1
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Chauhan C, Singh P, Muthu SA, Parvez S, Selvapandiyan A, Ahmad B. Plumbagin accelerates serum albumin's amyloid aggregation kinetics and generates fibril polymorphism by inducing non-native β-sheet structures. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141028. [PMID: 38849109 DOI: 10.1016/j.bbapap.2024.141028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
The ligand-induced conformational switch of proteins has great significance in understanding the biophysics and biochemistry of their self-assembly. In this work, we have investigated the ability of plumbagin (PL), a hydroxynaphthoquinone compound found in the root of the medicinal plant Plumbago zeylanica, to modulate aggregation precursor state, aggregation kinetics and generate distinct fibril of human serum albumin (HSA). PL was found to moderately bind (binding constant Ka ∼ 10-4 M-1)) to domain-II of HSA in the stoichiometric ratio of 1:1. We found that PL-HSA complex aggregation was accelerated as compared to that of HSA aggregation and it may be through an independent pathway. We also detected that fibril produced in the presence of PL is wider in diameter, contains a higher amount of β-sheet (∼18%) and disordered (∼46%) structures, and is less stable. We concluded that the acceleration of aggregation reaction and generation of fibril polymorphism was mainly because of the higher extent of unfolding and high content of non-native β-sheet structure in the aggregation precursor state of PL-HSA complex. This study offers opportunities to explore the ability of ligand binding to modulate aggregation reactions and generate polymorphic protein fibrils.
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Affiliation(s)
- Chanchal Chauhan
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Poonam Singh
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai 400098, India
| | - Shivani A Muthu
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Suhel Parvez
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India
| | | | - Basir Ahmad
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India.
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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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Lehman SE, Karageorgos I, Filteau JR, Vreeland WN. Effect of Azide Preservative on Thermomechanical Aggregation of Purified Reference Protein Materials. J Pharm Sci 2021; 110:1948-1957. [PMID: 33453208 DOI: 10.1016/j.xphs.2021.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
Protein aggregation can affect the quality of protein-based therapeutics. Attempting to unravel factors influencing protein aggregation involves systematic studies. These studies often include sodium azide or similar preservatives in the aggregation buffer. This work shows effects of azide on aggregation of two highly purified reference proteins, both a bovine serum albumin (BSA) as well as a monoclonal antibody (NISTmAb). The proteins were aggregated by thermomechanical stress, consisting of simultaneous heating of the solution with gentle agitation. Protein aggregates were characterized by asymmetric flow field flow fractionation (AF4) with light scattering measurements along with quantification by UV spectroscopy, revealing strong time-dependent generation of aggregated protein and an increase in aggregate molar mass. Gel electrophoresis was used to probe the reversibility of the aggregation and demonstrated complete reversibility for the NISTmAb, but not so for the BSA. Kinetic fitting to a commonly implemented nucleated polymerization model was also employed to provide mechanistic details into the kinetic process. The model suggests that the aggregation of the NISTmAb proceeds via nucleated growth and aggregate-aggregate condensation in a way that is dependent on the concentration (and presence) of the azide anion. This work overall implicates azide preservatives as having demonstrable effects on thermomechanical stress and aggregation of proteins undergoing systematic aggregation and stability studies.
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Affiliation(s)
- Sean E Lehman
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Ioannis Karageorgos
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jeremy R Filteau
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Wyatt N Vreeland
- Biomolecular Measurement Division, Bioprocess Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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4
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Kim J, Thomas CA, Ewald JM, Kurien NM, Booker ME, Greve HJ, Albu TV. Studies on lysozyme modifications induced by substituted p-benzoquinones. Bioorg Chem 2019; 85:386-398. [PMID: 30665033 DOI: 10.1016/j.bioorg.2019.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/03/2019] [Accepted: 01/08/2019] [Indexed: 11/19/2022]
Abstract
Protein misfolding can facilitate a protein damaging process and makes it susceptible to a series of events such as unfolding, adduct formation, oligomerization, or aggregation. Loss of a protein's native structure may result in its biological malfunction and/or cellular toxicity that could cause associated diseases. Several factors were identified for causing structural changes of a protein, however quinone-induced protein modifications received very little attention whether for amyloidal or non-amyloidal proteins. In this paper, we report our investigation on lysozyme modifications upon treatment with selected benzoquinones (BQs), utilizing fluorescence spectroscopy including anisotropy determination, UV-Vis spectroscopy, and SDS-PAGE. Lysozyme was reacted with substituted BQs in order to examine substituent effects on protein modifications. In addition, we evaluated lysozyme modifications induced by 1,4-benzoquinone in concentration-, pH-, temperature-, and time-dependent studies. Our study shows that all BQs can readily modify lysozyme in a complex manner through adduct formation, oligomerization, polymeric aggregation, and/or fibrilization. Electrochemical properties of selected BQs were monitored using cyclic voltammetry in phosphate buffered aqueous solution, and it was found that quinone reduction potentials correlate well with their reactivity trend toward lysozyme.
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Affiliation(s)
- Jisook Kim
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA.
| | - Charles A Thomas
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Jacob M Ewald
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Neethu M Kurien
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Mary E Booker
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Hendrik J Greve
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Titus V Albu
- Department of Chemistry and Physics, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA.
