1
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Cheung DL. Aggregation of an Amyloidogenic Peptide on Gold Surfaces. Biomolecules 2023; 13:1261. [PMID: 37627326 PMCID: PMC10452923 DOI: 10.3390/biom13081261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Solid surfaces have been shown to affect the aggregation and assembly of many biomolecular systems. One important example is the formation of protein fibrils, which can occur on a range of biological and synthetic surfaces. The rate of fibrillation depends on both the protein structure and the surface chemistry, with the different molecular and oligomer structures adopted by proteins on surfaces likely to be crucial. In this paper, the aggregation of the model amyloidogenic peptide, Aβ(16-22), corresponding to a hydrophobic segment of the amyloid beta protein on a gold surface is studied using molecular dynamics simulation. Previous simulations of this peptide on gold surfaces have shown that it adopts conformations on surfaces that are quite different from those in bulk solution. These simulations show that this then leads to significant differences in the oligomer structures formed in solution and on gold surfaces. In particular, oligomers formed on the surface are low in beta-strands so are unlike the structures formed in bulk solution. When oligomers formed in solution adsorb onto gold surfaces they can then restructure themselves. This can then help explain the inhibition of Aβ(16-22) fibrillation by gold surfaces and nanoparticles seen experimentally.
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Affiliation(s)
- David L Cheung
- School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
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2
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Mao D, Wu YY, Tu Y. Unexpectedly resisting protein adsorption on self-assembled monolayers terminated with two hydrophilic hydroxyl groups. Phys Chem Chem Phys 2023; 25:21376-21382. [PMID: 37530059 DOI: 10.1039/d3cp02376a] [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: 08/03/2023]
Abstract
OH-terminated self-assembled monolayers, as protein-resistant surfaces, have significant potential in biocompatible implant devices, which can avoid or reduce adverse reactions caused by protein adhesion to biomaterial surfaces, such as thrombosis, immune response and inflammation. Here, molecular dynamics simulations were performed to evaluate the degree of protein adsorption on the self-assembled monolayer terminated with two hydrophilic OH groups ((OH)2-SAM) at packing densities (Σ) of 4.5 nm-2 and 6.5 nm-2, respectively. The results show that the structure of the (OH)2-SAM itself, i.e., a nearly perfect hexagonal-ice-like hydrogen bond structure in the OH matrix of the (OH)2-SAM at Σ = 4.5 nm-2 sharply reduces the number of hydrogen bonds (i.e., 0.7 ± 0.27) formed between the hydrophobic (OH)2-SAM surface and protein. While for Σ = 6.5 nm-2, the hydrophilic (OH)2-SAM surface can provide more hydrogen bonding sites to form hydrogen bonds (i.e., 6.2 ± 1.07) with protein. The number of hydrogen bonds formed between the (OH)2-SAM and protein at Σ = 6.5 nm-2 is ∼8 times higher than that at Σ = 4.5 nm-2, reflecting the excellent resistance to protein adsorption exhibited by the structure of the (OH)2-SAM itself at Σ = 4.5 nm-2. Compared with a traditional physical barrier effect formed by a large number of hydrogen bonds between the (OH)2-SAM and water at Σ = 6.5 nm-2, the structure of the (OH)2-SAM itself at Σ = 4.5 nm-2 proposed in this study significantly improves the performance of the (OH)2-SAM resistance to protein adsorption, which provides new insights into the mechanism of resistance to protein adsorption on the (OH)2-SAM.
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Affiliation(s)
- Dangxin Mao
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Yuan-Yan Wu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Yusong Tu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
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3
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Zhu M, Zeng L, Li Z, Wang C, Wu L, Jiang X. Revealing the Nanoarchitectonics of Amyloid β-Aggregation on Two-Dimensional Biomimetic Membranes by Surface-Enhanced Infrared Absorption Spectroscopy. ChemistryOpen 2023; 12:e202200253. [PMID: 36744594 PMCID: PMC9906390 DOI: 10.1002/open.202200253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Indexed: 02/07/2023] Open
Abstract
The in vivo folding of amyloid β (Aβ) is influenced by many factors among which biomembrane interfaces play an important role. Here, using surface-enhanced infrared absorption (SEIRA) spectroscopy and atomic force microscopy (AFM), the adsorption, structure, and morphology of Aβ42 aggregating on different two-dimensional interfaces were investigated. Results show that interfaces facilitate the aggregation of Aβ42 and are conducive to the formation of homogeneous aggregates, while the aggregates vary on different interfaces. On hydrophobic interfaces, strong hydrophobic interactions with the C-terminus of Aβ42 result in the formation of small oligomers with a small proportion of the β-sheet structure. On hydrophilic interfaces, hydrogen-bonding interactions and electrostatic interactions promote the formation of large aggregate particles with β-sheet structure. The hydration repulsion plays an important role in the interaction of Aβ42 with interfaces. These findings help to understand the nature of Aβ42 adsorption and aggregation on the biomembrane interface and the origin of heterogeneity and polymorphism of Aβ42 aggregates.
