1
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Smardz P, Anila MM, Rogowski P, Li MS, Różycki B, Krupa P. A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta. Int J Mol Sci 2024; 25:6698. [PMID: 38928405 PMCID: PMC11204378 DOI: 10.3390/ijms25126698] [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: 05/09/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental techniques due to their large-scale conformational fluctuations and transient structural elements. This work presents computational methods for studying IDPs at various resolutions using the Amber and Gromacs packages with both all-atom (Amber ff19SB with the OPC water model) and coarse-grained (Martini 3 and SIRAH) approaches. The effectiveness of these methodologies is demonstrated by examining the monomeric form of amyloid-β (Aβ42), an IDP, with and without disulfide bonds at different resolutions. Our results clearly show that the addition of a disulfide bond decreases the β-content of Aβ42; however, it increases the tendency of the monomeric Aβ42 to form fibril-like conformations, explaining the various aggregation rates observed in experiments. Moreover, analysis of the monomeric Aβ42 compactness, secondary structure content, and comparison between calculated and experimental chemical shifts demonstrates that all three methods provide a reasonable choice to study IDPs; however, coarse-grained approaches may lack some atomistic details, such as secondary structure recognition, due to the simplifications used. In general, this study not only explains the role of disulfide bonds in Aβ42 but also provides a step-by-step protocol for setting up, conducting, and analyzing molecular dynamics (MD) simulations, which is adaptable for studying other biomacromolecules, including folded and disordered proteins and peptides.
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Affiliation(s)
| | | | | | | | | | - Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland; (P.S.); (M.M.A.); (P.R.); (M.S.L.); (B.R.)
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2
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General method to stabilize mesophilic proteins in hyperthermal water. iScience 2021; 24:102503. [PMID: 34113834 PMCID: PMC8169989 DOI: 10.1016/j.isci.2021.102503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/14/2021] [Accepted: 04/29/2021] [Indexed: 11/23/2022] Open
Abstract
The stability of protein structures and biological functions at normal temperature is closely linked with the universal aqueous environment of organisms. Preserving bioactivities of proteins in hyperthermia water would expand their functional capabilities beyond those in native environments. However, only a limited number of proteins derived from hyperthermophiles are thermostable at elevated temperatures. Triggered by this, here we describe a general method to stabilize mesophilic proteins in hyperthermia water. The mesophilic proteins, protected by amphiphilic polymers with multiple binding sites, maintain their secondary and tertiary structures after incubation even in boiling water. This approach, outside the conventional environment for bioactivities of mesophilic proteins, provides a general strategy to dramatically increase the Tm (melting temperature) of mesophilic proteins without any changes to amino sequences of the native proteins. Current work offers a new insight with protein stability engineering for potential application, including vaccine storage and enzyme engineering. Preserving bioactivities of proteins in hyperthermia water is promising. Amphiphilic polymers could protect mesophilic proteins even in boiling water. Mesophilic proteins protected by amphiphilic polymers show dramatically increased Tm. The method offers application prospect for vaccine storage and enzyme engineering.
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3
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Narayan M. Revisiting the Formation of a Native Disulfide Bond: Consequences for Protein Regeneration and Beyond. Molecules 2020; 25:molecules25225337. [PMID: 33207635 PMCID: PMC7697891 DOI: 10.3390/molecules25225337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
Oxidative protein folding involves the formation of disulfide bonds and the regeneration of native structure (N) from the fully reduced and unfolded protein (R). Oxidative protein folding studies have provided a wealth of information on underlying physico-chemical reactions by which disulfide-bond-containing proteins acquire their catalytically active form. Initially, we review key events underlying oxidative protein folding using bovine pancreatic ribonuclease A (RNase A), bovine pancreatic trypsin inhibitor (BPTI) and hen-egg white lysozyme (HEWL) as model disulfide bond-containing folders and discuss consequential outcomes with regard to their folding trajectories. We re-examine the findings from the same studies to underscore the importance of forming native disulfide bonds and generating a “native-like” structure early on in the oxidative folding pathway. The impact of both these features on the regeneration landscape are highlighted by comparing ideal, albeit hypothetical, regeneration scenarios with those wherein a native-like structure is formed relatively “late” in the R→N trajectory. A special case where the desired characteristics of oxidative folding trajectories can, nevertheless, stall folding is also discussed. The importance of these data from oxidative protein folding studies is projected onto outcomes, including their impact on the regeneration rate, yield, misfolding, misfolded-flux trafficking from the endoplasmic reticulum (ER) to the cytoplasm, and the onset of neurodegenerative disorders.
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Affiliation(s)
- Mahesh Narayan
- The Department of Chemistry and Biochemistry, The University of Texas as El Paso, El Paso, TX 79968, USA
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4
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Amyloid formation of fish β-parvalbumin involves primary nucleation triggered by disulfide-bridged protein dimers. Proc Natl Acad Sci U S A 2020; 117:27997-28004. [PMID: 33093204 PMCID: PMC7668186 DOI: 10.1073/pnas.2015503117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Amyloid fibrils are generally related to neurodegenerative diseases, but they can also be part of normal protein function. Amyloid formation involves numerous steps and intermediate species. In this study, we investigated a fish protein, beta-parvalbumin, which readily forms amyloid on ligand removal. Using biophysical experiments, we provide evidence that the underlying mechanism of amyloid formation includes primary nucleation and elongation processes; we also reveal a key role for a disulfide-bridged dimer in the nucleation step. Little is known about intermolecular disulfides in amyloid formation, but covalent dimers and dimer-induced aggregation may be of clinical relevance, because oxidative stress, which can trigger covalent bond formation, is often a hallmark of human neurodegenerative diseases. Amyloid formation involves the conversion of soluble protein species to an aggregated state. Amyloid fibrils of β-parvalbumin, a protein abundant in fish, act as an allergen but also inhibit the in vitro assembly of the Parkinson protein α-synuclein. However, the intrinsic aggregation mechanism of β-parvalbumin has not yet been elucidated. We performed biophysical experiments in combination with mathematical modeling of aggregation kinetics and discovered that the aggregation of β-parvalbumin is initiated by the formation of dimers stabilized by disulfide bonds and then proceeds via primary nucleation and fibril elongation processes. Dimer formation is accelerated by H2O2 and hindered by reducing agents, resulting in faster and slower aggregation rates, respectively. Purified β-parvalbumin dimers readily assemble into amyloid fibrils with similar morphology as those formed when starting from monomer solutions. Furthermore, addition of preformed dimers accelerates the aggregation reaction of monomers. Aggregation of purified β-parvalbumin dimers follows the same kinetic mechanism as that of monomers, implying that the rate-limiting primary nucleus is larger than a dimer and/or involves structural conversion. Our findings demonstrate a folded protein system in which spontaneously formed intermolecular disulfide bonds initiate amyloid fibril formation by recruitment of monomers. This dimer-induced aggregation mechanism may be of relevance for human amyloid diseases in which oxidative stress is often an associated hallmark.
