation of amyloid fibril propagation of βM. We herein analyzed homo- and heterotypic seeding of amyloid fibrils of WT human βM and its N-terminally-truncated variants ΔN1 to ΔN6, lacking up to six residues at the N-terminus. At acidic pH 2.5, we produced amyloid fibrils from recombinant, WT βM and its six truncated variants, and found that ΔN6 βM fibrils exhibit a significantly lower conformational stability than WT βM fibrils. Importantly, under more physiological conditions (pH 6.2), we assembled amyloid fibrils only from recombinant, ΔN4, ΔN5, and ΔN6 βM but not from WT βM and its three truncated variants ΔN1 to ΔN3. Notably, the removal of the six, five or four residues at the N-terminus leads to enhanced fibril formation, and homo- and heterotypic seeding of ΔN6 fibrils strongly promotes amyloid fibril formation of WT βM and its six truncated variants, including at more physiological pH 6.2. Collectively, these results demonstrated that the residues 4 to 6 at the N-terminus particularly modulate amyloid fibril propagation of βM and the interactions of WT βM with N-terminally truncated variants, potentially indicating the direct relevance to the involvement of the protein's aggregation in dialysis-related amyloidosis.
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Affiliation(s)
- Haibin Dang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Zhixian Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Wang Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Xudong Luo
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | | | - Liqiang Wang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | - Jie Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China
| | | | | | - Yi Liang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China2.Wuhan University Shenzhen Research InstituteShenzhen 518057Chinaand 3.School of Civil EngineeringWuhan UniversityWuhan430072China,Correspondence address. Tel: +86-27-68754902; E-mail:
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12
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Oliveira NFB, Rodrigues FEP, Vitorino JNM, Loureiro RJS, Faísca PFN, Machuqueiro M. Predicting stable binding modes from simulated dimers of the D76N mutant of β 2-microglobulin. Comput Struct Biotechnol J 2021; 19:5160-5169. [PMID: 34630936 PMCID: PMC8473664 DOI: 10.1016/j.csbj.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
β2m D76N mutant populates an aggregation-prone monomer (I2) with unstructured termini. MD and MM-PBSA indicate that I2 dimers are stabilized by hydrophobic interactions. The termini regions and BC- and DE-loops are prevalent in the most stable interfaces. The most stable dimer has a limited growth potential without structural rearrangement.
The D76N mutant of the β2m protein is a biologically motivated model system to study protein aggregation. There is strong experimental evidence, supported by molecular simulations, that D76N populates a highly dynamic conformation (which we originally named I2) that exposes aggregation-prone patches as a result of the detachment of the two terminal regions. Here, we use Molecular Dynamics simulations to study the stability of an ensemble of dimers of I2 generated via protein–protein docking. MM-PBSA calculations indicate that within the ensemble of investigated dimers the major contribution to interface stabilization at physiological pH comes from hydrophobic interactions between apolar residues. Our structural analysis also reveals that the interfacial region associated with the most stable binding modes are particularly rich in residues pertaining to both the N- and C-terminus, as well residues from the BC- and DE-loops. On the other hand, the less stable interfaces are stabilized by intermolecular interactions involving residues from the CD- and EF-loops. By focusing on the most stable binding modes, we used a simple geometric rule to propagate the corresponding dimer interfaces. We found that, in the absence of any kind of structural rearrangement occurring at an early stage of the oligomerization pathway, some interfaces drive a self-limited growth process, while others can be propagated indefinitely allowing the formation of long, polymerized chains. In particular, the interfacial region of the most stable binding mode reported here falls in the class of self-limited growth.
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Affiliation(s)
- Nuno F B Oliveira
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| | - Filipe E P Rodrigues
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| | - João N M Vitorino
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
| | - Rui J S Loureiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Patrícia F N Faísca
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Physics, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal
| | - Miguel Machuqueiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.,Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisboa 1749-016, Portugal
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13
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Good SC, Dewison KM, Radford SE, van Oosten-Hawle P. Global Proteotoxicity Caused by Human β 2 Microglobulin Variants Impairs the Unfolded Protein Response in C. elegans. Int J Mol Sci 2021; 22:10752. [PMID: 34639093 PMCID: PMC8509642 DOI: 10.3390/ijms221910752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Aggregation of β2 microglobulin (β2m) into amyloid fibrils is associated with systemic amyloidosis, caused by the deposition of amyloid fibrils containing the wild-type protein and its truncated variant, ΔN6 β2m, in haemo-dialysed patients. A second form of familial systemic amyloidosis caused by the β2m variant, D76N, results in amyloid deposits in the viscera, without renal dysfunction. Although the folding and misfolding mechanisms of β2 microglobulin have been widely studied in vitro and in vivo, we lack a comparable understanding of the molecular mechanisms underlying toxicity in a cellular and organismal environment. Here, we established transgenic C. elegans lines expressing wild-type (WT) human β2m, or the two highly amyloidogenic naturally occurring variants, D76N β2m and ΔN6 β2m, in the C. elegans bodywall muscle. Nematodes expressing the D76N β2m and ΔN6 β2m variants exhibit increased age-dependent and cell nonautonomous proteotoxicity associated with reduced motility, delayed development and shortened lifespan. Both β2m variants cause widespread endogenous protein aggregation contributing to the increased toxicity in aged animals. We show that expression of β2m reduces the capacity of C. elegans to cope with heat and endoplasmic reticulum (ER) stress, correlating with a deficiency to upregulate BiP/hsp-4 transcripts in response to ER stress in young adult animals. Interestingly, protein secretion in all β2m variants is reduced, despite the presence of the natural signal sequence, suggesting a possible link between organismal β2m toxicity and a disrupted ER secretory metabolism.
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Affiliation(s)
| | | | | | - Patricija van Oosten-Hawle
- Faculty of Biological Sciences, School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (S.C.G.); (K.M.D.); (S.E.R.)
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14
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Roterman I, Stapor K, Fabian P, Konieczny L. In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model. Int J Mol Sci 2021; 22:10587. [PMID: 34638925 PMCID: PMC8508659 DOI: 10.3390/ijms221910587] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 11/17/2022] Open
Abstract
The role of the environment in amyloid formation based on the fuzzy oil drop model (FOD) is discussed here. This model assumes that the hydrophobicity distribution within a globular protein is consistent with a 3D Gaussian (3DG) distribution. Such a distribution is interpreted as the idealized effect of the presence of a polar solvent-water. A chain with a sequence of amino acids (which are bipolar molecules) determined by evolution recreates a micelle-like structure with varying accuracy. The membrane, which is a specific environment with opposite characteristics to the polar aquatic environment, directs the hydrophobic residues towards the surface. The modification of the FOD model to the FOD-M form takes into account the specificity of the cell membrane. It consists in "inverting" the 3DG distribution (complementing the Gaussian distribution), which expresses the exposure of hydrophobic residues on the surface. It turns out that the influence of the environment for any protein (soluble or membrane-anchored) is the result of a consensus factor expressing the participation of the polar environment and the "inverted" environment. The ratio between the proportion of the aqueous and the "reversed" environment turns out to be a characteristic property of a given protein, including amyloid protein in particular. The structure of amyloid proteins has been characterized in the context of prion, intrinsically disordered, and other non-complexing proteins to cover a wider spectrum of molecules with the given characteristics based on the FOD-M model.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Medyczna 7, 30-688 Kraków, Poland
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Kraków, Poland;
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15
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Cornwell O, Ault JR, Bond NJ, Radford SE, Ashcroft AE. Investigation of D76N β 2-Microglobulin Using Protein Footprinting and Structural Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1583-1592. [PMID: 33586970 PMCID: PMC9282677 DOI: 10.1021/jasms.0c00438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NMR studies and X-ray crystallography have shown that the structures of the 99-residue amyloidogenic protein β2-microglobulin (β2m) and its more aggregation-prone variant, D76N, are indistinguishable, and hence, the reason for the striking difference in their aggregation propensities remains elusive. Here, we have employed two protein footprinting methods, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), in conjunction with ion mobility-mass spectrometry, to probe the differences in conformational dynamics of the two proteins. Using HDX-MS, a clear difference in HDX protection is observed between these two proteins in the E-F loop (residues 70-77) which contains the D76N substitution, with a significantly higher deuterium uptake being observed in the variant protein. Conversely, following FPOP-MS only minimal differences in the level of oxidation between the two proteins are observed in the E-F loop region, suggesting only modest side-chain movements in that area. Together the HDX-MS and FPOP-MS data suggest that a tangible perturbation to the hydrogen-bonding network in the E-F loop has taken place in the D76N variant and furthermore illustrate the benefit of using multiple complementary footprinting methods to address subtle, but possibly biologically important, differences between highly similar proteins.