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5
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Patel JR, Xu Y, Capitini C, Chiti F, De Simone A. Backbone NMR assignments of HypF-N under conditions generating toxic and non-toxic oligomers. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:273-277. [PMID: 29786756 PMCID: PMC6132818 DOI: 10.1007/s12104-018-9822-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
The HypF protein is involved in the maturation and regulation of hydrogenases. The N-terminal domain of HypF (HypF-N) has served as a key model system to study the pathways of protein amyloid formation and the nature of the toxicity of pre-fibrilar protein oligomers. This domain can aggregate into two forms of oligomers having significantly different toxic effects when added to neuronal cultures. Here, NMR assignments of HypF-N backbone resonances are presented in its native state and under the conditions favouring the formation of toxic and non-toxic oligomers. The analyses of chemical shifts provide insights into the protein conformational state and the possible pathways leading to the formation of different types of oligomers.
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Affiliation(s)
- Jayneil R Patel
- Department of Life Sciences, Imperial College London, South Kensington, London, SW72AZ, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, South Kensington, London, SW72AZ, UK
| | - Claudia Capitini
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134, Firenze, Italy
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134, Firenze, Italy
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, SW72AZ, UK.
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6
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Eftekharzadeh B, Piai A, Chiesa G, Mungianu D, García J, Pierattelli R, Felli IC, Salvatella X. Sequence Context Influences the Structure and Aggregation Behavior of a PolyQ Tract. Biophys J 2017; 110:2361-2366. [PMID: 27276254 DOI: 10.1016/j.bpj.2016.04.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/13/2016] [Accepted: 04/19/2016] [Indexed: 12/19/2022] Open
Abstract
Expansions of polyglutamine (polyQ) tracts in nine different proteins cause a family of neurodegenerative disorders called polyQ diseases. Because polyQ tracts are potential therapeutic targets for these pathologies there is great interest in characterizing the conformations that they adopt and in understanding how their aggregation behavior is influenced by the sequences flanking them. We used solution NMR to study at single-residue resolution a 156-residue proteolytic fragment of the androgen receptor that contains a polyQ tract associated with the disease spinobulbar muscular atrophy, also known as Kennedy disease. Our findings indicate that a Leu-rich region preceding the polyQ tract causes it to become α-helical and appears to protect the protein against aggregation, which represents a new, to our knowledge, mechanism by which sequence context can minimize the deleterious properties of these repetitive regions. Our results have implications for drug discovery for polyQ diseases because they suggest that the residues flanking these repetitive sequences may represent viable therapeutic targets.
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Affiliation(s)
- Bahareh Eftekharzadeh
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Alessandro Piai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy
| | - Giulio Chiesa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Daniele Mungianu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Florence, Italy
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; ICREA, Barcelona, Spain.
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7
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Ghobeh M, Ahmadian S, Meratan AA, Ebrahim-Habibi A, Ghasemi A, Shafizadeh M, Nemat-Gorgani M. Interaction of Aβ(25-35) fibrillation products with mitochondria: Effect of small-molecule natural products. Biopolymers 2016; 102:473-86. [PMID: 25297917 DOI: 10.1002/bip.22572] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/18/2014] [Accepted: 10/06/2014] [Indexed: 12/25/2022]
Abstract
The 25-35 fragment of the amyloid β (Aβ) peptide is a naturally occurring proteolytic by-product that retains the pathophysiology of its larger parent molecule, whose deposition has been shown to involve mitochondrial dysfunction. Hence, disruption of Aβ(25-35) aggregates could afford an effective remedial strategy for Alzheimer's disease (AD). In the present study, the effect of a number of selected small-molecule natural products (polyphenols: resveratrol, quercetin, biochanin A, and indoles: indole-3-acetic acid, indole-3-carbinol (I3C)) on Aβ(25-35) fibrillogenesis was explored under physiological conditions, and interaction of the resulting structures with rat brain mitochondria was investigated. Several techniques, including fluorescence, circular dichroism, and transmission electron microscopy were utilized to characterize the aggregation products, and possible mitochondrial membrane permeabilization was determined following release of marker enzymes. Results demonstrate the capacity of Aβ(25-35) fibrils to damage mitochondria and suggest how small molecules may afford protection. While I3C appeared more effective in inhibiting the fibrillation process, all natural products behaved similarly in destabilizing preformed aggregates. It is concluded that elucidation of such protection may provide important insights into the development of preventive and therapeutic agents for AD.
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Affiliation(s)
- Maryam Ghobeh
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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8
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Hu R, Zhang M, Chen H, Jiang B, Zheng J. Cross-Seeding Interaction between β-Amyloid and Human Islet Amyloid Polypeptide. ACS Chem Neurosci 2015; 6:1759-68. [PMID: 26255739 DOI: 10.1021/acschemneuro.5b00192] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alzheimer's disease (AD) and type 2 diabetes (T2D) are two common protein misfolding diseases. Increasing evidence suggests that these two diseases may be correlated with each other via cross-sequence interactions between β-amyloid peptide (Aβ) associated with AD and human islet amyloid polypeptide (hIAPP) associated with T2D. However, little is known about how these two peptides work and how they interact with each other to induce amyloidogenesis. In this work, we study the effect of cross-sequence interactions between Aβ and hIAPP peptides on hybrid amyloid structures, conformational changes, and aggregation kinetics using combined experimental and simulation approaches. Experimental results confirm that Aβ and hIAPP can interact with each other to aggregate into hybrid amyloid fibrils containing β-sheet-rich structures morphologically similar to pure Aβ and hIAPP. The cross-seeding of Aβ and hIAPP leads to the coexistence of both a retarded process at the initial nucleation stage and an accelerated process at the fibrillization stage, in conjunction with a conformational transition from random structures to α-helix to β-sheet. Further molecular dynamics simulations reveal that Aβ and hIAPP oligomers can efficiently cross-seed each other via the association of two highly similar U-shaped β-sheet structures; thus, conformational compatibility between Aβ and hIAPP aggregates appears to play a key role in determining barriers to cross-seeding. The cross-seeding effects in this work may provide new insights into the molecular mechanisms of interactions between AD and T2D.