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Affiliation(s)
- Manyu Zhu
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
| | - Li Zeng
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing100085P. R. China
| | - Zihao Li
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
| | - Chen Wang
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
| | - Lie Wu
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
| | - Xiue Jiang
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
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4
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Wang S, Ou X, Yi M, Li J. Spontaneous desorption of protein from self-assembled monolayer (SAM)-coated gold nanoparticles induced by high temperature. Phys Chem Chem Phys 2022; 24:2363-2370. [PMID: 35018922 DOI: 10.1039/d1cp04000f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nonspecific binding of proteins with nanomaterials (NMs) is a dynamic reversible process including both protein adsorption and desorption parts, which is crucial for controlled release of protein drug loaded by nanocarriers. The nonspecific binding of proteins is susceptible to high temperature, whereas its underlying mechanism still remains elusive. Here, the binding behavior of human serum albumin (HSA) with an amino-terminated self-assembled monolayer (SAM)-coated gold (111) surface was investigated by using molecular dynamics (MD) simulations. HSA binds to the SAM surface through salt bridges at 300 K. As the temperature increases to 350 K, HSA maintains its native structure, while the salt bridges largely diminish owing to the considerable lateral diffusion of HSA on the SAM. Moreover, the interfacial water located between HSA and the SAM gets increased and prevents the reformation of the salt bridges of HSA with the SAM, which reduces the binding affinity of HSA. And HSA eventually desorbs from the SAM. The depiction of thermally induced spontaneous protein desorption enriches our understanding of reversible binding behavior of protein with NMs, and may provide new insights into the controlled release of protein drugs delivered by using nanocarriers under the regulation of high temperature.
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Affiliation(s)
- Shuai Wang
- College of informatics, Huazhong Agricultural University, Wuhan 430070, China.,Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Xinwen Ou
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China.
| | - Jingyuan Li
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
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5
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Liu H, Zhong H, Liu H, Yao X. Molecular dynamics simulations reveal the disruption mechanism of a 2,4-thiazolidinedione derivative C30 against tau hexapeptide (PHF6) oligomer. Proteins 2021; 90:142-154. [PMID: 34331342 DOI: 10.1002/prot.26196] [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: 03/22/2021] [Revised: 07/17/2021] [Accepted: 07/23/2021] [Indexed: 11/08/2022]
Abstract
Derivatives of 2,4-thiazolidinedione have been reported to inhibit the aggregation of tau protein, in which compound 30 (C30) not only inhibit 80% of paired helical filament 6 (PHF6) aggregation, but also inhibit K18 and full-length tau aggregation. However, its inhibitory mechanism is unclear. In this study, to investigate the effect of C30 on tau protein, all-atom molecular dynamics simulation was performed on the PHF6 oligomer with and without C30. The results show that C30 can cause significant conformational changes in the PHF6 oligomer. The nematic order parameter P2 and secondary structure analyses show that C30 destroys the ordered structure of PHF6 oligomer, reduces the content of β-sheet structure, and transforms β-sheet into random coil structure. By clustering analysis, it was found that C30 has four possible binding sites on the PFH6 oligomer, and the binding ability order is S1 > S2 > S4 > S3. Following a more in-depth analyses of each site, it was determined that the S1 site is the most possible binding site mainly located between layers of L1 and L3. The hydrophobic interaction is the driving force for the binding of C30 to PHF6 oligomer. In addition, L1P4_Y310, L1P5_Y310, L3P1_V309, and L3P2_V309 are key residues for C30 binding to oligomer. Moreover, π-π interaction formed by L1P4_Y310 and L1P5_Y310 with C30 and the hydrogen bonding interaction formed by C30 with L3P3_Q307 are beneficial to the combination of C30 and oligomer. The fully understanding disrupt the mechanism of 2,4-thiazolidinedione derivative on PHF6 oligomer and the identification of binding sites will help design and discover new AD inhibitors in the future.
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Affiliation(s)
- Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.,School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Haiyang Zhong
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, 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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6
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Gaudreault R, Hervé V, van de Ven TGM, Mousseau N, Ramassamy C. Polyphenol-Peptide Interactions in Mitigation of Alzheimer's Disease: Role of Biosurface-Induced Aggregation. J Alzheimers Dis 2021; 81:33-55. [PMID: 33749653 DOI: 10.3233/jad-201549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder, responsible for nearly two-thirds of all dementia cases. In this review, we report the potential AD treatment strategies focusing on natural polyphenol molecules (green chemistry) and more specifically on the inhibition of polyphenol-induced amyloid aggregation/disaggregation pathways: in bulk and on biosurfaces. We discuss how these pathways can potentially alter the structure at the early stages of AD, hence delaying the aggregation of amyloid-β (Aβ) and tau. We also discuss multidisciplinary approaches, combining experimental and modelling methods, that can better characterize the biochemical and biophysical interactions between proteins and phenolic ligands. In addition to the surface-induced aggregation, which can occur on surfaces where protein can interact with other proteins and polyphenols, we suggest a new concept referred as "confinement stability". Here, on the contrary, the adsorption of Aβ and tau on biosurfaces other than Aβ- and tau-fibrils, e.g., red blood cells, can lead to confinement stability that minimizes the aggregation of Aβ and tau. Overall, these mechanisms may participate directly or indirectly in mitigating neurodegenerative diseases, by preventing protein self-association, slowing down the aggregation processes, and delaying the progression of AD.