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Affiliation(s)
- Owen Cornwell
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - James R. Ault
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Nicholas J. Bond
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alison E. Ashcroft
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
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16
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Morand J, Nunes A, Faísca PFN. The folding space of protein β2-microglobulin is modulated by a single disulfide bridge. Phys Biol 2021; 18. [PMID: 34098544 DOI: 10.1088/1478-3975/ac08ec] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/07/2021] [Indexed: 11/11/2022]
Abstract
Protein beta-2-microglobulin (β2m) is classically considered the causative agent of dialysis related amyloidosis, a conformational disorder that affects patients undergoing long-term hemodialysis. The wild type (WT) form, the ΔN6 structural variant, and the D76N mutant have been extensively used as model systems ofβ2m aggregation. In all of them, the native structure is stabilized by a disulfide bridge between the sulphur atoms of the cysteine residues 25 (at B strand) and 80 (at F strand), which has been considered fundamental inβ2m fibrillogenesis. Here, we use extensive discrete molecular dynamics simulations of a full atomistic structure-based model to explore the role of this disulfide bridge as a modulator of the folding space ofβ2m. In particular, by considering different models for the disulfide bridge, we explore the thermodynamics of the folding transition, and the formation of intermediate states that may have the potential to trigger the aggregation cascade. Our results show that the dissulfide bridge affects folding transition and folding thermodynamics of the considered model systems, although to different extents. In particular, when the interaction between the sulphur atoms is stabilized relative to the other intramolecular interactions, or even locked (i.e. permanently established), the WT form populates an intermediate state featuring a well preserved core and two unstructured termini, which was previously detected only for the D76N mutant. The formation of this intermediate state may have important implications in our understanding ofβ2m fibrillogenesis.
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Affiliation(s)
- Jules Morand
- Departamento de Física and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, CampoGrande, Ed. C8, 1749-016 Lisboa, Portugal
| | - Ana Nunes
- Departamento de Física and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, CampoGrande, Ed. C8, 1749-016 Lisboa, Portugal
| | - Patrícia F N Faísca
- Departamento de Física and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, CampoGrande, Ed. C8, 1749-016 Lisboa, Portugal
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17
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Strategies to load therapeutics into polysaccharide-based nanogels with a focus on microfluidics: A review. Carbohydr Polym 2021; 266:118119. [PMID: 34044935 DOI: 10.1016/j.carbpol.2021.118119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/04/2021] [Accepted: 04/15/2021] [Indexed: 01/05/2023]
Abstract
Nowadays nanoparticles are increasingly investigated for the targeted and controlled delivery of therapeutics, as suggested by the high number of research articles (2400 in 2000 vs 8500 in 2020). Among them, almost 2% investigated nanogels in 2020. Nanogels or nanohydrogels (NGs) are nanoparticles formed by a swollen three-dimensional network of synthetic polymers or natural macromolecules such as polysaccharides. NGs represent a highly versatile nanocarrier, able to deliver a number of therapeutics. Currently, NGs are undergoing clinical trials for the delivery of anti-cancer vaccines. Herein, the strategies to load low molecular weight drugs, (poly)peptides and genetic material into polysaccharide NGs as well as to formulate NGs-based vaccines are summarized, with a focus on the microfluidics approach.
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18
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Maschio MC, Fregoni J, Molteni C, Corni S. Proline isomerization effects in the amyloidogenic protein β2-microglobulin. Phys Chem Chem Phys 2021; 23:356-367. [DOI: 10.1039/d0cp04780e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein β2-microglobulin can aggregate in insoluble amyloid fibrils. By relying on extensive sampling simulations, we study the Pro32 isomerization as a possible triggering factor leading to structural modifications in β2-m.
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Affiliation(s)
| | - Jacopo Fregoni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| | - Carla Molteni
- Department of Physics
- King's College London
- Strand
- London WC2R 2LS
- UK
| | - Stefano Corni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
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19
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Yoshimura Y, So M, Miyanoiri Y. Carbonyl 13C-detect solution-state protein NMR experiments to circumvent amide-solvent exchange broadening: Application to β 2-microglobulin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140593. [PMID: 33359410 DOI: 10.1016/j.bbapap.2020.140593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The 15N-1H heteronuclear single-quantum correlation (HSQC) technique in protein NMR spectroscopy suffers from line-broadening effects, such as chemical exchange of labile protons with solvent, and exchange broadening for residues undergoing conformational dynamics. The amide resonance of β2-microglobulin residue S88 is not observed in the HSQC spectrum but can be obtained through 13C-detect experiments that circumvent the problem of amide-solvent exchange broadening. Line broadening of S88 resonance beyond detection in the HSQC spectrum is not attributed to conformational exchange but rather to solvent exchange occurring on the order of ~103 s-1.
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Affiliation(s)
- Yuichi Yoshimura
- Institute for Protein Research, Osaka University, Yamada-oka 3-2, Suita, 565-0871 Osaka, Japan; Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, 739-8526 Hiroshima, Japan; Lifematics West-Japan Branch, Hirano-machi 4-6-16, Chuo-ku, 541-0046 Osaka, Japan.
| | - Masatomo So
- Institute for Protein Research, Osaka University, Yamada-oka 3-2, Suita, 565-0871 Osaka, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Yamada-oka 3-2, Suita, 565-0871 Osaka, Japan
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20
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Ulamec SM, Brockwell DJ, Radford SE. Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins. Front Neurosci 2020; 14:611285. [PMID: 33335475 PMCID: PMC7736610 DOI: 10.3389/fnins.2020.611285] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid proteins are involved in many neurodegenerative disorders such as Alzheimer’s disease [Tau, Amyloid β (Aβ)], Parkinson’s disease [alpha-synuclein (αSyn)], and amyotrophic lateral sclerosis (TDP-43). Driven by the early observation of the presence of ordered structure within amyloid fibrils and the potential to develop inhibitors of their formation, a major goal of the amyloid field has been to elucidate the structure of the amyloid fold at atomic resolution. This has now been achieved for a wide variety of sequences using solid-state NMR, microcrystallography, X-ray fiber diffraction and cryo-electron microscopy. These studies, together with in silico methods able to predict aggregation-prone regions (APRs) in protein sequences, have provided a wealth of information about the ordered fibril cores that comprise the amyloid fold. Structural and kinetic analyses have also shown that amyloidogenic proteins often contain less well-ordered sequences outside of the amyloid core (termed here as flanking regions) that modulate function, toxicity and/or aggregation rates. These flanking regions, which often form a dynamically disordered “fuzzy coat” around the fibril core, have been shown to play key parts in the physiological roles of functional amyloids, including the binding of RNA and in phase separation. They are also the mediators of chaperone binding and membrane binding/disruption in toxic amyloid assemblies. Here, we review the role of flanking regions in different proteins spanning both functional amyloid and amyloid in disease, in the context of their role in aggregation, toxicity and cellular (dys)function. Understanding the properties of these regions could provide new opportunities to target disease-related aggregation without disturbing critical biological functions.
