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Xing Y, Andrikopoulos N, Zhang Z, Sun Y, Ke PC, Ding F. Modulating Nanodroplet Formation En Route to Fibrillization of Amyloid Peptides with Designed Flanking Sequences. Biomacromolecules 2022; 23:4179-4191. [PMID: 36137260 PMCID: PMC9618360 DOI: 10.1021/acs.biomac.2c00642] [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] [Indexed: 11/28/2022]
Abstract
Soluble oligomers populating early amyloid aggregation can be regarded as nanodroplets of liquid-liquid phase separation (LLPS). Amyloid peptides typically contain hydrophobic aggregation-prone regions connected by hydrophilic linkers and flanking sequences, and such a sequence hydropathy pattern drives the formation of supramolecular structures in the nanodroplets and modulates subsequent fibrillization. Here, we studied LLPS and fibrillization of coarse-grained amyloid peptides with increasing flanking sequences. Nanodroplets assumed lamellar, cylindrical micellar, and spherical micellar structures with increasing peptide hydrophilic/hydrophobic ratios, and such morphologies governed subsequent fibrillization processes. Adding glycine-serine repeats as flanking sequences to Aβ16-22, the amyloidogenic core of amyloid-β, our computational predictions of morphological transitions were corroborated experimentally. The uncovered inter-relationships between the peptide sequence pattern, oligomer/nanodroplet morphology, and fibrillization pathway, kinetics, and structure may contribute to our understanding of pathogenic amyloidosis in aging, facilitate future efforts ameliorating amyloidosis through peptide engineering, and aid in the design of novel amyloid-based functional nanobiomaterials and nanocomposites.
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Affiliation(s)
- Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Nicholas Andrikopoulos
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Pu Chun Ke
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Nanomedicine Center, The GBA National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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2
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Naranda J, Bračič M, Vogrin M, Maver U, Trojner T. Practical Use of Quartz Crystal Microbalance Monitoring in Cartilage Tissue Engineering. J Funct Biomater 2022; 13:jfb13040159. [PMID: 36278628 PMCID: PMC9590066 DOI: 10.3390/jfb13040159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 11/29/2022] Open
Abstract
Quartz crystal microbalance (QCM) is a real-time, nanogram-accurate technique for analyzing various processes on biomaterial surfaces. QCM has proven to be an excellent tool in tissue engineering as it can monitor key parameters in developing cellular scaffolds. This review focuses on the use of QCM in the tissue engineering of cartilage. It begins with a brief discussion of biomaterials and the current state of the art in scaffold development for cartilage tissue engineering, followed by a summary of the potential uses of QCM in cartilage tissue engineering. This includes monitoring interactions with extracellular matrix components, adsorption of proteins onto biomaterials, and biomaterial–cell interactions. In the last part of the review, the material selection problem in tissue engineering is highlighted, emphasizing the importance of surface nanotopography, the role of nanofilms, and utilization of QCM as a “screening” tool to improve the material selection process. A step-by-step process for scaffold design is proposed, as well as the fabrication of thin nanofilms in a layer-by-layer manner using QCM. Finally, future trends of QCM application as a “screening” method for 3D printing of cellular scaffolds are envisioned.
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Affiliation(s)
- Jakob Naranda
- Department of Orthopaedics, University Medical Centre Maribor, SI-2000 Maribor, Slovenia
- Department of Orthopaedics, Faculty of Medicine, University of Maribor, SI-2000 Maribor, Slovenia
- Correspondence: (J.N.); (M.B.); Tel.: +386-2-321-1541 (J.N.); +386-2-220-7929 (M.B.)
| | - Matej Bračič
- Laboratory for Characterisation and Processing of Polymers (LCPP), Faculty of Mechanical Engineering, University of Maribor, SI-2000 Maribor, Slovenia
- Correspondence: (J.N.); (M.B.); Tel.: +386-2-321-1541 (J.N.); +386-2-220-7929 (M.B.)