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Affiliation(s)
- Roger Gaudreault
- Department of Physics, Université de Montréal, Montreal, QC, Canada
| | - Vincent Hervé
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | | | - Normand Mousseau
- Department of Physics, Université de Montréal, Montreal, QC, Canada
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7
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Amirkulova DB, Chakraborty M, White AD. Experimentally Consistent Simulation of Aβ 21-30 Peptides with a Minimal NMR Bias. J Phys Chem B 2020; 124:8266-8277. [PMID: 32845146 DOI: 10.1021/acs.jpcb.0c07129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misfolded amyloid peptides are neurotoxic molecules associated with Alzheimer's disease. The Aβ21-30 peptide fragment is a decapeptide fragment of the complete Aβ42 peptide which is a hypothesized cause of Alzheimer's disease via amyloid fibrillogenesis. Aβ21-30 is investigated here with a combination of NMR (nuclear magnetic resonance) spectroscopy experiments and molecular dynamics simulations with experiment directed simulation (EDS). EDS is a maximum entropy biasing method that augments a molecular dynamics simulation with experimental data (NMR chemical shifts) to improve agreement with experiments and thus accuracy. EDS molecular dynamics shows that the Aβ21-30 monomer has a β turn stabilized by the following interactions: S26-K28, D23-S26, and D23-K28. NMR, total correlation spectroscopy, and rotating frame Overhauser effect spectroscopy experiments provide independent agreement. Subsequent two- and four-monomer EDS simulations show aggregation. Diffusion coefficients calculated from molecular simulation also agreed with experimentally measured values only after using EDS, providing independent assessment of accuracy. This work demonstrates how accuracy can be improved by directly using experimental data in molecular dynamics of complex processes like self-assembly.
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Affiliation(s)
- Dilnoza B Amirkulova
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
| | - Maghesree Chakraborty
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
| | - Andrew D White
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, United States
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8
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Cholko T, Barnum J, Chang CEA. Amyloid-β (Aβ42) Peptide Aggregation Rate and Mechanism on Surfaces with Widely Varied Properties: Insights from Brownian Dynamics Simulations. J Phys Chem B 2020; 124:5549-5558. [PMID: 32525673 DOI: 10.1021/acs.jpcb.0c02926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Amyloid-β (Aβ) plaques, which form by aggregation of harmless Aβ peptide monomers into larger fibrils, are characteristic of neurodegenerative disorders such as Alzheimer's disease. Efforts to treat Alzheimer's disease focus on stopping or reversing the aggregation process that leads to fibril formation. However, effective treatments are elusive due to certain unknown aspects of the process. Many hypotheses point to disruption of cell membranes by adsorbed Aβ monomers or oligomers, but how Aβ behaves and aggregates on surfaces of widely varying properties, such as those present in a cell, is unclear. Elucidating the effects of various surfaces on the dynamics of Aβ and the kinetics of the aggregation process from bulk solution to a surface-adsorbed multimer can help identify what drives aggregation, leading to new methods of intervention by inhibitory drugs or other means. In this work, we used all-atom Brownian dynamics simulations to study the association of two distinct Aβ42 monomer conformations with a surface-adsorbed or free-floating Aβ42 dimer. We calculated the association time, surface interaction energy, surface diffusion coefficient, surface residence time, and the mechanism of association on four different surfaces and two different bulk solution scenarios. In the presence of a surface, the majority of monomers underwent a two-dimensional surface-mediated association that depended primarily on an Aβ42 electrostatic interaction with the self-assembled monolayer (SAM) surfaces. Moreover, aggregation could be inhibited greatly by surfaces with high affinity for Aβ42 and heterogeneous charge distribution. Our results can be used to identify new opportunities for disrupting or reversing the Aβ42 aggregation process.