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Affiliation(s)
- Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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21
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Cawood EE, Guthertz N, Ebo JS, Karamanos TK, Radford SE, Wilson AJ. Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules. J Am Chem Soc 2020; 142:20845-20854. [PMID: 33253560 PMCID: PMC7729939 DOI: 10.1021/jacs.0c10629] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Protein–protein
interactions (PPIs) are involved in many
of life’s essential biological functions yet are also an underlying
cause of several human diseases, including amyloidosis. The modulation
of PPIs presents opportunities to gain mechanistic insights into amyloid
assembly, particularly through the use of methods which can trap specific
intermediates for detailed study. Such information can also provide
a starting point for drug discovery. Here, we demonstrate that covalently
tethered small molecule fragments can be used to stabilize specific
oligomers during amyloid fibril formation, facilitating the structural
characterization of these assembly intermediates. We exemplify the
power of covalent tethering using the naturally occurring truncated
variant (ΔN6) of the human protein β2-microglobulin
(β2m), which assembles into amyloid fibrils associated
with dialysis-related amyloidosis. Using this approach, we have trapped
tetramers formed by ΔN6 under conditions which would normally
lead to fibril formation and found that the degree of tetramer stabilization
depends on the site of the covalent tether and the nature of the protein–fragment
interaction. The covalent protein–ligand linkage enabled structural
characterization of these trapped, off-pathway oligomers using X-ray
crystallography and NMR, providing insight into why tetramer stabilization
inhibits amyloid assembly. Our findings highlight the power of “post-translational
chemical modification” as a tool to study biological molecular
mechanisms.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, 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, University of Leeds, Leeds LS2 9JT, United Kingdom.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
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22
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Childers MC, Daggett V. Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions. Biophys J 2020; 119:1995-2009. [PMID: 33091379 DOI: 10.1016/j.bpj.2020.08.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/09/2020] [Accepted: 08/31/2020] [Indexed: 01/18/2023] Open
Abstract
During amyloidogenesis, proteins undergo conformational changes that allow them to aggregate and assemble into insoluble, fibrillar structures. Soluble oligomers that form during this process typically contain 2-24 monomeric subunits and are cytotoxic. Before the formation of these soluble oligomers, monomeric species first adopt aggregation-competent conformations. Knowledge of the structures of these intermediate states is invaluable to the development of molecular strategies to arrest pathological amyloid aggregation. However, the highly dynamic and interconverting nature of amyloidogenic species limits biophysical characterization of their structures during amyloidogenesis. Here, we use molecular dynamics simulations to probe conformations sampled by monomeric transthyretin under amyloidogenic conditions. We show that certain β-strands in transthyretin tend to unfold and sample nonnative conformations and that the edge strands in one β-sheet (the DAGH sheet) are particularly susceptible to conformational changes in the monomeric state. We also find that changes in the tertiary structure of transthyretin can be associated with disruptions to the secondary structure. We evaluated the conformations produced by molecular dynamics by calculating how well molecular-dynamics-derived structures reproduced NMR-derived interatomic distances. Finally, we leverage our computational results to produce experimentally testable hypotheses that may aid experimental explorations of pathological conformations of transthyretin.
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Affiliation(s)
- Matthew C Childers
- Department of Bioengineering, University of Washington, Seattle, Washington.
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, Washington
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23
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He W, Zhang J, Sachsenhauser V, Wang L, Bardwell JCA, Quan S. Increased surface charge in the protein chaperone Spy enhances its anti-aggregation activity. J Biol Chem 2020; 295:14488-14500. [PMID: 32817055 PMCID: PMC7573262 DOI: 10.1074/jbc.ra119.012300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Chaperones are essential components of the protein homeostasis network. There is a growing interest in optimizing chaperone function, but exactly how to achieve this aim is unclear. Here, using a model chaperone, the bacterial protein Spy, we demonstrate that substitutions that alter the electrostatic potential of Spy's concave, client-binding surface enhance Spy's anti-aggregation activity. We show that this strategy is more efficient than one that enhances the hydrophobicity of Spy's surface. Our findings thus challenge the traditional notion that hydrophobic interactions are the major driving forces that guide chaperone-substrate binding. Kinetic data revealed that both charge- and hydrophobicity-enhanced Spy variants release clients more slowly, resulting in a greater "holdase" activity. However, increasing short-range hydrophobic interactions deleteriously affected Spy's ability to capture substrates, thus reducing its in vitro chaperone activity toward fast-aggregating substrates. Our strategy in chaperone surface engineering therefore sought to fine-tune the different molecular forces involved in chaperone-substrate interactions rather than focusing on enhancing hydrophobic interactions. These results improve our understanding of the mechanistic basis of chaperone-client interactions and illustrate how protein surface-based mutational strategies can facilitate the rational improvement of molecular chaperones.
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Affiliation(s)
- Wei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Jiayin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Veronika Sachsenhauser
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lili Wang
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
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24
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Loureiro RJS, Faísca PFN. The Early Phase of β2-Microglobulin Aggregation: Perspectives From Molecular Simulations. Front Mol Biosci 2020; 7:578433. [PMID: 33134317 PMCID: PMC7550760 DOI: 10.3389/fmolb.2020.578433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022] Open
Abstract
Protein β2-microglobulin is the causing agent of two amyloidosis, dialysis related amyloidosis (DRA), affecting the bones and cartilages of individuals with chronic renal failure undergoing long-term hemodialysis, and a systemic amyloidosis, found in one French family, which impairs visceral organs. The protein’s small size and its biomedical significance attracted the attention of theoretical scientists, and there are now several studies addressing its aggregation mechanism in the context of molecular simulations. Here, we review the early phase of β2-microglobulin aggregation, by focusing on the identification and structural characterization of monomers with the ability to trigger aggregation, and initial small oligomers (dimers, tetramers, hexamers etc.) formed in the so-called nucleation phase. We focus our analysis on results from molecular simulations and integrate our views with those coming from in vitro experiments to provide a broader perspective of this interesting field of research. We also outline directions for future computer simulation studies.
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Affiliation(s)
- Rui J S Loureiro
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Patrícia F N Faísca
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal.,Department of Physics, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
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25
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Ratha BN, Kar RK, Brender JR, Pariary R, Sahoo B, Kalita S, Bhunia A. High-resolution structure of a partially folded insulin aggregation intermediate. Proteins 2020; 88:1648-1659. [PMID: 32683793 DOI: 10.1002/prot.25983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 06/11/2020] [Accepted: 07/12/2020] [Indexed: 01/01/2023]
Abstract
Insulin has long been served as a model for protein aggregation, both due to the importance of aggregation in the manufacture of insulin and because the structural biology of insulin has been extensively characterized. Despite intensive study, details about the initial triggers for aggregation have remained elusive at the molecular level. We show here that at acidic pH, the aggregation of insulin is likely initiated by a partially folded monomeric intermediate. High-resolution structures of the partially folded intermediate show that it is coarsely similar to the initial monomeric structure but differs in subtle details-the A chain helices on the receptor interface are more disordered and the B chain helix is displaced from the C-terminal A chain helix when compared to the stable monomer. The result of these movements is the creation of a hydrophobic cavity in the center of the protein that may serve as nucleation site for oligomer formation. Knowledge of this transition may aid in the engineering of insulin variants that retain the favorable pharamacokinetic properties of monomeric insulin but are more resistant to aggregation.
