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Li Q, Zhu Y, Meng X, Tong HHY, Liu H. Experiment and molecular dynamics simulations reveal proanthocyanidin B2 and B3 can inhibit prion aggregation by different mechanisms. J Biomol Struct Dyn 2024; 42:2424-2436. [PMID: 37144732 DOI: 10.1080/07391102.2023.2209663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Prion diseases are a group of fatal neurodegenerative diseases caused by the misfolding and aggregation of prion protein (PrP), and the inhibition of PrP aggregation is one of the most effective therapeutic strategies. Proanthocyanidin B2 (PB2) and B3 (PB3), the effective natural antioxidants have been evaluated for the inhibition of amyloid-related protein aggregation. Since PrP has similar aggregation mechanism with other amyloid-related proteins, will PB2 and PB3 affect the aggregation of PrP? In this paper, experimental and molecular dynamics (MD) simulation methods were combined to investigate the influence of PB2 and PB3 on PrP aggregation. Thioflavin T assays showed PB2 and PB3 could inhibit PrP aggregation in a concentrate-dependent manner in vitro. To understand the underlying mechanism, we performed 400 ns all-atom MD simulations. The results suggested PB2 could stabilize the α2 C-terminus and the hydrophobic core of protein by stabilizing two important salt bridges R156-E196 and R156-D202, and consequently made global structure of protein more stable. Surprisingly, PB3 could not stabilize PrP, which may inhibit PrP aggregation through a different mechanism. Since dimerization is the first step of aggregation, will PB3 inhibit PrP aggregation by inhibiting the dimerization? To verify our assumption, we then explored the effect of PB3 on protein dimerization by performing 800 ns MD simulations. The results suggested PB3 could reduce the residue contacts and hydrogen bonds between two monomers, preventing dimerization process of PrP. The possible inhibition mechanism of PB2 and PB3 on PrP aggregation could provide useful information for drug development against prion diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qin Li
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Yongchang Zhu
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Henry H Y Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
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2
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Zhang T, Pan Y, Kandapal S, Sun X, Xu B. Following the Aggregation of Human Prion Protein on Heparin Functionalized Gold Surface in Real Time. ACS APPLIED BIO MATERIALS 2022; 5:5457-5464. [PMID: 36228282 DOI: 10.1021/acsabm.2c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The aggregation of the prion protein (PrP) plays a key role in the development of prion diseases and is believed to be an autocatalytic process with a very high kinetic barrier. Intensive studies have focused on overcoming the kinetic barriers under extremely nonphysiological in vitro conditions by altering the pH of PrP solution on solid surfaces, such as gold, mica, and a lipid bilayer. Importantly, sulfated glycosaminoglycans (GAGs), including heparin, were found to be associated with PrP misfolding and aggregation, suggesting GAGs have catalytic roles in PrP aggregation processes. However, the exact role and details of GAGs in the PrP aggregation are not clear and need a thorough perusal. Here, we investigate the PrP aggregation process on a heparin functionalized gold surface by in situ, real-time monitoring of the atomic scale details of the whole aggregation process by single molecule atomic force microscopy (AFM), combining simultaneous topographic and recognition (TREC) imaging and single molecule force spectroscopy (SMFS). We observed the whole aggregation process for full-length human recombinant PrP (23-231) aggregation on the heparin modified gold surface, from the formation of oligomers, to the assembly of protofibrils and short fibers, and the formation of elongated mature fibers. Heparin is found to promote the PrP aggregation by facilitating the formation of oligomers during the early nucleation stage.
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Affiliation(s)
- Tong Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Yangang Pan
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Sneha Kandapal
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Xin Sun
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
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Martí D, Martín-Martínez E, Torras J, Betran O, Turon P, Alemán C. In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold. Colloids Surf B Biointerfaces 2022; 213:112400. [PMID: 35158221 PMCID: PMC8820101 DOI: 10.1016/j.colsurfb.2022.112400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/26/2022]
Abstract
The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.
