1
|
Yagi-Utsumi M, Kato K. Conformational Variability of Amyloid-β and the Morphological Diversity of Its Aggregates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154787. [PMID: 35897966 PMCID: PMC9369837 DOI: 10.3390/molecules27154787] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022]
Abstract
Protein folding is the most fundamental and universal example of biomolecular self-organization and is characterized as an intramolecular process. In contrast, amyloidogenic proteins can interact with one another, leading to protein aggregation. The energy landscape of amyloid fibril formation is characterized by many minima for different competing low-energy structures and, therefore, is much more enigmatic than that of multiple folding pathways. Thus, to understand the entire energy landscape of protein aggregation, it is important to elucidate the full picture of conformational changes and polymorphisms of amyloidogenic proteins. This review provides an overview of the conformational diversity of amyloid-β (Aβ) characterized from experimental and theoretical approaches. Aβ exhibits a high degree of conformational variability upon transiently interacting with various binding molecules in an unstructured conformation in a solution, forming an α-helical intermediate conformation on the membrane and undergoing a structural transition to the β-conformation of amyloid fibrils. This review also outlines the structural polymorphism of Aβ amyloid fibrils depending on environmental factors. A comprehensive understanding of the energy landscape of amyloid formation considering various environmental factors will promote drug discovery and therapeutic strategies by controlling the fibril formation pathway and targeting the consequent morphology of aggregated structures.
Collapse
Affiliation(s)
- Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Correspondence: (M.Y.-U.); (K.K.)
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Correspondence: (M.Y.-U.); (K.K.)
| |
Collapse
|
2
|
Wang M, Liu Y, Liu Y, Xia Z. MOFs and PDA-supported immobilization of BSA in open tubular affinity capillary electrochromatography: Prediction and study on drug-protein interactions. Talanta 2022; 237:122959. [PMID: 34736684 DOI: 10.1016/j.talanta.2021.122959] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022]
Abstract
Owing to the satisfactory properties such as high specific surface area, finely tunable chemical composition, large yet adjustable pore sizes, and diverse architecture, metal-organic frameworks (MOFs) have the potential to be used as a stable, efficient, reusable and protective biomacromolecule immobilization carrier in capillary electrophoresis. Herein, a novel immobilized receptor open-tubular affinity capillary electrochromatography (OT-ACEC) strategy was developed for the first time to rapidly investigate the interactions between a set of drugs and bovine serum albumin (BSA). To further increase the amount of immobilized BSA and maintain the bioactivity of BSA, BSA was immobilized on the inner capillary surface by using polydopamine (PDA) as the adhesion layer and surface functionalization agent, a MOF namely dresden university of technology-5 (DUT-5) as supporting platform and biomacromolecule immobilization carrier, respectively. The amount of immobilized BSA on the capillary surface of the BSA@capillary and the PDA/MOFs/BSA@capillary column are separately calculated as 0.00756 nmol and 0.01812 nmol. Besides, the PDA/MOFs/BSA@capillary column was applied to investigate the interactions between BSA and flavonoids, fluoroquinolones. Under the optimal interaction conditions, three flavonoids and three fluoroquinolones are able to achieve baseline separation in the PDA/MOFs/BSA@capillary column (with resolution values of three flavonoids, 5.78 and 4.13; three fluoroquinolones, 1.72 and 1.68). The PDA/MOFs/BSA@capillary column shows good stability and reproducibility over 100 runs (relative standard deviation (RSD)<5%). In addition, the normalized capacity factor (KRCE) in this method replaced the binding constant and was used as an evaluation index to fast predict the activities of 20 drugs, some of which have not yet been reported for their interactions with BSA. Spectroscopy and molecular docking further illuminated the binding mechanism.