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5
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Dumoulin M. Reflections on professor Sir Christopher M. Dobson (1949-2019). Biophys Rev 2020; 12:13-18. [PMID: 31981089 DOI: 10.1007/s12551-020-00612-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2020] [Indexed: 12/11/2022] Open
Abstract
I have been invited to summarize my career with an emphasis on the time I spent in the laboratory of Prof Christopher M. Dobson, who sadly passed away on September 8th 2019, and to describe his role as a mentor. I accepted this slightly unusual request as it constitutes a unique way for me to express my deep gratitude and admiration for Chris.
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Affiliation(s)
- Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBios, Departement of Life Sciences, University of Liege, Liege, Belgium.
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6
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Göbl C, Morris VK, van Dam L, Visscher M, Polderman PE, Hartlmüller C, de Ruiter H, Hora M, Liesinger L, Birner-Gruenberger R, Vos HR, Reif B, Madl T, Dansen TB. Cysteine oxidation triggers amyloid fibril formation of the tumor suppressor p16 INK4A. Redox Biol 2020; 28:101316. [PMID: 31539802 PMCID: PMC6812003 DOI: 10.1016/j.redox.2019.101316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/28/2019] [Accepted: 09/01/2019] [Indexed: 02/09/2023] Open
Abstract
The tumor suppressor p16INK4A induces cell cycle arrest and senescence in response to oncogenic transformation and is therefore frequently lost in cancer. p16INK4A is also known to accumulate under conditions of oxidative stress. Thus, we hypothesized it could potentially be regulated by reversible oxidation of cysteines (redox signaling). Here we report that oxidation of the single cysteine in p16INK4A in human cells occurs under relatively mild oxidizing conditions and leads to disulfide-dependent dimerization. p16INK4A is an all α-helical protein, but we find that upon cysteine-dependent dimerization, p16INK4A undergoes a dramatic structural rearrangement and forms aggregates that have the typical features of amyloid fibrils, including binding of diagnostic dyes, presence of cross-β sheet structure, and typical dimensions found in electron microscopy. p16INK4A amyloid formation abolishes its function as a Cyclin Dependent Kinase 4/6 inhibitor. Collectively, these observations mechanistically link the cellular redox state to the inactivation of p16INK4A through the formation of amyloid fibrils.
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Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Vanessa K Morris
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Loes van Dam
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Marieke Visscher
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Paulien E Polderman
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Hesther de Ruiter
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Manuel Hora
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Laura Liesinger
- Omics Center Graz, BioTechMed-Graz, Graz, Austria; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Omics Center Graz, BioTechMed-Graz, Graz, Austria; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010, Graz, Austria
| | - Harmjan R Vos
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Bernd Reif
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010, Graz, Austria; BioTechMed-Graz, Austria.
| | - Tobias B Dansen
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands.
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7
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Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 557] [Impact Index Per Article: 111.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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8
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Khan AN, Hassan MN, Khan RH. Gallic acid: A naturally occurring bifunctional inhibitor of amyloid and metal induced aggregation with possible implication in metal-based therapy. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Tao F, Han Q, Yang P. Developing Biopolymer Mesocrystals by Crystallization of Secondary Structures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:183-193. [PMID: 30554509 DOI: 10.1021/acs.langmuir.8b03300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Particle-based mesocrystals have been known for over 10 years; however, examples of biopolymer mesocrystals are rather scarce. The synthesis of particle precursors of biopolymers, the identification of particle-mediated crystallization processes, and thus the synthesis of mesocrystals of biopolymers are challenging. Here, we summarize the existing examples of biopolymer crystallization based on self-assembly of the secondary structures, which could induce the formation of biopolymer mesocrystals. As basic building units, simple secondary structures such as β-sheets or α-helixes could provide a useful tool for the design of biopolymer mesocrystals.
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Affiliation(s)
- Fei Tao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Qian Han
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , China
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10
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Satoh JI, Kino Y, Yanaizu M, Ishida T, Saito Y. Microglia express gamma-interferon-inducible lysosomal thiol reductase in the brains of Alzheimer's disease and Nasu-Hakola disease. Intractable Rare Dis Res 2018; 7:251-257. [PMID: 30560017 PMCID: PMC6290847 DOI: 10.5582/irdr.2018.01119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Gamma-interferon-inducible lysosomal thiol reductase (GILT), expressed in antigen-presenting cells (APCs), facilitates the reduction of disulfide bonds of endocytosed proteins in the endocytic pathway and they are further processed for presentation of immunogenic peptides loaded on major histocompatibility complex (MHC) class II. Although the constitutive and IFNγ-inducible expression of GILT was observed in various APCs, such as dendritic cells, monocytes/macrophages, and B cells, GILT-expressing cell types remain unknown in the human central nervous system (CNS). Nasu-Hakola disease (NHD) is a rare autosomal recessive disorder characterized by sclerosing leukoencephalopathy and multifocal bone cysts, caused by a loss-of-function mutation of either TYROBP (DAP12) or TREM2, both of which are expressed on microglia. A rare heterozygous variant of the TREM2 gene encoding p.Arg47His causes a 3-fold increase in the risk for late-onset Alzheimer's disease (LOAD), suggesting that both NHD and AD are induced by dysfunction of the microglial TREM2 signaling pathway in the brains. We studied by immunohistochemistry GILT expression in NHD and AD brains. GILT was expressed on amoeboid microglia with the highest levels of expression in AD brains, compared with those in non-neurological control (NC) brains and in NHD brains. In AD brains, the clusters of amoeboid microglia surrounding amyloid-beta (Aꞵ) deposition strongly expressed GILT. Furthermore, a human microglial cell line expressed GILT in response to IFNγ. These results indicate that microglia, expressing constitutively high levels of GILT, act as a principal cell type of APCs in AD brains, in contrast to baseline levels of GILT expression in NHD brains.
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Affiliation(s)
- Jun-ichi Satoh
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
- Address correspondence to:Dr. Jun-ichi Satoh, Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan. E-mail:
| | - Yoshihiro Kino
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Motoaki Yanaizu
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Tsuyoshi Ishida
- Department of Pathology and Laboratory Medicine, Kohnodai Hospital, NCGM, Chiba, Japan
| | - Yuko Saito
- Department of Laboratory Medicine, National Center Hospital, NCNP, Tokyo, Japan
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11
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Bocedi A, Cattani G, Martelli C, Cozzolino F, Castagnola M, Pucci P, Ricci G. The extreme hyper-reactivity of Cys94 in lysozyme avoids its amorphous aggregation. Sci Rep 2018; 8:16050. [PMID: 30375487 PMCID: PMC6207692 DOI: 10.1038/s41598-018-34439-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/17/2018] [Indexed: 02/08/2023] Open
Abstract
Many proteins provided with disulfide bridges in the native state undergo amorphous irreversible aggregation when these bonds are not formed. Here we show that egg lysozyme displays a clever strategy to prevent this deleterious aggregation during the nascent phase when disulfides are still absent. In fact, when the reduced protein assembles into a molten globule state, its cysteines acquire strong hyper-reactivity towards natural disulfides. The most reactive residue, Cys94, reacts with oxidized glutathione (GSSG) 3000 times faster than an unperturbed protein cysteine. A low pKa of its sulfhydryl group (6.6/7.1) and a productive complex with GSSG (KD = 0.3 mM), causes a fast glutathionylation of this residue (t1/2 = 3 s) and a complete inhibition of the protein aggregation. Other six cysteines display 70 times higher reactivity toward GSSG. The discovery of extreme hyper-reactivity in cysteines only devoted to structural roles opens new research fields for Alzheimer's and Parkinson diseases.