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Affiliation(s)
- Rundong Hu
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Mingzhen Zhang
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Hong Chen
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Binbo Jiang
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Jie Zheng
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
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9
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Relini A, Marano N, Gliozzi A. Misfolding of amyloidogenic proteins and their interactions with membranes. Biomolecules 2013; 4:20-55. [PMID: 24970204 PMCID: PMC4030986 DOI: 10.3390/biom4010020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 01/07/2023] Open
Abstract
In this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. Many of these proteins are implicated in serious illnesses such as Alzheimer’s disease and Parkinson’s disease. Misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. Oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membrane damage. We focus on the structure of these aggregates and their interactions with model membranes. Study of interactions of amlyoidogenic proteins with model and natural membranes has shown the importance of the lipid bilayer in protein misfolding and aggregation and has led to the development of several models for membrane permeabilization by the resulting amyloid aggregates. We discuss several of these models: formation of structured pores by misfolded amyloidogenic proteins, extraction of lipids, interactions with receptors in biological membranes, and membrane destabilization by amyloid aggregates perhaps analogous to that caused by antimicrobial peptides.
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Affiliation(s)
- Annalisa Relini
- Department of Physics, University of Genoa, Genoa 16146, Italy.
| | - Nadia Marano
- Department of Physics, University of Genoa, Genoa 16146, Italy.
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10
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Cations as switches of amyloid-mediated membrane disruption mechanisms: calcium and IAPP. Biophys J 2013; 104:173-84. [PMID: 23332070 DOI: 10.1016/j.bpj.2012.11.3811] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 11/09/2012] [Accepted: 11/21/2012] [Indexed: 12/15/2022] Open
Abstract
Disruption of the integrity of the plasma membrane by amyloidogenic proteins is linked to the pathogenesis of a number of common age-related diseases. Although accumulating evidence suggests that adverse environmental stressors such as unbalanced levels of metal ions may trigger amyloid-mediated membrane damage, many features of the molecular mechanisms underlying these events are unknown. Using human islet amyloid polypeptide (hIAPP, aka amylin), an amyloidogenic peptide associated with β-cell death in type 2 diabetes, we demonstrate that the presence of Ca(2+) ions inhibits membrane damage occurring immediately after the interaction of freshly dissolved hIAPP with the membrane, but significantly enhances fiber-dependent membrane disruption. In particular, dye leakage, quartz crystal microbalance, atomic force microscopy, and NMR experiments show that Ca(2+) ions promote a shallow membrane insertion of hIAPP, which leads to the removal of lipids from the bilayer through a detergent-like mechanism triggered by fiber growth. Because both types of membrane-damage mechanisms are common to amyloid toxicity by most amyloidogenic proteins, it is likely that unregulated ion homeostasis, amyloid aggregation, and membrane disruption are all parts of a self-perpetuating cycle that fuels amyloid cytotoxicity.
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11
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Salvatella X. Structural aspects of amyloid formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:73-101. [PMID: 23663966 DOI: 10.1016/b978-0-12-386931-9.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Amyloid fibrils are highly organized and generally insoluble protein aggregates rich in β secondary structure that can be formed by a wide range of sequences. They have been the object of intense scrutiny because their formation has been associated with a number of neurodegenerative disorders such as Alzheimer's, Parkinson's, Huntington's, and Creutzfeldt-Jakob's diseases. As a consequence of these efforts, much is now known about the properties of proteins that render them prone to form amyloid fibrils, about the mechanism of fibrillation, about the molecular structures of the fibrils, and about the forces that stabilize them. The relationship between the structural properties of the monomeric protein and those of the corresponding aggregate has been, in particular, intensively studied. In this chapter, we will provide an account of current knowledge on this intriguing relationship and provide the reader with key references about this topic.
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12
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Salt Anions Promote the Conversion of HypF-N into Amyloid-Like Oligomers and Modulate the Structure of the Oligomers and the Monomeric Precursor State. J Mol Biol 2012; 424:132-49. [DOI: 10.1016/j.jmb.2012.09.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 09/11/2012] [Accepted: 09/26/2012] [Indexed: 11/17/2022]
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13
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Ciaccio NA, Reynolds TS, Middaugh CR, Laurence JS. Influence of the valine zipper region on the structure and aggregation of the basic leucine zipper (bZIP) domain of activating transcription factor 5 (ATF5). Mol Pharm 2012; 9:3190-9. [PMID: 23067245 DOI: 10.1021/mp300288n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein aggregation is a major problem for biopharmaceuticals. While the control of aggregation is critically important for the future of protein pharmaceuticals, mechanisms of aggregate assembly, particularly the role that structure plays, are still poorly understood. Increasing evidence indicates that partially folded intermediates critically influence the aggregation pathway. We have previously reported the use of the basic leucine zipper (bZIP) domain of activating transcription factor 5 (ATF5) as a partially folded model system to investigate protein aggregation. This domain contains three regions with differing structural propensity: a N-terminal polybasic region, a central helical leucine zipper region, and a C-terminal extended valine zipper region. Additionally, a centrally positioned cysteine residue readily forms an intermolecular disulfide bond that reduces aggregation. Computational analysis of ATF5 predicts that the valine zipper region facilitates self-association. Here we test this hypothesis using a truncated mutant lacking the C-terminal valine zipper region. We compare the structure and aggregation of this mutant to the wild-type (WT) form under both reducing and nonreducing conditions. Our data indicate that removal of this region results in a loss of α-helical structure in the leucine zipper and a change in the mechanism of self-association. The mutant form displays increased association at low temperature but improved resistance to thermally induced aggregation.