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Affiliation(s)
- Timothy Cholko
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Joseph Barnum
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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9
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Computational studies of protein aggregation mediated by amyloid: Fibril elongation and secondary nucleation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:461-504. [DOI: 10.1016/bs.pmbts.2019.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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10
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Azouz M, Cullin C, Lecomte S, Lafleur M. Membrane domain modulation of Aβ 1-42 oligomer interactions with supported lipid bilayers: an atomic force microscopy investigation. NANOSCALE 2019; 11:20857-20867. [PMID: 31657431 DOI: 10.1039/c9nr06361g] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Alzheimer's disease is a devastating pathology affecting an increasing number of individuals following the general rise in life expectancy. Amyloid peptide Aβ1-42 has been identified as one of the main culprits of the disease. The peptide has been shown to have major effects on lipid membranes, including membrane fragmentation. The membrane composition has been identified as a factor that plays a pivotal role in regulating peptide/membrane interactions and several results suggest that lipid domains, or rafts, can promote peptide-induced membrane damage. In this work, we examined the effects of lipid segregation on the membrane-perturbing ability of Aβ1-42 and an oligomeric mutant (G37C), a peptide that shares common features with the suspected toxic intermediates involved in the neurodegeneration process. Atomic force microscopy (AFM) was used to determine the impact of these peptides on the supported lipid bilayers of various compositions. In 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phosphocholine/cholesterol (DOPC/DPPC/cholesterol) and DOPC/sphingomyelin/cholesterol ternary mixtures, two systems exhibiting liquid-liquid phase separations, it was shown that Aβ1-42 and G37C exclusively aggregated on liquid-disordered-phase domains, creating large deposits and even causing membrane fragmentation for the latter composition. Cholesterol and ganglioside GM1, the two most documented lipids in the context of Alzheimer's disease, are also considered to play a crucial role in promoting detrimental interactions with amyloid peptides. We show that, in model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes, the presence of either cholesterol or GM1 in a proportion of 10 mol%, a content supposed to lead to domain formation, favoured the association of both Aβ1-42 and G37C, leading to a harmful membrane fragmentation. The AFM results established that the presence of domains favoured membrane perturbations induced by the amyloid peptides. It is proposed that lipid packing defects at the domain interface could act as adsorption and nucleation sites for the amyloid peptides. The more extensive bilayer perturbations induced by G37C compared to Aβ1-42 supported this hypothesis, indicating that oligomers that cannot mature to the fibril state can present considerable toxicity.
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Affiliation(s)
- Mehdi Azouz
- Chimie et Biologie des Membranes et Nanoobjets, CBMN CNRS UMR 5248, Université de Bordeaux, Allée Geoffroy de Saint-Hilaire, 33600 Pessac, France and Department of Chemistry, Université de Montréal, Montréal, Québec, Canada.
| | - Christophe Cullin
- Chimie et Biologie des Membranes et Nanoobjets, CBMN CNRS UMR 5248, Université de Bordeaux, Allée Geoffroy de Saint-Hilaire, 33600 Pessac, France
| | - Sophie Lecomte
- Chimie et Biologie des Membranes et Nanoobjets, CBMN CNRS UMR 5248, Université de Bordeaux, Allée Geoffroy de Saint-Hilaire, 33600 Pessac, France
| | - Michel Lafleur
- Department of Chemistry, Université de Montréal, Montréal, Québec, Canada.
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Liu Z, Zou Y, Zhang Q, Chen P, Liu Y, Qian Z. Distinct Binding Dynamics, Sites and Interactions of Fullerene and Fullerenols with Amyloid-β Peptides Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2019; 20:E2048. [PMID: 31027286 PMCID: PMC6514889 DOI: 10.3390/ijms20082048] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/21/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
The pathology Alzheimer's disease (AD) is associated with the self-assembly of amyloid-β (Aβ) peptides into β-sheet enriched fibrillar aggregates. A promising treatment strategy is focused on the inhibition of amyloid fibrillization of Aβ peptide. Fullerene C60 is proved to effectively inhibit Aβ fibrillation while the poor water-solubility restricts its use as a biomedicine agent. In this work, we examined the interaction of fullerene C60 and water-soluble fullerenol C60(OH)6/C60(OH)12 (C60 carrying 6/12 hydroxyl groups) with preformed Aβ40/42 protofibrils by multiple molecular dynamics simulations. We found that when binding to the Aβ42 protofibril, C60, C60(OH)6 and C60(OH)12 exhibit distinct binding dynamics, binding sites and peptide interaction. The increased number of hydroxyl groups C60 carries leads to slower binding dynamics and weaker binding strength. Binding free energy analysis demonstrates that the C60/C60(OH)6 molecule primarily binds to the C-terminal residues 31-41, whereas C60(OH)12 favors to bind to N-terminal residues 4-14. The hydrophobic interaction plays a critical role in the interplay between Aβ and all the three nanoparticles, and the π-stacking interaction gets weakened as C60 carries more hydroxyls. In addition, the C60(OH)6 molecule has high affinity to form hydrogen bonds with protein backbones. The binding behaviors of C60/C60(OH)6/C60(OH)12 to the Aβ40 protofibril resemble with those to Aβ42. Our work provides a detailed picture of fullerene/fullerenols binding to Aβ protofibril, and is helpful to understand the underlying inhibitory mechanism.
