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Lan J, Peng Y, Liang L, Duan X, Kong Z, Zhang L, Shen JW. Theoretical study of protein adsorption on graphene/h-BN heterostructures. Phys Chem Chem Phys 2023; 25:31206-31221. [PMID: 37955184 DOI: 10.1039/d3cp03303a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The biological characteristics of planar heterojunction nanomaterials and their interactions with biomolecules are crucial for the potential application of these materials in the biomedical field. This study employed molecular dynamics (MD) simulations to investigate the interactions between proteins with distinct secondary structures (a single α-helix representing the minimal oligomeric domain protein, a single β-sheet representing the WW structural domain of the Yap65 protein, and a mixed α/β structure representing the BBA protein) and a planar two-dimensional heterojunction (a GRA/h-BN heterojunction consisting of a graphene nanoplate (GRA) and a hexagonal boron nitride nanoplate (h-BN)). The results indicate that all three kinds of protein can be quickly and stably adsorbed on the GRA/h-BN heterojunction due to the strong van der Waals interaction, regardless of their respective types, structures and initial orientations. Moreover, the proteins exhibit a pronounced binding preference for the hBN region of the GRA/h-BN heterojunction. Upon adsorption, the α-helix structure of the minimal oligomeric domain protein experiences partial or complete denaturation. Conversely, while the secondary structure of the single β-sheet and mixed α/β structure (BBA protein) undergoes slight changes (focus on the coil and turn regions), the main α-helix and β-sheet structures remain intact. The initial orientation significantly impacts the degree of protein adsorption and its position on the GRA/h-BN heterojunction. However, regardless of the initial orientation, proteins can ultimately be adsorbed onto the GRA/h-BN heterojunction. Furthermore, the initial orientation has a minor influence on the structural changes of proteins. Significantly, the combination of different secondary structures helps mitigate the denaturation of a single α-helix structure to some extent. Overall, the adsorption of proteins on GRA/h-BN is primarily driven by van der Waals and hydrophobic interactions. Proteins with β-sheet or mixed structures exhibit stronger biocompatibility on the GRA/h-BN heterojunction. Our research elucidated the biological characteristics of GRA/h-BN heterojunction nanomaterials and their interactions with proteins possessing diverse secondary structures. It offers a theoretical foundation for considering heterojunction nanomaterials as promising candidates for biomedical applications.
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Affiliation(s)
- Jun Lan
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Yiran Peng
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Lijun Liang
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Xing Duan
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Zhe Kong
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Li Zhang
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jia-Wei Shen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
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2
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Detection and modulation of neurodegenerative processes using graphene-based nanomaterials: Nanoarchitectonics and applications. Adv Colloid Interface Sci 2023; 311:102824. [PMID: 36549182 DOI: 10.1016/j.cis.2022.102824] [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: 10/03/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Neurodegenerative disorders (NDDs) are caused by progressive loss of functional neurons following the aggregation and fibrillation of proteins in the central nervous system. The incidence rate continues to rise alarmingly worldwide, particularly in aged population, and the success of treatment remains limited to symptomatic relief. Graphene nanomaterials (GNs) have attracted immense interest on the account of their unique physicochemical and optoelectronic properties. The research over the past two decades has recognized their ability to interact with aggregation-prone neuronal proteins, regulate autophagy and modulate the electrophysiology of neuronal cells. Graphene can prevent the formation of higher order protein aggregates and facilitate the clearance of such deposits. In this review, after highlighting the role of protein fibrillation in neurodegeneration, we have discussed how GN-protein interactions can be exploited for preventing neurodegeneration. A comprehensive understanding of such interactions would contribute to the exploration of novel modalities for controlling neurodegenerative processes.
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Jia X, Liu Y, Qu Y, Li YQ, Liu X, Liu P, Li W. Electric Field-Controlled Peptide Self-Assembly through Funnel-Shaped Two-Dimensional Nanopores. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51183-51189. [PMID: 36329605 DOI: 10.1021/acsami.2c13590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Self-assembly of biomolecules is critical for the realization of biological functions. Thus, the precise control of self-assembly has great significance in the design of biochips and biomedical agents. In this report, we design a Y-shaped funnel on a two-dimensional (2D) heterostructure, called 2D funnel, based on monolayered polyaniline carbon nitride (C3N) and boron carbide (BC3), and study its application in the self-assembly state regulation of the peptide oligomer, using Aβ16-21 as the representative model. Structurally, the 2D funnel is composed of three regions: channel area, triangle area, and barrier area. The channel and triangle areas show higher binding affinity to the peptide than that of the barrier area, which leads to the confinement of the peptide in the 2D funnel. Our results show that when an external electric field is applied along the 2D funnel, the oligomer is driven to migrate across the funnel. Its trajectory is confined inside the narrow channel area, which effectively causes peptide dissociation into the individual peptide chains. Then, when the external electric field is turned off, the separated peptide chains spontaneously assemble in the triangle area and tend to reunite. Our present findings propose a novel heterostructure platform, which enables the manipulation of the self-assembly state of peptides by switching the electric field, which could guide the design and fabrication of nanodevices for sensing and sequencing applications.
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Affiliation(s)
- Xiao Jia
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yang Liu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yong-Qiang Li
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Xiangdong Liu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Peng Liu
- Institute of Frontier and Interdisciplinary Science and Key Laboratory of Particle Physics and Particle Irradiation (MOE), Shandong University, Qingdao, Shandong 266237, China
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, Shandong 250100, China
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4
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Probing both sides of the story. Proc Natl Acad Sci U S A 2022; 119:e2212419119. [PMID: 36070345 PMCID: PMC9499575 DOI: 10.1073/pnas.2212419119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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5
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Liang X, Wang Y, Song J, Xia D, Li Q, Dong M. Nontoxic silicene photothermal agents with high near-infrared absorption for disassembly of Alzheimer's amyloid‑β fibrils. Colloids Surf B Biointerfaces 2022; 216:112575. [PMID: 35636323 DOI: 10.1016/j.colsurfb.2022.112575] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
The disassembly and eliminating the amyloid-β (Aβ) aggregates has become an effective way to treat Alzheimer's disease (AD). Herein, for the first time, the near-infrared (NIR) activated silicene nanosheets (SNSs) have been identified as an effective nontoxic photothermal conversion agent for irreversibly disassembly of the Aβ33-42 aggregates. The SNSs synthesized by a combination of mild oxidation method and liquid exfoliation method possess good biocompatibility and biodegradability, and high near-infrared photothermal conversion capabilities. Under NIR light, the SNSs could disassemble the large and dense Aβ33-42 mature fibrils into short fibrils and even form thin films, leading to the degradation rate of 96.47%. The circular dichroism spectrum, fluorescent spectra, and nanostructure were analyzed to monitor the photothermal degradation of mature Aβ33-42 fibrils for elaborating the mechanism beneath. This study might provide a clue for developing potential therapeutic strategy for AD and related neurodegenerative diseases.
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Affiliation(s)
- Xiaoteng Liang
- Tianjin Key Laboratory of Materials Laminating Fabrication and Interface Control Technology; School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yin Wang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Jie Song
- Tianjin Key Laboratory of Materials Laminating Fabrication and Interface Control Technology; School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Dan Xia
- Tianjin Key Laboratory of Materials Laminating Fabrication and Interface Control Technology; School of Materials Science and Engineering, Hebei University of Technology, Tianjin 300130, China.
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China.
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark.