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Affiliation(s)
- Alessio Bocedi
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome, Italy
| | - Giada Cattani
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome, Italy
| | - Claudia Martelli
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica and Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Flora Cozzolino
- CEINGE Biotecnologie Avanzate and Department of Chemical Science, University of Naples "Federico II", Naples, Italy
| | - Massimo Castagnola
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica and Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Pietro Pucci
- CEINGE Biotecnologie Avanzate and Department of Chemical Science, University of Naples "Federico II", Naples, Italy
| | - Giorgio Ricci
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome, Italy.
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12
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Marinelli P, Navarro S, Baño-Polo M, Morel B, Graña-Montes R, Sabe A, Canals F, Fernandez MR, Conejero-Lara F, Ventura S. Global Protein Stabilization Does Not Suffice to Prevent Amyloid Fibril Formation. ACS Chem Biol 2018; 13:2094-2105. [PMID: 29966079 DOI: 10.1021/acschembio.8b00607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations or cellular conditions that destabilize the native protein conformation promote the population of partially unfolded conformations, which in many cases assemble into insoluble amyloid fibrils, a process associated with multiple human pathologies. Therefore, stabilization of protein structures is seen as an efficient way to prevent misfolding and subsequent aggregation. This has been suggested to be the underlying reason why proteins living in harsh environments, such as the extracellular space, have evolved disulfide bonds. The effect of protein disulfides on the thermodynamics and kinetics of folding has been extensively studied, but much less is known on its effect on aggregation reactions. Here, we designed a single point mutation that introduces a disulfide bond in the all-α FF domain, a protein that, despite being devoid of preformed β-sheets, forms β-sheet-rich amyloid fibrils. The novel and unique covalent bond in the FF domain dramatically increases its thermodynamic stability and folding speed. Nevertheless, these optimized properties cannot counteract the inherent aggregation propensity of the protein, thus indicating that a high global protein stabilization does not suffice to prevent amyloid formation unless it contributes to hide from exposure the specific regions that nucleate the aggregation reaction.
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Affiliation(s)
- Patrizia Marinelli
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Manuel Baño-Polo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Ricardo Graña-Montes
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Anna Sabe
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron University Hospital, 08135 Barcelona, Spain
| | - Francesc Canals
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron University Hospital, 08135 Barcelona, Spain
| | - Maria Rosario Fernandez
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
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13
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Ridgway Z, Zhang X, Wong AG, Abedini A, Schmidt AM, Raleigh DP. Analysis of the Role of the Conserved Disulfide in Amyloid Formation by Human Islet Amyloid Polypeptide in Homogeneous and Heterogeneous Environments. Biochemistry 2018; 57:3065-3074. [PMID: 29697253 DOI: 10.1021/acs.biochem.8b00017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) is a hormone secreted from β-cells in the Islets of Langerhans in response to the same stimuli that lead to insulin secretion. hIAPP plays an adaptive role in glucose homeostasis but misfolds to form insoluble, fibrillar aggregates in type II diabetes that are associated with the disease. Along the misfolding pathway, hIAPP forms species that are toxic to β-cells, resulting in reduced β-cell mass. hIAPP contains a strictly conserved disulfide bond between residues 2 and 7, which forms a small loop at the N-terminus of the molecule. The loop is located outside of the cross β-core in all models of the hIAPP amyloid fibrils. Mutations in this region are rare, and the disulfide loop plays a role in receptor binding; however, the contribution of this region to the aggregation of hIAPP is not well understood. We define the role of the disulfide by analyzing a collection of analogues that remove the disulfide, by mutation of Cys to Ser, by reduction and modification of the Cys residues, or by deletion of the first seven residues. The cytotoxic properties of hIAPP are retained in the Cys to Ser disulfide-free mutant. Removal of the disulfide bond accelerates amyloid formation in all constructs, both in solution and in the presence of model membranes. Removal of the disulfide weakens the ability of hIAPP to induce leakage of vesicles consisting of POPS and POPC. Smaller effects are observed with vesicles that contain 40 mol % cholesterol, although N-terminal truncation still reduces the extent of leakage.
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Affiliation(s)
- Zachary Ridgway
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Xiaoxue Zhang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Amy G Wong
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Andisheh Abedini
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine , New York University School of Medicine , New York , New York 10016 , United States
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine , New York University School of Medicine , New York , New York 10016 , United States
| | - Daniel P Raleigh
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States.,Laufer Center for Quantitative Biology , Stony Brook University , Stony Brook , New York 11794-3400 , United States
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14
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Saha B, Chowdhury S, Sanyal D, Chattopadhyay K, Suresh Kumar G. Comparative Study of Toluidine Blue O and Methylene Blue Binding to Lysozyme and Their Inhibitory Effects on Protein Aggregation. ACS OMEGA 2018; 3:2588-2601. [PMID: 30023840 PMCID: PMC6044680 DOI: 10.1021/acsomega.7b01991] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/19/2018] [Indexed: 06/01/2023]
Abstract
A comparative binding interaction of toluidine blue O (TBO) and methylene blue (MB) with lysozyme was investigated by multifaceted biophysical approaches as well as from the aspects of in silico biophysics. The bindings were static, and it occurred via ground-state complex formation as confirmed from time-resolved fluorescence experiments. From steady-state fluorescence and anisotropy, binding constants were calculated, and it was found that TBO binds more effectively than MB. Synchronous fluorescence spectra revealed that binding of dyes to lysozyme causes polarity changes around the tryptophan (Trp) moiety, most likely at Trp 62 and 63. Calorimetric titration also depicts the higher binding affinity of TBO over MB, and the interactions were exothermic and entropy-driven. In silico studies revealed the potential binding pockets in lysozyme and the participation of residues Trp 62 and 63 in ligand binding. Furthermore, calculations of thermodynamic parameters from the theoretical docking studies were in compliance with experimental observations. Moreover, an inhibitory effect of these dyes to lysozyme fibrillogenesis was examined, and the morphology of the formed fibril was scanned by atomic force microscopy imaging. TBO was observed to exhibit higher potential in inhibiting the fibrillogenesis than MB, and this phenomenon stands out as a promising antiamyloid therapeutic strategy.
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Affiliation(s)
- Baishakhi Saha
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Sourav Chowdhury
- Structural
Biology and Bioinformatics Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Dwipanjan Sanyal
- Structural
Biology and Bioinformatics Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Krishnananda Chattopadhyay
- Structural
Biology and Bioinformatics Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India
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15
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Li C, Xu L, Zuo YY, Yang P. Tuning protein assembly pathways through superfast amyloid-like aggregation. Biomater Sci 2018; 6:836-841. [DOI: 10.1039/c8bm00066b] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three structural elements for protein assembly are proposed, which guide superfast amyloid-like globular protein aggregation towards macroscopic nanofilms and microparticles.