Collapse
Affiliation(s)
- Min Wang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Yi Liu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China; Chongqing Chemical Industry Vocational College, Chongqing, 401228, China
| | - Yao Liu
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhining Xia
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
3
|
Effendi SSW, Tan SI, Ting WW, Ng IS. Genetic design of co-expressed Mesorhizobium loti carbonic anhydrase and chaperone GroELS to enhancing carbon dioxide sequestration. Int J Biol Macromol 2020; 167:326-334. [PMID: 33275972 DOI: 10.1016/j.ijbiomac.2020.11.189] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/20/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022]
Abstract
Mesorhizobium loti carbonic anhydrase (MlCA), an intrinsically high catalytic enzyme, has been employed for carbon dioxide capture and sequestration. However, recombinant expression of MlCA in Escherichia coli often forms inclusion bodies. Hence, protein partners such as fusion-tags and molecular chaperones are involved in regarding reduce the harshness of protein folding. TrxA-tag and GroELS have been chosen to co-express with MlCA in E. coli under an inducible T7 promoter or a constitutive J23100 promoter to compare productivity and activity. The results possessed that coupling protein partners effectively increased soluble MlCA up to 2.9-folds under T7 promoter, thus enhancing the CA activity by 120% and achieving a 5.2-folds turnover rate. Besides, it has also shifted the optimum temperature from 40 °C to 50 °C, promoted stability in the broad pH range (4.5 to 9.5) and the presence of various metal ions. Based on the in vitro assay and isothermal titration calorimetry (ITC) analysis, GroELS enhancing CA activity was due to change the intrinsic thermodynamic properties of the enzyme from endothermic to exothermic reaction (i.e., ∆H = 89.8 to -121.8 kJ/mol). Therefore, the collaboration of TrxA-MlCA with GroELS successfully augmented CO2 biomineralization.
Collapse
Affiliation(s)
- Sefli Sri Wahyu Effendi
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC.
| |
Collapse
|
4
|
Hu Y, Li C, He L, Jin C, Liu M. Mechanisms of Chaperones as Active Assistant/Protector for Proteins: Insights from NMR Studies. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.201900441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, Peking University Beijing 100871 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| |
Collapse
|
5
|
Yagi-Utsumi M. NMR Characterization of Conformational Dynamics and Molecular Assemblies of Proteins. Biol Pharm Bull 2019; 42:867-872. [PMID: 31155585 DOI: 10.1248/bpb.b19-00115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dynamic conformational transitions and molecular assemblies are essential properties of proteins, and relevant to their biological and pathological functions. Neurodegenerative diseases are known to be caused by abnormal, toxic assemblies of related proteins, e.g., amyloid β (Aβ) in Alzheimer's disease. Growing evidence indicates that the aggregation of various amyloidogenic proteins, including Aβ, can be highly enhanced at glycolipid membranes, suggesting that dynamic glycolipid-dependent conformational changes of proteins constitute crucial steps for their subsequent pathogenic amyloid fibril formation. It has also been proposed that several proteins, including molecular chaperones, can capture amyloidogenic proteins and thereby suppress their fibrillization. NMR spectroscopy provides a powerful tool for characterizing the conformational dynamics and intermolecular interactions of proteins, as well as for exploring transiently formed weak interactions among proteins in solution with various biomolecules, such as glycolipids. Our research group therefore attempted to elucidate the structural basis of protein-glycolipid and protein-protein interactions that either promote or suppress molecular assemblies of amyloidogenic proteins, using both solution and solid-state NMR methods in conjunction with other biophysical techniques. Our findings provide structural views of molecular processes involving amyloidogenic proteins of clinical and pathological interest and offer clues for the development of drugs to prevent and treat neurodegenerative diseases.
Collapse
Affiliation(s)
- Maho Yagi-Utsumi
- Institute for Molecular Science, National Institutes of National Sciences.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of National Sciences.,Graduate School of Pharmaceutical Sciences, Nagoya City University
| |
Collapse
|
6
|
Horvath I, Blockhuys S, Šulskis D, Holgersson S, Kumar R, Burmann BM, Wittung-Stafshede P. Interaction between Copper Chaperone Atox1 and Parkinson's Disease Protein α-Synuclein Includes Metal-Binding Sites and Occurs in Living Cells. ACS Chem Neurosci 2019; 10:4659-4668. [PMID: 31600047 DOI: 10.1021/acschemneuro.9b00476] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Alterations in copper ion homeostasis appear coupled to neurodegenerative disorders, but mechanisms are unknown. The cytoplasmic copper chaperone Atox1 was recently found to inhibit amyloid formation in vitro of α-synuclein, the amyloidogenic protein in Parkinson's disease. As α-synuclein may have copper-dependent functions, and free copper ions promote α-synuclein amyloid formation, it is important to characterize the Atox1 interaction with α-synuclein on a molecular level. Here we applied solution-state nuclear magnetic resonance spectroscopy, with isotopically labeled α-synuclein and Atox1, to define interaction regions in both proteins. The α-synuclein interaction interface includes the whole N-terminal part up to Gln24; in Atox1, residues around the copper-binding cysteines (positions 11-16) are mostly perturbed, but additional effects are also found for residues elsewhere in both proteins. Because α-synuclein is N-terminally acetylated in vivo, we established that Atox1 also inhibits amyloid formation of this variant in vitro, and proximity ligation in human cell lines demonstrated α-synuclein-Atox1 interactions in situ. Thus, this interaction may provide the direct link between copper homeostasis and amyloid formation in vivo.