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Affiliation(s)
- Bhisma N Ratha
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Jeffrey R Brender
- Radiation Biology Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Ranit Pariary
- Department of Biophysics, Bose Institute, Kolkata, India
| | | | - Sujan Kalita
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, India
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26
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Smith HI, Guthertz N, Cawood EE, Maya-Martinez R, Breeze AL, Radford SE. The role of the I T-state in D76N β 2-microglobulin amyloid assembly: A crucial intermediate or an innocuous bystander? J Biol Chem 2020; 295:12474-12484. [PMID: 32661194 PMCID: PMC7458819 DOI: 10.1074/jbc.ra120.014901] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/06/2020] [Indexed: 02/05/2023] Open
Abstract
The D76N variant of human β2-microglobulin (β2m) is the causative agent of a hereditary amyloid disease. Interestingly, D76N-associated amyloidosis has a distinctive pathology compared with aggregation of WT-β2m, which occurs in dialysis-related amyloidosis. A folding intermediate of WT-β2m, known as the IT-state, which contains a nonnative trans Pro-32, has been shown to be a key precursor of WT-β2m aggregation in vitro. However, how a single amino acid substitution enhances the rate of aggregation of D76N-β2m and gives rise to a different amyloid disease remained unclear. Using real-time refolding experiments monitored by CD and NMR, we show that the folding mechanisms of WT- and D76N-β2m are conserved in that both proteins fold slowly via an IT-state that has similar structural properties. Surprisingly, however, direct measurement of the equilibrium population of IT using NMR showed no evidence for an increased population of the IT-state for D76N-β2m, ruling out previous models suggesting that this could explain its enhanced aggregation propensity. Producing a kinetically trapped analog of IT by deleting the N-terminal six amino acids increases the aggregation rate of WT-β2m but slows aggregation of D76N-β2m, supporting the view that although the folding mechanisms of the two proteins are conserved, their aggregation mechanisms differ. The results exclude the IT-state as the origin of the rapid aggregation of D76N-β2m, suggesting that other nonnative states must cause its high aggregation rate. The results highlight how a single substitution at a solvent-exposed site can affect the mechanism of aggregation and the resulting disease.
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Affiliation(s)
- Hugh I Smith
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Roberto Maya-Martinez
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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27
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Arden BG, Borotto NB, Burant B, Warren W, Akiki C, Vachet RW. Measuring the Energy Barrier of the Structural Change That Initiates Amyloid Formation. Anal Chem 2020; 92:4731-4735. [PMID: 32159946 DOI: 10.1021/acs.analchem.0c00368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Obtaining kinetic and thermodynamic information for protein amyloid formation can yield new insight into the mechanistic details of this biomedically important process. The kinetics of the structural change that initiates the amyloid pathway, however, has been challenging to access for any amyloid protein system. Here, using the protein β-2-microglobulin (β2m) as a model, we measure the kinetics and energy barrier associated with an initial amyloidogenic structural change. Using covalent labeling and mass spectrometry, we measure the decrease in solvent accessibility of one of β2m's Trp residues, which is buried during the initial structural change, as a way to probe the kinetics of this structural change at different temperatures and under different amyloid forming conditions. Our results provide the first-ever measure of the activation barrier for a structural change that initiates the amyloid formation pathway. The results also yield new mechanistic insight into β2m's amyloidogenic structural change, especially the role of Pro32 isomerization in this reaction.
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Affiliation(s)
- Blaise G Arden
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Nicholas B Borotto
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Brittney Burant
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - William Warren
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Christine Akiki
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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28
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Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K. Fast time-resolved NMR with non-uniform sampling. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:40-55. [PMID: 32130958 DOI: 10.1016/j.pnmrs.2019.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy is a versatile tool for studying time-dependent processes: chemical reactions, phase transitions or macromolecular structure changes. However, time-resolved NMR is usually based on the simplest among available techniques - one-dimensional spectra serving as "snapshots" of the studied process. One of the reasons is that multidimensional experiments are very time-expensive due to costly sampling of evolution time space. In this review we summarize efforts to alleviate the problem of limited applicability of multidimensional NMR in time-resolved studies. We focus on techniques based on sparse or non-uniform sampling (NUS), which lead to experimental time reduction by omitting a significant part of the data during measurement and reconstructing it mathematically, adopting certain assumptions about the spectrum. NUS spectra are faster to acquire than conventional ones and thus better suited to the role of "snapshots", but still suffer from non-stationarity of the signal i.e. amplitude and frequency variations within a dataset. We discuss in detail how these instabilities affect the spectra, and what are the optimal ways of sampling the non-stationary FID signal. Finally, we discuss related areas of NMR where serial experiments are exploited and how they can benefit from the same NUS-based approaches.
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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Vladislav Orekhov
- Department of Chemistry & Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden.
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29
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Qi H, Yang L, Shan P, Zhu S, Ding H, Xue S, Wang Y, Yuan X, Li P. The Stability Maintenance of Protein Drugs in Organic Coatings Based on Nanogels. Pharmaceutics 2020; 12:E115. [PMID: 32024083 PMCID: PMC7076513 DOI: 10.3390/pharmaceutics12020115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Abstract
Protein drugs are often loaded on scaffolds with organic coatings to realize a spatiotemporal controlled release. The stability or activity of protein drugs, however, is largely affected by the organic coating, particularly with organic solvents, which can dramatically reduce their delivery efficiency and limit their application scope. In spite of this, little attention has been paid to maintaining the stability of protein drugs in organic coatings, to date. Here, we used catalase as a model protein drug to exploit a kind of chemically cross-linked nanogel that can efficiently encapsulate protein drugs. The polymeric shells of nanogels can maintain the surface hydration shell to endow them with a protein protection ability against organic solvents. Furthermore, the protection efficiency of nanogels is higher when the polymeric shell is more hydrophilic. In addition, nanogels can be dispersed in polylactic acid (PLA) solution and subsequently coated on scaffolds to load catalase with high activity. To the best of our knowledge, this is the first use of hydrophilic nanogels as a protection niche to load protein drugs on scaffolds through an organic coating, potentially inspiring researchers to exploit new methods for protein drug loading.
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Affiliation(s)
- Hongzhao Qi
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; (P.S.); (S.Z.); (H.D.); (S.X.); (Y.W.); (P.L.)
| | - Lijun Yang
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China;
| | - Peipei Shan
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; (P.S.); (S.Z.); (H.D.); (S.X.); (Y.W.); (P.L.)
| | - Sujie Zhu
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; (P.S.); (S.Z.); (H.D.); (S.X.); (Y.W.); (P.L.)
| | - Han Ding
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; (P.S.); (S.Z.); (H.D.); (S.X.); (Y.W.); (P.L.)
| | - Sheng Xue
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; (P.S.); (S.Z.); (H.D.); (S.X.); (Y.W.); (P.L.)
| | - Yin Wang
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; (P.S.); (S.Z.); (H.D.); (S.X.); (Y.W.); (P.L.)
| | - Xubo Yuan
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China;
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China; (P.S.); (S.Z.); (H.D.); (S.X.); (Y.W.); (P.L.)
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30
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Hoop CL, Zhu J, Bhattacharya S, Tobita CA, Radford SE, Baum J. Collagen I Weakly Interacts with the β-Sheets of β 2-Microglobulin and Enhances Conformational Exchange To Induce Amyloid Formation. J Am Chem Soc 2020; 142:1321-1331. [PMID: 31875390 PMCID: PMC7135851 DOI: 10.1021/jacs.9b10421] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Amyloidogenesis is
significant in both protein function and pathology.
Amyloid formation of folded, globular proteins is commonly initiated
by partial or complete unfolding. However, how this unfolding event
is triggered for proteins that are otherwise stable in their native
environments is not well understood. The accumulation of the immunoglobulin
protein β2-microglobulin (β2m) into
amyloid plaques in the joints of long-term hemodialysis patients is
the hallmark of dialysis-related amyloidosis (DRA). While β2m does not form amyloid unassisted near neutral pH in vitro, the localization of β2m deposits
to joint spaces suggests a role for the local extracellular matrix
(ECM) proteins, specifically collagens, in promoting amyloid formation.