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Affiliation(s)
- Natalie A Ciaccio
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
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14
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Aguado-Llera D, Bacarizo J, Gregorio-Teruel L, Taberner FJ, Cámara-Artigas A, Neira JL. Biophysical characterization of the isolated C-terminal region of the transient receptor potential vanilloid 1. FEBS Lett 2012; 586:1154-9. [DOI: 10.1016/j.febslet.2012.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 03/14/2012] [Accepted: 03/14/2012] [Indexed: 11/28/2022]
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15
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Kim J, Vaughn AR, Cho C, Albu TV, Carver EA. Modifications of ribonuclease A induced by p-benzoquinone. Bioorg Chem 2011; 40:92-98. [PMID: 22138305 DOI: 10.1016/j.bioorg.2011.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 11/10/2011] [Accepted: 11/12/2011] [Indexed: 10/15/2022]
Abstract
The nature of ribonuclease A (RNase) modifications induced by p-benzoquinone (pBQ) was investigated using several analysis methods. SDS-PAGE experiments revealed that pBQ was efficient in producing oligomers and polymeric aggregates when RNase was incubated with pBQ. The fluorescence behavior and anisotropy changes of the modified RNase were monitored for a series of incubation reactions where RNase (0.050 mM) was incubated with pBQ (0.050, 0.25, 0.50, 1.50 mM) at 37 °C in phosphate buffer (pH 7.0, 50 mM). The modified RNase exhibited less intense fluorescence and slightly higher anisotropy than the unmodified RNase. UV-Vis spectroscopy indicated that pBQ formed covalent bonds to the modified RNase. Confocal imaging analysis confirmed the formation of the polymeric RNase aggregates with different sizes upon exposure of RNase to high concentrations of pBQ. The interaction between the modified RNase and salts affecting biomineralization of salts was also investigated by scanning electron microscopy. Overall, our results show that pBQ can induce formation of both RNase adducts and aggregates thus providing a better understanding of its biological activity.
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Affiliation(s)
- Jisook Kim
- Department of Chemistry, Box 2252, University of Tennessee at Chattanooga, Chattanooga, TN 37403, United States.
| | - Albert R Vaughn
- Department of Chemistry, Box 2252, University of Tennessee at Chattanooga, Chattanooga, TN 37403, United States
| | - Chris Cho
- Department of Chemistry, Box 2252, University of Tennessee at Chattanooga, Chattanooga, TN 37403, United States
| | - Titus V Albu
- Department of Chemistry, Box 5055, Tennessee Technological University, Cookeville, TN 38505, United States
| | - Ethan A Carver
- Department of Biological and Environmental Sciences, Box 2653, University of Tennessee at Chattanooga, Chattanooga, TN 37403, United States
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16
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Peng T, Lim S. Trimer-Based Design of pH-Responsive Protein Cage Results in Soluble Disassembled Structures. Biomacromolecules 2011; 12:3131-8. [DOI: 10.1021/bm2005438] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tao Peng
- Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457
| | - Sierin Lim
- Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457
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17
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Xie J, Qin M, Cao Y, Wang W. Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: the interplay between hydrophobic interactions and formation of intermolecular disulfide bonds. Proteins 2011; 79:2505-16. [PMID: 21661057 DOI: 10.1002/prot.23074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 04/21/2011] [Accepted: 04/26/2011] [Indexed: 11/05/2022]
Abstract
Recently, it was reported that ultraviolet (UV) illumination could trigger the unfolding of proteins by disrupting the buried disulfide bonds. However, the consequence of such unfolding has not been adequately evaluated. Here, we report that unfolded chicken egg white lysozyme (CEWL) triggered by UV illumination can form uniform globular aggregates as confirmed by dynamic light scattering, atomic force microscopy, and transmission electron microscopy. The assembling process of such aggregates was also monitored by several other methods, such as circular dichroism, fluorescence spectroscopy, mass spectrometry based on chymotrypsin digestion, ANS-binding assay, Ellman essay, and SDS-PAGE. Our finding is that due to the dissociation of the native disulfide bonds by UV illumination, CEWL undergoes drastic conformational changes resulting in the exposure of some hydrophobic residues and free thiols. Subsequently, these partially unfolded molecules self-assemble into small granules driven by intermolecular hydrophobic interaction. With longer UV illumination or longer incubation time, these granules can further self-assemble into larger globular aggregates. The combined effects from both the hydrophobic interaction and the formation of intermolecular disulfide bonds dominate this process. Additionally, similar aggregation behavior can also be found in other three typical disulfide-bonded proteins, that is, α-lactalbumin, RNase A, and bovine serum albumin. Thus, we propose that such aggregation behavior might be a general mechanism for some disulfide-bonded proteins under UV irradiation.