| | - Matjaž Vogrin
- Department of Orthopaedics, University Medical Centre Maribor, SI-2000 Maribor, Slovenia
- Department of Orthopaedics, Faculty of Medicine, University of Maribor, SI-2000 Maribor, Slovenia
| | - Uroš Maver
- Institute of Biomedical Sciences, Faculty of Medicine, University of Maribor, SI-2000 Maribor, Slovenia
- Department of Pharmacology, Faculty of Medicine, University of Maribor, SI-2000 Maribor, Slovenia
| | - Teodor Trojner
- Department of Orthopaedics, University Medical Centre Maribor, SI-2000 Maribor, Slovenia
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3
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Direct observation of heterogeneous formation of amyloid spherulites in real-time by super-resolution microscopy. Commun Biol 2022; 5:850. [PMID: 35987792 PMCID: PMC9392779 DOI: 10.1038/s42003-022-03810-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Protein misfolding in the form of fibrils or spherulites is involved in a spectrum of pathological abnormalities. Our current understanding of protein aggregation mechanisms has primarily relied on the use of spectrometric methods to determine the average growth rates and diffraction-limited microscopes with low temporal resolution to observe the large-scale morphologies of intermediates. We developed a REal-time kinetics via binding and Photobleaching LOcalization Microscopy (REPLOM) super-resolution method to directly observe and quantify the existence and abundance of diverse aggregate morphologies of human insulin, below the diffraction limit and extract their heterogeneous growth kinetics. Our results revealed that even the growth of microscopically identical aggregates, e.g., amyloid spherulites, may follow distinct pathways. Specifically, spherulites do not exclusively grow isotropically but, surprisingly, may also grow anisotropically, following similar pathways as reported for minerals and polymers. Combining our technique with machine learning approaches, we associated growth rates to specific morphological transitions and provided energy barriers and the energy landscape at the level of single aggregate morphology. Our unifying framework for the detection and analysis of spherulite growth can be extended to other self-assembled systems characterized by a high degree of heterogeneity, disentangling the broad spectrum of diverse morphologies at the single-molecule level. Real-time super-resolution microscopy analysis reveals the growth kinetics, morphology, and abundance of human insulin amyloid spherulites with different growth pathways.
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Noi K, Ikenaka K, Mochizuki H, Goto Y, Ogi H. Disaggregation Behavior of Amyloid β Fibrils by Anthocyanins Studied by Total-Internal-Reflection-Fluorescence Microscopy Coupled with a Wireless Quartz-Crystal Microbalance Biosensor. Anal Chem 2021; 93:11176-11183. [PMID: 34351734 DOI: 10.1021/acs.analchem.1c01720] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid fibrils are formed from various proteins, some of which cause the corresponding neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. It has been reported that many compounds inhibit the formation of amyloid fibrils. Anthocyanins are flavonoid pigments present in fruits and vegetables, which are known to suppress symptoms related with Alzheimer's disease. However, the influence of anthocyanins on the amyloid fibril remains unclear. Here, we succeeded in the direct monitoring of the disaggregation reaction of single amyloid β (Aβ) fibrils by anthocyanins using total-internal-reflection-fluorescence microscopy with a quartz-crystal microbalance (TIRFM-QCM). It is found that the disassembly activity to the Aβ fibrils depends on the number of hydroxyl groups in six-membered ring B of anthocyanin, and only delphinidin-3-galactoside, possessing three hydroxyl groups there, shows high disassembly activity. Our results show the importance of the number of hydroxyl groups and demonstrate the usefulness of TIRFM-QCM as a powerful tool in studying interactions between amyloid fibrils and compounds.
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Affiliation(s)
- Kentaro Noi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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Mobed A, Hasanzadeh M. Biosensing: The best alternative for conventional methods in detection of Alzheimer's disease biomarkers. Int J Biol Macromol 2020; 161:59-71. [PMID: 32504710 DOI: 10.1016/j.ijbiomac.2020.05.257] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/29/2022]
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Migoń D, Wasilewski T, Suchy D. Application of QCM in Peptide and Protein-Based Drug Product Development. Molecules 2020; 25:E3950. [PMID: 32872496 PMCID: PMC7504752 DOI: 10.3390/molecules25173950] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
AT-cut quartz crystals vibrating in the thickness-shear mode (TSM), especially quartz crystal resonators (QCRs), are well known as very efficient mass sensitive systems because of their sensitivity, accuracy, and biofunctionalization capacity. They are highly reliable in the measurement of the mass of deposited samples, in both gas and liquid matrices. Moreover, they offer real-time monitoring, as well as relatively low production and operation costs. These features make mass sensitive systems applicable in a wide range of different applications, including studies on protein and peptide primary packaging, formulation, and drug product manufacturing process development. This review summarizes the information on some particular implementations of quartz crystal microbalance (QCM) instruments in protein and peptide drug product development as well as their future prospects.
