1
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Xia N, Xu L, Xu D, Huang M, Li Y, Mei Z, Yu Z. Neuroprotective effect of emodin on Aβ 25-35-induced cytotoxicity in PC12 cells involves Nrf2/GPX4 and TLR4/p-NF-κB/NLRP3 pathways. Brain Res 2024; 1841:149019. [PMID: 38795791 DOI: 10.1016/j.brainres.2024.149019] [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: 03/25/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
The present study aims to investigate the neuroprotective effects of emodin in Alzheimer's disease (AD). PC12 cells were used to explore the underlying mechanism and were incubated with Aβ25-35 for 24 h as the model group, incubated with emodin at different concentrations (2.5, 5, 10 μM) as the drug administration groups. The content of MDA and the enzymic activities of CAT, GSH-Px were detected by the corresponding commercial kits. The ROS level in Aβ25-35 induced cells was decreased by emodin dose-dependently, but the MMP in these cells were elevated. The expressions of AChE, TLR4, p-NF-κB, NLRP3, IL-1β, and TNF-α in PC12 cells were increased by Aβ25-35 treatment, the expressions of Nrf2, HO-1, GPX4, xCT were decreased, all the levels of expressions were reversed by emodin. Besides, ultraviolet spectrophotometry and infrared spectrophotometry were ultilized to ascertain the production of emodin-Fe (Ⅱ) complex. The FerroOrange results showed that emodin reduced free Fe2+ in cells. The immunofluorescent intensities of Nrf2, GPX4, and p-NF-κB offered direct visible evidence for emodin's multi-targets in AD treatment. Collectively, emodin could inhibit the activity of AChE and exert neuroprotective effects against AD through antioxidant, anti-ferroptotic, anti-inflammatory properties via Nrf2/GPX4 and TLR4/p-NF-κB/NLRP3 pathways.
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Affiliation(s)
- Nengyin Xia
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Lingyun Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Dengrui Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mengyuan Huang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yang Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Zhinan Mei
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zejun Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China.
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2
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Chen Q, Zheng J. Self-assembly and structures of nanoscale double emulsion droplets through coarse-grained molecular dynamics simulations. SOFT MATTER 2023; 19:7731-7743. [PMID: 37789812 DOI: 10.1039/d3sm00656e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Examples of self-assembled multiple emulsion droplets on the nanometre scale are very rare. In this work, we use coarse-grained (CG) molecular dynamics simulations to study the self-assembly of ternary mixtures consisting of water, n-heptane, and nonionic surfactant tetraethylene glycol monododecyl ether (C12E4). The water volume fractions studied are 1%, 3%, and 5%, respectively. Various nanoscale emulsions are obtained in a spontaneous process. When the water/surfactant volume ratio vm/s = 1.0/1.0, the obtained emulsion droplets are identified as oil-in-water-in-oil (O/W/O) double types, consisting of an oil core, an inner surfactant layer, a water layer, and an outer surfactant layer. The water molecules are distributed around the hydrophilic ends of the surfactants, while the hydrophobic ends of the surfactants wrap the oil cores and penetrate into the oil bulk. Hydrogen-bond interactions among water and the hydrophilic ends of the surfactants form cross-links that stabilize the double emulsion droplets. The sizes of all the oil cores inside the droplets are <6 nm in diameter, even with the highest water volume fraction of 5%. Both the concentration of free water molecules on the order of 10-6 mol/cm3 and the favourable energy change during emulsion formation indicate that the emulsion droplets are thermodynamically stable. In contrast, for vm/s = 1.0/5.5, no double emulsion but a simple water-in-oil emulsion was observed, with morphologies evolving from oblate to bicontinuous phases with an increase in the water volume fraction from 1% to 5%. Our coarse-grained molecular dynamics simulations provide valuable insight for the preparation of nanoscale double emulsions and the characterization of their structures.
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Affiliation(s)
- Qiubo Chen
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore.
| | - Jianwei Zheng
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Republic of Singapore.
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3
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Tang Y, Zhang D, Gong X, Zheng J. A mechanistic survey of Alzheimer's disease. Biophys Chem 2021; 281:106735. [PMID: 34894476 DOI: 10.1016/j.bpc.2021.106735] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most common, age-dependent neurodegenerative disorder. While AD has been intensively studied from different aspects, there is no effective cure for AD, largely due to a lack of a clear mechanistic understanding of AD. In this mini-review, we mainly focus on the discussion and summary of mechanistic causes of Alzheimer's disease (AD). While different AD mechanisms illustrate different molecular and cellular pathways in AD pathogenesis, they do not necessarily exclude each other. Instead, some of them could work together to initiate, trigger, and promote the onset and development of AD. In a broader viewpoint, some AD mechanisms (e.g., amyloid aggregation mechanism, microbial infection/neuroinflammation mechanism, and amyloid cross-seeding mechanism) could also be applicable to other amyloid diseases including type II diabetes, Parkinson's disease, and prion disease. Such common mechanisms for AD and other amyloid diseases explain not only the pathogenesis of individual amyloid diseases, but also the spreading of pathologies between these diseases, which will inspire new strategies for therapeutic intervention and prevention for AD.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, OH, United States of America
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America.