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Affiliation(s)
- Didac Martí
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Eduard Martín-Martínez
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
| | - Juan Torras
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain.
| | - Oscar Betran
- Departament de Física, EETAC, Universitat Politècnica de Catalunya (UPC), c/ Esteve Terrades, 7, 08860 Castelldefels, Spain
| | - Pau Turon
- B. Braun Surgical, S.A.U. Carretera de Terrasa 121, Rubí, 08191 Barcelona, Spain.
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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Mukhopadhyay S, Bera SC, Ramola K. Observation of two-step aggregation kinetics of Amyloid- βproteins from fractal analysis. Phys Biol 2022; 19. [PMID: 35381581 DOI: 10.1088/1478-3975/ac6478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/05/2022] [Indexed: 11/12/2022]
Abstract
Self-aggregation in proteins has long been studied and modeled due to its ubiquity and importance in many biological contexts. Several models propose a two step aggregation mechanism, consisting of linear growth of fibrils and secondary growth involving branch formation. Single molecule imaging techniques such as total internal reflection fluorescence (TIRF) microscopy can provide direct evidence of such mechanisms, however, analyzing such large data-sets is challenging. In this paper, we analyze for the first time, images of growing amyloid fibrils obtained from TIRF microscopy using the techniques of fractal geometry, which provides a natural framework to disentangle the two types of growth mechanisms at play. We find that after an initial linear growth phase, identified by a plateau in the average fractal dimension with time, the occurrence of branching events leads to a further increase in the fractal dimension, with a final saturation value ≈ 2. This provides direct evidence of the two-step nature of the aggregation kinetics of Amyloid-βproteins, with an initial linear elongation phase followed by branching at later times.
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Affiliation(s)
- Soham Mukhopadhyay
- Tata Institute of Fundamental Research Centre for Interdisciplinary Sciences, 36/P, Gopanpally Tanda, Serilingampally Mandal, Hyderabad, Telangana, 500046, INDIA
| | - Subhas C Bera
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, Erlangen, Bayern, 91058, GERMANY
| | - Kabir Ramola
- Tata Institute of Fundamental Research Centre for Interdisciplinary Sciences, 36/P, Gopanpally Tanda, Serilingampally Mandal, Hyderabad, Telangana, 500046, INDIA
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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6
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Sang JC, Lee JE, Dear AJ, De S, Meisl G, Thackray AM, Bujdoso R, Knowles TPJ, Klenerman D. Direct observation of prion protein oligomer formation reveals an aggregation mechanism with multiple conformationally distinct species. Chem Sci 2019; 10:4588-4597. [PMID: 31123569 PMCID: PMC6492631 DOI: 10.1039/c8sc05627g] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
The aggregation of the prion protein (PrP) plays a key role in the development of prion diseases. In the past decade, a similar process has been associated with other proteins, such as Aβ, tau, and α-synuclein, which participate in other neurodegenerative diseases. It is increasingly recognized that the small oligomeric species of aggregates can play an important role in the development of prion diseases. However, determining the nature of the oligomers formed during the aggregation process has been experimentally difficult due to the lack of suitable methods capable of the detection and characterization of the low level of oligomers that may form. To address this problem, we have utilized single-aggregate methods to study the early events associated with aggregation of recombinant murine PrP in vitro to approach the bona fide process in vivo. PrP aggregation resulted in the formation of thioflavin T (ThT)-inactive and ThT-active species of oligomers. The ThT-active oligomers undergo conversion from a Proteinase K (PK)-sensitive to PK-resistant conformer, from which mature fibrils can eventually emerge. Overall, our results show that single-aggregate methods can provide structural and mechanistic insights into PrP aggregation, identify the potential species that mediates cytotoxicity, and reveal that a range of distinct oligomeric species with different properties is formed during prion protein aggregation.