Indeed, collagen and other ECM components have been observed to facilitate
β2m amyloid formation, but the large size and anisotropy
of the complex, combined with the low affinity of these interactions,
have limited atomic-level elucidation of the amyloid-promoting mechanism(s)
by these molecules. Using solution NMR approaches that uniquely probe
weak interactions in large molecular weight complexes, we are able
to map the binding interfaces on β2m for collagen
I and detect collagen I-induced μs–ms time-scale dynamics
in the β2m backbone. By combining solution NMR relaxation
methods and 15N-dark-state exchange saturation transfer
experiments, we propose a model in which weak, multimodal collagen
I−β2m interactions promote exchange with a
minor population of amyloid-competent species to induce fibrillogenesis.
The results portray the intimate role of the environment in switching
an innocuous protein into an amyloid-competent state, rationalizing
the localization of amyloid deposits in DRA.
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Affiliation(s)
- Cody L Hoop
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Jie Zhu
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | | | - Caitlyn A Tobita
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
| | - Jean Baum
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
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31
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Pande M, Srivastava R. Molecular and clinical insights into protein misfolding and associated amyloidosis. Eur J Med Chem 2019; 184:111753. [PMID: 31622853 DOI: 10.1016/j.ejmech.2019.111753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/24/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022]
Abstract
The misfolding of normally soluble proteins causes their aggregation and deposition in the tissues which disrupts the normal structure and function of the corresponding organs. The proteins with high β-sheet contents are more prone to form amyloids as they exhibit high propensity of self-aggregation. The self aggregated misfolded proteins act as template for further aggregation that leads to formation of protofilaments and eventually amyloid fibrils. More than 30 different types of proteins are known to be associated with amyloidosis related diseases. Several aspects of the amyloidogenic behavior of proteins remain elusive. The exact reason that causes misfolding of the protein and its association into amyloid fibrils is not known. These misfolded intermediates surpass the over engaged quality control system of the cell which clears the misfolded intermediates. This promotes the self-aggregation, accumulation and deposition of these misfolded species in the form of amyloids in the different parts of the body. The amyloid deposition can be localized as in Alzheimer disease or systemic as reported in most of the amyloidosis. The amyloidosis can be of acquired type or familial. The current review aims at bringing together recent updates and comprehensive information about protein amyloidosis and associated diseases at one place.
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Affiliation(s)
- Monu Pande
- Department of Biochemistry, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ragini Srivastava
- Department of Biochemistry, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India.
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32
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Karamanos TK, Jackson MP, Calabrese AN, Goodchild SC, Cawood EE, Thompson GS, Kalverda AP, Hewitt EW, Radford SE. Structural mapping of oligomeric intermediates in an amyloid assembly pathway. eLife 2019; 8:46574. [PMID: 31552823 PMCID: PMC6783270 DOI: 10.7554/elife.46574] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/24/2019] [Indexed: 01/02/2023] Open
Abstract
Transient oligomers are commonly formed in the early stages of amyloid assembly. Determining the structure(s) of these species and defining their role(s) in assembly is key to devising new routes to control disease. Here, using a combination of chemical kinetics, NMR spectroscopy and other biophysical methods, we identify and structurally characterize the oligomers required for amyloid assembly of the protein ΔN6, a truncation variant of human β2-microglobulin (β2m) found in amyloid deposits in the joints of patients with dialysis-related amyloidosis. The results reveal an assembly pathway which is initiated by the formation of head-to-head non-toxic dimers and hexamers en route to amyloid fibrils. Comparison with inhibitory dimers shows that precise subunit organization determines amyloid assembly, while dynamics in the C-terminal strand hint to the initiation of cross-β structure formation. The results provide a detailed structural view of early amyloid assembly involving structured species that are not cytotoxic.
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Affiliation(s)
- Theodoros K Karamanos
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Matthew P Jackson
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Antonio N Calabrese
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sophia C Goodchild
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Emma E Cawood
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Gary S Thompson
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Arnout P Kalverda
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Eric W Hewitt
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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33
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Achour A, Broggini L, Han X, Sun R, Santambrogio C, Buratto J, Visentin C, Barbiroli A, De Luca CMG, Sormanni P, Moda F, De Simone A, Sandalova T, Grandori R, Camilloni C, Ricagno S. Biochemical and biophysical comparison of human and mouse beta-2 microglobulin reveals the molecular determinants of low amyloid propensity. FEBS J 2019; 287:546-560. [PMID: 31420997 DOI: 10.1111/febs.15046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/09/2019] [Accepted: 08/15/2019] [Indexed: 01/01/2023]
Abstract
The molecular bases of amyloid aggregation propensity are still poorly understood, especially for proteins that display a stable folded native structure. A prototypic example is human beta-2 microglobulin (β2m), which, when accumulated in patients, gives rise to dialysis-related amyloidosis. Interestingly, although the physiologic concentration of β2m in mice is five times higher than that found in human patients, no amyloid deposits are observed in mice. Moreover, murine β2m (mβ2m) not only displays a lower amyloid propensity both in vivo and in vitro but also inhibits the aggregation of human β2m in vitro. Here, we compared human and mβ2m for their aggregation propensity, ability to form soluble oligomers, stability, three-dimensional structure and dynamics. Our results indicate that mβ2m low-aggregation propensity is due to two concomitant aspects: the low-aggregation propensity of its primary sequence combined with the absence of high-energy amyloid-competent conformations under native conditions. The identification of the specific properties determining the low-aggregation propensity of mouse β2m will help delineate the molecular risk factors which cause a folded protein to aggregate.
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Affiliation(s)
- Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, Sweden
| | - Luca Broggini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Italy
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, Sweden
| | - Carlo Santambrogio
- Dipartimento di Biotecnologie e Bioscienze, Università Milano-Bicocca, Italy
| | - Jeremie Buratto
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, Sweden
| | | | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, Italy
| | - Chiara Maria Giulia De Luca
- Divisione di Neurologia 5 - Neuropatologia, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | | | - Fabio Moda
- Divisione di Neurologia 5 - Neuropatologia, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | | | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, Sweden
| | - Rita Grandori
- Dipartimento di Biotecnologie e Bioscienze, Università Milano-Bicocca, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Italy
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J S Loureiro R, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, F N Faísca P. The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant. Biomolecules 2019; 9:biom9080366. [PMID: 31416179 PMCID: PMC6722664 DOI: 10.3390/biom9080366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/08/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Human β2-microglobulin (b2m) protein is classically associated with dialysis-related amyloidosis (DRA). Recently, the single point mutant D76N was identified as the causative agent of a hereditary systemic amyloidosis affecting visceral organs. To get insight into the early stage of the β2m aggregation mechanism, we used molecular simulations to perform an in depth comparative analysis of the dimerization phase of the D76N mutant and the ΔN6 variant, a cleaved form lacking the first six N-terminal residues, which is a major component of ex vivo amyloid plaques from DRA patients. We also provide first glimpses into the tetramerization phase of D76N at physiological pH. Results from extensive protein–protein docking simulations predict an essential role of the C- and N-terminal regions (both variants), as well as of the BC-loop (ΔN6 variant), DE-loop (both variants) and EF-loop (D76N mutant) in dimerization. The terminal regions are more relevant under acidic conditions while the BC-, DE- and EF-loops gain importance at physiological pH. Our results recapitulate experimental evidence according to which Tyr10 (A-strand), Phe30 and His31 (BC-loop), Trp60 and Phe62 (DE-loop) and Arg97 (C-terminus) act as dimerization hot-spots, and further predict the occurrence of novel residues with the ability to nucleate dimerization, namely Lys-75 (EF-loop) and Trp-95 (C-terminus). We propose that D76N tetramerization is mainly driven by the self-association of dimers via the N-terminus and DE-loop, and identify Arg3 (N-terminus), Tyr10, Phe56 (D-strand) and Trp60 as potential tetramerization hot-spots.