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4
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Zhang Y, Zhang M, Liu Y, Zhang D, Tang Y, Ren B, Zheng J. Dual amyloid cross-seeding reveals steric zipper-facilitated fibrillization and pathological links between protein misfolding diseases. J Mater Chem B 2021; 9:3300-3316. [PMID: 33651875 DOI: 10.1039/d0tb02958k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amyloid cross-seeding, as a result of direct interaction and co-aggregation between different disease-causative peptides, is considered as a main mechanism for the spread of the overlapping pathology across different cells and tissues between different protein-misfolding diseases (PMDs). Despite the biomedical significance of amyloid cross-seeding in amyloidogenesis, it remains a great challenge to discover amyloid cross-seeding systems and reveal their cross-seeding structures and mechanisms. Herein, we are the first to report that GNNQQNY - a short fragment from yeast prion protein Sup35 - can cross-seed with both amyloid-β (Aβ, associated with Alzheimer's disease) and human islet amyloid polypeptide (hIAPP, associated with type II diabetes) to form β-structure-rich assemblies and to accelerate amyloid fibrillization. Dry, steric β-zippers, formed by the two β-sheets of different amyloid peptides, provide generally interactive and structural motifs to facilitate amyloid cross-seeding. The presence of different steric β-zippers in a variety of GNNQQNY-Aβ and GNNQQNY-hIAPP assemblies also explains amyloid polymorphism. In addition, alteration of steric zipper formation by single-point mutations of GNNQQNY and interactions of GNNQQNY with different Aβ and hIAPP seeds leads to different amyloid cross-seeding efficiencies, further confirming the existence of cross-seeding barriers. This work offers a better structural-based understanding of amyloid cross-seeding mechanisms linked to different PMDs.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering The University of Akron, Ohio, USA.
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5
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Lau CYJ, Mastrobattista E. Programming supramolecular peptide materials by modulating the intermediate steps in the complex assembly pathway: Implications for biomedical applications. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2020.101396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Lau CYJ, Fontana F, Mandemaker LDB, Wezendonk D, Vermeer B, Bonvin AMJJ, de Vries R, Zhang H, Remaut K, van den Dikkenberg J, Medeiros-Silva J, Hassan A, Perrone B, Kuemmerle R, Gelain F, Hennink WE, Weingarth M, Mastrobattista E. Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides. Commun Chem 2020; 3:164. [PMID: 36703336 PMCID: PMC9814929 DOI: 10.1038/s42004-020-00417-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/19/2020] [Indexed: 01/29/2023] Open
Abstract
Self-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different β-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.
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Affiliation(s)
- Chun Yin Jerry Lau
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Federico Fontana
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy
| | - Laurens D. B. Mandemaker
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Dennie Wezendonk
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Benjamin Vermeer
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Renko de Vries
- grid.4818.50000 0001 0791 5666Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Heyang Zhang
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Katrien Remaut
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Joep van den Dikkenberg
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - João Medeiros-Silva
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alia Hassan
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Barbara Perrone
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Fabrizio Gelain
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy ,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell’Ospedale Maggiore 3, 20162 Milan, Italy
| | - Wim E. Hennink
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Markus Weingarth
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Enrico Mastrobattista
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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7
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Nishikawa N, Sakae Y, Gouda T, Tsujimura Y, Okamoto Y. Structural Analysis of a Trimer of β 2-Microgloblin Fragment by Molecular Dynamics Simulations. Biophys J 2019; 116:781-790. [PMID: 30771855 DOI: 10.1016/j.bpj.2018.11.3143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 06/08/2018] [Accepted: 11/06/2018] [Indexed: 01/22/2023] Open
Abstract
A peptide β2-m21-31, which is a fragment from residue 21 to residue 31 of β2-microgloblin, is experimentally known to self-assemble and form amyloid fibrils. In order to understand the mechanism of amyloid fibril formations, we applied the replica-exchange molecular dynamics method to the system consisting of three fragments of β2-m21-31. From the analyses on the temperature dependence, we found that there is a clear phase transition temperature in which the peptides aggregate with each other. Moreover, we found by the free energy analyses that there are two major stable states: One of them is like amyloid fibrils and the other is amorphous aggregates.