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Affiliation(s)
- Chen Li
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Xi'an 710119
- China
| | - Lu Xu
- Department of Mechanical Engineering
- University of Hawaii at Manoa
- Honolulu
- USA
| | - Yi Y. Zuo
- Department of Mechanical Engineering
- University of Hawaii at Manoa
- Honolulu
- USA
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Xi'an 710119
- China
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16
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Wineman-Fisher V, Miller Y. Insight into a New Binding Site of Zinc Ions in Fibrillar Amylin. ACS Chem Neurosci 2017; 8:2078-2087. [PMID: 28692245 DOI: 10.1021/acschemneuro.7b00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Amylin peptides are secreted together with insulin and zinc ions from pancreatic β-cells. Under unknown conditions, the amylin peptides aggregate to produce oligomers and fibrils, and in some cases Zn2+ ions can bind to amylin peptides to form Zn2+-aggregate complexes. Consequently, these aggregates lead to the death of the β-cells and a decrease in insulin, which is one of the symptoms of type-2 diabetes (T2D). Therefore, it is crucial to investigate the binding sites of the Zn2+ ions in fibrillary amylin. It was previously found by in vitro and simulation studies that Zn2+ ion binds to two or four His residues in the turn domain of fibrillary amylin. In the current study, we present a new Zn2+ binding site in the N-terminus of fibrillary amylin with three different coordination modes. Our simulations showed that Zn2+ ions bind to polymorphic amylin fibrils with a preference to bind to four Cys residues rather than two Cys residues of two neighboring amylin monomers. The new binding site leads to conformational changes, increases the number of polymorphic states, and demonstrates the existence of competition between various binding sites. Our study provides insight into the molecular mechanisms through which Zn2+ ions that play a critical role in amylin aggregation can bind to amylin and promote amylin aggregation in T2D.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 84105, Israel
- Ilse Katz Institute for Nanoscale Science
and Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 84105, Israel
- Ilse Katz Institute for Nanoscale Science
and Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
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17
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Kong LX, Zeng CM. Effects of Seeding on Lysozyme Amyloid Fibrillation in the Presence of Epigallocatechin and Polyethylene Glycol. BIOCHEMISTRY (MOSCOW) 2017; 82:156-167. [PMID: 28320299 DOI: 10.1134/s0006297917020079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Preformed amyloid fibrils can act as seeds for accelerating protein fibrillation. In the present study, we examined the effects of preformed seeds on lysozyme amyloid fibrillation in the presence of two distinct inhibitors - epigallocatechin (EGC) and polyethylene glycol 2000 (PEG). The results demonstrated that the effects of fibrillar seeds on the acceleration of lysozyme fibrillation depended on the aggregation pathway directed by an inhibitor. EGC inhibited lysozyme fibrillation and modified the peptide chains with quinone moieties in a concentration-dependent manner. The resulting aggregates showed amorphous off-pathway morphology. Preformed fibril seeds did not promote lysozyme fibrillation in the presence of EGC. PEG also inhibited lysozyme fibrillation, and the resulting aggregates showed on-pathway protofibrillar morphology. In contrast, the addition of fibril seeds into the mixture of lysozyme and PEG significantly stimulated fibril growth. Assays of cell viability showed that both EGC and PEG inhibited the formation of cytotoxic species. In accordance with thioflavine T data, the seeds failed to alter the cell-damaging potency of the EGC-directed off-pathway aggregates, but increased the cytotoxicity of the PEG-directed on-pathway fibrils. We suggest that the pattern of interaction between lysozyme and an inhibitor determines the pathway of aggregation and therefore the effects of seeding on amyloid formation. EGC covalently modified lysozyme chains with quinones, directing the aggregation to proceed through an off-pathway, whereas PEG affected the protein in a noncovalent manner, and fibril growth could be stimulated under seeding through an on-pathway.
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Affiliation(s)
- Li-Xiu Kong
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, 710119, China.
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18
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Bemporad F, Ramazzotti M. From the Evolution of Protein Sequences Able to Resist Self-Assembly to the Prediction of Aggregation Propensity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:1-47. [PMID: 28109326 DOI: 10.1016/bs.ircmb.2016.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls. One of the possible outcomes of this misbehavior is cross-β aggregation, a super secondary structure which represents the hallmark of self-assembled, well organized, and extremely ordered structures termed amyloid fibrils. What if evolution would have not taken into account such possibilities? Twenty years of research point toward the idea that, in fact, evolution has constantly supervised the risk of errors and minimized their impact. In this review we tried to survey the major findings in the amyloid field, trying to describe what the real pitfalls of protein folding are-from an evolutionary perspective-and how sequence and structural features have evolved to balance the need for perfect, dynamic, functionally efficient structures, and the detrimental effects implicit in the dangerous process of folding. We will discuss how the knowledge obtained from these studies has been employed to produce computational methods able to assess, predict, and discriminate the aggregation properties of protein sequences.
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Affiliation(s)
- F Bemporad
- Università degli Studi di Firenze, Firenze, Italy.
| | - M Ramazzotti
- Università degli Studi di Firenze, Firenze, Italy.
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19
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Kurouski D, Van Duyne RP, Lednev IK. Exploring the structure and formation mechanism of amyloid fibrils by Raman spectroscopy: a review. Analyst 2016; 140:4967-80. [PMID: 26042229 DOI: 10.1039/c5an00342c] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amyloid fibrils are β-sheet rich protein aggregates that are strongly associated with various neurodegenerative diseases. Raman spectroscopy has been broadly utilized to investigate protein aggregation and amyloid fibril formation and has been shown to be capable of revealing changes in secondary and tertiary structures at all stages of fibrillation. When coupled with atomic force (AFM) and scanning electron (SEM) microscopies, Raman spectroscopy becomes a powerful spectroscopic approach that can investigate the structural organization of amyloid fibril polymorphs. In this review, we discuss the applications of Raman spectroscopy, a unique, label-free and non-destructive technique for the structural characterization of amyloidogenic proteins, prefibrilar oligomers, and mature fibrils.
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Affiliation(s)
- Dmitry Kurouski
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, USA.