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Immunospecific analysis of in vitro and ex vivo surface-immobilized protein complex. Biointerphases 2022; 17:021005. [PMID: 35477241 DOI: 10.1116/6.0001783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biomaterials used for blood contacting devices are inherently thrombogenic. Antithrombotic agents can be used as surface modifiers on biomaterials to reduce thrombus formation on the surface and to maintain device efficacy. For quality control and to assess the effectiveness of immobilization strategies, it is necessary to quantify the surface-immobilized antithrombotic agent directly. There are limited methods that allow direct quantification on device surfaces such as catheters. In this study, an enzyme immunoassay (EIA) has been developed to measure the density of a synthetic antithrombin-heparin (ATH) covalent complex immobilized on a catheter surface. The distribution of the immobilized ATH was further characterized by an immunohistochemical assay. This analyte-specific EIA is relatively simple and has high throughput, thus providing a tool for quantitative analysis of biomaterial surface modifications. These methods may be further modified to evaluate plasma proteins adsorbed and immobilized on various biomaterial surfaces of complex shapes, with a range of bioactive functionalities, as well as to assess conformational changes of proteins using specific antibodies.
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Chao Y, Zhang L. Biomimetic design of inhibitors of immune checkpoint LILRB4. Biophys Chem 2021; 282:106746. [PMID: 34963077 DOI: 10.1016/j.bpc.2021.106746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022]
Abstract
Immune checkpoint inhibitors have become a hot spot in the treatment of acute myeloid leukemia (AML), the most common acute leukemia (blood cancer) in adults. In the present study, molecular insights into the molecular interactions between an immune checkpoint leukocyte immunoglobulin-like receptor b4 (LILRB4) and its mAb h128-3 was explored using molecular dynamics (MD) simulation for the biomimetic design of peptide inhibitor of LILRB4. Both hydrophobic interaction and electrostatic interaction were found favorable for the binding of the mAb h128-3 on LILRB4, and hydrophobic interaction was identified as the main driving force. The key amino acid residues for the binding of mAb h128-3 on LILRB4 were identified as Y93, D94, D106, Y34, S103, W107, Y61, N30, E27, Y33, Y59, W95, S92 through MM-PBSA (molecular mechanics-Poisson-Boltzmann surface area) method. Based on this, an inhibitor library with the sequence of SXDXYXSY (Where X is an arbitrary amino acid residue) were designed. Two peptide inhibitors, SADHYHSY and SVDWYHSY were obtained through screening using molecular docking and MD simulations, and then validated by successful blocking of LILRB4 through the covering of LILRB4 surface by these inhibitors. These results would be helpful for the research and development of therapies for AML.
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Affiliation(s)
- Yuanyuan Chao
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China.
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8
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Randhawa S, Abidi SMS, Dar AI, Acharya A. The curious cases of nanoparticle induced amyloidosis during protein corona formation and anti-amyloidogenic nanomaterials: Paradox or prejudice? Int J Biol Macromol 2021; 193:1009-1020. [PMID: 34728302 DOI: 10.1016/j.ijbiomac.2021.10.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022]
Abstract
Protein corona (PC) formation remains a major hurdle in the successful delivery of nanomedicines to the target sites. Interacting proteins have been reported to undergo structural changes on the nanoparticle (NP) surface which invariably impacts their biological activities. Such structural changes are the result of opening of more binding sites of proteins to adsorb on the NP surface. The process of conversion of α-helix proteins to their β-sheet enriched counterpart is termed as amyloidosis and in case of PC formation, NPs apparently play the crucial role of being the nucleation centres where this process takes place. Conversely, increasing numbers of artificial nano-chaperones are being used to treat the protein misfolding disorders. Anti-amyloidogenic nanomaterials (NM) have been gaining utmost importance in inhibiting Aβ42 (hallmark peptide for Alzheimer's disease) and Hen egg white lysozyme (HEWL, model protein for systemic amyloidosis) aggregation. Interestingly, in this process, NPs inhibit protein β-sheet enrichment. These two seemingly opposite roles of NPs, propelling confirmatory change onto the smorgasbord of adsorbed native proteins and the ability of NPs in inhibiting amyloidosis creates a paradox, which has not been discussed earlier. Here, we highlight the key points from both the facets of the NP behaviour with respect to their physicochemical properties and the nature of proteins they adsorb onto them to unravel the mystery. BRIEF: Protein corona formation remains a major hurdle in achieving the desired efficacy of nanomedicine. Proteins when interact with nanoparticle (NP) surface, undergo both structural and biological changes. Again, NPs are known to exhibit anti-amyloidogenic behaviour where these play the crucial role of preventing any change in their native structure. Such seemingly different roles of NPs need sincere inquisition.
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Affiliation(s)
- Shiwani Randhawa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Syed M S Abidi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aqib Iqbal Dar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amitabha Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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9
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Sorout N, Chandra A. Interactions of the Aβ(1-42) Peptide with Boron Nitride Nanoparticles of Varying Curvature in an Aqueous Medium: Different Pathways to Inhibit β-Sheet Formation. J Phys Chem B 2021; 125:11159-11178. [PMID: 34605235 DOI: 10.1021/acs.jpcb.1c05805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The aggregation of amyloid β (Aβ) peptide triggered by its conformational changes leads to the commonly known neurodegenerative disease of Alzheimer's. It is believed that the formation of β sheets of the peptide plays a key role in its aggregation and subsequent fibrillization. In the current study, we have investigated the interactions of the Aβ(1-42) peptide with boron nitride nanoparticles and the effects of the latter on conformational transitions of the peptide through a series of molecular dynamics simulations. In particular, the effects of curvature of the nanoparticle surface are studied by considering boron nitride nanotubes (BNNTs) of varying diameter and also a planar boron nitride nanosheet (BNNS). Altogether, the current study involves the generation and analysis of 9.5 μs of dynamical trajectories of peptide-BNNT/BNNS pairs in an aqueous medium. It is found that BN nanoparticles of different curvatures that are studied in the present work inhibit the conformational transition of the peptide to its β-sheet form. However, such an inhibition effect follows different pathways for BN nanoparticles of different curvatures. For the BNNT with the highest surface curvature, i.e., (3,3) BNNT, the nanoparticle is found to inhibit β-sheet formation by stabilizing the helical structure of the peptide, whereas for planar BNNS, the β-sheet formation is prevented by making more favorable pathways available for transitions of the peptide to conformations of random coils and turns. The BNNTs with intermediate curvatures are found to exhibit diverse pathways of their interactions with the peptide, but in all cases, essentially no formation of the β sheet is found whereas substantial β-sheet formation is observed for Aβ(1-42) in water in the absence of any nanoparticle. The current study shows that BN nanoparticles have the potential to act as effective tools to prevent amyloid formation from Aβ peptides.
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Affiliation(s)
- Nidhi Sorout
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
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Kaumbekova S, Shah D. Early Aggregation Kinetics of Alzheimer’s Aβ 16–21 in the Presence of Ultrafine Fullerene Particles and Ammonium Nitrate. ACS CHEMICAL HEALTH & SAFETY 2021. [DOI: 10.1021/acs.chas.1c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samal Kaumbekova
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
| | - Dhawal Shah
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
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Gao F. Adsorption of Mussel Protein on Polymer Antifouling Membranes: A Molecular Dynamics Study. Molecules 2021; 26:5660. [PMID: 34577131 PMCID: PMC8468479 DOI: 10.3390/molecules26185660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Biofouling is one of the most difficult problems in the field of marine engineering. In this work, molecular dynamics simulation was used to study the adsorption process of mussel protein on the surface of two antifouling films-hydrophilic film and hydrophobic film-trying to reveal the mechanism of protein adsorption and the antifouling mechanism of materials at the molecular level. The simulated conclusion is helpful to design and find new antifouling coatings for the experiments in the future.