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Affiliation(s)
- Naohiro Nishikawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
| | - Yoshitake Sakae
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Takuya Gouda
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuichiro Tsujimura
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan; Information Technology Center, Nagoya University, Nagoya, Aichi, Japan; JST-CREST, Nagoya, Aichi, Japan.
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8
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Zheng S, Javidpour L, Shing KS, Sahimi M. Dynamics of proteins aggregation. I. Universal scaling in unbounded media. J Chem Phys 2017; 145:134306. [PMID: 27782447 DOI: 10.1063/1.4962837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
It is well understood that in some cases proteins do not fold correctly and, depending on their environment, even properly-folded proteins change their conformation spontaneously, taking on a misfolded state that leads to protein aggregation and formation of large aggregates. An important factor that contributes to the aggregation is the interactions between the misfolded proteins. Depending on the aggregation environment, the aggregates may take on various shapes forming larger structures, such as protein plaques that are often toxic. Their deposition in tissues is a major contributing factor to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and prion. This paper represents the first part in a series devoted to molecular simulation of protein aggregation. We use the PRIME, a meso-scale model of proteins, together with extensive discontinuous molecular dynamics simulation to study the aggregation process in an unbounded fluid system, as the first step toward MD simulation of the same phenomenon in crowded cellular environments. Various properties of the aggregates have been computed, including dynamic evolution of aggregate-size distribution, mean aggregate size, number of peptides that contribute to the formation of β sheets, number of various types of hydrogen bonds formed in the system, radius of gyration of the aggregates, and the aggregates' diffusivity. We show that many of such quantities follow dynamic scaling, similar to those for aggregation of colloidal clusters. In particular, at long times the mean aggregate size S(t) grows with time as, S(t) ∼ tz, where z is the dynamic exponent. To our knowledge, this is the first time that the qualitative similarity between aggregation of proteins and colloidal aggregates has been pointed out.
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Affiliation(s)
- Size Zheng
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Leili Javidpour
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
| | - Katherine S Shing
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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9
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [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: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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10
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Zhang M, Ren B, Chen H, Sun Y, Ma J, Jiang B, Zheng J. Molecular Simulations of Amyloid Structures, Toxicity, and Inhibition. Isr J Chem 2016. [DOI: 10.1002/ijch.201600075] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Hong Chen
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - 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 P. R. China
| | - Jie Ma
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
- State Key Laboratory of Pollution Control and Resource Reuse School of Environmental Science and Engineering Tongji University Shanghai 200092 P. R. China
| | - Binbo Jiang
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
- College of Chemical and Biological Engineering Zhejiang University Hangzhou Zhejiang 310027 P. R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
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11
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de Almeida NEC, Do TD, Tro M, LaPointe NE, Feinstein SC, Shea JE, Bowers MT. Opposing Effects of Cucurbit[7]uril and 1,2,3,4,6-Penta-O-galloyl-β-d-glucopyranose on Amyloid β25-35 Assembly. ACS Chem Neurosci 2016; 7:218-26. [PMID: 26629788 PMCID: PMC4758880 DOI: 10.1021/acschemneuro.5b00280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease characterized by extracellular deposits of amyloid β protein (Aβ) in the brain. The conversion of soluble monomers to amyloid Aβ fibrils is a complicated process and involves several transient oligomeric species, which are widely believed to be highly toxic and play a crucial role in the etiology of AD. The development of inhibitors to prevent formation of small and midsized oligomers is a promising strategy for AD treatment. In this work, we employ ion mobility spectrometry (IMS), transmission electron microscopy (TEM), and molecular dynamics (MD) simulations to elucidate the structural modulation promoted by two potential inhibitors of Aβ oligomerization, cucurbit[7]uril (CB[7]) and 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose (PGG), on early oligomer and fibril formation of the Aβ25-35 fragment. One and two CB[7] molecules bind to Aβ25-35 monomers and dimers, respectively, and suppress aggregation by remodeling early oligomer structures and inhibiting the formation of higher-order oligomers. On the other hand, nonselective binding was observed between PGG and Aβ25-35. The interactions between PGG and Aβ25-35, surprisingly, enhanced the formation of Aβ aggregates by promoting extended Aβ25-35 conformations in both homo- and hetero-oligomers. When both ligands were present, the inhibitory effect of CB[7] overrode the stimulatory effect of PGG on Aβ25-35 aggregation, suppressing the formation of large amyloid oligomers and eliminating the structural conversion from isotropic to β-rich topologies induced by PGG. Our results provide mechanistic insights into CB[7] and PGG action on Aβ oligomerization. They also demonstrate the power of the IMS technique to investigate mechanisms of multiple small-molecule agents on the amyloid formation process.