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Affiliation(s)
- Zhiwei Liu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Peijie Chen
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Yu Liu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education), School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
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12
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Rangachari V, Dean DN, Rana P, Vaidya A, Ghosh P. Cause and consequence of Aβ - Lipid interactions in Alzheimer disease pathogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1652-1662. [PMID: 29526709 PMCID: PMC6133763 DOI: 10.1016/j.bbamem.2018.03.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 12/14/2022]
Abstract
Self-templating propagation of protein aggregate conformations is increasingly becoming a significant factor in many neurological diseases. In Alzheimer disease (AD), intrinsically disordered amyloid-β (Aβ) peptides undergo aggregation that is sensitive to environmental conditions. High-molecular weight aggregates of Aβ that form insoluble fibrils are deposited as senile plaques in AD brains. However, low-molecular weight aggregates called soluble oligomers are known to be the primary toxic agents responsible for neuronal dysfunction. The aggregation process is highly stochastic involving both homotypic (Aβ-Aβ) and heterotypic (Aβ with interacting partners) interactions. Two of the important members of interacting partners are membrane lipids and surfactants, to which Aβ shows a perpetual association. Aβ-membrane interactions have been widely investigated for more than two decades, and this research has provided a wealth of information. Although this has greatly enriched our understanding, the objective of this review is to consolidate the information from the literature that collectively showcases the unique phenomenon of lipid-mediated Aβ oligomer generation, which has largely remained inconspicuous. This is especially important because Aβ aggregate "strains" are increasingly becoming relevant in light of the correlations between the structure of aggregates and AD phenotypes. Here, we will focus on aspects of Aβ-lipid interactions specifically from the context of how lipid modulation generates a wide variety of biophysically and biochemically distinct oligomer sub-types. This, we believe, will refocus our thinking on the influence of lipids and open new approaches in delineating the mechanisms of AD pathogenesis. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry & Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA.
| | - Dexter N Dean
- Department of Chemistry & Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pratip Rana
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Ashwin Vaidya
- Department of Mathematical Science, Montclair State University, Montclair, NJ 07043, USA
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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13
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Yang S, Liu J, Quan X, Zhou J. Bilirubin Oxidase Adsorption onto Charged Self-Assembled Monolayers: Insights from Multiscale Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9818-9828. [PMID: 30044918 DOI: 10.1021/acs.langmuir.8b01974] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The efficient immobilization and orientation of bilirubin oxidase (BOx) on different solid substrates are essential for its application in biotechnology. The T1 copper site within BOx is responsible for the electron transfer. In order to obtain quick direct electron transfer (DET), it is important to keep the distance between the T1 copper site and electrode surface small and to maintain the natural structure of BOx at the same time. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of BOx from Myrothecium verrucaria (MvBOx) adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (±0.05 and ±0.19 C·m-2). The results show that MvBOx adsorbs on negatively charged surfaces with a "back-on" orientation, whereas on positively charged surfaces, MvBOx binds with a "lying-on" orientation. The locations of the T1 copper site are closer to negatively charged surfaces. Furthermore, for negatively charged surfaces, the T1 copper site prefers to orient closer to the surface with lower surface charge density. Therefore, the negatively charged surface with low surface charge density is more suitable for the DET of MvBOx on electrodes. Besides, the structural changes primarily take place on the relatively flexible turns, coils, and α-helix. The native structure of MvBOx is well preserved when it adsorbs on both charged surfaces. This work sheds light on the controlling orientation and conformational information on MvBOx on charged surfaces at the atomistic level. This understanding would certainly promote our understanding of the mechanism of MvBOx immobilization and provide theoretical support for BOx-based bioelectrode design.
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Affiliation(s)
- Shengjiang Yang
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640 , P. R. China
| | - Jie Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology , Wuhan 430073 , P. R. China
| | - Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640 , 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 510640 , P. R. China
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14
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Ning L, Mu Y. Aggregation of PrP106-126 on surfaces of neutral and negatively charged membranes studied by molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1936-1948. [PMID: 29550288 DOI: 10.1016/j.bbamem.2018.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 01/28/2023]
Abstract