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Affiliation(s)
- Fengfeng Gao
- Department of Chemical Engineering, Zibo Vocational Institute, Zibo 255300, China
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Kaumbekova S, Torkmahalleh MA, Shah D. Impact of ultrafine particles and secondary inorganic ions on early onset and progression of amyloid aggregation: Insights from molecular simulations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117147. [PMID: 33894535 DOI: 10.1016/j.envpol.2021.117147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder, associated with the aggregation of amyloid beta (Aβ) peptides and formation of plaques. The impact of airborne particulate matter (PM) and ultrafine particles (UFPs), on early onset and progression of AD has been recently hypothesized. Considering their small size, carbon black nanoparticles and UFPs can penetrate into human organism and affect Alzheimer's progression. While experiments show that the exposure of PM and UFPs can lead to enhanced concentrations of Aβ peptides, the interactions between the peptides and UFPs remain obscured. Particularly, the impact of UFPs on the initial rate of aggregation of the peptides is ambiguous. Herein, we perform molecular dynamics simulations to investigate the aggregation of Aβ16-21 peptides, an aggregation-prone segment of Aβ, in the presence of UFPs, mimicked by C60, under different salt solutions suggesting the presence of the inorganic constituents of PM in the blood. In particular, the simulations were performed in the presence of Na+, Cl- and CO3-2 ions to characterize typical buffer environments and electrolytes present in human blood. Furthermore, NH4+, NO3- and SO4-2 ions, found in PM, were used in the simulations. The results revealed high propensity for the aggregation of Aβ16-21 peptides. Moreover, the peptides made clusters with C60 molecules, that would be expected to act as a nucleation site for the formation of amyloid plaques. Taken together, the results showed that UFPs affected the peptide aggregation differently, depending on the type of ions present in the simulation environment. In the presence of C60, SO4-2 and NO3- ions accelerated the aggregation of Aβ16-21 peptides, however, NH4+ ions decelerated their aggregation. In addition, UFP lowered β-sheets amounts at all environments, except NaCl solution.
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Affiliation(s)
- Samal Kaumbekova
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kazakhstan
| | - Mehdi Amouei Torkmahalleh
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kazakhstan
| | - Dhawal Shah
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kazakhstan.
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Huang Y, Chang Y, Liu L, Wang J. Nanomaterials for Modulating the Aggregation of β-Amyloid Peptides. Molecules 2021; 26:4301. [PMID: 34299575 PMCID: PMC8305396 DOI: 10.3390/molecules26144301] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
The aberrant aggregation of amyloid-β (Aβ) peptides in the brain has been recognized as the major hallmark of Alzheimer's disease (AD). Thus, the inhibition and dissociation of Aβ aggregation are believed to be effective therapeutic strategiesforthe prevention and treatment of AD. When integrated with traditional agents and biomolecules, nanomaterials can overcome their intrinsic shortcomings and boost their efficiency via synergistic effects. This article provides an overview of recent efforts to utilize nanomaterials with superior properties to propose effective platforms for AD treatment. The underlying mechanismsthat are involved in modulating Aβ aggregation are discussed. The summary of nanomaterials-based modulation of Aβ aggregation may help researchers to understand the critical roles in therapeutic agents and provide new insight into the exploration of more promising anti-amyloid agents and tactics in AD theranostics.
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Affiliation(s)
- Yaliang Huang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China;
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China;
| | - Yong Chang
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China;
| | - Lin Liu
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China;
| | - Jianxiu Wang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China;
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Kang N, Hua J, Gao L, Zhang B, Pang J. The Interplay between Whey Protein Fibrils with Carbon Nanotubes or Carbon Nano-Onions. MATERIALS (BASEL, SWITZERLAND) 2021; 14:608. [PMID: 33525699 PMCID: PMC7865974 DOI: 10.3390/ma14030608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/30/2022]
Abstract
Whey protein isolate (WPI) fibrils were prepared using an acid hydrolysis induction process. Carbon nanotubes (CNTs) and carbon nano-onions (CNOs) were made via the catalytic chemical vapor deposition (CVD) of methane. WPI fibril-CNTs and WPI fibril-CNOs were prepared via hydrothermal synthesis at 80 °C. The composites were characterized by SEM, TEM, FTIR, XRD, Raman, and TG analyses. The interplay between WPI fibrils and CNTs and CNOs were studied. The WPI fibrils with CNTs and CNOs formed uniform gels and films. CNTs and CNOs were highly dispersed in the gels. Hydrogels of WPI fibrils with CNTs (or CNOs) could be new materials with applications in medicine or other fields. The CNTs and CNOs shortened the WPI fibrils, which might have important research value for curing fibrosis diseases such as Parkinson's and Alzheimer's diseases. The FTIR revealed that CNTs and CNOs both had interactions with WPI fibrils. The XRD analysis suggested that most of the CNTs were wrapped in WPI fibrils, while CNOs were partially wrapped. This helped to increase the biocompatibility and reduce the cytotoxicity of CNTs and CNOs. HR-TEM and Raman spectroscopy studies showed that the graphitization level of CNTs was higher than for CNOs. After hybridization with WPI fibrils, more defects were created in CNTs, but some original defects were dismissed in CNOs. The TG results indicated that a new phase of WPI fibril-CNTs or CNOs was formed.
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Affiliation(s)
- Ning Kang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China;
- Taiyuan Customs District, Taiyuan 030006, China;
| | - Jin Hua
- Taiyuan Customs District, Taiyuan 030006, China;
| | - Lizhen Gao
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China;
| | - Bin Zhang
- Key Laboratory of Coal Science, Technology of the Ministry of Education, Taiyuan University of Technology, Taiyuan 030024, China
| | - Jiewen Pang
- College of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan 030024, China;
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Rissanou AN, Keliri A, Arnittali M, Harmandaris V. Self-assembly of diphenylalanine peptides on graphene via detailed atomistic simulations. Phys Chem Chem Phys 2021; 22:27645-27657. [PMID: 33283818 DOI: 10.1039/d0cp03671d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom molecular dynamics simulations. Two interfacial systems are studied, with different concentrations of dipeptides and the results are compared with an aqueous solution of FF at room temperature. Corresponding length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface. A hierarchical formation of FF structures is observed involving two sequential processes: first, a stabilized interfacial layer of dipeptides onto the graphene surface is formulated, which next is followed by the development of a structure of self-aggregated dipeptides on top of this layer. The whole procedure is completed in almost 200 ns, whereas self-assembly in the system without graphene is accomplished much faster; in less than 50 ns cylindrical structures, the microscopic signal of the macroscopic fibrillar ones, are formed. Strong π-π* interactions between FF and the graphene lead to a parallel orientation to the graphene layer of the phenyl rings within a characteristic time of 80 ns, similar to the one indicated by the time evolution of the number of adsorbed FF atoms at the surface. Reduction in the number of hydrogen bonds between FF peptides is observed because of the graphene layer, since it disturbs their self-assembly propensity. The self-assembly of dipeptides and their adsorption onto the graphene surface destruct the hydrogen bond network of water, in the vicinity of FF, however, the total number of hydrogen bonds in all systems increases, promoting the formed structures.
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Affiliation(s)
- Anastassia N Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
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16
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Li Y, Tang H, Andrikopoulos N, Javed I, Cecchetto L, Nandakumar A, Kakinen A, Davis TP, Ding F, Ke PC. The membrane axis of Alzheimer's nanomedicine. ADVANCED NANOBIOMED RESEARCH 2021; 1:2000040. [PMID: 33748816 PMCID: PMC7971452 DOI: 10.1002/anbr.202000040] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Alzheimer's disease (AD) is a major neurological disorder impairing its carrier's cognitive function, memory and lifespan. While the development of AD nanomedicine is still nascent, the field is evolving into a new scientific frontier driven by the diverse physicochemical properties and theranostic potential of nanomaterials and nanocomposites. Characteristic to the AD pathology is the deposition of amyloid plaques and tangles of amyloid beta (Aβ) and tau, whose aggregation kinetics may be curbed by nanoparticle inhibitors via sequence-specific targeting or nonspecific interactions with the amyloidogenic proteins. As literature implicates cell membrane as a culprit in AD pathogenesis, here we summarize the membrane axis of AD nanomedicine and present a new rationale that the field development may greatly benefit from harnessing our existing knowledge of Aβ-membrane interaction, nanoparticle-membrane interaction and Aβ-nanoparticle interaction.