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Affiliation(s)
- Jinbing Xie
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
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18
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Buell AK, Dhulesia A, Mossuto MF, Cremades N, Kumita JR, Dumoulin M, Welland ME, Knowles TP, Salvatella X, Dobson CM. Population of nonnative states of lysozyme variants drives amyloid fibril formation. J Am Chem Soc 2011; 133:7737-7743. [PMID: 21528861 PMCID: PMC4982536 DOI: 10.1021/ja109620d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The propensity of protein molecules to self-assemble into highly ordered, fibrillar aggregates lies at the heart of understanding many disorders ranging from Alzheimer's disease to systemic lysozyme amyloidosis. In this paper we use highly accurate kinetic measurements of amyloid fibril growth in combination with spectroscopic tools to quantify the effect of modifications in solution conditions and in the amino acid sequence of human lysozyme on its propensity to form amyloid fibrils under acidic conditions. We elucidate and quantify the correlation between the rate of amyloid growth and the population of nonnative states, and we show that changes in amyloidogenicity are almost entirely due to alterations in the stability of the native state, while other regions of the global free-energy surface remain largely unmodified. These results provide insight into the complex dynamics of a macromolecule on a multidimensional energy landscape and point the way for a better understanding of amyloid diseases.
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Affiliation(s)
- Alexander K. Buell
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, Cambridge CB3 0FF, UK
| | - Anne Dhulesia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Maria F. Mossuto
- Institute for Research in Biomedicine (IRB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Nunilo Cremades
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Mireille Dumoulin
- Centre for Protein Engineering, University of Liège, Sart Tilman, 4000 Liège, Belgium
| | - Mark E. Welland
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, Cambridge CB3 0FF, UK
| | - Tuomas P.J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB), Baldiri Reixac 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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19
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Ahmad B, Vigliotta I, Tatini F, Campioni S, Mannini B, Winkelmann J, Tiribilli B, Chiti F. The induction of α-helical structure in partially unfolded HypF-N does not affect its aggregation propensity. Protein Eng Des Sel 2011; 24:553-63. [PMID: 21518735 DOI: 10.1093/protein/gzr018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The conversion of proteins into structured fibrillar aggregates is a central problem in protein chemistry, biotechnology, biology and medicine. It is generally accepted that aggregation takes place from partially structured states of proteins. However, the role of the residual structure present in such conformational states is not yet understood. In particular, it is not yet clear as to whether the α-helical structure represents a productive or counteracting structural element for protein aggregation. We have addressed this issue by studying the aggregation of pH-unfolded HypF-N. It has previously been shown that the two native α-helices of HypF-N retain a partial α-helical structure in the pH-unfolded state and that these regions are also involved in the formation of the cross-β structure of the aggregates. We have introduced mutations in such stretches of the sequence, with the aim of increasing the α-helical structure in the key regions of the pH-unfolded state, while minimizing the changes of other factors known to influence protein aggregation, such as hydrophobicity, β-Sheet propensity, etc. The resulting HypF-N mutants have higher contents of α-helical structure at the site(s) of mutation in their pH-unfolded states, but such an increase does not correlate with a change of aggregation rate. The results suggest that stabilisation of α-helical structure in amyloidogenic regions of the sequence of highly dynamic states does not have remarkable effects on the rate of protein aggregation from such conformational states. Comparison with other protein systems indicate that the effect of increasing α-helical propensity can vary if the stabilised helices are in non-amyloidogenic stretches of initially unstructured peptides (accelerating effect), in amyloidogenic stretches of initially unstructured peptides (no effect) or in amyloidogenic stretches of initially stable helices (decelerating effect).
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Affiliation(s)
- B Ahmad
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale Morgagni 50, 50134 Firenze, Italy
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20
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Dhulesia A, Cremades N, Kumita JR, Hsu STD, Mossuto MF, Dumoulin M, Nietlispach D, Akke M, Salvatella X, Dobson CM. Local cooperativity in an amyloidogenic state of human lysozyme observed at atomic resolution. J Am Chem Soc 2010; 132:15580-8. [PMID: 20958028 PMCID: PMC2974344 DOI: 10.1021/ja103524m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Indexed: 12/22/2022]
Abstract
The partial unfolding of human lysozyme underlies its conversion from the soluble state into amyloid fibrils observed in a fatal hereditary form of systemic amyloidosis. To understand the molecular origins of the disease, it is critical to characterize the structural and physicochemical properties of the amyloidogenic states of the protein. Here we provide a high-resolution view of the unfolding process at low pH for three different lysozyme variants, the wild-type protein and the mutants I56T and I59T, which show variable stabilities and propensities to aggregate in vitro. Using a range of biophysical techniques that includes differential scanning calorimetry and nuclear magnetic resonance spectroscopy, we demonstrate that thermal unfolding under amyloidogenic solution conditions involves a cooperative loss of native tertiary structure, followed by progressive unfolding of a compact, molten globule-like denatured state ensemble as the temperature is increased. The width of the temperature window over which the denatured ensemble progressively unfolds correlates with the relative amyloidogenicity and stability of these variants, and the region of lysozyme that unfolds first maps to that which forms the core of the amyloid fibrils formed under similar conditions. Together, these results present a coherent picture at atomic resolution of the initial events underlying amyloid formation by a globular protein.