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20
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Wineman-Fisher V, Tudorachi L, Nissim E, Miller Y. The removal of disulfide bonds in amylin oligomers leads to the conformational change of the ‘native’ amylin oligomers. Phys Chem Chem Phys 2016; 18:12438-42. [DOI: 10.1039/c6cp01196a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Removal of the Cys2–Cys7 disulfide bonds in amylin oligomers decreases polymorphism and induces cross-β structures in the N-termini.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beér Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| | | | - Einav Nissim
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beér Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| | - Yifat Miller
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beér Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
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21
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Klus P, Ponti RD, Livi CM, Tartaglia GG. Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets. BMC Genomics 2015; 16:1071. [PMID: 26673865 PMCID: PMC4681139 DOI: 10.1186/s12864-015-2280-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/08/2015] [Indexed: 01/27/2023] Open
Abstract
Background Comparison between multiple protein datasets requires the choice of an appropriate reference system and a number of variables to describe their differences. Here we introduce an innovative approach to discriminate multiple protein datasets (multiCM) and to measure enrichments in gene ontology terms (cleverGO) using semantic similarities. Results We illustrate the powerfulness of our approach by investigating the links between RNA-binding ability and other protein features, such as structural disorder and aggregation, in S. cerevisiae, C. elegans, M. musculus and H. sapiens. Our results are in striking agreement with available experimental evidence and unravel features that are key to understand the mechanisms regulating cellular homeostasis. Conclusions In an intuitive way, multiCM and cleverGO provide accurate classifications of physico-chemical features and annotations of biological processes, molecular functions and cellular components, which is extremely useful for the discovery and characterization of new trends in protein datasets. The multiCM and cleverGO can be freely accessed on the Web at http://www.tartaglialab.com/cs_multi/submission and http://www.tartaglialab.com/GO_analyser/universal. Each of the pages contains links to the corresponding documentation and tutorial. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2280-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Petr Klus
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Riccardo Delli Ponti
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Carmen Maria Livi
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluís Companys, 08010, Barcelona, Spain.
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22
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Jeong HR, An SSA. Causative factors for formation of toxic islet amyloid polypeptide oligomer in type 2 diabetes mellitus. Clin Interv Aging 2015; 10:1873-9. [PMID: 26604727 PMCID: PMC4655906 DOI: 10.2147/cia.s95297] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human islet amyloid polypeptide (h-IAPP) is a peptide hormone that is synthesized and cosecreted with insulin from insulin-secreting pancreatic β-cells. Recently, h-IAPP was proposed to be the main component responsible for the cytotoxic pancreatic amyloid deposits in patients with type 2 diabetes mellitus (T2DM). Since the causative factors of IAPP (or amylin) oligomer aggregation are not fully understood, this review will discuss the various forms of h-IAPP aggregation. Not all forms of IAPP aggregates trigger the destruction of β-cell function and loss of β-cell mass; however, toxic oligomers do trigger these events. Once these toxic oligomers form under abnormal metabolic conditions in T2DM, they can lead to cell disruption by inducing cell membrane destabilization. In this review, the various factors that have been shown to induce toxic IAPP oligomer formation will be presented, as well as the potential mechanism of oligomer and fibril formation from pro-IAPPs. Initially, pro-IAPPs undergo enzymatic reactions to produce the IAPP monomers, which can then develop into oligomers and fibrils. By this mechanism, toxic oligomers could be generated by diverse pathway components. Thus, the interconnections between factors that influence amyloid aggregation (eg, absence of PC2 enzyme, deamidation, reduction of disulfide bonds, environmental factors in the cell, genetic mutations, copper metal ions, and heparin) will be presented. Hence, this review will aid in understanding the fundamental causative factors contributing to IAPP oligomer formation and support studies for investigating novel T2DM therapeutic approaches, such as the development of inhibitory agents for preventing oligomerization at the early stages of diabetic pathology.
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Affiliation(s)
- Hye Rin Jeong
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Gyeonggi-do, Republic of Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Gyeonggi-do, Republic of Korea
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23
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Fang X, Yang T, Wang L, Yu J, Wei X, Zhou Y, Wang C, Liang W. Nano-cage-mediated refolding of insulin by PEG-PE micelle. Biomaterials 2015; 77:139-48. [PMID: 26595505 DOI: 10.1016/j.biomaterials.2015.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 10/22/2022]
Abstract
Insulin aggregation has pronounced pharmaceutical implications and biological importance. Deposition of insulin aggregates is associated with type II diabetes and instability of pharmaceutical formulations. We present in this study the renaturation effect of PEG-PE micelle on dithiothreitol (DTT)-denatured insulin revealed by techniques including turbidity assay, circular dichroism (CD), thioflavinT (ThT) binding assay, bis-ANS binding assay, agarose gel electrophoresis and MALDI-TOF MS. The obtained results show that PEG-PE micelle having a hydrophilic nano-cage-like structure in which with a negative charge layer, can capture DTT-induced insulin A and B chains, and block their hydrophobic interaction, thereby preventing aggregation. The reduced insulin A and B chain in the nano-cage are capable of recognizing each other and form the native insulin with yields of ∼30% as measured by hypoglycemic activity analysis in mice. The observed insulin refolding assisted by PEG-PE micelle may be applicable to other proteins.
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Affiliation(s)
- Xiaocui Fang
- Protein & Peptide Pharmaceutical Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
| | - Tao Yang
- Protein & Peptide Pharmaceutical Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Luoyang Wang
- Protein & Peptide Pharmaceutical Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jibing Yu
- Protein & Peptide Pharmaceutical Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Xiuli Wei
- Protein & Peptide Pharmaceutical Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yinjian Zhou
- Protein & Peptide Pharmaceutical Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Chen Wang
- CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, No.11 ZhongGuanCun BeiYiTiao, Beijing 100190, China.
| | - Wei Liang
- Protein & Peptide Pharmaceutical Laboratory, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.
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24
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Jayaram DT, Shankar BH, Ramaiah D. Effective Amyloid Defibrillation by Polyhydroxyl-Substituted Squaraine Dyes. Chem Asian J 2015; 10:2689-94. [PMID: 26289494 DOI: 10.1002/asia.201500780] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Indexed: 12/14/2022]
Abstract
With an objective to develop β-amyloid destabilizing agents, we have investigated the interactions of a few water-soluble near-infrared (NIR)-absorbing squaraine dyes 1-3 with lysozyme and its amyloid aggregates through photophysical and biophysical techniques. These dyes exhibited strong interactions with lysozyme and β-amyloids in addition to serum albumins as evidenced by the absorption and emission changes. The interactions were found to be spontaneous with association constant values in the range of approximately 10(4)-10(5) m(-1), as confirmed through half-reciprocal analysis and isothermal calorimetric measurements. Uniquely, such effective interactions of the dyes have led to the complete disassembly of the β-amyloid fibrillar structures to form spherical particles approximately 350 nm in size, as confirmed through photophysical, thioflavin assay, circular dichroism (CD), atomic force microscopy (AFM), TEM, and selected-area electron diffraction (SAED) techniques. These results demonstrate that the squaraine dyes 1-3 under investigation act as effective protein-labelling and destabilizing agents of the protein amyloidogenesis.
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Affiliation(s)
- Dhanya T Jayaram
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695019, Kerala, India
| | - Balaraman H Shankar
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695019, Kerala, India
| | - Danaboyina Ramaiah
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695019, Kerala, India. , , .,CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India. , ,
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25
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Li M, Zhao C, Ren J, Qu X. Chiral Metallo-Supramolecular Complex Directed Enantioselective Self-Assembly of β-Sheet Breaker Peptide for Amyloid Inhibition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4651-4655. [PMID: 26136296 DOI: 10.1002/smll.201501329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 05/29/2015] [Indexed: 06/04/2023]
Abstract
Chiral recognition plays an important role for biomacromolecules involved self-assembly and further affects their biological functions. Herein, it is demonstrated that two chiral metal complexes can enantioselectively bind with Aβ15-20, leading to the formation of different self-assembled nanostructures. With the ability of both metal complexes and Aβ15-20 to inhibit Aβ1-40 aggregation, the NiM@P hybrid particles can act as bifunctional Aβ inhibitors.