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Affiliation(s)
- Rui J S Loureiro
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrícia F N Faísca
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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Benseny-Cases N, Karamanos TK, Hoop CL, Baum J, Radford SE. Extracellular matrix components modulate different stages in β 2-microglobulin amyloid formation. J Biol Chem 2019; 294:9392-9401. [PMID: 30996004 PMCID: PMC6579475 DOI: 10.1074/jbc.ra119.008300] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Indexed: 11/26/2022] Open
Abstract
Amyloid deposition of WT human β2-microglobulin (WT-hβ2m) in the joints of long-term hemodialysis patients is the hallmark of dialysis-related amyloidosis. In vitro, WT-hβ2m does not form amyloid fibrils at physiological pH and temperature unless co-solvents or other reagents are added. Therefore, understanding how fibril formation is initiated and maintained in the joint space is important for elucidating WT-hβ2m aggregation and dialysis-related amyloidosis onset. Here, we investigated the roles of collagen I and the commonly administered anticoagulant, low-molecular-weight (LMW) heparin, in the initiation and subsequent aggregation phases of WT-hβ2m in physiologically relevant conditions. Using thioflavin T fluorescence to study the kinetics of amyloid formation, we analyzed how these two agents affect specific stages of WT-hβ2m assembly. Our results revealed that LMW-heparin strongly promotes WT-hβ2m fibrillogenesis during all stages of aggregation. However, collagen I affected WT-hβ2m amyloid formation in contrasting ways: decreasing the lag time of fibril formation in the presence of LMW-heparin and slowing the rate at higher concentrations. We found that in self-seeded reactions, interaction of collagen I with WT-hβ2m amyloid fibrils attenuates surface-mediated growth of WT-hβ2m fibrils, demonstrating a key role of secondary nucleation in WT-hβ2m amyloid formation. Interestingly, collagen I fibrils did not suppress surface-mediated assembly of WT-hβ2m monomers when cross-seeded with fibrils formed from the N-terminally truncated variant ΔN6-hβ2m. Together, these results provide detailed insights into how collagen I and LMW-heparin impact different stages in the aggregation of WT-hβ2m into amyloid, which lead to dramatic effects on the time course of assembly.
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Affiliation(s)
- Núria Benseny-Cases
- From the Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Theodoros K Karamanos
- From the Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Cody L Hoop
- the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Jean Baum
- the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Sheena E Radford
- From the Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and
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36
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Serio TR. [PIN+]ing down the mechanism of prion appearance. FEMS Yeast Res 2019; 18:4923032. [PMID: 29718197 PMCID: PMC5889010 DOI: 10.1093/femsyr/foy026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/03/2018] [Indexed: 11/13/2022] Open
Abstract
Prions are conformationally flexible proteins capable of adopting a native state and a spectrum of alternative states associated with a change in the function of the protein. These alternative states are prone to assemble into amyloid aggregates, which provide a structure for self-replication and transmission of the underlying conformer and thereby the emergence of a new phenotype. Amyloid appearance is a rare event in vivo, regulated by both the aggregation propensity of prion proteins and their cellular environment. How these forces normally intersect to suppress amyloid appearance and the ways in which these restrictions can be bypassed to create protein-only phenotypes remain poorly understood. The most widely studied and perhaps most experimentally tractable system to explore the mechanisms regulating amyloid appearance is the [PIN+] prion of Saccharomyces cerevisiae. [PIN+] is required for the appearance of the amyloid state for both native yeast proteins and for human proteins expressed in yeast. These observations suggest that [PIN+] facilitates the bypass of amyloid regulatory mechanisms by other proteins in vivo. Several models of prion appearance are compatible with current observations, highlighting the complexity of the process and the questions that must be resolved to gain greater insight into the mechanisms regulating these events.
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Affiliation(s)
- Tricia R Serio
- The University of Massachusetts-Amherst, Department of Biochemistry and Molecular Biology, 240 Thatcher Rd, N360, Amherst, MA 01003, USA
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37
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van der Kant R, van Durme J, Rousseau F, Schymkowitz J. SolubiS: Optimizing Protein Solubility by Minimal Point Mutations. Methods Mol Biol 2019; 1873:317-333. [PMID: 30341620 DOI: 10.1007/978-1-4939-8820-4_21] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein solubility is adapted to endogeneous protein abundance in the cell where protein folding is also assisted by multiple chaperones. During recombinant protein production, purification and storage proteins are frequently handled at concentrations that are several orders of magnitude above their physiological concentration, often resulting in protein aggregation. Here we describe SolubiS, a method allowing for (1) detection of aggregation prone linear segments within a protein sequence and (2) identification of mutations that abolish the aggregation propensity of these segments without affecting the thermodynamic stability of the protein. Provided the availability of structural information this method is applicable to all globular proteins including antibodies, resulting both in increased in vitro protein solubility and in better protein production yields.
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Affiliation(s)
- Rob van der Kant
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
| | - Joost van Durme
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven, Belgium.
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John T, Gladytz A, Kubeil C, Martin LL, Risselada HJ, Abel B. Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles. NANOSCALE 2018; 10:20894-20913. [PMID: 30225490 DOI: 10.1039/c8nr04506b] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Society is increasingly exposed to nanoparticles as they are ubiquitous in nature and introduced as man-made air pollutants and as functional ingredients in cosmetic products as well as in nanomedicine. Nanoparticles differ in size, shape and material properties. In addition to their intended function, the side effects on biochemical processes in organisms remain unclear. Nanoparticles can significantly influence the nucleation and aggregation process of peptides. The development of several neurodegenerative diseases, such as Alzheimer's disease, is related to the aggregation of peptides into amyloid fibrils. However, there is no comprehensive or universal mechanism to predict or explain apparent acceleration or inhibition of these aggregation processes. In this work, selected studies and possible mechanisms for amyloid peptide nucleation and aggregation, in the presence of nanoparticles, are highlighted. These studies are discussed in the context of recent data from our group on the role of gold nanoparticles in amyloid peptide aggregation using experimental methods and large-scale molecular dynamics simulations. A complex interplay of the surface properties of the nanoparticles, the properties of the peptides, as well as the resulting forces between both the nanoparticles and the peptides, appear to determine whether amyloid peptide aggregation is influenced, catalysed or inhibited by the presence of nanoparticles.
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Affiliation(s)
- Torsten John
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany.
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39
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Cornwell O, Radford SE, Ashcroft AE, Ault JR. Comparing Hydrogen Deuterium Exchange and Fast Photochemical Oxidation of Proteins: a Structural Characterisation of Wild-Type and ΔN6 β 2-Microglobulin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2413-2426. [PMID: 30267362 PMCID: PMC6276068 DOI: 10.1007/s13361-018-2067-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 05/23/2023]
Abstract
Hydrogen deuterium exchange (HDX) coupled to mass spectrometry (MS) is a well-established technique employed in the field of structural MS to probe the solvent accessibility, dynamics and hydrogen bonding of backbone amides in proteins. By contrast, fast photochemical oxidation of proteins (FPOP) uses hydroxyl radicals, liberated from the photolysis of hydrogen peroxide, to covalently label solvent accessible amino acid side chains on the microsecond-millisecond timescale. Here, we use these two techniques to study the structural and dynamical differences between the protein β2-microglobulin (β2m) and its amyloidogenic truncation variant, ΔN6. We show that HDX and FPOP highlight structural/dynamical differences in regions of the proteins, localised to the region surrounding the N-terminal truncation. Further, we demonstrate that, with carefully optimised LC-MS conditions, FPOP data can probe solvent accessibility at the sub-amino acid level, and that these data can be interpreted meaningfully to gain more detailed understanding of the local environment and orientation of the side chains in protein structures. Graphical Abstract ᅟ.