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Affiliation(s)
- Jason C Sang
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Ji-Eun Lee
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Alexander J Dear
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Suman De
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Alana M Thackray
- Department of Veterinary Medicine , University of Cambridge , Madingley Road , Cambridge , CB3 0ES , UK
| | - Raymond Bujdoso
- Department of Veterinary Medicine , University of Cambridge , Madingley Road , Cambridge , CB3 0ES , UK
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - David Klenerman
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
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7
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Zhu Y, Guo J, Zhang A, Li L, Liu X, Liu H, Yao X. How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study. ENVIRONMENTAL RESEARCH 2019; 171:1-10. [PMID: 30641367 DOI: 10.1016/j.envres.2018.12.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 12/15/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
As the broad application of graphene in the biomedical field, it is urgent and important to evaluate how the graphene affects the structure and function of the proteins in our body, especially the amyloid-related proteins. Prion protein, as a typical amyloid protein, it misfolding and aggregation will lead to serious prion diseases. To explore if graphene promotes or inhibits the formation of amyloid, here, we combined the experimental and molecular dynamics (MD) simulation methods to study the influence of graphene on the globular domain of prion protein (PrP117-231). The results from fluorescence quenching and circular dichroism spectrum showed that the addition of graphene changed the secondary structure of prion protein largely, mainly reflecting in the reduced α-helix structure and the increased coil structure, indicating graphene may strengthen the misfolding inclination of prion. To further uncover the mechanism of conformational change of prion under the induction of graphene, the all-atoms MD simulations in explicit solvent were performed. Our simulations suggest that prion protein can be quickly and tightly adsorbed onto graphene together with the weak conformational rearrangement and may reorient when approaching the surface. The Van der Waals' force drive the adsorption process. In the induction of graphene, H1 and S2-H2 loop regions of prion become unstable and prion begins to misfold partially. Our work shows that graphene can induce the misfolding of prion protein and may cause the potential risk to biosystems.
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Affiliation(s)
- Yongchang Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jingjing Guo
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Ai Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Lanlan Li
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xuewei Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
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8
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Synthesis of Fe₃C@C from Pyrolysis of Fe₃O₄-Lignin Clusters and Its Application for Quick and Sensitive Detection of PrP Sc through a Sandwich SPR Detection Assay. Int J Mol Sci 2019; 20:ijms20030741. [PMID: 30744182 PMCID: PMC6387304 DOI: 10.3390/ijms20030741] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 02/06/2023] Open
Abstract
The prion protein (PrPSc) has drawn widespread attention due to its pathological potential to cause prion diseases. Herein, we successfully synthesized Fe₃C@C by carbonizing Fe₃O₄-lignin clusters, which were prepared through a facile hydrogen bonding interaction between ≡Fe-OH and hydroxyl groups of lignin. Our in-depth investigation confirmed that the composites were Fe₃C@C core/shell particles. We constructed a novel sandwich surface plasmon resonance (SPR) detection assay for sensitive PrPSc detection, utilizing bare gold surface and aptamer-modified Fe₃C@C (Fe₃C@C-aptamer). Due to the highly specific affinity of Fe₃C@C-aptamer towards PrPSc, the sandwich type SPR sensor exhibited excellent analytical performance towards the discrimination and quantitation of PrPSc. A good linear relationship was obtained between the SPR responses and the logarithm of PrPSc concentrations over a range of 0.1⁻200 ng/mL. The detection sensitivity for PrPSc was improved by ~10 fold compared with the SPR direct detection format. The required detection time was only 20 min. The specificity of the present biosensor was also confirmed by PrPC and other reagents as controls. This proposed approach could also be used to isolate and detect other highly pathogenic biomolecules with similar structural characteristics by altering the corresponding aptamer in the Fe₃C@C conjugates.
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Huang Q, Wang H, Gao H, Cheng P, Zhu L, Wang C, Yang Y. In Situ Observation of Amyloid Nucleation and Fibrillation by FastScan Atomic Force Microscopy. J Phys Chem Lett 2019; 10:214-222. [PMID: 30543438 DOI: 10.1021/acs.jpclett.8b03143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amyloidogenic proteins are key components in various amyloid diseases. The aggregation process and the local structural changes of the toxic species from toxic oligomers to protofibrils and subsequently to mature fibrils are crucial for understanding the molecular mechanism of the amyloidgenic process and also for developing a treatment strategy. Exploration on amyloid aggregation dynamics in situ under real liquid condition is feasible for reflection of the whole process with biological correlations. Herein we report the in situ dynamic study and structure exploration of Amylin1-37 aggregation by FastScan atomic force microscopy. Amylin1-37 nucleation process was observed in which smaller oligomers or monomers were assimilated by the surrounding big oligomers. Amylin1-37 protofibril aggregation was positively correlated with monomer concentration, whereas no direct relationship was observed between fibril elongation and monomer concentration. Growing end and passivated end were found during Amylin1-37 fibrillation. In the assembly process, the growing end kept its structure, and its stiffness was lower than the aggregate body, whereas the passivated end might experience rearrangements of β-structures, which eventually enabled fibril growth from this end. This work is beneficial to the insights of amyloid fibrillation and may shed light on the development of drugs targeting the specific phase of amyloid aggregation.