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Affiliation(s)
- Meng Li
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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26
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Tokunaga Y, Matsumoto M, Sugimoto Y. Amyloid fibril formation from a 9 amino acid peptide, 55th–63rd residues of human lysozyme. Int J Biol Macromol 2015; 80:208-16. [DOI: 10.1016/j.ijbiomac.2015.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
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27
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Abstract
Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.
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Affiliation(s)
- Maria Francesca Mossuto
- Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Diletta Ami
- 1] Department of Physics, University of Milano-Bicocca [2] Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Tiziana Anelli
- 1] Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy [2] Vita-Salute San Raffaele University, Milan, Italy
| | - Claudio Fagioli
- Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Maria Doglia
- 1] Department of Physics, University of Milano-Bicocca [2] Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Roberto Sitia
- 1] Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy [2] Vita-Salute San Raffaele University, Milan, Italy
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28
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Quinopeptide formation associated with the disruptive effect of epigallocatechin-gallate on lysozyme fibrils. Int J Biol Macromol 2015; 78:389-95. [DOI: 10.1016/j.ijbiomac.2015.04.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/02/2015] [Accepted: 04/20/2015] [Indexed: 02/05/2023]
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29
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Yang M, Dutta C, Tiwari A. Disulfide-bond scrambling promotes amorphous aggregates in lysozyme and bovine serum albumin. J Phys Chem B 2015; 119:3969-81. [PMID: 25689578 DOI: 10.1021/acs.jpcb.5b00144] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Disulfide bonds are naturally formed in more than 50% of amyloidogenic proteins, but the exact role of disulfide bonds in protein aggregation is still not well-understood. The intracellular reducing agents and/or improper use of antioxidants in extracellular environment can break proteins disulfide bonds, making them unstable and prone to misfolding and aggregation. In this study, we report the effect of disulfide-reducing agent dithiothreitol (DTT) on hen egg white lysozyme (lysozyme) and bovine serum albumin (BSA) aggregation at pH 7.2 and 37 °C. BSA and lysozyme proteins treated with disulfide-reducing agents form very distinct amorphous aggregates as observed by scanning electron microscope. However, proteins with intact disulfide bonds were stable and did not aggregate over time. BSA and lysozyme aggregates show unique but measurable differences in 8-anilino-1-naphthalenesulfonic acid (ANS) and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) fluorescence, suggesting a loose and flexible aggregate structure for lysozyme but a more compact aggregate structure for BSA. Scrambled disulfide-bonded protein aggregates were observed by nonreducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) for both proteins. Similar amorphous aggregates were also generated using a nonthiol-based reducing agent, tris(2-carboxyethyl)phosphine (TCEP), at pH 7.2 and 37 °C. In summary, formation of distinct amorphous aggregates by disulfide-reduced BSA and lysozyme suggests an alternate pathway for protein aggregation that may be relevant to several proteins.
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Affiliation(s)
- Mu Yang
- Department of Chemistry, Michigan Technological University , Houghton, Michigan 49931, United States
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Zhang J, Ogorzalek Loo RR, Loo JA. Increasing Fragmentation of Disulfide-Bonded Proteins for Top-Down Mass Spectrometry by Supercharging. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 377:546-556. [PMID: 26028988 PMCID: PMC4448141 DOI: 10.1016/j.ijms.2014.07.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The disulfide bond is an important post-translational modification to form and maintain the native structure and biological functions of proteins. Characterization of disulfide bond linkages is therefore of essential interest in the structural elucidation of proteins. Top-down mass spectrometry (MS) of disulfide-bonded proteins has been hindered by relatively low sequence coverage due to disulfide cross-linking. In this study, we employed top-down ESI-MS with Fourier-transform ion cyclotron resonance (FT-ICR) MS with electron capture dissociation (ECD) and collisionally activated dissociation (CAD) to study the fragmentation of supercharged proteins with multiple intramolecular disulfide bonds. With charge enhancement upon the addition of sulfolane to the analyte solution, improved protein fragmentation and disulfide bond cleavage efficiency was observed for proteins including bovine β-lactoglobulin, soybean trypsin inhibitor, human proinsulin, and chicken lysozyme. Both the number and relative abundances of product ions representing disulfide cleavage increase with increasing charge states for the proteins studied. Our studies suggest supercharging ESI-MS is a promising tool to aid in the top-down MS analysis of disulfide-bonded proteins, providing potentially useful information for the determination of disulfide bond linkages.
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Affiliation(s)
- Jiang Zhang
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, 90095, United States
| | - Rachel R. Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, California, 90095, United States
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California, 90095, United States
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, 90095, United States
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, California, 90095, United States
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California, 90095, United States
- Corresponding author. Tel.: +1 310 794 7023; fax: +1 310 206 4038. (J.A. Loo)
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Rosario-Alomar MF, Quiñones-Ruiz T, Kurouski D, Sereda V, Ferreira EB, Jesús-Kim LD, Hernández-Rivera S, Zagorevski DV, López-Garriga J, Lednev IK. Hydrogen sulfide inhibits amyloid formation. J Phys Chem B 2015; 119:1265-74. [PMID: 25545790 PMCID: PMC4315425 DOI: 10.1021/jp508471v] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Amyloid
fibrils are large aggregates of misfolded proteins, which
are often associated with various neurodegenerative diseases such
as Alzheimer’s, Parkinson’s, Huntington’s, and
vascular dementia. The amount of hydrogen sulfide (H2S)
is known to be significantly reduced in the brain tissue of people
diagnosed with Alzheimer’s disease relative to that of healthy
individuals. These findings prompted us to investigate the effects
of H2S on the formation of amyloids in vitro using a model fibrillogenic protein hen egg white lysozyme (HEWL).
HEWL forms typical β-sheet rich fibrils during the course of
70 min at low pH and high temperatures. The addition of H2S completely inhibits the formation of β-sheet and amyloid
fibrils, as revealed by deep UV resonance Raman (DUVRR) spectroscopy
and ThT fluorescence. Nonresonance Raman spectroscopy shows that disulfide
bonds undergo significant rearrangements in the presence of H2S. Raman bands corresponding to disulfide (RSSR) vibrational
modes in the 550–500 cm–1 spectral range
decrease in intensity and are accompanied by the appearance of a new
490 cm–1 band assigned to the trisulfide group (RSSSR)
based on the comparison with model compounds. The formation of RSSSR
was proven further using a reaction with TCEP reduction agent and
LC-MS analysis of the products. Intrinsic tryptophan fluorescence
study shows a strong denaturation of HEWL containing trisulfide bonds.
The presented evidence indicates that H2S causes the formation
of trisulfide bridges, which destabilizes HEWL structure, preventing
protein fibrillation. As a result, small spherical aggregates of unordered
protein form, which exhibit no cytotoxicity by contrast with HEWL
fibrils.