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21
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Relini A, Torrassa S, Ferrando R, Rolandi R, Campioni S, Chiti F, Gliozzi A. Detection of populations of amyloid-like protofibrils with different physical properties. Biophys J 2010; 98:1277-84. [PMID: 20371327 DOI: 10.1016/j.bpj.2009.11.052] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 11/20/2009] [Accepted: 11/30/2009] [Indexed: 11/19/2022] Open
Abstract
We used tapping mode atomic force microscopy to study the morphology of the amyloid protofibrils formed at fixed conditions (low pH with high ionic strength) by self-assembly of the N-terminal domain of the hydrogenase maturation factor HypF. Although all protofibrils in the sample share a beaded structure and similar values of height and width, an accurate analysis of contour length and end-to-end distance and the comparison of experimental data with theoretical predictions based on the worm-like chain model show that two different populations of protofibrils are present. These populations are characterized by different physical properties, such as persistence length, bending rigidity and Young's modulus. Fluorescence quenching measurements on earlier globular intermediates provide an independent evidence of the existence of different populations. The finding that differences in mechanical properties exist even within the same sample of protofibrils indicates the presence of different subpopulations of prefibrillar aggregates with potentially diverse tendencies to react with undesired molecular targets. This study describes a strategy to discriminate between such different subpopulations that are otherwise difficult to identify with conventional analyses.
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Affiliation(s)
- Annalisa Relini
- Department of Physics, University of Genoa, and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Genoa, Italy.
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22
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Wang L, Schubert D, Sawaya MR, Eisenberg D, Riek R. Multidimensional structure-activity relationship of a protein in its aggregated states. Angew Chem Int Ed Engl 2010; 49:3904-8. [PMID: 20397175 PMCID: PMC3004770 DOI: 10.1002/anie.201000068] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lei Wang
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
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23
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Abstract
Gut microbiota is an assortment of microorganisms inhabiting the length and width of the mammalian gastrointestinal tract. The composition of this microbial community is host specific, evolving throughout an individual's lifetime and susceptible to both exogenous and endogenous modifications. Recent renewed interest in the structure and function of this "organ" has illuminated its central position in health and disease. The microbiota is intimately involved in numerous aspects of normal host physiology, from nutritional status to behavior and stress response. Additionally, they can be a central or a contributing cause of many diseases, affecting both near and far organ systems. The overall balance in the composition of the gut microbial community, as well as the presence or absence of key species capable of effecting specific responses, is important in ensuring homeostasis or lack thereof at the intestinal mucosa and beyond. The mechanisms through which microbiota exerts its beneficial or detrimental influences remain largely undefined, but include elaboration of signaling molecules and recognition of bacterial epitopes by both intestinal epithelial and mucosal immune cells. The advances in modeling and analysis of gut microbiota will further our knowledge of their role in health and disease, allowing customization of existing and future therapeutic and prophylactic modalities.
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Affiliation(s)
- Inna Sekirov
- Michael Smith Laboratories, Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
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24
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Buell AK, White DA, Meier C, Welland ME, Knowles TPJ, Dobson CM. Surface Attachment of Protein Fibrils via Covalent Modification Strategies. J Phys Chem B 2010; 114:10925-38. [DOI: 10.1021/jp101579n] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Alexander K. Buell
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, CB3 0FF, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, U.K
| | - Duncan A. White
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, CB3 0FF, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, U.K
| | - Christoph Meier
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, CB3 0FF, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, U.K
| | - Mark E. Welland
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, CB3 0FF, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, U.K
| | - Tuomas P. J. Knowles
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, CB3 0FF, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, U.K
| | - Christopher M. Dobson
- Nanoscience Centre, University of Cambridge, 11 JJ Thomson Avenue, CB3 0FF, U.K., and Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, U.K
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25
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Wang L, Schubert D, Sawaya M, Eisenberg D, Riek R. Multidimensional Structure-Activity Relationship of a Protein in Its Aggregated States. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Neira JL, Contreras LM, de los Paños OR, Sánchez-Hidalgo M, Martínez-Bueno M, Maqueda M, Rico M. Structural characterisation of the natively unfolded enterocin EJ97. Protein Eng Des Sel 2010; 23:507-18. [PMID: 20385607 DOI: 10.1093/protein/gzq020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteriocins belong to the wide variety of antimicrobial ribosomal peptides synthesised by bacteria. Enterococci are Gram-positive, catalase-negative bacteria that produce lactic acid as the major end product of glucose fermentation. Many enterococcal strains produce bacteriocins, named enterocins. We describe in this work, the structural characterisation of the 44 residues-long enterocin EJ97, produced by Enterococcus faecalis EJ97. To this end, we have used a combined theoretical and experimental approach. First, we have characterised experimentally the conformational properties of EJ97 in solution under different conditions by using a number of spectroscopic techniques, namely fluorescence, CD, FTIR and NMR. Then, we have used several bioinformatic tools as an aid to complement the experimental information about the conformational properties of EJ97. We have shown that EJ97 is monomeric in aqueous solution and that it appears to be chiefly unfolded, save some flickering helical- or turn-like structures, probably stabilised by hydrophobic clustering. Accordingly, EJ97 does not show a cooperative sigmoidal transition when heated or upon addition of GdmCl. These conformational features are essentially pH-independent, as shown by NMR assignments at pHs 5.9 and 7.0. The computational results were puzzling, since some algorithms revealed the natively unfolded character of EJ97 (FoldIndex, the mean scaled hydropathy), whereas some others suggested the presence of ordered structure in its central region (PONDR, RONN and IUPRED). A future challenge is to produce much more experimental results to aid the development of accurate software tools for predicting disorder in proteins.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Edificio Torregaitán, 50009 Zaragoza, Spain.