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Affiliation(s)
- Owen Cornwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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40
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Hashimoto Y, Mukai S, Sasaki Y, Akiyoshi K. Nanogel Tectonics for Tissue Engineering: Protein Delivery Systems with Nanogel Chaperones. Adv Healthc Mater 2018; 7:e1800729. [PMID: 30221496 DOI: 10.1002/adhm.201800729] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/12/2018] [Indexed: 12/15/2022]
Abstract
Amphiphilic polysaccharide self-assembled (SA) nanogels are promising protein carriers owing to their chaperone-like activity that allows them to nanoencapsulate proteins within their polymer networks. The chaperoning function is an important concept that has led to breakthroughs in the development of effective protein drug delivery systems by stabilizing formulations and controlling the quality of unstable proteins. Recently, nanogel-tectonic materials that integrate SA nanogels as building blocks have been designed as new hydrogel biomaterials. This article describes recent progress and applications of SA nanogel tectonic materials as protein delivery systems for tissue engineering.
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Affiliation(s)
- Yoshihide Hashimoto
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo‐ku Kyoto 615‐8510 Japan
- Japan Science and Technology Agency (JST) The Exploratory Research for Advanced Technology (ERATO) Bio‐Nanotransporter Project Katsura Int'tech Center Katsura, Nishikyo‐ku Kyoto 615‐8530 Japan
- Department of Material‐based Medical Engineering Institute of Biomaterials and Bioengineering Tokyo Medical and Dental University 2‐3‐10 Kanda‐Surugadai Chiyoda‐ku Tokyo 101‐0062 Japan
| | - Sada‐atsu Mukai
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo‐ku Kyoto 615‐8510 Japan
- Japan Science and Technology Agency (JST) The Exploratory Research for Advanced Technology (ERATO) Bio‐Nanotransporter Project Katsura Int'tech Center Katsura, Nishikyo‐ku Kyoto 615‐8530 Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo‐ku Kyoto 615‐8510 Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo‐ku Kyoto 615‐8510 Japan
- Japan Science and Technology Agency (JST) The Exploratory Research for Advanced Technology (ERATO) Bio‐Nanotransporter Project Katsura Int'tech Center Katsura, Nishikyo‐ku Kyoto 615‐8530 Japan
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41
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The structure of a β 2-microglobulin fibril suggests a molecular basis for its amyloid polymorphism. Nat Commun 2018; 9:4517. [PMID: 30375379 PMCID: PMC6207761 DOI: 10.1038/s41467-018-06761-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/20/2018] [Indexed: 11/08/2022] Open
Abstract
All amyloid fibrils contain a cross-β fold. How this structure differs in fibrils formed from proteins associated with different diseases remains unclear. Here, we combine cryo-EM and MAS-NMR to determine the structure of an amyloid fibril formed in vitro from β2-microglobulin (β2m), the culprit protein of dialysis-related amyloidosis. The fibril is composed of two identical protofilaments assembled from subunits that do not share β2m's native tertiary fold, but are formed from similar β-strands. The fibrils share motifs with other amyloid fibrils, but also contain unique features including π-stacking interactions perpendicular to the fibril axis and an intramolecular disulfide that stabilises the subunit fold. We also describe a structural model for a second fibril morphology and show that it is built from the same subunit fold. The results provide insights into the mechanisms of fibril formation and the commonalities and differences within the amyloid fold in different protein sequences.
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42
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Dongmo Foumthuim CJ, Corazza A, Esposito G, Fogolari F. Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces. MOLECULAR BIOSYSTEMS 2018; 13:2625-2637. [PMID: 29051937 DOI: 10.1039/c7mb00464h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.
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Zhao J, Zhang B, Zhu J, Nussinov R, Ma B. Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2294-2303. [PMID: 29241665 PMCID: PMC5927852 DOI: 10.1016/j.bbadis.2017.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
Amyloid formation and deposition of immunoglobulin light-chain proteins in systemic amyloidosis (AL) cause major organ failures. While the κ light-chain is dominant (λ/κ=1:2) in healthy individuals, λ is highly overrepresented (λ/κ=3:1) in AL patients. The structural basis of the amyloid formation and the sequence preference are unknown. We examined the correlation between sequence and structural stability of dimeric variable domains of immunoglobulin light chains using molecular dynamics simulations of 24 representative dimer interfaces, followed by energy evaluation of conformational ensembles for 20 AL patients' light chain sequences. We identified a stable interface with displaced N-terminal residues, provides the structural basis for AL protein fibrils formation. Proline isomerization may cause the N-terminus to adopt amyloid-prone conformations. We found that λ light-chains prefer misfolded dimer conformation, while κ chain structures are stabilized by a natively folded dimer. Our study may facilitate structure-based small molecule and antibody design to inhibit AL. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Baohong Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jianwei Zhu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Jecho Laboratories, Inc., 7320A Executive Way, Frederick, MD 21704, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
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Valdés-García G, Millán-Pacheco C, Pastor N. Convergent mechanisms favor fast amyloid formation in two lambda 6a Ig light chain mutants. Biopolymers 2018; 107. [PMID: 28509352 DOI: 10.1002/bip.23027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/05/2017] [Accepted: 05/05/2017] [Indexed: 12/30/2022]
Abstract
Extracellular deposition as amyloids of immunoglobulin light chains causes light chain amyloidosis. Among the light chain families, lambda 6a is one of the most frequent in light chain amyloidosis patients. Its germline protein, 6aJL2, and point mutants, R24G and P7S, are good models to study fibrillogenesis, because their stability and fibril formation characteristics have been described. Both mutations make the germline protein unstable and speed up its ability to aggregate. To date, there is no molecular mechanism that explains how these differences in amyloidogenesis can arise from a single mutation. To look into the structural and dynamical differences in the native state of these proteins, we carried out molecular dynamics simulations at room temperature. Despite the structural similarity of the germline protein and the mutants, we found differences in their dynamical signatures that explain the mutants' increased tendency to form amyloids. The contact network alterations caused by the mutations, though different, converge in affecting two anti-aggregation motifs present in light chain variable domains, suggesting a different starting point for aggregation in lambda chains compared to kappa chains.
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Affiliation(s)
- Gilberto Valdés-García
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - César Millán-Pacheco
- Facultad de Farmacia; Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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45
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Brancolini G, Maschio MC, Cantarutti C, Corazza A, Fogolari F, Bellotti V, Corni S, Esposito G. Citrate stabilized gold nanoparticles interfere with amyloid fibril formation: D76N and ΔN6 β2-microglobulin variants. NANOSCALE 2018; 10:4793-4806. [PMID: 29469914 DOI: 10.1039/c7nr06808e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein aggregation including the formation of dimers and multimers in solution, underlies an array of human diseases such as systemic amyloidosis which is a fatal disease caused by misfolding of native globular proteins damaging the structure and function of affected organs. Different kind of interactors can interfere with the formation of protein dimers and multimers in solution. A very special class of interactors are nanoparticles thanks to the extremely efficient extension of their interaction surface. In particular citrate-coated gold nanoparticles (cit-AuNPs) were recently investigated with amyloidogenic protein β2-microglobulin (β2m). Here we present the computational studies on two challenging models known for their enhanced amyloidogenic propensity, namely ΔN6 and D76N β2m naturally occurring variants, and disclose the role of cit-AuNPs on their fibrillogenesis. The proposed interaction mechanism lies in the interference of the cit-AuNPs with the protein dimers at the early stages of aggregation, that induces dimer disassembling. As a consequence, natural fibril formation can be inhibited. Relying on the comparison between atomistic simulations at multiple levels (enhanced sampling molecular dynamics and Brownian dynamics) and protein structural characterisation by NMR, we demonstrate that the cit-AuNPs interactors are able to inhibit protein dimer assembling. As a consequence, the natural fibril formation is also inhibited, as found in experiment.