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Affiliation(s)
- Dorian Migoń
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland;
- Polpharma Biologics S.A., Trzy Lipy 3, 80-172 Gdańsk, Poland;
| | - Tomasz Wasilewski
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland;
| | - Dariusz Suchy
- Polpharma Biologics S.A., Trzy Lipy 3, 80-172 Gdańsk, Poland;
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Nakajima K, Yamazaki T, Kimura Y, So M, Goto Y, Ogi H. Time-Resolved Observation of Evolution of Amyloid-β Oligomer with Temporary Salt Crystals. J Phys Chem Lett 2020; 11:6176-6184. [PMID: 32687370 DOI: 10.1021/acs.jpclett.0c01487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aggregation behavior of amyloid-β (Aβ) peptides remains unclarified despite the fact that it is closely related to the pathogenic mechanism of Alzheimer's disease. Aβ peptides form diverse oligomers with various diameters before nucleation, making clarification of the mechanism involved a complex problem with conventional macroscopic analysis methods. Time-resolved single-molecule level analysis in bulk solution is thus required to fully understand their early stage aggregation behavior. Here, we perform time-resolved observation of the aggregation dynamics of Aβ oligomers in bulk solution using liquid-state transmission electron microscopy. Our observations reveal previously unknown behaviors. The most important discovery is that a salt crystal can precipitate even with a concentration much lower than its solubility, and it then dissolves in a short time, during which the aggregation reaction of Aβ peptides is significantly accelerated. These findings will provide new insights in the evolution of the Aβ oligomer.
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Affiliation(s)
- Kichitaro Nakajima
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoya Yamazaki
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Yuki Kimura
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Masatomo So
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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8
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The growth of amyloid fibrils: rates and mechanisms. Biochem J 2019; 476:2677-2703. [DOI: 10.1042/bcj20160868] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022]
Abstract
AbstractAmyloid fibrils are β-sheet-rich linear protein polymers that can be formed by a large variety of different proteins. These assemblies have received much interest in recent decades, due to their role in a range of human disorders. However, amyloid fibrils are also found in a functional context, whereby their structural, mechanical and thermodynamic properties are exploited by biological systems. Amyloid fibrils form through a nucleated polymerisation mechanism with secondary processes acting in many cases to amplify the number of fibrils. The filamentous nature of amyloid fibrils implies that the fibril growth rate is, by several orders of magnitude, the fastest step of the overall aggregation reaction. This article focusses specifically on in vitro experimental studies of the process of amyloid fibril growth, or elongation, and summarises the state of knowledge of its kinetics and mechanisms. This work attempts to provide the most comprehensive summary, to date, of the available experimental data on amyloid fibril elongation rate constants and the temperature and concentration dependence of amyloid fibril elongation rates. These data are compared with those from other types of protein polymers. This comparison with data from other polymerising proteins is interesting and relevant because many of the basic ideas and concepts discussed here were first introduced for non-amyloid protein polymers, most notably by the Japanese school of Oosawa and co-workers for cytoskeletal filaments.
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9
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Xu Y, Safari MS, Ma W, Schafer NP, Wolynes PG, Vekilov PG. Steady, Symmetric, and Reversible Growth and Dissolution of Individual Amyloid-β Fibrils. ACS Chem Neurosci 2019; 10:2967-2976. [PMID: 31099555 DOI: 10.1021/acschemneuro.9b00179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Oligomers and fibrils of the amyloid-β (Aβ) peptide are implicated in the pathology of Alzheimer's disease. Here, we monitor the growth of individual Aβ40 fibrils by time-resolved in situ atomic force microscopy and thereby directly measure fibril growth rates. The measured growth rates in a population of fibrils that includes both single protofilaments and bundles of filaments are independent of the fibril thickness, indicating that cooperation between adjacent protofilaments does not affect incorporation of monomers. The opposite ends of individual fibrils grow at similar rates. In contrast to the "stop-and-go" kinetics that has previously been observed for amyloid-forming peptides, growth and dissolution of the Aβ40 fibrils are relatively steady for peptide concentration of 0-10 μM. The fibrils readily dissolve in quiescent peptide-free solutions at a rate that is consistent with the microscopic reversibility of growth and dissolution. Importantly, the bimolecular rate coefficient for the association of a monomer to the fibril end is significantly smaller than the diffusion limit, implying that the transition state for incorporation of a monomer into a fibril is associated with a relatively high free energy.