Prion diseases are neurodegenerative disorders characterized by the aggregation of an abnormal form of prion protein. The interaction of prion protein and cellular membrane is crucial to elucidate the occurrence and development of prion diseases. Its fragment, residues 106-126, has been proven to maintain the pathological properties of misfolded prion and was used as a model peptide. In this study, explicit solvent molecular dynamics (MD) simulations were carried out to investigate the adsorption, folding and aggregation of PrP106-126 with different sizes (2-peptides, 4-peptides and 6-peptides) on the surface of both pure neutral POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and negatively charged POPC/POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol) (3:1) lipids. MD simulation results show that PrP106-126 display strong affinity with POPC/POPG but does not interact with pure POPC. The positively charged and polar residues participating hydrogen bonding with membrane promote the adsorption of PrP106-126. The presence of POPC and POPC/POPG exert limited influence on the secondary structures of PrP106-126 and random coil structures are predominant in all simulation systems. Upon the adsorption on the POPC/POPG surface, the aggregation states of PrP106-126 have been changed and more small oligomers were observed. This work provides insights into the interactions of PrP106-126 and membranes with different compositions in atomic level, which expand our understanding the role membrane plays in the development of prion diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Lulu Ning
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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15
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Zhao W, Ai H. Effect of pH on Aβ 42 Monomer and Fibril-like Oligomers-Decoding in Silico of the Roles of pK Values of Charged Residues. Chemphyschem 2018; 19:1103-1116. [PMID: 29380494 DOI: 10.1002/cphc.201701384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 01/10/2023]
Abstract
Amyloid beta-peptide (Aβ) is the key to developing Alzheimer's disease. Experiments have confirmed that different acidity influences directly not only the structural morphology and population of Aβ oligomers, but also the toxicity. The atomic-level association between the pH, charged residues, and Aβ properties remains obscure. Herein, conformational changes of Aβ42 monomer, fibril-like trimer, and pentamer in the medium pH range of 4.0-7.5 are studied. The results reveal that, as the pH changes from 7.5 to the isoelectric pH, His6, His13, and His14 are protonated in turn, successively approach the center of mass of folded Aβ monomer, trigger ionic interactions and changes of neighboring turns (Asp7-Ser8, His14-Lys16) and even a distant one (Leu34-Met35), as well as concomitant changes of secondary structure, and promote the conformation transition from unfolded to folded. This observation discloses that protonation can convert these charged residues from originally hydrophilic to "hydrophobic-like". For fibril-like oligomers, the pH susceptibility essentially stems from the pK values of charged residues in the context of the Aβ fibril, and in turn one can predict the dynamic behavior of these residues in the processes of dissociation or stabilization of a fibril by comparing the pK values of residues involved in salt bridges in the normal state with those in the current context. This idea is justified by two fibril models and appears to be applicable to other peptides and their fibril systems.
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Affiliation(s)
- Wei Zhao
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
| | - Hongqi Ai
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
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16
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Liu Y, Ren B, Zhang Y, Sun Y, Chang Y, Liang G, Xu L, Zheng J. Molecular simulation aspects of amyloid peptides at membrane interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1906-1916. [PMID: 29421626 DOI: 10.1016/j.bbamem.2018.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022]
Abstract
The interactions of amyloid peptides with cell membranes play an important role in maintaining the integrity and functionality of cell membrane. A thorough molecular-level understanding of the structure, dynamics, and interactions between amyloid peptides and cell membranes is critical to amyloid aggregation and toxicity mechanisms for the bench-to-bedside applications. Here we review the most recent computational studies of amyloid peptides at model cell membranes. Different mechanisms of action of amyloid peptides on/in cell membranes, targeted by different computational techniques at different lengthscales and timescales, are rationally discussed. Finally, we have proposed some new insights into the remaining challenges and perspectives for future studies to improve our understanding of the activity of amyloid peptides associated with protein-misfolding diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Yonglan Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yung Chang
- R&D Center for Membrane Technology and Department of Chemical EngineeringChung Yuan Christian University, Chung-Li, Taoyuan 320, Taiwan
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Lijian Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
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17
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Tian R, Luo M, Li J. Spontaneous protein desorption from self-assembled monolayer (SAM)-coated gold nanoparticles. Phys Chem Chem Phys 2018; 20:68-74. [DOI: 10.1039/c7cp05515c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Interfacial water molecules and lateral diffusion of protein reduce the adsorption affinity of protein and promote protein desorption.
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Affiliation(s)
- Ranran Tian
- Department of Physics
- Zhejiang University
- Hangzhou
- China
| | - Mengbo Luo
- Department of Physics
- Zhejiang University
- Hangzhou
- China
| | - Jingyuan Li
- Department of Physics
- Zhejiang University
- Hangzhou
- China
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18
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Xiang N, Lyu Y, Zhu X, Narsimhan G. Investigation of the interaction of amyloid β peptide (11–42) oligomers with a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane using molecular dynamics simulation. Phys Chem Chem Phys 2018; 20:6817-6829. [PMID: 29299557 DOI: 10.1039/c7cp07148e] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism of pore formation in model neural cell membranes by β amyloid (Aβ) peptides was investigated using molecular dynamics simulation which indicated that Aβ oligomers of size equal or greater than 3 has a higher tendency for pore formation than monomers and that cholesterol tends to retard Aβ binding and insertion into the membrane.