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Affiliation(s)
- Qunxing Huang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Huayi Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Houqian Gao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Peng Cheng
- State Key Laboratory of Tribology, Department of Mechanical Engineering , Tsinghua University , Beijing 100084 , China
| | - Ling Zhu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
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Yang B, Adams DJ, Marlow M, Zelzer M. Surface-Mediated Supramolecular Self-Assembly of Protein, Peptide, and Nucleoside Derivatives: From Surface Design to the Underlying Mechanism and Tailored Functions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15109-15125. [PMID: 30032622 DOI: 10.1021/acs.langmuir.8b01165] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Among the many parameters that have been explored to exercise control over self-assembly processes, the influence of surface properties on self-assembly has been recognized as important but has received considerably less attention than other factors. This is particularly true for biomolecule-derived self-assembling molecules such as protein, peptide, and nucleobase derivatives. Because of their relevance to biomaterial and drug delivery applications, interest in these materials is increasing. As the formation of supramolecular structures from these biomolecule derivatives inevitably brings them into contact with the surfaces of surrounding materials, understanding and controlling the impact of the properties of these surfaces on the self-assembly process are important. In this feature article, we present an overview of the different surface parameters that have been used and studied for the direction of the self-assembly of protein, peptide, and nucleoside-based molecules. The current mechanistic understanding of these processes will be discussed, and potential applications of surface-mediated self-assembly will be outlined.
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Affiliation(s)
- Bin Yang
- Department of Pharmacy , University of Nottingham , Nottingham NG2 7RD , U.K
| | - Dave J Adams
- School of Chemistry , University of Glasgow , Glasgow G12 8QQ , U.K
| | - Maria Marlow
- Department of Pharmacy , University of Nottingham , Nottingham NG2 7RD , U.K
| | - Mischa Zelzer
- Department of Pharmacy , University of Nottingham , Nottingham NG2 7RD , U.K
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11
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Qualitative and Quantitative Detection of PrP Sc Based on the Controlled Release Property of Magnetic Microspheres Using Surface Plasmon Resonance (SPR). NANOMATERIALS 2018; 8:nano8020107. [PMID: 29438353 PMCID: PMC5853738 DOI: 10.3390/nano8020107] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/01/2023]
Abstract
Prion protein (PrPSc) has drawn widespread attention due to its pathological potential to prion diseases. In this work, we constructed a novel surface plasmon resonance (SPR) detection assay involving magnetic microspheres (MMs) and its controlled release property, for selective capture, embedding, concentration, and SPR detection of PrPSc with high sensitivity and specificity. Aptamer-modified magnetic particles (AMNPs) were used to specifically capture PrPSc. Amphiphilic copolymer was used to embed the labeled PrPSc and form magnetic microspheres to isolate PrPSc from the external environment. Static magnetic and alternating magnetic fields were used to concentrate and control release the embedded PrPSc, respectively. Finally, the released AMNPs-labeled PrPSc was detected by SPR which was equipped with a bare gold sensing film. A good linear relationship was obtained between SPR responses and the logarithm of PrPSc concentrations over a range of 0.01-1000 ng/mL. The detection sensitivity for PrPSc was improved by 10 fold compared with SPR direct detection format. The specificity of the present biosensor was also determined by PrPC and other reagents as controls. This proposed approach could also be used to isolate and detect other highly pathogenic biomolecules with similar structural characteristics by altering the corresponding aptamer in the AMNPs conjugates.