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Affiliation(s)
- Yuechuan Xu
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Mohammad S. Safari
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Wenchuan Ma
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Nicholas P. Schafer
- Center for Theoretical Biological Physics, Rice University, P.O. Box 1892, MS 654, Houston, Texas 77251-1892, United States
- Department of Chemistry, Rice University, P.O. Box 1892, MS 60, Houston, Texas 77251-1892, United States
| | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Rice University, P.O. Box 1892, MS 654, Houston, Texas 77251-1892, United States
- Department of Chemistry, Rice University, P.O. Box 1892, MS 60, Houston, Texas 77251-1892, United States
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, Texas 77204-5003, United States
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10
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Hao X, Zheng J, Sun Y, Dong X. Seeding and Cross-Seeding Aggregations of Aβ 40 and Its N-Terminal-Truncated Peptide Aβ 11-40. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2821-2831. [PMID: 30681866 DOI: 10.1021/acs.langmuir.8b03599] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In the amyloid plaques of Alzheimer's disease (AD) patients, a large number of N-terminal-truncated amyloid β (Aβ) peptides such as Aβ11-40 have been identified in addition to the full-length Aβ peptides. However, little is known about the roles of the N-terminal-truncated peptides in AD pathological process. Herein, seeding and cross-seeding aggregations of Aβ40 and its N-terminal-truncated Aβ11-40 were investigated in the solution and on the surfaces of chips with immobilized seeds by extensive biophysical and biological analyses. The results showed that Aβ40 and Aβ11-40 aggregates could seed both homologous and heterologous aggregations of the two monomers. However, the capability and characteristics of the seeding (homologous aggregation) and cross-seeding (heterologous aggregation) were significantly different. Aβ40 seeds showed stronger acceleration effects on the aggregations than Aβ11-40 seeds and induced β-sheet-rich fibrous aggregates of similar cytotoxicities for the two monomers. This indicates that Aβ40 and Aβ11-40 had similar aggregation pathways in the seeding and cross-seeding on Aβ40 seeds. By contrast, Aβ11-40 seeds led to different aggregation pathways of Aβ40 and Aβ11-40. Pure Aβ11-40 aggregates had higher toxicity than Aβ40 aggregates, and as seeds, Aβ11-40 seeds induced Aβ40 to form aggregates of higher cytotoxicity. However, homologous Aβ11-40 aggregates induced by Aβ11-40 seeds showed lower cytotoxicity than pure Aβ11-40 aggregates. The results suggest that Aβ11-40 plays an important role in the pathological process of AD.
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Affiliation(s)
- Xiuping Hao
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering , The University of Akron , Akron , Ohio 44325 , United States
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
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Zheng Y, Xu L, Yang J, Peng X, Wang H, Yu N, Hua Y, Zhao J, He J, Hong T. The effects of fluorescent labels on Aβ42
aggregation detected by fluorescence correlation spectroscopy. Biopolymers 2018; 109:e23237. [DOI: 10.1002/bip.23237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 09/02/2018] [Accepted: 09/13/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Yanpeng Zheng
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Lingwan Xu
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Jingfa Yang
- Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Xianglei Peng
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - He Wang
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Na Yu
- School of Sciences; Beijing Jiaotong University; Beijing China
- Shandong Xinchuang Biological Technology Co., Ltd.; Jinan China
| | - Ying Hua
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Jiang Zhao
- Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Jinsheng He
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Tao Hong
- School of Sciences; Beijing Jiaotong University; Beijing China
- Institute for Viral Disease Control and Prevention; Chinese Centre for Disease Control and Prevention; Beijing China
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Lai YT, Ogi H, Noi K, Kato F. Viscoelasticity Response during Fibrillation of Amyloid β Peptides on a Quartz-Crystal-Microbalance Biosensor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5474-5479. [PMID: 29697982 DOI: 10.1021/acs.langmuir.8b00639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Unlike previous in vitro measurements where Amyloid β (Aβ) aggregation was studied in bulk solutions, we detect the structure change of the Aβ aggregate on the surface of a wireless quartz-crystal-microbalance biosensor, which resembles more closely the aggregation process on the cell membrane. Using a 58 MHz quartz crystal, we monitored changes in the viscoelastic properties of the aggregate formed on the quartz surface from monomers to oligomers and then to fibrils, involving up to the 7th overtone mode (406 MHz). With atomic-force microscopy observations, we found a significant stiffness increase as well as thinning of the protein layer during the structure change from oligomer to fibrils at 20 h, which indicates that the stiffness of the fibril is much higher. Viscoelasticity can provide a significant index of fibrillation and can be useful for evaluating inhibitory medicines in drug development.