Collapse
Affiliation(s)
- Istvan Horvath
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Stéphanie Blockhuys
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Darius Šulskis
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 405 30, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Stellan Holgersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Ranjeet Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 405 30, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| |
Collapse
|
7
|
Hiller S, Burmann BM. Chaperone-client complexes: A dynamic liaison. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 289:142-155. [PMID: 29544626 DOI: 10.1016/j.jmr.2017.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 06/08/2023]
Abstract
Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.
Collapse
Affiliation(s)
- Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University for Gothenburg, 405 30 Göteborg, Sweden.
| |
Collapse
|
8
|
Fukui N, Araki K, Hongo K, Mizobata T, Kawata Y. Modulating the Effects of the Bacterial Chaperonin GroEL on Fibrillogenic Polypeptides through Modification of Domain Hinge Architecture. J Biol Chem 2016; 291:25217-25226. [PMID: 27742838 DOI: 10.1074/jbc.m116.751925] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/05/2016] [Indexed: 11/06/2022] Open
Abstract
The isolated apical domain of the Escherichia coli GroEL subunit displays the ability to suppress the irreversible fibrillation of numerous amyloid-forming polypeptides. In previous experiments, we have shown that mutating Gly-192 (located at hinge II that connects the apical domain and the intermediate domain) to a tryptophan results in an inactive chaperonin whose apical domain is disoriented. In this study, we have utilized this disruptive effect of Gly-192 mutation to our advantage, by substituting this residue with amino acid residues of varying van der Waals volumes with the intent to modulate the affinity of GroEL toward fibrillogenic peptides. The affinities of GroEL toward fibrillogenic polypeptides such as Aβ(1-40) (amyloid-β(1-40)) peptide and α-synuclein increased in accordance to the larger van der Waals volume of the substituent amino acid side chain in the G192X mutants. When we compared the effects of wild-type GroEL and selected GroEL G192X mutants on α-synuclein fibril formation, we found that the effects of the chaperonin on α-synuclein fibrillation were different; the wild-type chaperonin caused changes in both the initial lag phase and the rate of fibril extension, whereas the effects of the G192X mutants were more specific toward the nucleus-forming lag phase. The chaperonins also displayed differential effects on α-synuclein fibril morphology, suggesting that through mutation of Gly-192, we may induce changes to the intermolecular affinities between GroEL and α-synuclein, leading to more efficient fibril suppression, and in specific cases, modulation of fibril morphology.
Collapse
Affiliation(s)
- Naoya Fukui
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, and
| | - Kiho Araki
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, and
| | - Kunihiro Hongo
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, and.,the Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori 680-8552, Japan
| | - Tomohiro Mizobata
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, and.,the Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori 680-8552, Japan
| | - Yasushi Kawata
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, and .,the Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori 680-8552, Japan
| |
Collapse
|
9
|
Ojha B, Fukui N, Hongo K, Mizobata T, Kawata Y. Suppression of amyloid fibrils using the GroEL apical domain. Sci Rep 2016; 6:31041. [PMID: 27488469 PMCID: PMC4973282 DOI: 10.1038/srep31041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/12/2016] [Indexed: 01/09/2023] Open
Abstract
In E. coli cells, rescue of non-native proteins and promotion of native state structure is assisted by the chaperonin GroEL. An important key to this activity lies in the structure of the apical domain of GroEL (GroEL-AD) (residue 191–376), which recognizes and binds non-native protein molecules through hydrophobic interactions. In this study, we investigated the effects of GroEL-AD on the aggregation of various client proteins (α-Synuclein, Aβ42, and GroES) that lead to the formation of distinct protein fibrils in vitro. We found that GroEL-AD effectively inhibited the fibril formation of these three proteins when added at concentrations above a critical threshold; the specific ratio differed for each client protein, reflecting the relative affinities. The effect of GroEL-AD in all three cases was to decrease the concentration of aggregate-forming unfolded client protein or its early intermediates in solution, thereby preventing aggregation and fibrillation. Binding affinity assays revealed some differences in the binding mechanisms of GroEL-AD toward each client. Our findings suggest a possible applicability of this minimal functioning derivative of the chaperonins (the “minichaperones”) as protein fibrillation modulators and detectors.