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Affiliation(s)
- Manuel F Rosario-Alomar
- Department of Chemistry and ‡Department of Biology, University of Puerto Rico at Mayagüez , Mayagüez, Puerto Rico 00693
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Jakhria T, Hellewell AL, Porter MY, Jackson MP, Tipping KW, Xue WF, Radford SE, Hewitt EW. β2-microglobulin amyloid fibrils are nanoparticles that disrupt lysosomal membrane protein trafficking and inhibit protein degradation by lysosomes. J Biol Chem 2014; 289:35781-94. [PMID: 25378395 PMCID: PMC4276847 DOI: 10.1074/jbc.m114.586222] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fragmentation of amyloid fibrils produces fibrils that are reduced in length but have an otherwise unchanged molecular architecture. The resultant nanoscale fibril particles inhibit the cellular reduction of the tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), a substrate commonly used to measure cell viability, to a greater extent than unfragmented fibrils. Here we show that the internalization of β2-microglobulin (β2m) amyloid fibrils is dependent on fibril length, with fragmented fibrils being more efficiently internalized by cells. Correspondingly, inhibiting the internalization of fragmented β2m fibrils rescued cellular MTT reduction. Incubation of cells with fragmented β2m fibrils did not, however, cause cell death. Instead, fragmented β2m fibrils accumulate in lysosomes, alter the trafficking of lysosomal membrane proteins, and inhibit the degradation of a model protein substrate by lysosomes. These findings suggest that nanoscale fibrils formed early during amyloid assembly reactions or by the fragmentation of longer fibrils could play a role in amyloid disease by disrupting protein degradation by lysosomes and trafficking in the endolysosomal pathway.
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Affiliation(s)
- Toral Jakhria
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew L Hellewell
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Morwenna Y Porter
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Matthew P Jackson
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Kevin W Tipping
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Wei-Feng Xue
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sheena E Radford
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Eric W Hewitt
- From the School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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Fraga H, Graña-Montes R, Illa R, Covaleda G, Ventura S. Association between foldability and aggregation propensity in small disulfide-rich proteins. Antioxid Redox Signal 2014; 21:368-83. [PMID: 24635049 PMCID: PMC4076991 DOI: 10.1089/ars.2013.5543] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS Disulfide-rich domains (DRDs) are small proteins whose native structure is stabilized by the presence of covalent disulfide bonds. These domains are versatile and can perform a wide range of functions. Many of these domains readily unfold on disulfide bond reduction, suggesting that in the absence of covalent bonding they might display significant disorder. RESULTS Here, we analyzed the degree of disorder in 97 domains representative of the different DRDs families and demonstrate that, in terms of sequence, many of them can be classified as intrinsically disordered proteins (IDPs) or contain predicted disordered regions. The analysis of the aggregation propensity of these domains indicates that, similar to IDPs, their sequences are more soluble and have less aggregating regions than those of other globular domains, suggesting that they might have evolved to avoid aggregation after protein synthesis and before they can attain its compact and covalently linked native structure. INNOVATION AND CONCLUSION DRDs, which resemble IDPs in the reduced state and become globular when their disulfide bonds are formed, illustrate the link between protein folding and aggregation propensities and how these two properties cannot be easily dissociated, determining the main traits of the folding routes followed by these small proteins to attain their native oxidized states.
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Affiliation(s)
- Hugo Fraga
- Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona , Barcelona, Spain
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Ravi VK, Goel M, Kotamarthi HC, Ainavarapu SRK, Swaminathan R. Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates. PLoS One 2014; 9:e87012. [PMID: 24551048 PMCID: PMC3925087 DOI: 10.1371/journal.pone.0087012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 12/16/2013] [Indexed: 12/21/2022] Open
Abstract
Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL) at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control) and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL) on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.
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Affiliation(s)
- Vijay Kumar Ravi
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Mohit Goel
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, Maharashtra, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, Maharashtra, India
| | - Rajaram Swaminathan
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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35
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The effect of exposing a critical hydrophobic patch on amyloidogenicity and fibril structure of insulin. Biochem Biophys Res Commun 2013; 440:56-61. [DOI: 10.1016/j.bbrc.2013.09.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/05/2013] [Indexed: 11/23/2022]
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36
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Kurouski D, Luo H, Sereda V, Robb FT, Lednev IK. Deconstruction of stable cross-Beta fibrillar structures into toxic and nontoxic products using a mutated archaeal chaperonin. ACS Chem Biol 2013; 8:2095-101. [PMID: 23875676 DOI: 10.1021/cb400238a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our group recently determined that a mutant archaeal chaperonin (Hsp 60) exhibited substantially enhanced protein folding activity at low temperatures and was able to deconstruct refractory protein aggregates. ATP dependent conversion of fibril structures into amorphous aggregates was observed in insulin amyloid preparations (Kurouski et al. Biochem. Biophys. Res. Commun. 2012). In the current study, mechanistic insights into insulin fibril deconstruction were obtained by examination of early stage complexes between Hsp60 and fibrils in the absence of ATP. Activity of the Hsp60 was significantly curtailed without ATP; however, some fibril deconstruction occurred, which is consistent with some models of the folding cycle that predict initial removal of unproductive protein folds. Chaperonin molecules adsorbed on the fibril surface and formed chaperonin clusters with no ATP present. We propose that there are specific locations on the fibril surface where chaperonin can unravel the fibril to release short fragments. Spontaneous coagulation of these fibril fragments resulted in the formation of amorphous aggregates without the release of insulin into solution. The addition of ATP significantly increased the toxicity of the insulin fibril-chaperonin reaction products toward mammalian cells.
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Affiliation(s)
- Dmitry Kurouski
- Department of Chemistry, University
at Albany, State University of New York, Albany, New York 12222, United States
| | - Haibin Luo
- Department of Microbiology and
Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, Maryland 21201, United States
| | - Valentin Sereda
- Department of Chemistry, University
at Albany, State University of New York, Albany, New York 12222, United States
| | - Frank T. Robb
- Department of Microbiology and
Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, Maryland 21201, United States
| | - Igor K. Lednev
- Department of Chemistry, University
at Albany, State University of New York, Albany, New York 12222, United States
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37
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Li Y, Yan J, Zhang X, Huang K. Disulfide bonds in amyloidogenesis diseases related proteins. Proteins 2013; 81:1862-73. [DOI: 10.1002/prot.24338] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/16/2013] [Accepted: 05/23/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Yang Li
- Tongji School of Pharmacy; Huazhong University of Science and Technology; Wuhan Hubei People's Republic of China 430030
| | - Juan Yan
- Tongji School of Pharmacy; Huazhong University of Science and Technology; Wuhan Hubei People's Republic of China 430030
| | - Xin Zhang
- Tongji School of Pharmacy; Huazhong University of Science and Technology; Wuhan Hubei People's Republic of China 430030
| | - Kun Huang
- Tongji School of Pharmacy; Huazhong University of Science and Technology; Wuhan Hubei People's Republic of China 430030
- Centre for Biomedicine Research; Wuhan Institute of Biotechnology; Wuhan Hubei People's Republic of China 430074
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38
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Disulfide bonding in neurodegenerative misfolding diseases. Int J Cell Biol 2013; 2013:318319. [PMID: 23983694 PMCID: PMC3747422 DOI: 10.1155/2013/318319] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/16/2013] [Indexed: 01/27/2023] Open
Abstract
In recent years an increasing number of neurodegenerative diseases has been linked to the misfolding of a specific protein and its subsequent accumulation into aggregated species, often toxic to the cell. Of all the factors that affect the behavior of these proteins, disulfide bonds are likely to be important, being very conserved in protein sequences and being the enzymes devoted to their formation among the most conserved machineries in mammals. Their crucial role in the folding and in the function of a big fraction of the human proteome is well established. The role of disulfide bonding in preventing and managing protein misfolding and aggregation is currently under investigation. New insights into their involvement in neurodegenerative diseases, their effect on the process of protein misfolding and aggregation, and into the role of the cellular machineries devoted to disulfide bond formation in neurodegenerative diseases are emerging. These studies mark a step forward in the comprehension of the biological base of neurodegenerative disorders and highlight the numerous questions that still remain open.