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27
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Winkelmann J, Calloni G, Campioni S, Mannini B, Taddei N, Chiti F. Low-level expression of a folding-incompetent protein in Escherichia coli: search for the molecular determinants of protein aggregation in vivo. J Mol Biol 2010; 398:600-13. [PMID: 20346957 DOI: 10.1016/j.jmb.2010.03.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 03/04/2010] [Accepted: 03/17/2010] [Indexed: 11/30/2022]
Abstract
Aggregation of peptides and proteins into insoluble amyloid fibrils or related intracellular inclusions is the hallmark of many degenerative diseases, including Alzheimer's disease, Parkinson's disease, and various forms of amyloidosis. In spite of the considerable progress carried out in vitro in elucidating the molecular determinants of the conversion of purified and isolated proteins into amyloid fibrils, very little is known on factors governing this process in the complex environment of living organisms. Taking advantage of increasing evidence that bacterial inclusion bodies consist of amyloid-like aggregates, we have expressed in Escherichia coli both wild type and 21 single-point mutants of the N-terminal domain of the E. coli protein HypF. All variants were expressed as folding-incompetent units in a controlled manner, at low and comparable levels. Their solubilities were measured by quantifying the protein amount contained in the soluble and insoluble fractions by Western blot analysis. A significant negative correlation was found between the solubility of the variants in E. coli and their intrinsic propensity to form amyloid fibrils, predicted using an algorithm previously validated experimentally in vitro on a number of unfolded peptides and proteins, and considering hydrophobicity, beta-sheet propensity, and charge as major sequence determinants of the aggregation process. These findings show that the physicochemical parameters previously recognized to govern amyloid formation by fully or partially unfolded proteins are largely applicable in vivo and pave the way for the molecular exploration of a process as complex as protein aggregation in living organisms.
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Affiliation(s)
- Julia Winkelmann
- Department of Biochemical Sciences, University of Florence, Viale Morgagni 50, 50134 Firenze, Italy
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28
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Aguado-Llera D, Goormaghtigh E, de Geest N, Quan XJ, Prieto A, Hassan BA, Gómez J, Neira JL. The basic helix-loop-helix region of human neurogenin 1 is a monomeric natively unfolded protein which forms a "fuzzy" complex upon DNA binding. Biochemistry 2010; 49:1577-89. [PMID: 20102160 DOI: 10.1021/bi901616z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Neuronal specification is regulated by the activity of transcription factors containing the basic helix-loop-helix motif (bHLH); these regulating proteins include, among others, the neurogenin (Ngn) family, related to the atonal family of genes. Neurogenin 1 (NGN1) is a 237-residue protein that contains a bHLH domain and is involved in neuronal differentiation. In this work, we synthesized the bHLH region of NGN1 (bHLHN) comprising residues 90-150 of the full-length NGN1. The domain is a monomeric natively unfolded protein with a pH-dependent premolten globule conformation, as shown by several spectroscopic techniques (namely, NMR, fluorescence, FTIR, and circular dichroism). The unfolded character of the domain also explains, first, the impossibility of its overexpression in several Escherichia coli strains and, second, its insolubility in aqueous buffers. To the best of our knowledge, this is the first extensive study of the conformational preferences of a bHLH domain under different solution conditions. Upon binding to two DNA E-boxes, the protein forms "fuzzy" complexes (that is, the complexes were not fully folded). The affinities of bHLHN for both DNA boxes were smaller than those of other bHLH domains, which might explain why the protein-DNA complexes were not fully folded.
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Affiliation(s)
- David Aguado-Llera
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
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29
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Junker M, Clark PL. Slow formation of aggregation-resistant beta-sheet folding intermediates. Proteins 2010; 78:812-24. [PMID: 19847915 DOI: 10.1002/prot.22609] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein folding has been studied extensively for decades, yet our ability to predict how proteins reach their native state from a mechanistic perspective is still rudimentary at best, limiting our understanding of folding-related processes in vivo and our ability to manipulate proteins in vitro. Here, we investigate the in vitro refolding mechanism of a large beta-helix protein, pertactin, which has an extended, elongated shape. At 55 kDa, this single domain, all-beta-sheet protein allows detailed analysis of the formation of beta-sheet structure in larger proteins. Using a combination of fluorescence and far-UV circular dichroism spectroscopy, we show that the pertactin beta-helix refolds remarkably slowly, with multiexponential kinetics. Surprisingly, despite the slow refolding rates, large size, and beta-sheet-rich topology, pertactin refolding is reversible and not complicated by off-pathway aggregation. The slow pertactin refolding rate is not limited by proline isomerization, and 30% of secondary structure formation occurs within the rate-limiting step. Furthermore, site-specific labeling experiments indicate that the beta-helix refolds in a multistep but concerted process involving the entire protein, rather than via initial formation of the stable core substructure observed in equilibrium titrations. Hence pertactin provides a valuable system for studying the refolding properties of larger, beta-sheet-rich proteins, and raises intriguing questions regarding the prevention of aggregation during the prolonged population of partially folded, beta-sheet-rich refolding intermediates. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Mirco Junker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
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30
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Cytotoxic aggregation and amyloid formation by the myostatin precursor protein. PLoS One 2010; 5:e9170. [PMID: 20161792 PMCID: PMC2820090 DOI: 10.1371/journal.pone.0009170] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 01/19/2010] [Indexed: 11/19/2022] Open
Abstract
Myostatin, a negative regulator of muscle growth, has been implicated in sporadic inclusion body myositis (sIBM). sIBM is the most common age-related muscle-wastage disease with a pathogenesis similar to that of amyloid disorders such as Alzheimer's and Parkinson's diseases. Myostatin precursor protein (MstnPP) has been shown to associate with large molecular weight filamentous inclusions containing the Alzheimer's amyloid beta peptide in sIBM tissue, and MstnPP is upregulated following ER stress. The mechanism for how MstnPP contributes to disease pathogenesis is unknown. Here, we show for the first time that MstnPP is capable of forming amyloid fibrils in vitro. When MstnPP-containing Escherichia coli inclusion bodies are refolded and purified, a proportion of MstnPP spontaneously misfolds into amyloid-like aggregates as characterised by electron microscopy and binding of the amyloid-specific dye thioflavin T. When subjected to a slightly acidic pH and elevated temperature, the aggregates form straight and unbranched amyloid fibrils 15 nm in diameter and also exhibit higher order amyloid structures. Circular dichroism spectroscopy reveals that the amyloid fibrils are dominated by beta-sheet and that their formation occurs via a conformational change that occurs at a physiologically relevant temperature. Importantly, MstnPP aggregates and protofibrils have a negative effect on the viability of myoblasts. These novel results show that the myostatin precursor protein is capable of forming amyloid structures in vitro with implications for a role in sIBM pathogenesis.