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Affiliation(s)
- Giorgia Brancolini
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.
| | | | - Cristina Cantarutti
- Dipartimento di Scienza Mediche e Biologiche (DSMB), University of Udine, Piazzale Kolbe 3, 33100 Udine, Italy
| | - Alessandra Corazza
- Dipartimento di Scienza Mediche e Biologiche (DSMB), University of Udine, Piazzale Kolbe 3, 33100 Udine, Italy and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy
| | - Federico Fogolari
- Dipartimento di Scienza Mediche e Biologiche (DSMB), University of Udine, Piazzale Kolbe 3, 33100 Udine, Italy and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy
| | - Vittorio Bellotti
- Dipartimento di Medicina Molecolare, Universita' di Pavia, Via Taramelli 3, 27100 Pavia, Italy and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy and Division of Medicine, University College of London, London NW3 2PF, UK
| | - Stefano Corni
- Department of Chemical Science, University of Padova, via VIII Febbraio 2, 35122 Padova and Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Gennaro Esposito
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy. and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy and Science and Math Division, New York University at Abu Dhabi, Abu Dhabi, United Arab Emirates.
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A mechanistic insight into protein-ligand interaction, folding, misfolding, aggregation and inhibition of protein aggregates: An overview. Int J Biol Macromol 2018; 106:1115-1129. [DOI: 10.1016/j.ijbiomac.2017.07.185] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 07/28/2017] [Accepted: 07/30/2017] [Indexed: 11/22/2022]
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47
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Morgan GJ, Usher GA, Kelly JW. Incomplete Refolding of Antibody Light Chains to Non-Native, Protease-Sensitive Conformations Leads to Aggregation: A Mechanism of Amyloidogenesis in Patients? Biochemistry 2017; 56:6597-6614. [PMID: 29200282 DOI: 10.1021/acs.biochem.7b00579] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Genetic, biochemical, and pharmacologic evidence supports the hypothesis that conformationally altered or misfolded protein states enable aggregation and cytotoxicity in the systemic amyloid diseases. Reversible structural fluctuations of natively folded proteins are involved in the aggregation of many degenerative disease associated proteins. Herein, we use antibody light chains (LCs) that form amyloid fibrils in AL amyloidosis to consider an alternative hypothesis of amyloidogenesis: that transient unfolding and incomplete extracellular refolding of secreted proteins can lead to metastable, alternatively folded states that are more susceptible to aggregation or to endoproteolysis that can release aggregation-prone fragments. Refolding of full-length λ6a LC dimers comprising an interchain disulfide bond from heat- or chaotrope-denatured ensembles in buffers yields the native dimeric state as well as alternatively folded dimers and aggregates. LC variants lacking an interchain disulfide bond appear to refold fully reversibly to the native state. The conformation of a backbone peptidyl-proline amide in the LC constant domain, which is cis in the native state, may determine whether the LC refolds back to the native state. A proline to alanine (P147A) LC variant, which cannot form the native cis-amide conformation, forms amyloid fibrils from the alternatively folded ensemble, whereas all the full-length λ6a LCs we have studied to date do not form amyloid under analogous conditions. P147A LC variants are susceptible to endoproteolysis by thrombin, enabling amyloidogenesis of the fragments released. Thus, non-native LC structural ensembles containing a tyrosine 146-proline 147 trans-amide bond can initiate and propagate amyloid formation, either directly or after aberrant endoproteolysis.
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Affiliation(s)
- Gareth J Morgan
- Departments of Chemistry and Molecular Medicine, and ‡The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Grace A Usher
- Departments of Chemistry and Molecular Medicine, and ‡The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Departments of Chemistry and Molecular Medicine, and ‡The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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Abstract
Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates.
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Affiliation(s)
- Derek R Dee
- a Department of Physics , University of Alberta , Edmonton , AB , Canada
| | - Michael T Woodside
- a Department of Physics , University of Alberta , Edmonton , AB , Canada;,b National Institute for Nanotechnology, National Research Council , Edmonton , AB , Canada
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Fukasawa K, Higashimoto Y, Ando Y, Motomiya Y. Selection of DNA Aptamer That Blocks the Fibrillogenesis of a Proteolytic Amyloidogenic Fragment of β 2 m. Ther Apher Dial 2017; 22:61-66. [PMID: 28960840 DOI: 10.1111/1744-9987.12591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/22/2017] [Accepted: 06/14/2017] [Indexed: 01/10/2023]
Abstract
Dialysis-related amyloidosis (DRA) is a severe complication of hemodialysis that results in progressive destruction of bones and joints. Elevated concentrations of the β2 -microglobulin (β2 m) level in the serum of subjects on hemodialysis promote the formation of amyloid fibrils in osteoarticular tissues. β2 m lacking the N-terminal six residues of the mature protein (ΔN6β2 m) constitutes 25-30% of β2 m in ex vivo DRA amyloid. Unlike full-length wild-type β2 m, ΔN6β2 m forms amyloid fibrils at neutral pH in vitro. However, the role of ΔN6β2 m in DRA is, at present, poorly understood. In the present study, we screened novel phosphorothioate-modified aptamers directed against ΔN6β2 m using combinatorial chemistry in vitro. We identified 11 ΔN6β2 m aptamers; among the identified aptamers, clone #2, #8, and #10 aptamers had higher binding affinity to ΔN6β2 m than the others. Biolayer interferometry analysis revealed that KD values of clone #2, #8, and #10 aptamers were 56, 23, and 44 nM, respectively. Furthermore, the clone #8 aptamer inhibited fibril formation in a dose-dependent manner, as assessed by Thioflavin T fluorescence assay. Fibrils formed from ΔN6β2 m bind to Congo red, displaying changes in the absorbance spectrum of the dye characteristic of binding to amyloid fibrils, which was completely blocked by treatment with clone #8 aptamer. These results suggest the potential of ΔN6β2 m aptamers as tools for elucidating co-assembly mechanisms in amyloid formation.
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Affiliation(s)
- Kanon Fukasawa
- Department of Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Yuichiro Higashimoto
- Department of Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Yukio Ando
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Honjo, Kumamoto, Japan
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50
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Prakash A, Kumar V, Pandey P, Bharti DR, Vishwakarma P, Singh R, Hassan MI, Lynn AM. Solvent sensitivity of protein aggregation in Cu, Zn superoxide dismutase: a molecular dynamics simulation study. J Biomol Struct Dyn 2017; 36:2605-2617. [PMID: 28782426 DOI: 10.1080/07391102.2017.1364670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Misfolding and aggregation of Cu, Zn Superoxide Dismutase (SOD1) is often found in amyotrophic lateral sclerosis (ALS) patients. The central apo SOD1 barrel was involved in protein maturation and pathological aggregation in ALS. In this work, we employed atomistic molecular dynamics (MD) simulations to study the conformational dynamics of SOD1barrel monomer in different concentrations of trifluoroethanol (TFE). We find concentration dependence unusual structural and dynamical features, characterized by the local unfolding of SOD1barrel. This partially unfolded structure is characterized by the exposure of hydrophobic core, is highly dynamic in nature, and is the precursor of aggregation seen in SOD1barrel. Our computational studies supports the hypothesis of the formation of aggregation 'building blocks' by means of local unfolding of apo monomer as the mechanism of SOD1 fibrillar aggregation. The non-monotonic TFE concentration dependence of protein conformational changes was explored through simulation studies. Our results suggest that altered protein conformation and dynamics within its structure may underlie the aggregation of SOD1 in ALS.
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Affiliation(s)
- Amresh Prakash
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Vijay Kumar
- b Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
| | - Preeti Pandey
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Deepak R Bharti
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Poonam Vishwakarma
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Ruhar Singh
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
| | - Md Imtaiyaz Hassan
- b Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
| | - Andrew M Lynn
- a School of Computational & Integrative Sciences , Jawaharlal Nehru University , New Delhi , 110067 , India
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