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39
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Neue Mitglieder der National Academy of Sciences Wolfson-Forschungspreise der Royal Society. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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New Members of the National Academy of Sciences Royal Society Wolfson Research Merit Awards. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201303907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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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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42
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Ahn M, De Genst E, Kaminski Schierle GS, Erdelyi M, Kaminski CF, Dobson CM, Kumita JR. Analysis of the native structure, stability and aggregation of biotinylated human lysozyme. PLoS One 2012; 7:e50192. [PMID: 23166837 PMCID: PMC3500338 DOI: 10.1371/journal.pone.0050192] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/22/2012] [Indexed: 11/29/2022] Open
Abstract
Fibril formation by mutational variants of human lysozyme is associated with a fatal form of hereditary non-neuropathic systemic amyloidosis. Defining the mechanistic details of lysozyme aggregation is of crucial importance for understanding the origin and progression of this disease and related misfolding conditions. In this study, we show that a biotin moiety can be introduced site-specifically at Lys33 of human lysozyme. We demonstrate, using biophysical techniques, that the structure and stability of the native-state of the protein are not detectably altered by this modification, and that the ability to form amyloid fibrils is unchanged. By taking advantage of biotin-avidin interactions, we show that super-resolution fluorescence microscopy can generate detailed images of the mature fibrils. This methodology can readily enable the introduction of additional probes into the protein, thereby providing the means through which to understand, in detail, the nature of the aggregation process of lysozyme and its variants under a variety of conditions.
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Affiliation(s)
- Minkoo Ahn
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Miklos Erdelyi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
- National Physics Laboratory, Teddington, United Kingdom
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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43
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Feng S, Song XH, Zeng CM. Inhibition of amyloid fibrillation of lysozyme by phenolic compounds involves quinoprotein formation. FEBS Lett 2012; 586:3951-5. [DOI: 10.1016/j.febslet.2012.09.037] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 09/08/2012] [Accepted: 09/24/2012] [Indexed: 12/26/2022]
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Disulfide bridges remain intact while native insulin converts into amyloid fibrils. PLoS One 2012; 7:e36989. [PMID: 22675475 PMCID: PMC3365881 DOI: 10.1371/journal.pone.0036989] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 04/11/2012] [Indexed: 11/19/2022] Open
Abstract
Amyloid fibrils are β-sheet-rich protein aggregates commonly found in the organs and tissues of patients with various amyloid-associated diseases. Understanding the structural organization of amyloid fibrils can be beneficial for the search of drugs to successfully treat diseases associated with protein misfolding. The structure of insulin fibrils was characterized by deep ultraviolet resonance Raman (DUVRR) and Nuclear Magnetic Resonance (NMR) spectroscopy combined with hydrogen-deuterium exchange. The compositions of the fibril core and unordered parts were determined at single amino acid residue resolution. All three disulfide bonds of native insulin remained intact during the aggregation process, withstanding scrambling. Three out of four tyrosine residues were packed into the fibril core, and another aromatic amino acid, phenylalanine, was located in the unordered parts of insulin fibrils. In addition, using all-atom MD simulations, the disulfide bonds were confirmed to remain intact in the insulin dimer, which mimics the fibrillar form of insulin.
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45
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Silvers R, Sziegat F, Tachibana H, Segawa SI, Whittaker S, Günther UL, Gabel F, Huang JR, Blackledge M, Wirmer-Bartoschek J, Schwalbe H. Modulation of structure and dynamics by disulfide bond formation in unfolded states. J Am Chem Soc 2012; 134:6846-54. [PMID: 22414027 DOI: 10.1021/ja3009506] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During oxidative folding, the formation of disulfide bonds has profound effects on guiding the protein folding pathway. Until now, comparatively little is known about the changes in the conformational dynamics in folding intermediates of proteins that contain only a subset of their native disulfide bonds. In this comprehensive study, we probe the conformational landscape of non-native states of lysozyme containing a single native disulfide bond utilizing nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), circular dichroism (CD) data, and modeling approaches. The impact on conformational dynamics varies widely depending on the loop size of the single disulfide variants and deviates significantly from random coil predictions for both NMR and SAXS data. From these experiments, we conclude that the introduction of single disulfides spanning a large portion of the polypeptide chain shifts the structure and dynamics of hydrophobic core residues of the protein so that these regions exhibit levels of order comparable to the native state on the nanosecond time scale.
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Affiliation(s)
- Robert Silvers
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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46
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Graña-Montes R, de Groot NS, Castillo V, Sancho J, Velazquez-Campoy A, Ventura S. Contribution of disulfide bonds to stability, folding, and amyloid fibril formation: the PI3-SH3 domain case. Antioxid Redox Signal 2012; 16:1-15. [PMID: 21797671 DOI: 10.1089/ars.2011.3936] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIMS The failure of proteins to fold or to remain folded very often leads to their deposition into amyloid fibrils and is the origin of a variety of human diseases. Accordingly, mutations that destabilize the native conformation are associated with pathological phenotypes in several protein models. Protein backbone cyclization by disulfide bond crosslinking strongly reduces the entropy of the unfolded state and, usually, increases protein stability. The effect of protein cyclization on the thermodynamic and kinetics of folding has been extensively studied, but little is know on its effect on aggregation reactions. RESULTS The SRC homology 3 domain (SH3) of p85α subunit of bovine phosphatidyl-inositol-3'-kinase (PI3-SH3) domain is a small globular protein, whose folding and amyloid properties are well characterized. Here we describe the effect of polypeptide backbone cyclization on both processes. INNOVATION We show that a cyclized PI3-SH3 variant is more stable, folds faster, aggregates slower, and forms conformationally and functionally different amyloid fibrils than the wild-type domain. CONCLUSION Disulfide bridges may act as key molecular determinants of both productive protein folding and deleterious aggregation reactions.
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Affiliation(s)
- Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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