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31
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Ahmad B, Winkelmann J, Tiribilli B, Chiti F. Searching for conditions to form stable protein oligomers with amyloid-like characteristics: The unexplored basic pH. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:223-34. [DOI: 10.1016/j.bbapap.2009.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 09/21/2009] [Accepted: 10/07/2009] [Indexed: 10/20/2022]
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32
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Hosszu LLP, Trevitt CR, Jones S, Batchelor M, Scott DJ, Jackson GS, Collinge J, Waltho JP, Clarke AR. Conformational properties of beta-PrP. J Biol Chem 2009; 284:21981-21990. [PMID: 19369250 PMCID: PMC2755922 DOI: 10.1074/jbc.m809173200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly alpha-helical conformation to one dominated by beta-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91-231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant beta-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a beta-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126-227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state.
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Affiliation(s)
- Laszlo L. P. Hosszu
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Clare R. Trevitt
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Samantha Jones
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Mark Batchelor
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - David J. Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Graham S. Jackson
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - John Collinge
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jonathan P. Waltho
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Anthony R. Clarke
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
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33
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Neira JL, Román-Trufero M, Contreras LM, Prieto J, Singh G, Barrera FN, Renart ML, Vidal M. The transcriptional repressor RYBP is a natively unfolded protein which folds upon binding to DNA. Biochemistry 2009; 48:1348-60. [PMID: 19170609 DOI: 10.1021/bi801933c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RYBP (Ring1A and YY1 binding protein) is a zinc finger protein with an essential role during embryonic development, which binds transcriptional factors, Polycomb products, and mediators of apoptosis, suggesting roles in, apparently, unrelated functions. To investigate mechanisms underlying its association with functionally diverse partners, we set out to study its structural properties using a number of biophysical (fluorescence, circular dichroism, Fourier transform infrared, and NMR spectroscopies) and hydrodynamic (analytical ultracentrifugation, DOSY-NMR, and gel filtration chromatography) techniques. We find RYBP to be a noncompact protein with little residual secondary structure, lacking a well-defined tertiary structure. These observations are also supported by theoretical calculations using neural networks and pairwise energy content, suggesting that RYBP is a natively unfolded protein. In addition, structural studies on its binding to the C-terminal region of the Polycomb protein Ring1B or to DNA show conformational changes in the complexed RYBP, consistent with the acquisition of a folded structure. The data provide a structural explanation for RYBP engagement in functionally unrelated pathways by means of its assembly into various macromolecular complexes as an unstructured protein with the ability to acquire a well-structured fold due to its association with different partners.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernandez, 03202 Elche (Alicante), Spain.
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Ganguly D, Chen J. Structural interpretation of paramagnetic relaxation enhancement-derived distances for disordered protein states. J Mol Biol 2009; 390:467-77. [PMID: 19447112 DOI: 10.1016/j.jmb.2009.05.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 04/27/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
Abstract
Paramagnetic relaxation enhancement (PRE) is a powerful technique for studying transient tertiary organizations of unfolded and partially folded proteins. The heterogeneous and dynamic nature of disordered protein states, together with the r(-6) dependence of PRE, presents significant challenges for reliable structural interpretation of PRE-derived distances. Without additional knowledge of accessible conformational substates, ensemble-simulation-based protocols have been used to calculate structure ensembles that appear to be consistent with the PRE distance restraints imposed on the ensemble level with the proper r(-6) weighting. However, rigorous assessment of the reliability of such protocols has been difficult without intimate knowledge of the true nature of disordered protein states. Here we utilize sets of theoretical PRE distances derived from simulated structure ensembles that represent the folded, partially folded and unfolded states of a small protein to investigate the efficacy of ensemble-simulation-based structural interpretation of PRE distances. The results confirm a critical limitation that, due to r(-6) weighting, only one or a few members need to satisfy the distance restraints and the rest of the ensemble are essentially unrestrained. Consequently, calculated structure ensembles will appear artificially heterogeneous no matter whether the PRE distances are derived from the folded, partially unfolded or unfolded state. Furthermore, the nature of the heterogeneous ensembles is largely determined by the protein model employed in structure calculation and reflects little on the true nature of the underlying disordered state. These findings suggest that PRE measurements on disordered protein states alone generally do not contain enough information for a reliable structural interpretation and that the latter will require additional knowledge of accessible conformational substates. Interestingly, when a very large number of PRE measurements is available, faithful structural interpretation might be possible with intermediate ensemble sizes under ideal conditions.
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Affiliation(s)
- Debabani Ganguly
- Department of Biochemistry, Kansas State University, Manhattan, 66506, USA
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