Collapse
Affiliation(s)
- Bimlesh Ojha
- Department of Chemistry and Biotechnology, Graduate School of Engineering Tottori University, Tottori 680-8552, Japan
| | - Naoya Fukui
- Department of Chemistry and Biotechnology, Graduate School of Engineering Tottori University, Tottori 680-8552, Japan
| | - Kunihiro Hongo
- Department of Chemistry and Biotechnology, Graduate School of Engineering Tottori University, Tottori 680-8552, Japan.,Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori 680-8552, Japan
| | - Tomohiro Mizobata
- Department of Chemistry and Biotechnology, Graduate School of Engineering Tottori University, Tottori 680-8552, Japan.,Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori 680-8552, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering Tottori University, Tottori 680-8552, Japan.,Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori 680-8552, Japan
| |
Collapse
|
10
|
Mangione MR, Vilasi S, Marino C, Librizzi F, Canale C, Spigolon D, Bucchieri F, Fucarino A, Passantino R, Cappello F, Bulone D, San Biagio PL. Hsp60, amateur chaperone in amyloid-beta fibrillogenesis. Biochim Biophys Acta Gen Subj 2016; 1860:2474-2483. [PMID: 27474204 DOI: 10.1016/j.bbagen.2016.07.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/14/2016] [Accepted: 07/24/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Molecular chaperones are a very special class of proteins that play essential roles in many cellular processes like folding, targeting and transport of proteins. Moreover, recent evidence indicates that chaperones can act as potentially strong suppressor agents in Alzheimer's disease (AD). Indeed, in vitro experiments demonstrate that several chaperones are able to significantly slow down or suppress aggregation of Aβ peptide and in vivo studies reveal that treatment with specific chaperones or their overexpression can ameliorate some distinct pathological signs characterizing AD. METHODS Here we investigate using a biophysical approach (fluorescence, circular dichroism (CD), transmission electron (TEM) and atomic force (AFM) microscopy, size exclusion chromatography (SEC)) the effect of the human chaperonin Hsp60 on Aβ fibrillogenesis. RESULTS We found that Hsp60 powerfully inhibits Aβ amyloid aggregation, by closing molecular pathways leading to peptide fibrillogenesis. CONCLUSIONS We observe that Hsp60 inhibits Aβ aggregation through a more complex mechanism than a simple folding chaperone action. The action is specifically directed toward the early oligomeric species behaving as aggregation seeds for on-pathway amyloid fibrillogenesis. GENERAL SIGNIFICANCE Understanding the specificity of the molecular interactions of Hsp60 with amyloid Aβ peptide allowed us to emphasize the important aspects to be taken into consideration when considering the recent promising therapeutic strategies for neurodegeneration.
Collapse
Affiliation(s)
| | - Silvia Vilasi
- Institute of Biophysics, National Research Council, Palermo, Italy.
| | - Claudia Marino
- Institute of Biophysics, National Research Council, Palermo, Italy; Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA; Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Italy
| | - Fabio Librizzi
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Claudio Canale
- Nanophysics Department, Istituto Italiano di Tecnologia, Italy
| | - Dario Spigolon
- Institute of Biophysics, National Research Council, Palermo, Italy; Department of Physics and Chemistry, University of Palermo, Palermo, Italy
| | - Fabio Bucchieri
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Italy; Institute of Biomedicine and Molecular Immunology, National Research Council, Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
| | - Alberto Fucarino
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
| | - Rosa Passantino
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Francesco Cappello
- Institute of Biophysics, National Research Council, Palermo, Italy; Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
| | - Donatella Bulone
- Institute of Biophysics, National Research Council, Palermo, Italy
| | | |
Collapse
|
11
|
Liu C, Zhang X, Jing H, Miao Y, Zhao L, Han Y, Cui C. Research on drug-receptor interactions and prediction of drug activity via oriented immobilized receptor capillary electrophoresis. Electrophoresis 2016; 36:2433-41. [PMID: 26105113 DOI: 10.1002/elps.201400583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 05/22/2015] [Accepted: 06/01/2015] [Indexed: 02/06/2023]
Abstract
Oriented covalent immobilized β2 -adrenergic receptor (β2 -AR) CE (OIRCE) was developed to determine the interactions between a set of natural extracts of Radix Paeoniae Rubra (NERPR) and β2 -AR, and to predict the activity of NERPR. The inner capillary surface is chemically bonded with stable β2 -AR coating via microwave-assisted technical synthesis. The modified capillaries were characterized via infrared spectroscopy and fluorescence microscopy. Furthermore, the bonding amounts of β2 -AR were first obtained via fluorescence spectroscopy method. In determining the amount of bonded β2 -AR, the regression equation A = 576 707C + 35.449 and the correlation coefficient 0.9995 were obtained. This result revealed an excellent linear relationship in the range of 2 × 10(-4) mg/mL to 1 × 10(-3) mg/mL. The normalized capacity factor (KRCE ) was obtained using OIRCE in evaluating drug-receptor interactions. Related theories and equations were used to calculate KRCE values from apparent migration times of a solute and EOF. The order of KRCE and the binding constant (Kb ) values between drugs and β2 -AR was well consistent. The results confirmed that the OIRCE and KRCE values can be effectually used to investigate drug-receptor interactions, and OIRCE has the potential to predict drug activity and to select leading compounds from natural chemicals.