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Affiliation(s)
- Natália E. C. de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Thanh D. Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Nichole E. LaPointe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Corresponding author: Michael T. Bowers. Tel: +1-805-893-2673;
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12
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Hu R, Zhang M, Chen H, Jiang B, Zheng J. Cross-Seeding Interaction between β-Amyloid and Human Islet Amyloid Polypeptide. ACS Chem Neurosci 2015; 6:1759-68. [PMID: 26255739 DOI: 10.1021/acschemneuro.5b00192] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alzheimer's disease (AD) and type 2 diabetes (T2D) are two common protein misfolding diseases. Increasing evidence suggests that these two diseases may be correlated with each other via cross-sequence interactions between β-amyloid peptide (Aβ) associated with AD and human islet amyloid polypeptide (hIAPP) associated with T2D. However, little is known about how these two peptides work and how they interact with each other to induce amyloidogenesis. In this work, we study the effect of cross-sequence interactions between Aβ and hIAPP peptides on hybrid amyloid structures, conformational changes, and aggregation kinetics using combined experimental and simulation approaches. Experimental results confirm that Aβ and hIAPP can interact with each other to aggregate into hybrid amyloid fibrils containing β-sheet-rich structures morphologically similar to pure Aβ and hIAPP. The cross-seeding of Aβ and hIAPP leads to the coexistence of both a retarded process at the initial nucleation stage and an accelerated process at the fibrillization stage, in conjunction with a conformational transition from random structures to α-helix to β-sheet. Further molecular dynamics simulations reveal that Aβ and hIAPP oligomers can efficiently cross-seed each other via the association of two highly similar U-shaped β-sheet structures; thus, conformational compatibility between Aβ and hIAPP aggregates appears to play a key role in determining barriers to cross-seeding. The cross-seeding effects in this work may provide new insights into the molecular mechanisms of interactions between AD and T2D.
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Affiliation(s)
- Rundong Hu
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Mingzhen Zhang
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Hong Chen
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Binbo Jiang
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Jie Zheng
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
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13
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Zhang M, Hu R, Chen H, Chang Y, Ma J, Liang G, Mi J, Wang Y, Zheng J. Polymorphic cross-seeding amyloid assemblies of amyloid-β and human islet amyloid polypeptide. Phys Chem Chem Phys 2015; 17:23245-56. [PMID: 26283068 DOI: 10.1039/c5cp03329b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Epidemiological studies have shown that the development of Alzheimer's disease (AD) is associated with type 2 diabetes (T2D), but it still remains unclear how AD and T2D are connected. Heterologous cross-seeding between the causative peptides of Aβ and hIAPP may represent a molecular link between AD and T2D. Here, we computationally modeled and simulated a series of cross-seeding double-layer assemblies formed by Aβ and hIAPP peptides using all-atom and coarse-gained molecular dynamics (MD) simulations. The cross-seeding Aβ-hIAPP assemblies showed a wide range of polymorphic structures via a combination of four β-sheet-to-β-sheet interfaces and two packing orientations, focusing on a comparison of different matches of β-sheet layers. Two cross-seeding Aβ-hIAPP assemblies with different interfacial β-sheet packings exhibited high structural stability and favorable interfacial interactions in both oligomeric and fibrillar states. Both Aβ-hIAPP assemblies displayed interfacial dehydration to different extents, which in turn promoted Aβ-hIAPP association depending on interfacial polarity and geometry. Furthermore, computational mutagenesis studies revealed that disruption of interfacial salt bridges largely disfavor the β-sheet-to-β-sheet association, highlighting the importance of salt bridges in the formation of cross-seeding assemblies. This work provides atomic-level information on the cross-seeding interactions between Aβ and hIAPP, which may be involved in the interplay between these two disorders.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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14
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Zhang M, Zhao J, Zheng J. Molecular understanding of a potential functional link between antimicrobial and amyloid peptides. SOFT MATTER 2014; 10:7425-7451. [PMID: 25105988 DOI: 10.1039/c4sm00907j] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antimicrobial and amyloid peptides do not share common sequences, typical secondary structures, or normal biological activity but both the classes of peptides exhibit membrane-disruption ability to induce cell toxicity. Different membrane-disruption mechanisms have been proposed for antimicrobial and amyloid peptides, individually, some of which are not exclusive to either peptide type, implying that certain common principles may govern the folding and functions of different cytolytic peptides and associated membrane disruption mechanisms. Particularly, some antimicrobial and amyloid peptides have been identified to have dual complementary amyloid and antimicrobial properties, suggesting a potential functional link between amyloid and antimicrobial peptides. Given that some similar structural and membrane-disruption characteristics exist between the two classes of peptides, this review summarizes major findings, recent advances, and future challenges related to antimicrobial and amyloid peptides and strives to illustrate the similarities, differences, and relationships in the sequences, structures, and membrane interaction modes between amyloid and antimicrobial peptides, with a special focus on direct interactions of the peptides with the membranes. We hope that this review will stimulate further research at the interface of antimicrobial and amyloid peptides - which has been studied less intensively than either type of peptides - to decipher a possible link between both amyloid pathology and antimicrobial activity, which can guide drug design and peptide engineering to influence peptide-membrane interactions important in human health and diseases.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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15