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Affiliation(s)
- Ning Xiang
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
| | - Yuan Lyu
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
| | - Xiao Zhu
- ItaP
- Research Computing
- Rosen Center for Advanced Computing
- Purdue University
- West Lafayette
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering
- Purdue University
- West Lafayette
- USA
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19
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Liu J, Xie Y, Peng C, Yu G, Zhou J. Molecular Understanding of Laccase Adsorption on Charged Self-Assembled Monolayers. J Phys Chem B 2017; 121:10610-10617. [DOI: 10.1021/acs.jpcb.7b08738] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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, P. R. China
- Key
Laboratory for Green Chemical Process of Ministry of Education, School
of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, P. R. China
| | - Yun Xie
- Huizhou University, Huizhou 516007, 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 510640, P. R. 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, P. R. China
- School
of Materials and Chemical Engineering, Hainan University, Haikou 570228, 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 510640, P. R. China
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20
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Dong X, Sun Y, Wei G, Nussinov R, Ma B. Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning. Phys Chem Chem Phys 2017; 19:27556-27569. [PMID: 28979963 PMCID: PMC5647258 DOI: 10.1039/c7cp05959k] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease, a common neurodegenerative disease, is characterized by the aggregation of amyloid-β (Aβ) peptides. The interactions of Aβ with membranes cause changes in membrane morphology and ion permeation, which are responsible for its neurotoxicity and can accelerate fibril growth. However, the Aβ-lipid interactions and how these induce membrane perturbation and disruption at the atomic level and the consequences for the Aβ organization are not entirely understood. Here, we perform multiple atomistic molecular dynamics simulations on three protofibrillar Aβ9-40 trimers. Our simulations show that, regardless of the morphologies and the initial orientations of the three different protofibrillar Aβ9-40 trimers, the N-terminal β-sheet of all trimers preferentially binds to the membrane surface. The POPG lipid bilayers enhance the structural stability of protofibrillar Aβ trimers by stabilizing inter-peptide β-sheets and D23-K28 salt-bridges. The interaction causes local membrane thinning. We found that the trimer structure related to Alzheimer's disease brain tissue () is the most stable both in water solution and at membrane surface, and displays slightly stronger membrane perturbation capability. These results provide mechanistic insights into the membrane-enhanced structural stability of protofibrillar Aβ oligomers and the first step of Aβ-induced membrane disruption at the atomic level.
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Affiliation(s)
- Xuewei Dong
- Department of Physics, State Key Laboratory of Surface physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People's Republic of China
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21
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Yang QH, Luo MB. Dynamics of adsorbed polymers on attractive homogeneous surfaces. Sci Rep 2016; 6:37156. [PMID: 27849002 PMCID: PMC5111053 DOI: 10.1038/srep37156] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/25/2016] [Indexed: 02/07/2023] Open
Abstract
Dynamic behaviors of polymer chains adsorbed on an attractive, homogeneous surface are studied by using dynamic Monte Carlo simulations. The translational diffusion coefficient Dxy parallel to the surface decreases as the intra-polymer attraction strength EPP or the polymer-surface attraction strength EPS increases. The rotational relaxation time τR increases with EPS, but the dependence of τR on EPP is dependent on the adsorption state of the polymer. We find that τR decreases with increasing EPP for a partially adsorbed polymer but it increases with EPP for a fully adsorbed polymer. Scaling relations Dxy ~ N−α and τR ~ Nβ are found for long polymers. The scaling exponent α is independent of EPS for long polymers but increases with EPP from α = 1.06 at EPP = 0. While β ≈ 2.7 is also roughly independent of EPS for the adsorbed polymer at EPP = 0, but β increases with EPS at EPP > 0. Moreover, we find that β always decreases with increasing EPP. Our results reveal different effects of the attractive surface on the diffusion and rotation of adsorbed polymers.
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Affiliation(s)
- Qing-Hui Yang
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China.,Collaborative Innovation Center of Advanced Microstructures, Nanjing, China
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22
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DeBenedictis EP, Liu J, Keten S. Adhesion mechanisms of curli subunit CsgA to abiotic surfaces. SCIENCE ADVANCES 2016; 2:e1600998. [PMID: 28138525 PMCID: PMC5262458 DOI: 10.1126/sciadv.1600998] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/13/2016] [Indexed: 05/24/2023]
Abstract
Curli fibers are functional amyloids that play a key role in biofilm structure and adhesion to various surfaces. Strong bioinspired adhesives comprising curli fibers have recently been created; however, the mechanisms curli uses to attach onto abiotic surfaces are still uncharacterized. Toward a materials-by-design approach for curli-based adhesives and multifunctional materials, we examine curli subunit adsorption onto graphene and silica surfaces through atomistic simulation. We find that both structural features and sequence influence adhesive strength, enabling the CsgA subunit to adhere strongly to both polar and nonpolar surfaces. Specifically, flexible regions facilitate adhesion to both surfaces, charged and polar residues (Arg, Lys, and Gln) enable strong interactions with silica, and six-carbon aromatic rings (Tyr and Phe) adsorb strongly to graphene. We find that adsorption not only lowers molecular mobility but also leads to loss of secondary structure, factors that must be well balanced for effective surface attachment. Both events appear to propagate through the CsgA structure as correlated motion between clusters of residues, often H-bonded between rows on adjacent β strands. To quantify this, we present a correlation analysis approach to detecting collective motion between residue groups. We find that certain clusters of residues have a higher impact on the stability of the rest of the protein structure, often polar and bulky groups within the helix core. These findings lend insight into bacterial adhesion mechanisms and reveal strategies for theory-driven design of engineered curli fibers that harness point mutations and conjugates for stronger adhesion.