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12
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Lou Z, Han H, Zhou M, Wan J, Sun Q, Zhou X, Gu N. Fabrication of Magnetic Conjugation Clusters via Intermolecular Assembling for Ultrasensitive Surface Plasmon Resonance (SPR) Detection in a Wide Range of Concentrations. Anal Chem 2017; 89:13472-13479. [PMID: 29164862 DOI: 10.1021/acs.analchem.7b03768] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, a novel sandwich surface plasmon resonance (SPR) detection assay, which utilizes prion disease-associated isoform (PrPSc) conjugating magnetic nanoparticle clusters (nanoparticle-organic clusters, NOCs) as signal amplification reagents, is constructed for the ultrasensitive detection of PrPSc. Due to the highly specific affinity of aptamer-Fe3O4 nanoparticles (AMNPs) toward PrPSc and the intermolecular assembly behaviors among PrPSc, PrPSc conjugating magnetic nanoparticle clusters were obtained after the incubation of AMNPs and PrPSc and the subsequent concentration processes in an external magnetic field. The conjugation clusters were further injected into the SPR cuvette and captured by the gold sensing film via the Au-S bonding interaction, inducing intense SPR responses. Meanwhile, a traditional sandwich SPR detection format using a gold/PrPSc/AMNPs amplification mode was conducted for the detection of PrPSc as comparison. The results reveal that the synthesized NOCs permitted a 215-fold increase of the SPR signal, while the sandwich format permitted only a 65-fold increase. Moreover, a lower detection limit (1 × 10-4 ng/mL) and a wider quantitation range (1 × 10-4-1 × 105 ng/mL) were demonstrated. The formation of the conjugation clusters and the capture of these clusters were confirmed by high-resolution AFM imaging and molecular simulations. This conjugation-cluster-induced signal amplification strategy has great potential for the detection of small analytes with similar structural characteristics in trace level concentrations with high selectivity and sensitivity by altering the corresponding aptamer labeled to magnetic particles.
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Affiliation(s)
- Zhichao Lou
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China.,State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - He Han
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Ming Zhou
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Jinfeng Wan
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Qian Sun
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Xiaoyan Zhou
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
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13
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Zhang Y, Lou Z, Lin X, Wang Q, Cao M, Gu N. Optimizing purification process of MIM-I-BAR domain by introducing atomic force microscope and dynamics simulations. Colloids Surf B Biointerfaces 2017. [PMID: 28623696 DOI: 10.1016/j.colsurfb.2017.05.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
MIM (missing in metastasis) is a member of I-BAR (inverse BAR) domain protein family, which functions as a putative metastasis suppressor. However, methods of gaining high purity MIM-I-BAR protein are barely reported. Here, by optimizing the purification process including changing the conditions of cell lysate and protein elution, we successfully purified MIM protein. The purity of the obtained protein was up to ∼90%. High-resolution atomic force microscope (AFM) provides more visual images, ensuring that we can observe the microenvironment around the target protein, as well as the conformations of the purification products following each purification process. MIM protein with two different sizes were observed on mica surface with AFM. Combining with molecular dynamics simulations, these molecules were revealed as MIM monomer and dimer. Furthermore, our study attaches importance to the usage of imidazole with suitable concentrations during the affinity chromatography process, as well as the removal of excessive imidazole after the affinity chromatography process. All these results indicate that the method described here was successful in purifying MIM protein and maintaining their natural properties, and is supposed to be used to purify other proteins with low solubility.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China; Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou 215123, China
| | - Zhichao Lou
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China; College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xubo Lin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Qiwei Wang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China; Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou 215123, China
| | - Meng Cao
- Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou 215123, China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China; Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou 215123, China.