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Affiliation(s)
- Yuhuan Li
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Luca Cecchetto
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemical and Pharmaceutical Science, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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17
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Zheng H, Yang SJ, Zheng YC, Cui Y, Zhang Z, Zhong JY, Zhou J. Electrostatic Effect of Functional Surfaces on the Activity of Adsorbed Enzymes: Simulations and Experiments. ACS APPLIED MATERIALS & INTERFACES 2020; 12:35676-35687. [PMID: 32649833 DOI: 10.1021/acsami.0c08080] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The efficient immobilization of haloalkane dehalogenase (DhaA) on carriers with retaining of its catalytic activity is essential for its application in environmental remediation. In this work, adsorption orientation and conformation of DhaA on different functional surfaces were investigated by computer simulations; meanwhile, the mechanism of varying the catalytic activity was also probed. The corresponding experiments were then carried out to verify the simulation results. (The simulations of DhaA on SAMs provided parallel insights into DhaA adsorption in carriers. Then, the theory-guided experiments were carried out to screen the best surface functional groups for DhaA immobilization.) The electrostatic interaction was considered as the main impact factor for the regulation of enzyme orientation, conformation, and enzyme bioactivity during DhaA adsorption. The synergy of overall conformation, enzyme substrate tunnel structural parameters, and distance between catalytic active sites and surfaces codetermined the catalytic activity of DhaA. Specifically, it was found that the positively charged surface with suitable surface charge density was helpful for the adsorption of DhaA and retaining its conformation and catalytic activity and was favorable for higher enzymatic catalysis efficiency in haloalkane decomposition and environmental remediation. The neutral, negatively charged surfaces and positively charged surfaces with high surface charge density always caused relatively larger DhaA conformation change and decreased catalytic activity. This study develops a strategy using a combination of simulation and experiment, which can be essential for guiding the rational design of the functionalization of carriers for enzyme adsorption, and provides a practical tool to rationally screen functional groups for the optimization of adsorbed enzyme functions on carriers. More importantly, the strategy is general and can be applied to control behaviors of different enzymes on functional carrier materials.
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Affiliation(s)
- He Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Sheng-Jiang Yang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yong-Chao Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Yan Cui
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Zhe Zhang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Jin-Yi Zhong
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
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18
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Sorout N, Chandra A. Effects of Boron Nitride Nanotube on the Secondary Structure of Aβ(1–42) Trimer: Possible Inhibitory Effect on Amyloid Formation. J Phys Chem B 2020; 124:1928-1940. [DOI: 10.1021/acs.jpcb.9b11986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nidhi Sorout
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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He Z, Li J, Chen SH, Zhou R. Surface Inhomogeneity of Graphene Oxide Influences Dissociation of Aβ 16-21 Peptide Assembly. J Phys Chem B 2019; 123:9098-9103. [PMID: 31566974 DOI: 10.1021/acs.jpcb.9b07359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abnormal peptide assembly and aggregation is associated with an array of neurodegenerative diseases including Alzheimer's disease (AD). A detailed understanding of how nanostructured materials such as oxidized graphene perturb the peptide assembly and subsequently induce fibril dissociation may open new directions for the development of potential AD treatments. Here, we investigate the impact of surface inhomogeneity of graphene oxide (GO) on the assembly of amyloid-beta Aβ16-21 peptides on GO surfaces with different degrees of oxidation using molecular dynamics simulations. Interestingly, nonuniform GO nanosheets (in terms of oxidation sites) have a much stronger perturbation effect on the structure of Aβ16-21 assembly. The Aβ peptides exhibit a remarkable tendency in binding to the scattered interfaces between unoxidized and oxidized regions, which induces the dissociation of Aβ amyloid fibril. These findings should deepen our understanding of surface-induced peptide dissociation and stimulate discovery of alternative AD treatments.
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Affiliation(s)
| | | | - Serena H Chen
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
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20
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Wang X, Han Q, Liu X, Wang C, Yang R. Multifunctional inhibitors of β-amyloid aggregation based on MoS 2/AuNR nanocomposites with high near-infrared absorption. NANOSCALE 2019; 11:9185-9193. [PMID: 31038146 DOI: 10.1039/c9nr01845j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recent advances in nanotechnology have developed a lot of opportunities for biological applications. In this work, multifunctional MoS2/AuNR nanocomposites with unique high NIR absorption were designed via combining MoS2 nanosheets and gold nanorods (AuNRs). The nanocomposites were synthesized through electrostatic self-assembly and showed high stability and good biocompatibility. Then they were used to modulate the aggregation of amyloid-β peptides, destabilize mature fibrils under NIR irradiation, and eliminate Aβ-induced ROS against neurotoxicity. The inhibition and destabilization effects were confirmed by Thioflavin T (ThT) fluorescence assay and transmission electron microscopy (TEM). Cell viability assay and ROS assay revealed that MoS2/AuNR nanocomposites could alleviate Aβ-induced oxidative stress and cell toxicity. More importantly, both MoS2 nanosheets and AuNRs can be used as NIR photothermal agents, MoS2/AuNR nanocomposites have enhanced ability of disrupting Aβ fibrils and improved cell viability by generating local heat under low power NIR irradiation. Our results provide new insights into the design of new multifunctional systems for the treatment of amyloid-related diseases.
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Affiliation(s)
- Xinhuan Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Center of Materials Science and Optoelectronics Engineering, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 1000190, P. R. China.
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21
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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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22
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Mo Y, Brahmachari S, Lei J, Gilead S, Tang Y, Gazit E, Wei G. The Inhibitory Effect of Hydroxylated Carbon Nanotubes on the Aggregation of Human Islet Amyloid Polypeptide Revealed by a Combined Computational and Experimental Study. ACS Chem Neurosci 2018; 9:2741-2752. [PMID: 29986579 DOI: 10.1021/acschemneuro.8b00166] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Fibrillar deposits formed by the aggregation of the human islet amyloid polypeptide (hIAPP) are the major pathological hallmark of type 2 diabetes mellitus (T2DM). Inhibiting the aggregation of hIAPP is considered the primary therapeutic strategy for the treatment of T2DM. Hydroxylated carbon nanoparticles have received great attention in impeding amyloid protein fibrillation owing to their reduced cytotoxicity compared to the pristine ones. In this study, we investigated the influence of hydroxylated single-walled carbon nanotubes (SWCNT-OHs) on the first step of hIAPP aggregation: dimerization by performing explicit solvent replica exchange molecular dynamics (REMD) simulations. Extensive REMD simulations demonstrate that SWCNT-OHs can dramatically inhibit interpeptide β-sheet formation and completely suppress the previously reported β-hairpin amyloidogenic precursor of hIAPP. On the basis of our simulation results, we proposed that SWCNT-OH can hinder hIAPP fibrillation. This was further confirmed by our systematic turbidity measurements, thioflavin T fluorescence, circular dichroism (CD), transmission electron microscope (TEM), and atomic force microscopy (AFM) experiments. Detailed analyses of hIAPP-SWCNT-OH interactions reveal that hydrogen bonding, van der Waals, and π-stacking interactions between hIAPP and SWCNT-OH significantly weaken the inter- and intrapeptide interactions that are crucial for β-sheet formation. Our collective computational and experimental data reveal not only the inhibitory effect but also the inhibitory mechanism of SWCNT-OH against hIAPP aggregation, thus providing new clues for the development of future drug candidates against T2DM.
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Affiliation(s)
- Yuxiang Mo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
- College of Physical Science and Technology, Guangxi Normal University, 15 Yucai Road, Guilin 541004, People’s Republic of China
| | - Sayanti Brahmachari
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jiangtao Lei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
| | - Sharon Gilead
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yiming Tang
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
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Roccatano D, Sarukhanyan E, Zangi R. Adsorption mechanism of an antimicrobial peptide on carbonaceous surfaces: A molecular dynamics study. J Chem Phys 2018; 146:074703. [PMID: 28228017 DOI: 10.1063/1.4975689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptaken by living cells, and their high surface-to-volume ratio facilitates the adsorption of molecules of different natures. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutical agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A-Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surfaces through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalizable Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to the loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus into the interior of the CNT, was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion.