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Tsai HHG, Lee JB, Shih YC, Wan L, Shieh FK, Chen CY. Location and Conformation of Amyloid β(25-35) Peptide and its Sequence-Shuffled Peptides within Membranes: Implications for Aggregation and Toxicity in PC12 Cells. ChemMedChem 2014; 9:1002-11. [DOI: 10.1002/cmdc.201400062] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Indexed: 12/18/2022]
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16
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GhattyVenkataKrishna PK, Mostofian B. Dynamics of water in the amphiphilic pore of amyloid β fibrils. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex. PLoS One 2013; 8:e66935. [PMID: 23776704 PMCID: PMC3680412 DOI: 10.1371/journal.pone.0066935] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/13/2013] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus protein A (SpA) is the most popular affinity ligand for immunoglobulin G1 (IgG1). However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1) in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154) of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137) in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex.
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18
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Li W, Park IS, Kang SK, Lee M. Smart hydrogels from laterally-grafted peptide assembly. Chem Commun (Camb) 2012; 48:8796-8. [DOI: 10.1039/c2cc34528e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Polymorphic structures of Alzheimer's β-amyloid globulomers. PLoS One 2011; 6:e20575. [PMID: 21687730 PMCID: PMC3110195 DOI: 10.1371/journal.pone.0020575] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 05/04/2011] [Indexed: 01/25/2023] Open
Abstract
Background Misfolding and self-assembly of Amyloid-β (Aβ) peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphic Aβ structures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation. Methods and Findings Here, we model a series of molecular structures of Aβ globulomers assembled by monomer and dimer building blocks using our peptide-packing program and explicit-solvent molecular dynamics (MD) simulations. Structural and energetic analysis shows that although Aβ globulomers could adopt different energetically favorable but structurally heterogeneous conformations in a rugged energy landscape, they are still preferentially organized by dynamic dimeric subunits with a hydrophobic core formed by the C-terminal residues independence of initial peptide packing and organization. Such structural organizations offer high structural stability by maximizing peptide-peptide association and optimizing peptide-water solvation. Moreover, curved surface, compact size, and less populated β-structure in Aβ globulomers make them difficult to convert into other high-order Aβ aggregates and fibrils with dominant β-structure, suggesting that they are likely to be off-pathway species to amyloid fibrils. These Aβ globulomers are compatible with experimental data in overall size, subunit organization, and molecular weight from AFM images and H/D amide exchange NMR. Conclusions Our computationally modeled Aβ globulomers provide useful insights into structure, dynamics, and polymorphic nature of Aβ globulomers which are completely different from Aβ fibrils, suggesting that these globulomers are likely off-pathway species and explaining the independence of the aggregation kinetics between Aβ globulomers and fibrils.
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Spill YG, Pasquali S, Derreumaux P. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model. J Chem Theory Comput 2011; 7:1502-10. [DOI: 10.1021/ct100619p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yannick G. Spill
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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21
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Zhao J, Yu X, Liang G, Zheng J. Heterogeneous Triangular Structures of Human Islet Amyloid Polypeptide (Amylin) with Internal Hydrophobic Cavity and External Wrapping Morphology Reveal the Polymorphic Nature of Amyloid Fibrils. Biomacromolecules 2011; 12:1781-94. [DOI: 10.1021/bm2001507] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Xiang Yu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Guizhao Liang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- Key Laboratory of Biorheological Science and Technology Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
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Zhao J, Yu X, Liang G, Zheng J. Structural Polymorphism of Human Islet Amyloid Polypeptide (hIAPP) Oligomers Highlights the Importance of Interfacial Residue Interactions. Biomacromolecules 2010; 12:210-20. [DOI: 10.1021/bm101159p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
| | - Xiang Yu
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
| | - Guizhao Liang
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
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