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Affiliation(s)
- Yen-Ting Lai
- Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Kentaro Noi
- Graduate School of Engineering , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Fumihito Kato
- Department of Mechanical Engineering , Nippon Institute of Technology , 4-1 Gakuendai , Minamisaitama-gun, Saitama 345-8501 , Japan
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13
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Kamgar-Parsi K, Hong L, Naito A, Brooks CL, Ramamoorthy A. Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time. J Biol Chem 2017; 292:14963-14976. [PMID: 28739873 PMCID: PMC5592673 DOI: 10.1074/jbc.m117.791236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/19/2017] [Indexed: 11/06/2022] Open
Abstract
The role of the peptide hormone calcitonin in skeletal protection has led to its use as a therapeutic for osteoporosis. However, calcitonin aggregation into amyloid fibrils limits its therapeutic efficacy, necessitating a modification of calcitonin's aggregation kinetics. Here, we report a direct relationship between human calcitonin (hCT) concentration and aggregation lag time. This kinetic trend was contrary to the conventional understanding of amyloid aggregation and persisted over a range of aggregation conditions, as confirmed by thioflavin-T kinetics assays, CD spectroscopy, and transmission EM. Dynamic light scattering, 1H NMR experiments, and seeded thioflavin-T assay results indicated that differences in initial peptide species contribute to this trend more than variations in the primary nucleus formation rate. On the basis of kinetics modeling results, we propose a mechanism whereby a structural conversion of hCT monomers is needed before incorporation into the fibril. Our kinetic mechanism recapitulates the experimentally observed relationship between peptide concentration and lag time and represents a novel mechanism in amyloid aggregation. Interestingly, hCT at low pH and salmon calcitonin (sCT) exhibited the canonical inverse relationship between concentration and lag time. Comparative studies of hCT and sCT with molecular dynamics simulations and CD indicated an increased α-helical structure in sCT and low-pH hCT monomers compared with neutral-pH hCT, suggesting that α-helical monomers represent a growth-competent species, whereas unstructured random coil monomers represent a growth-incompetent species. Our finding that initial monomer concentration is positively correlated with lag time in hCT aggregation could help inform future efforts for improving therapeutic applications of CT.
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Affiliation(s)
- Kian Kamgar-Parsi
- From the Applied Physics Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan, and
| | - Charles L Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
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14
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He RY, Chao SH, Tsai YJ, Lee CC, Yu CY, Gao HD, Huang YA, Hwang E, Lee HM, Huang JJT. Photocontrollable Probe Spatiotemporally Induces Neurotoxic Fibrillar Aggregates and Impairs Nucleocytoplasmic Trafficking. ACS NANO 2017; 11:6795-6807. [PMID: 28653830 DOI: 10.1021/acsnano.7b01645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The abnormal assembly of misfolded proteins into neurotoxic aggregates is the hallmark associated with neurodegenerative diseases. Herein, we establish a photocontrollable platform to trigger amyloidogenesis to recapitulate the pathogenesis of amyotrophic lateral sclerosis (ALS) by applying a chemically engineered probe as a "switch" in live cells. This probe is composed of an amyloidogenic peptide from TDP-43, a photolabile linker, a polycationic sequence both to mask amyloidogenicity and for cell penetration, and a fluorophore for visualization. The photocontrollable probe can self-assemble into a spherical vesicle but rapidly develops massive nanofibrils with amyloid properties upon photoactivation. The photoinduced in vitro fibrillization process is characterized by biophysical techniques. In cellular experiments, this cell-penetrable vesicle was retained in the cytoplasm, seeded the mislocalized endogenous TDP-43 into aggregates upon irradiation, and consequently initiated apoptosis. In addition, this photocontrollable vesicle interfered with nucleocytoplasmic protein transport and triggered cortical neuron degeneration. Our developed strategy provides in vitro and in vivo spatiotemporal control of neurotoxic fibrillar aggregate formation, which can be readily applied in the studies of protein misfolding, aggregation-induced protein mislocalization, and amyloid-induced pathogenesis in different diseases.