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Affiliation(s)
- Danilo Roccatano
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| | - Edita Sarukhanyan
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ronen Zangi
- Polymat and Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain
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Matsubara T, Nishihara M, Yasumori H, Nakai M, Yanagisawa K, Sato T. Size and Shape of Amyloid Fibrils Induced by Ganglioside Nanoclusters: Role of Sialyl Oligosaccharide in Fibril Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13874-13881. [PMID: 29148800 DOI: 10.1021/acs.langmuir.7b02091] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ganglioside-enriched microdomains in the presynaptic neuronal membrane play a key role in the initiation of amyloid ß-protein (Aß) assembly related to Alzheimer's disease. We previously isolated lipids from a detergent-resistant membrane microdomain fraction of synaptosomes prepared from aged mouse brain and found that spherical Aß assemblies were formed on Aß-sensitive ganglioside nanoclusters (ASIGN) of reconstituted lipid bilayers in the synaptosomal fraction. In the present study, we investigated the role of oligosaccharides in Aß fibril formation induced by ganglioside-containing mixed lipid membranes that mimic the features of ASIGN. Ganglioside nanoclusters were constructed as ternary mixed lipid bilayers composed of ganglioside (GM1, GM2, GM3, GD1a, or GT1b), sphingomyelin, and cholesterol, and their surface topography was visualized by atomic force microscopy. Aß fibril formation on the nanocluster was strongly induced in the presence of 10 mol % ganglioside, and Aß-sensitive features were observed at cholesterol contents of 35-55 mol %. GM1-, GD1a-, and GT1b-containing membranes induced longer fibrils than those containing GD1b and GM2, indicating that the terminal galactose of GM1 along with N-acetylneuraminic acid accelerates protofibril elongation. These results demonstrate that Aß fibril formation is induced by ASIGN that are highly enriched ganglioside nanoclusters with a limited number of components and that the generation and elongation of Aß protofibrils are regulated by the oligosaccharide structure of gangliosides.
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Affiliation(s)
- Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Masaya Nishihara
- Department of Biosciences and Informatics, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Hanaki Yasumori
- Department of Biosciences and Informatics, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Mako Nakai
- Department of Biosciences and Informatics, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Katsuhiko Yanagisawa
- Department of Alzheimer's Disease Research, Center for Development of Advanced Medicine for Dementia , National Center for Geriatrics and Gerontology, 7-430 Morioka, Obu 474-8511, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
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Lai L, Jiang X, Han S, Zhao C, Du T, Rehman FU, Zheng Y, Li X, Liu X, Jiang H, Wang X. In Vivo Biosynthesized Zinc and Iron Oxide Nanoclusters for High Spatiotemporal Dual-Modality Bioimaging of Alzheimer's Disease. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9018-9024. [PMID: 28806518 DOI: 10.1021/acs.langmuir.7b01516] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Alzheimer's disease is still incurable and neurodegenerative, and there is a lack of detection methods with high sensitivity and specificity. In this study, by taking different month old Alzheimer's mice as models, we have explored the possibility of the target bioimaging of diseased sites through the initial injection of zinc gluconate solution into Alzheimer's model mice post-tail vein and then the combination of another injection of ferrous chloride (FeCl2) solution into the same Alzheimer's model mice post-stomach. Our observations indicate that both zinc gluconate solution and FeCl2 solution could cross the blood-brain barrier (BBB) to biosynthesize the fluorescent zinc oxide nanoclusters and magnetic iron oxide nanoclusters, respectively, in the lesion areas of the AD model mice, thus enabling high spatiotemporal dual-modality bioimaging (i.e., including fluorescence bioimaging (FL) and magnetic resonance imaging (MRI)) of Alzheimer's disease for the first time. The result presents a novel promising strategy for the rapid and early diagnosis of Alzheimer's disease.
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Affiliation(s)
- Lanmei Lai
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Xuerui Jiang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Shanying Han
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Chunqiu Zhao
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Tianyu Du
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Fawad Ur Rehman
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Youkun Zheng
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Xiaoqi Li
- Nanjing Foreign Language School, Nanjing 210096, China
| | - Xiaoli Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Hui Jiang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
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26
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A molecular dynamics study on the adsorption of a mussel protein on two different films: Polymer film and a SAM. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Zou X, Wei S, Jasensky J, Xiao M, Wang Q, Brooks Iii CL, Chen Z. Molecular Interactions between Graphene and Biological Molecules. J Am Chem Soc 2017; 139:1928-1936. [PMID: 28092440 DOI: 10.1021/jacs.6b11226] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e.g., to detect analytes in solution). To control and characterize peptide behavior on a graphene surface in solution is difficult. Here we successfully probed the molecular interactions between two peptides (cecropin P1 and MSI-78(C1)) and graphene in situ and in real-time using sum frequency generation (SFG) vibrational spectroscopy and molecular dynamics (MD) simulation. We demonstrated that the distribution of various planar (including aromatic (Phe, Trp, Tyr, and His)/amide (Asn and Gln)/Guanidine (Arg)) side-chains and charged hydrophilic (such as Lys) side-chains in a peptide sequence determines the orientation of the peptide adsorbed on a graphene surface. It was found that peptide interactions with graphene depend on the competition between both planar and hydrophilic residues in the peptide. Our results indicated that part of cecropin P1 stands up on graphene due to an unbalanced distribution of planar and hydrophilic residues, whereas MSI-78(C1) lies down on graphene due to an even distribution of Phe residues and hydrophilic residues. With such knowledge, we could rationally design peptides with desired residues to manipulate peptide-graphene interactions, which allows peptides to adopt optimized structure and exhibit excellent activity for nanobio-technological applications. This research again demonstrates the power to combine SFG vibrational spectroscopy and MD simulation in studying interfacial biological molecules.
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Affiliation(s)
- Xingquan Zou
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shuai Wei
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Joshua Jasensky
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Minyu Xiao
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Qiuming Wang
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks Iii
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
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Ban DK, Paul S. Nano Zinc Oxide Inhibits Fibrillar Growth and Suppresses Cellular Toxicity of Lysozyme Amyloid. ACS APPLIED MATERIALS & INTERFACES 2016; 8:31587-31601. [PMID: 27801574 DOI: 10.1021/acsami.6b11549] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Deposition of amyloid fibers has been a common pathological event in many neurodegenerations, such as Alzheimer's disease, Parkinson's disease, and Prion disease. Although various therapeutic interventions have been reported, nanoparticles have recently been considered as possible inhibitors of amyloid fibrillation. Here, we reported the effect of three different forms of zinc oxide nanoparticles (ZnONP): uncapped (ZnONPuncap), starch-capped (ZnONPST), and self-assembled (ZnONPassmb) (average sizes of 10, 30, and 163 nm, respectively), having a core size of 10-15 nm, in the amyloid growth of hen egg white lysozyme (HEWL). We monitored the amyloid growth by electron microscopy as well as Thioflavin-T (ThT) measurement. We observed that ZnONP demonstrated a dose-dependent inhibition of fibrillar amyloid growth of HEWL, with the greatest effect being exhibited by ZnONPST. Such inhibition was also associated with a decrease in cross β-sheet amount, surface hydrophobicity as well as increase of stability of proteins. Furthermore, we observed that ZnONPST prolonged the nucleation phase and shortened the elongation phase of HEWL amyloid growth. Although pure amyloid caused profound cellular toxicity in both mouse carcinoma N2a and normal cells such as human keratinocytes HaCaT cells, amyloid formed in the presence of ZnONP showed much reduced cellular toxicity. We also observed that the inhibition of amyloid growth was effective when ZnONP was administered during the lag phase. When our amyloid inhibition results were compared with a well-known inhibitor curcumin, we observed that ZnONPST demonstrated a better inhibitory effect than curcumin. Overall, here, we reported the inhibitory activity of three different forms of ZnONP to amyloid fibrillation of HEWL and amyloid-mediated cytotoxicity to different extents, while starch-capped ZnONP showed the highest fibrillation inhibitory effect.