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14
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Lou Z, Wan J, Zhang X, Zhang H, Zhou X, Cheng S, Gu N. Quick and sensitive SPR detection of prion disease-associated isoform (PrP Sc) based on its self-assembling behavior on bare gold film and specific interactions with aptamer-graphene oxide (AGO). Colloids Surf B Biointerfaces 2017; 157:31-39. [PMID: 28570989 DOI: 10.1016/j.colsurfb.2017.05.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/18/2017] [Accepted: 05/23/2017] [Indexed: 01/31/2023]
Abstract
Herein, we constructed a novel sandwich surface plasmon resonance (SPR) detection assay for sensitive prion disease-associated isoform (PrPSc) detection, utilizing bare gold film and apatamer-graphene oxide (AGO). Due to the self-assembling behavior of PrPSc on gold surface, the non-modified gold surface can be directly used as sensing surface for the quick detection, for the purpose to avoid the interference from the traditional, complex and changeable probe-modified sensing surface. And due to the highly specific affinity of AGO towards PrPSc, the sandwich type SPR sensor exhibits excellent analytical performance towards the discrimination and quantitation of PrPSc. A good linear relationship was obtained between SPR responses and the logarithm of PrPSc concentrations over a range of 0.001-1ng/mL. The detection sensitivity for PrPSc was improved by ∼156 orders of AGO compared with SPR direct detection format. Besides, morphological changes of the sensing film surfaces were investigated by high resolution AFM imaging, confirming the capture of PrPSc molecules and their further specific recognition by AGO. The specificity of the present biosensor was also investigated by PrPC and other regents as controls. By compared with other reported methods, the AGO enhanced sandwich SPR assay was confirmed to be efficient, sensitive, and with wide working range.
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Affiliation(s)
- Zhichao Lou
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, China; State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jinfeng Wan
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaohong Zhang
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Haiqian Zhang
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Xiaoyan Zhou
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Su Cheng
- Zhongda Hospital, Southeast University, Nanjing 210009, China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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15
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Wang B, Lou Z, Zhang H, Xu B. Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level. J Chem Phys 2016; 144:114701. [DOI: 10.1063/1.4943878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Bin Wang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
| | - Zhichao Lou
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, People’s Republic of China
| | - Haiqian Zhang
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, People’s Republic of China
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science, and Engineering Center, University of Georgia, Athens, Georgia 30605, USA
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Protective V127 prion variant prevents prion disease by interrupting the formation of dimer and fibril from molecular dynamics simulations. Sci Rep 2016; 6:21804. [PMID: 26906032 PMCID: PMC4764842 DOI: 10.1038/srep21804] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/01/2016] [Indexed: 12/12/2022] Open
Abstract
Recent studies uncovered a novel protective prion protein variant: V127 variant, which was reported intrinsically resistant to prion conversion and propagation. However, the structural basis of its protective effect is still unknown. To uncover the origin of the protective role of V127 variant, molecular dynamics simulations were performed to explore the influence of G127V mutation on two key processes of prion propagation: dimerization and fibril formation. The simulation results indicate V127 variant is unfavorable to form dimer by reducing the main-chain H-bond interactions. The simulations of formed fibrils consisting of β1 strand prove V127 variant will make the formed fibril become unstable and disorder. The weaker interaction energies between layers and reduced H-bonds number for V127 variant reveal this mutation is unfavorable to the formation of stable fibril. Consequently, we find V127 variant is not only unfavorable to the formation of dimer but also unfavorable to the formation of stable core and fibril, which can explain the mechanism on the protective role of V127 variant from the molecular level. Our findings can deepen the understanding of prion disease and may guide the design of peptide mimetics or small molecule to mimic the protective effect of V127 variant.
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17
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Li Q, Zhang T, Pan Y, Ciacchi LC, Xu B, Wei G. AFM-based force spectroscopy for bioimaging and biosensing. RSC Adv 2016. [DOI: 10.1039/c5ra22841g] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AFM-based force spectroscopy shows wide bio-related applications especially for bioimaging and biosensing.
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Affiliation(s)
- Qing Li
- Hybrid Materials Interfaces Group
- Faculty of Production Engineering
- University of Bremen
- D-28359 Bremen
- Germany
| | - Tong Zhang
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Altens
- USA
| | - Yangang Pan
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Altens
- USA
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group
- Faculty of Production Engineering
- University of Bremen
- D-28359 Bremen
- Germany
| | - Bingqian Xu
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Altens
- USA
| | - Gang Wei
- Hybrid Materials Interfaces Group
- Faculty of Production Engineering
- University of Bremen
- D-28359 Bremen
- Germany
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