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Affiliation(s)
- Ruei-Yu He
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Shu-Han Chao
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Yu-Ju Tsai
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Chi-Chang Lee
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Chu-Yi Yu
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Hua-De Gao
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University , Taipei 106, Taiwan
| | - Yung-An Huang
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, and Institute of Molecular Medicine and Bioengineering, National Chiao Tung University , Hsinchu 30068, Taiwan
| | - Eric Hwang
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, and Institute of Molecular Medicine and Bioengineering, National Chiao Tung University , Hsinchu 30068, Taiwan
| | - Hsien-Ming Lee
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica , No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
- Department of Applied Chemistry, National Chiayi University , Chiayi 60004, Taiwan
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15
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An B, Wang X, Cui M, Gui X, Mao X, Liu Y, Li K, Chu C, Pu J, Ren S, Wang Y, Zhong G, Lu TK, Liu C, Zhong C. Diverse Supramolecular Nanofiber Networks Assembled by Functional Low-Complexity Domains. ACS NANO 2017; 11:6985-6995. [PMID: 28609612 DOI: 10.1021/acsnano.7b02298] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Self-assembling supramolecular nanofibers, common in the natural world, are of fundamental interest and technical importance to both nanotechnology and materials science. Despite important advances, synthetic nanofibers still lack the structural and functional diversity of biological molecules, and the controlled assembly of one type of molecule into a variety of fibrous structures with wide-ranging functional attributes remains challenging. Here, we harness the low-complexity (LC) sequence domain of fused in sarcoma (FUS) protein, an essential cellular nuclear protein with slow kinetics of amyloid fiber assembly, to construct random copolymer-like, multiblock, and self-sorted supramolecular fibrous networks with distinct structural features and fluorescent functionalities. We demonstrate the utilities of these networks in the templated, spatially controlled assembly of ligand-decorated gold nanoparticles, quantum dots, nanorods, DNA origami, and hybrid structures. Owing to the distinguishable nanoarchitectures of these nanofibers, this assembly is structure-dependent. By coupling a modular genetic strategy with kinetically controlled complex supramolecular self-assembly, we demonstrate that a single type of protein molecule can be used to engineer diverse one-dimensional supramolecular nanostructures with distinct functionalities.
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Affiliation(s)
- Bolin An
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032, China
| | - Xinyu Wang
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Shanghai Institute of Ceramics, Chinese Academy of Sciences , Shanghai 200050, China
| | - Mengkui Cui
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032, China
| | - Xinrui Gui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science , Shanghai 200032, China
| | - Xiuhai Mao
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Yan Liu
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Ke Li
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Shanghai Institute of Ceramics, Chinese Academy of Sciences , Shanghai 200050, China
| | - Cenfeng Chu
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Jiahua Pu
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Susu Ren
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032, China
| | - Yanyi Wang
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Guisheng Zhong
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139-4307, United States
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science , Shanghai 200032, China
| | - Chao Zhong
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
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16
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Nanoscale Control of Amyloid Self-Assembly Using Protein Phase Transfer by Host-Guest Chemistry. Sci Rep 2017; 7:5710. [PMID: 28720896 PMCID: PMC5516018 DOI: 10.1038/s41598-017-06181-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/09/2017] [Indexed: 12/19/2022] Open
Abstract
Amyloid fibrils have recently been highlighted for their diverse applications as functional nanomaterials in modern chemistry. However, tight control to obtain a targeted fibril length with low heterogeneity has not been achieved because of the complicated nature of amyloid fibrillation. Herein, we demonstrate that fibril assemblies can be homogeneously manipulated with desired lengths from ~40 nm to ~10 μm by a phase transfer of amyloid proteins based on host-guest chemistry. We suggest that host-guest interactions with cucurbit[6]uril induce a phase transfer of amyloid proteins (human insulin, human islet amyloid polypeptide, hen egg lysozyme, and amyloid-β 1–40 & 1–42) from the soluble state to insoluble state when the amount of cucurbit[6]uril exceeds its solubility limit in solution. The phase transfer of the proteins kinetically delays the nucleation of amyloid proteins, while the nuclei formed in the early stage are homogeneously assembled to fibrils. Consequently, supramolecular assemblies of amyloid proteins with heterogeneous kinetics can be controlled by protein phase transfer based on host-guest interactions.