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Affiliation(s)
- Deependra Kumar Ban
- Department of Biotechnology and Medical Engineering, National Institute of Technology , Rourkela-769008, Odisha, India
| | - Subhankar Paul
- Department of Biotechnology and Medical Engineering, National Institute of Technology , Rourkela-769008, Odisha, India
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29
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Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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30
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Shezad K, Zhang K, Hussain M, Dong H, He C, Gong X, Xie X, Zhu J, Shen L. Surface Roughness Modulates Diffusion and Fibrillation of Amyloid-β Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8238-8244. [PMID: 27466062 DOI: 10.1021/acs.langmuir.6b01756] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The presence of surfaces influences the kinetics of amyloid-β (Aβ) peptide fibrillation. Although it has been generally recognized that the fibrillation process can be assisted or accelerated by surface chemistry, the impact of surface topography, i.e., roughness, on peptide fibrillation is relatively little understood. Here we study the role of surface roughness on surface-mediated fibrillation using polymer coatings of varying roughness as well as polymer microparticles. Using single-molecule tracking, atomic force microscopy, and the thioflavin T fluorescence technique, we show that a rough surface decelerates the two-dimensional (2D) diffusion of peptides and retards the surface-mediated fibrillation. A higher degree of roughness that presents an obstacle to peptide diffusion is found to inhibit the fibrillation process.
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Affiliation(s)
- Khurram Shezad
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Kejun Zhang
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Mubashir Hussain
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Hai Dong
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Chuanxin He
- College of Chemistry and Environmental Engineering, Shenzhen University , Shenzhen 518060, China
| | - Xiangjun Gong
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510640, China
| | - Xiaolin Xie
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Jintao Zhu
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Lei Shen
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
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31
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Bag S, Sett A, DasGupta S, Dasgupta S. Hydropathy: the controlling factor behind the inhibition of Aβ fibrillation by graphene oxide. RSC Adv 2016. [DOI: 10.1039/c6ra23570k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Fibrillation of Aβ25–35 peptide is inhibited in presence of graphene oxide.
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Affiliation(s)
- Sudipta Bag
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Ayantika Sett
- Department of Chemical Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Sunando DasGupta
- Department of Chemical Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Swagata Dasgupta
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
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32
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Shigeno M, Sawato T, Yamaguchi M. Fibril Film Formation of Pseudoenantiomeric Oxymethylenehelicene Oligomers at the Liquid-Solid Interface: Structural Changes, Aggregation, and Discontinuous Heterogeneous Nucleation. Chemistry 2015; 21:17676-82. [DOI: 10.1002/chem.201503224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 12/21/2022]
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33
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Wang X, Weber JK, Liu L, Dong M, Zhou R, Li J. A novel form of β-strand assembly observed in Aβ(33-42) adsorbed onto graphene. NANOSCALE 2015; 7:15341-15348. [PMID: 26331805 DOI: 10.1039/c5nr00555h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Peptide assembly plays a seminal role in the fabrication of structural and functional architectures in cells. Characteristically, peptide assemblies are often dominated by β-sheet structures, wherein component molecules are connected by backbone hydrogen bonds in a parallel or an antiparallel fashion. While β-rich peptide scaffolds are implicated in an array of neurodegenerative diseases, the mechanisms by which toxic peptides assemble and mediate neuropathic effects are still poorly understood. In this work, we employ molecular dynamics simulations to study the adsorption and assembly of the fragment Aβ33-42 (taken from the Aβ-42 peptide widely associated with Alzheimer's disease) on a graphene surface. We observe that such Aβ33-42 fragments, which are largely hydrophobic in character, readily adsorb onto the graphitic surface and coalesce into a well-structured, β-strand-like assembly. Strikingly, the structure of such complex is quite unique: hydrophobic side-chains extend over the graphene surface and interact with adjacent peptides, yielding a well-defined mosaic of hydrophobic interaction patches. This ordered structure is markedly depleted of backbone hydrogen bonds. Hence, our simulation results reveal a distinct type of β-strand assembly, maintained by hydrophobic side-chain interactions. Our finding suggests the backbone hydrogen bond is no longer crucial to the peptide assembly. Further studies concerning whether such β-strand assembly can be realized in other peptide systems and in biologically-relevant contexts are certainly warranted.
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Affiliation(s)
- Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.
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34
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Liu J, Peng C, Yu G, Zhou J. Molecular simulation study of feruloyl esterase adsorption on charged surfaces: effects of surface charge density and ionic strength. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10751-10763. [PMID: 26379082 DOI: 10.1021/acs.langmuir.5b01491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a nonmodular type-A feruloyl esterase from Aspergillus niger (AnFaeA) on charged surfaces was investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics (AAMD) simulations at different surface charge densities (±0.05 and ±0.16 C·m(-2)) and ionic strengths (0.007 and 0.154 M). The adsorption energy, orientation, and conformational changes were analyzed. Simulation results show that whether AnFaeA can adsorb onto a charged surface is mainly controlled by electrostatic interactions between AnFaeA and the charged surface. The electrostatic interactions between AnFaeA and charged surfaces are weakened when the ionic strength increases. The positively charged surface at low surface charge density and high ionic strength conditions can maximize the utilization of the immobilized AnFaeA. The counterion layer plays a key role in the adsorption of AnFaeA on the negatively charged COOH-SAM. The native conformation of AnFaeA is well preserved under all of these conditions. The results of this work can be used for the controlled immobilization of AnFaeA.
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Affiliation(s)
- Jie Liu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, PR China
| | - Chunwang Peng
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, PR China
| | - Gaobo Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, PR China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, PR China
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35
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Long noncoding RNA SPRY4-IT1 predicts poor patient prognosis and promotes tumorigenesis in gastric cancer. Tumour Biol 2015; 53:2016-2028. [PMID: 25835973 DOI: 10.1007/s12035-015-9142-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/12/2015] [Indexed: 12/16/2022] Open
Abstract
Gastric cancer (GC) is the second common cause of cancer-related death worldwide. Long noncoding RNAs (lncRNAs) are emerging as novel regulators in the cancer paradigm. However, investigation of lncRNAs on GC is still in its infancy. In this study, we focused on lncRNA SPRY4 intronic transcript 1 (SPRY4-IT1) and investigated its expression pattern, clinical significance, biological function, and molecular mechanism in GC. SPRY4-IT1 expression was examined, and its correlation with clinicopathological characteristics and patient prognosis was analyzed. A series of assays were performed to understand the role of SPRY4-IT1 in GC. SPRY4-IT1 expression was elevated in GC tissues and cell lines, and SPRY4-IT1 levels were highly positively correlated with tumor size, invasion depth, distant metastasis, TNM stage, and reduced overall survival (OS) and disease-free survival (DFS). A multivariate analysis showed that SPRY4-IT1 expression is an independent prognostic factor of OS and DFS in patients with GC. Additionally, the results of in vitro assays showed that the suppression of SPRY4-IT1 expression in GC cell line MKN-45 significantly reduced cell proliferation, colony formation, and cell migration/invasion. Moreover, the tumorigenic effects of SPRY4-IT1 were partially mediated by the regulation of certain cyclins and matrix metalloproteinases (MMPs)-related genes. Our data suggest that SPRY4-IT1 plays a critical role in GC tumorigenesis and may represent a novel prognostic marker and potential therapeutic target in patients with GC.