Collapse
Affiliation(s)
- Chunye Liu
- School of Pharmacy, Xi'an Medical University, Xi'an, P. R. China
| | - Xuejiao Zhang
- School of Pharmacy, Xi'an Medical University, Xi'an, P. R. China
| | - Hui Jing
- School of Pharmacy, Xi'an Medical University, Xi'an, P. R. China
| | - Yanqing Miao
- School of Pharmacy, Xi'an Medical University, Xi'an, P. R. China
| | - Lingzhi Zhao
- School of Pharmacy, Xi'an Medical University, Xi'an, P. R. China
| | - Yan Han
- School of Pharmacy, Xi'an Medical University, Xi'an, P. R. China
| | - Cuixia Cui
- School of Pharmacy, Xi'an Medical University, Xi'an, P. R. China
| |
Collapse
|
12
|
Yagi-Utsumi M, Satoh T, Kato K. Structural basis of redox-dependent substrate binding of protein disulfide isomerase. Sci Rep 2015; 5:13909. [PMID: 26350503 PMCID: PMC4563560 DOI: 10.1038/srep13909] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/13/2015] [Indexed: 01/09/2023] Open
Abstract
Protein disulfide isomerase (PDI) is a multidomain enzyme, operating as an essential folding catalyst, in which the b′ and a′ domains provide substrate binding sites and undergo an open–closed domain rearrangement depending on the redox states of the a′ domain. Despite the long research history of this enzyme, three-dimensional structural data remain unavailable for its ligand-binding mode. Here we characterize PDI substrate recognition using α-synuclein (αSN) as the model ligand. Our nuclear magnetic resonance (NMR) data revealed that the substrate-binding domains of PDI captured the αSN segment Val37–Val40 only in the oxidized form. Furthermore, we determined the crystal structure of an oxidized form of the b′–a′ domains in complex with an undecapeptide corresponding to this segment. The peptide-binding mode observed in the crystal structure with NMR validation, was characterized by hydrophobic interactions on the b′ domain in an open conformation. Comparison with the previously reported crystal structure indicates that the a′ domain partially masks the binding surface of the b′ domain, causing steric hindrance against the peptide in the reduced form of the b′–a′ domains that exhibits a closed conformation. These findings provide a structural basis for the mechanism underlying the redox-dependent substrate binding of PDI.
Collapse
Affiliation(s)
- Maho Yagi-Utsumi
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| |
Collapse
|
13
|
Zhang D, Xu J, He W, Tong Q, Chen L, Zhou J, Su X. Characterization of Enterobacter cloacae under phoxim stress by two-dimensional gel electrophoresis. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0771-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
14
|
Burmann BM, Hiller S. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:41-64. [PMID: 25919198 DOI: 10.1016/j.pnmrs.2015.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 05/20/2023]
Abstract
The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.
Collapse
Affiliation(s)
- Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
| |
Collapse
|
15
|
Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 326] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| |
Collapse
|
16
|
Reddy KD, DeForte S, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (July-August-September, 2013). INTRINSICALLY DISORDERED PROTEINS 2014; 2:e27833. [PMID: 28232877 PMCID: PMC5314876 DOI: 10.4161/idp.27833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 12/26/2022]
Abstract
The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a new issue of reader's digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
Collapse
Affiliation(s)
- Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah, Saudi Arabia; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| |
Collapse
|