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17
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Zhao R, So M, Maat H, Ray NJ, Arisaka F, Goto Y, Carver JA, Hall D. Measurement of amyloid formation by turbidity assay-seeing through the cloud. Biophys Rev 2016; 8:445-471. [PMID: 28003859 PMCID: PMC5135725 DOI: 10.1007/s12551-016-0233-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022] Open
Abstract
Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations are used to interrogate the literature concerned with in vitro drug screening and the assessment of amyloid aggregation mechanisms.
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Affiliation(s)
- Ran Zhao
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Masatomo So
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Hendrik Maat
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Nicholas J Ray
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Fumio Arisaka
- College of Bio-resource Sciences, Nihon University, Chiyoda-ku, Tokyo, 102-8275, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - John A Carver
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia
| | - Damien Hall
- Research School of Chemistry, Australian National University, Acton ACT, 2601, Australia. .,Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan.
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18
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Cho H, Choi JY, Hwang MS, Kim YJ, Lee HM, Lee HS, Lee JH, Ryu YH, Lee MS, Lyoo CH. In vivo cortical spreading pattern of tau and amyloid in the Alzheimer disease spectrum. Ann Neurol 2016; 80:247-58. [PMID: 27323247 DOI: 10.1002/ana.24711] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/03/2016] [Accepted: 06/05/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To determine the in vivo cortical spreading pattern of tau and amyloid and to establish positron emission tomography (PET) image-based tau staging in the Alzheimer disease (AD) spectrum. METHODS We included 195 participants (53 AD, 52 amnestic mild cognitive impairment [MCI], 23 nonamnestic MCI, and 67 healthy controls) who underwent 2 PET scans ((18) F-florbetaben for amyloid-β and (18) F-AV-1451 for tau). We assumed that regions with earlier appearances of pathology may show increased binding in a greater number of participants and acquired spreading order of tau accumulation by sorting the regional frequencies of involvement. We classified each participant into image-based tau stage based on the Z score of the composite region for each stage. RESULTS Tau accumulation was most frequently observed in the medial temporal regions and spread stepwise to the basal and lateral temporal, inferior parietal, posterior cingulate, and other association cortices, and then ultimately to the primary cortical regions. In contrast, amyloid accumulation was found with similar frequency in the diffuse neocortical areas and then finally spread to the medial temporal regions. The image-based tau stage correlated with the general cognitive status, whereas cortical thinning was found only in the advanced tau stages: medial temporal region in stage V and widespread cortex in stage VI. INTERPRETATION Our PET study replicated postmortem spreading patterns of tau and amyloid-β pathologies. Unlike the diffuse accumulation of amyloid throughout the neocortex, tau spreading occurred in a stepwise fashion through the networks. Image-based tau staging may be useful for the objective assessment of AD progression. Ann Neurol 2016;80:247-258.
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Affiliation(s)
- Hanna Cho
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Jae Yong Choi
- Department of Nuclear Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Mi Song Hwang
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - You Jin Kim
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Hye Mi Lee
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Hye Sun Lee
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae Hoon Lee
- Department of Nuclear Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Young Hoon Ryu
- Department of Nuclear Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Myung Sik Lee
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine
| | - Chul Hyoung Lyoo
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine
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19
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Halfmann R. A glass menagerie of low complexity sequences. Curr Opin Struct Biol 2016; 38:18-25. [PMID: 27258703 DOI: 10.1016/j.sbi.2016.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/06/2016] [Accepted: 05/11/2016] [Indexed: 10/24/2022]
Abstract
Remarkably simple proteins play outsize roles in the execution of developmental complexity within biological systems. Sequence information determines structure and hence function, so how do low complexity sequences fulfill their functions? Recent discoveries are raising the curtain on a new dimension of the sequence-structure paradigm. In it, function derives not from the structures of individual proteins, but instead, from dynamic material properties of entire ensembles of the proteins acting in unison through phase changes. These phases include liquids, one-dimensional crystals, and - as elaborated herein - even glasses. The peculiar thermodynamics of glass-like protein assemblies, in particular, illuminate new principles of information flow through and, at times, orthogonal to the central dogma of molecular biology.