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36
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Bajda M, Filipek S. Study of early stages of amyloid Aβ13-23 formation using molecular dynamics simulation in implicit environments. Comput Biol Chem 2015; 56:13-8. [PMID: 25749181 DOI: 10.1016/j.compbiolchem.2015.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 02/09/2015] [Accepted: 02/21/2015] [Indexed: 02/07/2023]
Abstract
β-amyloid aggregation and formation of senile plaques is one of the hallmarks of Alzheimer's disease (AD). It leads to degeneration of neurons and decline of cognitive functions. The most aggregative and toxic form of β-amyloid is Aβ1-42 but in experiments, the shorter forms able to form aggregates are also used. The early stages of amyloid formation are of special interest due to the influence of this peptide on progression of AD. Here, we employed nine helices of undecapeptide Aβ13-23 and studied progress of amyloid formation using 500ns molecular dynamics simulation and implicit membrane environment. The small β-sheets emerged very early during simulation as separated two-strand structures and a presence of the membrane facilitated this process. Later, the larger β-sheets were formed. However, the ninth helix which did not form paired structure stayed unchanged till the end of MD simulation. Paired helix-helix interactions seemed to be a driving force of β-sheet formation at early stages of amyloid formation. Contrary, the specific interactions between α-helix and β-sheet can be very stable and be stabilized by the membrane.
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Affiliation(s)
- Marek Bajda
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Medical College, Jagiellonian University, Medyczna 9, 30-688 Cracow, Poland.
| | - Slawomir Filipek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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37
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Zhao D, Peng C, Zhou J. Lipase adsorption on different nanomaterials: a multi-scale simulation study. Phys Chem Chem Phys 2015; 17:840-50. [DOI: 10.1039/c4cp04696j] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Adsorption orientations of lipase on different nanomaterials with different surface chemistry.
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Affiliation(s)
- Daohui Zhao
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Chunwang Peng
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
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38
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Liu J, Yu G, Zhou J. Ribonuclease A adsorption onto charged self-assembled monolayers: A multiscale simulation study. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.07.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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39
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Peter EK, Agarwal M, Kim B, Pivkin IV, Shea JE. How water layers on graphene affect folding and adsorption of TrpZip2. J Chem Phys 2014; 141:22D511. [DOI: 10.1063/1.4896984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Mrigya Agarwal
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
| | - BongKeun Kim
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Igor V. Pivkin
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
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40
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Peng C, Liu J, Zhao D, Zhou J. Adsorption of hydrophobin on different self-assembled monolayers: the role of the hydrophobic dipole and the electric dipole. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:11401-11. [PMID: 25185838 DOI: 10.1021/la502595t] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this work, the adsorptions of hydrophobin (HFBI) on four different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by parallel tempering Monte Carlo and molecular dynamics simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions, while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of a hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of an electric dipole for charged surfaces. Therefore, the hydrophobic dipole may be applied to predict the probable orientations of protein adsorbed on hydrophobic surfaces.
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Affiliation(s)
- Chunwang Peng
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou, Guangdong 510640, P. R. China
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41
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Xie L, Luo Y, Lin D, Xi W, Yang X, Wei G. The molecular mechanism of fullerene-inhibited aggregation of Alzheimer's β-amyloid peptide fragment. NANOSCALE 2014; 6:9752-62. [PMID: 25004796 DOI: 10.1039/c4nr01005a] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Amyloid deposits are implicated in the pathogenesis of many neurodegenerative diseases such as Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. Increasing data show that nanoparticles can retard or promote the fibrillation of amyloid-β (Aβ) peptides depending on the physicochemical properties of nanoparticles, however, the underlying molecular mechanism remains elusive. In this study, our replica exchange molecular dynamics (REMD) simulations show that fullerene nanoparticle - C60 (with a fullerene : peptide molar ratio greater than 1 : 8) can dramatically prevent β-sheet formation of Aβ(16-22) peptides. Atomic force microscopy (AFM) experiments further confirm the inhibitory effect of C60 on Aβ(16-22) fibrillation, in support of our REMD simulations. An important finding from our REMD simulations is that fullerene C180, albeit with the same number of carbon atoms as three C60 molecules (3C60) and smaller surface area than 3C60, displays an unexpected stronger inhibitory effect on the β-sheet formation of Aβ(16-22) peptides. A detailed analysis of the fullerene-peptide interaction reveals that the stronger inhibition of β-sheet formation by C180 results from the strong hydrophobic and aromatic-stacking interactions of the fullerene hexagonal rings with the Phe rings relative to the pentagonal rings. The strong interactions between the fullerene nanoparticles and Aβ(16-22) peptides significantly weaken the peptide-peptide interaction that is important for β-sheet formation, thus retarding Aβ(16-22) fibrillation. Overall, our studies reveal the significant role of fullerene hexagonal rings in the inhibition of Aβ(16-22) fibrillation and provide novel insight into the development of drug candidates against Alzheimer's disease.
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Affiliation(s)
- Luogang Xie
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China.
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42
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Xie B, Li X, Dong XY, Sun Y. Insight into the inhibition effect of acidulated serum albumin on amyloid β-protein fibrillogenesis and cytotoxicity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:9789-9796. [PMID: 25083748 DOI: 10.1021/la5025197] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia, and aggregation of amyloid β-proteins (Aβ) into soluble oligomers and fibrils has been implicated in the pathogenesis of AD. Herein we developed acidulated serum albumin for the inhibition of Aβ42 fibrillogenesis. Bovine serum albumin (BSA) was modified with diglycolic anhydride, leading to the coupling of 14.5 more negative charges (carboxyl groups) on average on each protein surface. The acidulated BSA (A-BSA) was characterized and confirmed to keep the tertiary structure and stability of BSA. Extensive biophysical and biological analyses showed that A-BSA significantly inhibited Aβ42 fibrillogenesis and mitigated amyloid cytotoxicity. As compared to the Aβ42-treated group (cell viability, 50%), the cell viability increased to 88% by the addition of equimolar A-BSA. The inhibitory effect was remarkably higher than that of BSA at the same concentration. On the basis of the experimental findings, a mechanistic model was proposed. The model considers that Aβ42 is bound to the A-BSA surface by hydrophobic interactions, but the widely distributed negative charges on the A-BSA surface give rise to electrostatic repulsions to the bound Aβ42 that is also negatively charged. The two well-balanced opposite forces make Aβ42 adopt extended conformations instead of the β-sheet structure that is necessary for the on-pathway fibrillogenesis, even when the protein is released off the surface. Thus, A-BSA greatly slows down the fibrillation and changes the fibrillogenesis pathway, leading to the formation of less toxic aggregates. The findings and the mechanistic model offer new insights into the development of more potent inhibitors of Aβ fibrillogenesis and cytotoxicity.
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Affiliation(s)
- Baolong Xie
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, China
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43
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Vácha R, Linse S, Lund M. Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. J Am Chem Soc 2014; 136:11776-82. [DOI: 10.1021/ja505502e] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Robert Vácha
- National
Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kamenice
5, 625 00 Brno-Bohunice, Czech Republic
| | - Sara Linse
- Division
of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Mikael Lund
- Division
of Theoretical Chemistry, Lund University, Lund, Sweden
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44
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Li Y, Liu X, Dong X, Zhang L, Sun Y. Biomimetic design of affinity peptide ligand for capsomere of virus-like particle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8500-8508. [PMID: 24976378 DOI: 10.1021/la5017438] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Virus-like particle (VLP) of murine polyomavirus (MPV) is a T = 7d icosahedral capsid that self-assembles from 72 capsomeres (Caps), each of which is a pentamer of major coat protein VP1. VLP has great potential in vaccinology, gene therapy, drug delivery, and materials science. However, its application is hindered by high cost downstream processes, leading to an urgent demand of a highly efficient affinity ligand for the separation and purification of Cap by affinity chromatography. Herein a biomimetic design strategy of an affinity peptide ligand of Cap has been developed on the basis of the binding structure of the C-terminus of minor coat protein (VP2-C) on the inner surface of Cap. The molecular interactions between VP2-C and Cap were first examined using all-atom molecular dynamics (MD) simulations coupled with the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method, where V283, P285, D286, W287, L289, and Y296 of VP2-C were identified as the hot spots. An affinity peptide library (DWXLXLXY, X denotes arbitrary amino acids except cysteine) was then constructed for virtual screening sequently by docking with AUTODOCK VINA, binding structure comparison, and final docking with ROSETTA FlexPepDock. Ten peptide candidates were selected and further confirmed by MD simulations and MM/PBSA, where DWDLRLLY was found to have the highest affinity to Cap. In DWDLRLLY, six residues are favorable for the binding, including W2, L4, L6 and Y8 inheriting from VP2-C, and R5 and L7 selected in the virtual screening. This confirms the high efficiency and accuracy of the biomimetic design strategy. DWDLRLLY was then experimentally validated by a one-step purification of Cap from crude cell lysate using affinity chromatography with the octapeptide immobilized on Sepharose gel. The purified Caps were observed to self-assemble into VLP with consistent structure of authentic MPV.
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Affiliation(s)
- Yanying Li
- 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, People's Republic of China
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Qing G, Zhao S, Xiong Y, Lv Z, Jiang F, Liu Y, Chen H, Zhang M, Sun T. Chiral effect at protein/graphene interface: a bioinspired perspective to understand amyloid formation. J Am Chem Soc 2014; 136:10736-42. [PMID: 25011035 DOI: 10.1021/ja5049626] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein misfolding to form amyloid aggregates is the main cause of neurodegenerative diseases. While it has been widely acknowledged that amyloid formation in vivo is highly associated with molecular surfaces, particularly biological membranes, how their intrinsic features, for example, chirality, influence this process still remains unclear. Here we use cysteine enantiomer modified graphene oxide (GO) as a model to show that surface chirality strongly influences this process. We report that R-cysteine modification suppresses the adsorption, nucleation, and fiber elongation processes of Aβ(1-40) and thus largely inhibits amyloid fibril formation on the surface, while S-modification promotes these processes. And surface chirality also greatly influences the conformational transition of Aβ(1-40) from α-helix to β-sheet. More interestingly, we find that this effect is highly related to the distance between chiral moieties and GO surface, and inserting a spacer group of about 1-2 nm between them prevents the adsorption of Aβ(1-40) oligomers, which eliminates the chiral effect. Detailed study stresses the crucial roles of GO surface. It brings novel insights for better understanding the amyloidosis process on surface from a biomimetic perspective.
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Affiliation(s)
- Guangyan Qing
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, People's Republic of China
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Li Q, Liu L, Zhang S, Xu M, Wang X, Wang C, Besenbacher F, Dong M. Modulating aβ33-42 peptide assembly by graphene oxide. Chemistry 2014; 20:7236-40. [PMID: 24838837 DOI: 10.1002/chem.201402022] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 12/12/2022]
Abstract
Graphene oxide (GO) is utilized as the modulator to tune the formation and development of amyloid fibrils (Aβ33-42 ). Atomic force microscopy temporal evolution measurements reveal that the initial binding between the peptide monomer and the large available surface of the GO sheets can redirect the assembly pathway of amyloid beta. The results support the possibility to develop graphene-based materials to inhibit amyloidosis.
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Affiliation(s)
- Qiang Li
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark), Fax: (+45) 8942-3690
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Zhang L, Sun Y. Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: I. Construction of an affinity binding model. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4725-4733. [PMID: 24697616 DOI: 10.1021/la404599s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Platelet adhesion on a collagen surface through integrin α2β1 has been proven to be significant for the formation of arterial thrombus. However, the molecular determinants mediating the integrin-collagen complex remain unclear. In the present study, the dynamics of integrin-collagen binding and molecular interactions were investigated using molecular dynamics (MD) simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis. Hydrophobic interaction is identified as the major driving force for the formation of the integrin-collagen complex. On the basis of the MD simulation and MM-PBSA results, an affinity binding model (ABM) of integrin for collagen is constructed; it is composed of five residues, including Y157, N154, S155, R288, and L220. The ABM has been proven to capture the major binding motif contributing 84.8% of the total binding free energy. On the basis of the ABM, we expect to establish a biomimetic design strategy of platelet adhesion inhibitors, which would be beneficial for the development of potent peptide-based drugs for thrombotic diseases.
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Affiliation(s)
- Lin Zhang
- 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, People's Republic of China
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Heng Z, Li-mei H, Cun-guo L, Li W, Shi-ling Y. Molecular Dynamics Simulation of Interaction between Lysozyme and Non-fouling Polymer Membranes. ACTA POLYM SIN 2014. [DOI: 10.3724/sp.j.1105.2014.13164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Drolle E, Hane F, Lee B, Leonenko Z. Atomic force microscopy to study molecular mechanisms of amyloid fibril formation and toxicity in Alzheimer's disease. Drug Metab Rev 2014; 46:207-23. [PMID: 24495298 DOI: 10.3109/03602532.2014.882354] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disease characterized by dementia and memory loss for which no cure or effective prevention is currently available. Neurodegeneration in AD is linked to formation of amyloid plaques found in brain tissues of Alzheimer's patients during post-mortem examination. Amyloid plaques are composed of amyloid fibrils and small oligomers - insoluble protein aggregates. Although amyloid plaques are found on the neuronal cell surfaces, the mechanism of amyloid toxicity is still not well understood. Currently, it is believed that the cytotoxicity is a result of the nonspecific interaction of small soluble amyloid oligomers (rather than longer fibrils) with the plasma membrane. In recent years, nanotechnology has contributed significantly to understanding the structure and function of lipid membranes and to the study of the molecular mechanisms of membrane-associated diseases. We review the current state of research, including applications of the latest nanotechnology approaches, on the interaction of lipid membranes with the amyloid-β (Aβ) peptide in relation to amyloid toxicity. We discuss the interactions of Aβ with model lipid membranes with a focus to demonstrate that composition, charge and phase of the lipid membrane, as well as lipid domains and rafts, affect the binding of Aβ to the membrane and contribute to toxicity. Understanding the role of the lipid membrane in AD at the nanoscale and molecular level will contribute to the understanding of the molecular mechanism of amyloid toxicity and may aid into the development of novel preventive strategies to combat AD.
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Affiliation(s)
- Elizabeth Drolle
- Department of Biology, University of Waterloo , Waterloo, ON , Canada
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Luan Y, Li D, Wang Y, Liu X, Brash JL, Chen H. 125I-radiolabeling, surface plasmon resonance, and quartz crystal microbalance with dissipation: three tools to compare protein adsorption on surfaces of different wettability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:1029-1035. [PMID: 24393063 DOI: 10.1021/la403498w] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The extent of protein adsorption is an important consideration in the biocompatibility of biomaterials. Various experimental methods can be used to determine the quantity of protein adsorbed, but the results usually differ. In the present work, self-assembled monolayers (SAMs) were used to prepare a series of model gold surfaces varying systematically in water wettability, from hydrophilic to hydrophobic. Three commonly used methods, namely, surface plasmon resonance (SPR), quartz crystal microbalance with dissipation (QCM-D), and (125)I-radiolabeling, were employed to quantify fibrinogen (Fg) adsorption on these surfaces. This approach allows a direct comparison of the mass of Fg adsorbed using these three techniques. The results from all three methods showed that protein adsorption increases with increasing surface hydrophobicity. The increase in the mass of Fg adsorbed with increasing surface hydrophobicity in the SPR data was parallel to that from (125)I-radiolabeling, but the absolute values were different and there does not seem to be a "universally congruent" relationship between the two methods for surfaces with varying wettability. For QCM-D, the variation in protein adsorption with wettability was different from that for SPR and radiolabeling. On the more hydrophobic surfaces, QCM-D gave an adsorbed mass much higher than from the two other methods, possibly because QCM-D measures both the adsorbed Fg and its associated water. However, on the more hydrophilic surfaces, the adsorbed mass from QCM-D was slightly greater than that from SPR, and both were smaller than from (125)I-radiolabeling; this was true no matter whether the Sauerbrey equation or the Voigt model was used to convert QCM-D data to adsorbed mass.
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Affiliation(s)
- Yafei Luan
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University , 199 Ren-ai Road, Suzhou 215123, PR China
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