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Affiliation(s)
- Randal Halfmann
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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20
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Beun LH, Albertazzi L, van der Zwaag D, de Vries R, Cohen Stuart MA. Unidirectional Living Growth of Self-Assembled Protein Nanofibrils Revealed by Super-resolution Microscopy. ACS NANO 2016; 10:4973-4980. [PMID: 27124596 DOI: 10.1021/acsnano.6b01017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein-based nanofibrils are emerging as a promising class of materials that provide unique properties for applications such as biomedical and food engineering. Here, we use atomic force microscopy and stochastic optical reconstruction microscopy imaging to elucidate the growth dynamics, exchange kinetics, and polymerization mechanism for fibrils composed of a de novo designed recombinant triblock protein polymer. This macromolecule features a silk-inspired self-assembling central block composed of GAGAGAGH repeats, which are known to fold into a β roll with turns at each histidine and, once folded, to stack, forming a long, ribbon-like structure. We find several properties that allow the growth of patterned protein nanofibrils: the self-assembly takes place on only one side of the growing fibrils by the essentially irreversible addition of protein polymer subunits, and these fibril ends remain reactive indefinitely in the absence of monomer ("living ends"). Exploiting these characteristics, we can grow stable diblock protein nanofibrils by the sequential addition of differently labeled proteins. We establish control over the block length ratio by simply varying monomer feed conditions. Our results demonstrate the use of engineered protein polymers in creating precisely patterned protein nanofibrils and open perspectives for the hierarchical self-assembly of functional biomaterials.
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Affiliation(s)
- Lennart H Beun
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University , Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Lorenzo Albertazzi
- Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Bioengineering of Catalonia Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Daan van der Zwaag
- Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University , Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University , Dreijenplein 6, 6703 HB Wageningen, The Netherlands
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21
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Schwierz N, Frost CV, Geissler PL, Zacharias M. Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step. J Am Chem Soc 2016; 138:527-39. [PMID: 26694883 DOI: 10.1021/jacs.5b08717] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide-peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient.
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Affiliation(s)
- Nadine Schwierz
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Christina V Frost
- Physik Department, Technische Universität München , 85748 Garching, Germany
| | - Phillip L Geissler
- Chemistry Department, University of California , Berkeley, California 94720, United States
| | - Martin Zacharias
- Physik Department, Technische Universität München , 85748 Garching, Germany
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22
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Wördehoff MM, Bannach O, Shaykhalishahi H, Kulawik A, Schiefer S, Willbold D, Hoyer W, Birkmann E. Single fibril growth kinetics of α-synuclein. J Mol Biol 2015; 427:1428-1435. [PMID: 25659910 DOI: 10.1016/j.jmb.2015.01.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 01/26/2015] [Accepted: 01/29/2015] [Indexed: 01/13/2023]
Abstract
Neurodegenerative disorders associated with protein misfolding are fatal diseases that are caused by fibrillation of endogenous proteins such as α-synuclein (α-syn) in Parkinson's disease (PD) or amyloid-β in Alzheimer's disease. Fibrils of α-syn are a major pathological hallmark of PD and certain aggregation intermediates are postulated to cause synaptic failure and cell death of dopaminergic neurons in the substantia nigra. For the development of therapeutic approaches, the mechanistic understanding of the fibrillation process is essential. Here we report real-time observation of α-syn fibril elongation on a glass surface, imaged by total internal reflection fluorescence microscopy using thioflavin T fluorescence. Fibrillation on the glass surface occurred in the same time frame and yielded fibrils of similar length as fibrillation in solution. Time-resolved imaging of fibrillation on a single fibril level indicated that α-syn fibril elongation follows a stop-and-go mechanism; that is, fibrils either extend at a homogenous growth rate or stop to grow for variable time intervals. The fibril growth kinetics were compatible with a model featuring two states, a growth state and a stop state, which were approximately isoenergetic and interconverted with rate constants of ~1.5×10(-4) s(-1). In the growth state, α-syn monomers were incorporated into the fibril with a rate constant of 8.6×10(3) M(-1) s(-1). Fibril elongation of α-syn is slow compared to other amyloidogenic proteins.
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Affiliation(s)
- Michael M Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Oliver Bannach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Research Centre Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas Kulawik
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Research Centre Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Stephanie Schiefer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Research Centre Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Research Centre Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Eva Birkmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Research Centre Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
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