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Affiliation(s)
- Elizabeth P. DeBenedictis
- Departments of Civil and Environmental Engineering and Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Jenny Liu
- Northwestern University Medical Scientist Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Sinan Keten
- Departments of Civil and Environmental Engineering and Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
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23
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Zhao J, Ma B, Nussinov R. Compilation and Analysis of Enzymes, Engineered Antibodies, and Nanoparticles Designed to Interfere with Amyloid-β Aggregation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program; National Cancer Institute; Frederick Maryland 21702 USA
| | - Buyong Ma
- Basic Science Program; Leidos Biomedical Research, Inc.; Cancer and Inflammation Program; National Cancer Institute; Frederick Maryland 21702 USA
| | - Ruth Nussinov
- Basic Science Program; Leidos Biomedical Research, Inc.; Cancer and Inflammation Program; National Cancer Institute; Frederick Maryland 21702 USA
- Sackler Institute of Molecular Medicine; Department of Human Genetics and Molecular Medicine; Sackler School of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
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24
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Peng C, Liu J, Xie Y, Zhou J. Molecular simulations of cytochrome c adsorption on positively charged surfaces: the influence of anion type and concentration. Phys Chem Chem Phys 2016; 18:9979-89. [DOI: 10.1039/c6cp00170j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The influence of anion type and concentration on the adsorption of cytochrome c onto the positively charged NH2-SAM surface.
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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
- P. R. China
| | - Jie Liu
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Yun Xie
- School of Chemistry and Chemical Engineering
- Guangdong Pharmaceutical University
- Guangzhou 510006
- 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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25
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Parodi J, Ormeño D, Ochoa-de la Paz LD. Amyloid pore-channel hypothesis: effect of ethanol on aggregation state using frog oocytes for an Alzheimer's disease study. BMB Rep 2015; 48:13-8. [PMID: 25047445 PMCID: PMC4345636 DOI: 10.5483/bmbrep.2015.48.1.125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/01/2014] [Accepted: 07/17/2014] [Indexed: 11/29/2022] Open
Abstract
Alzheimer's disease severely compromises cognitive function. One of the mechanisms to explain the pathology of Alzheimer’s disease has been the hypotheses of amyloid-pore/channel formation by complex Aβ-aggregates. Clinical studies suggested the moderate alcohol consumption can reduces probability developing neurodegenerative pathologies. A recent report explored the ability of ethanol to disrupt the generation of complex Aβ in vitro and reduce the toxicity in two cell lines. Molecular dynamics simulations were applied to understand how ethanol blocks the aggregation of amyloid. On the other hand, the in silico modeling showed ethanol effect over the dynamics assembling for complex Aβ-aggregates mediated by break the hydrosaline bridges between Asp 23 and Lys 28, was are key element for amyloid dimerization. The amyloid pore/channel hypothesis has been explored only in neuronal models, however recently experiments suggested the frog oocytes such an excellent model to explore the mechanism of the amyloid pore/channel hypothesis. So, the used of frog oocytes to explored the mechanism of amyloid aggregates is new, mainly for amyloid/pore hypothesis. Therefore, this experimental model is a powerful tool to explore the mechanism implicates in the Alzheimer’s disease pathology and also suggests a model to prevent the Alzheimer’s disease pathology. [BMB Reports 2015; 48(1): 13-18]
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Affiliation(s)
- Jorge Parodi
- Laboratorio de Fisiología de la Reproducción, Núcleo de Investigaciónen Producción Alimentaria, Facultad de Recursos Naturales, Escuela de Medicina Veterinaria, Universidad Católica de Temuco, Temuco, Chile
| | - David Ormeño
- Laboratorio de Fisiología de la Reproducción, Núcleo de Investigaciónen Producción Alimentaria, Facultad de Recursos Naturales, Escuela de Medicina Veterinaria, Universidad Católica de Temuco, Temuco, Chile
| | - Lenin D Ochoa-de la Paz
- Laboratorio de Fisiología Celular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, México
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26
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Ma X, Shrotriya P. Molecular Dynamics Simulation of Conformational Transition and Frictional Performance Modulation of Densely Packed Self-Assembled Monolayers Based on Electrostatic Stimulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6729-6741. [PMID: 26053128 DOI: 10.1021/acs.langmuir.5b00956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Self-assembled monolayers (SAMs) terminated with functional end groups such as polyethylene glycols (PEG) have attracted considerable attention because of their unique and flexible structure that exhibits conformational transition under electrostatic stimulation. Molecular dynamics simulations are used to investigate the conformational transition and associated modulation of frictional performance of densely packed PEG-terminated SAMs subjected to electrical field stimulation. Previously reported empirical potentials and atomic charges were used to model the intrachain bonds and electrostatic and interchain interactions. Simulation results indicate that significant conformational transition is generated because of the electrostatic forces. Under positive electrical fields, PEG groups are compressed and twisted into the helical form, "gauche" state, whereas under negative electrical fields, PEG groups are stretched into the straight form, "all-trans" state. Such conformational transition may lead to substantial alteration of frictional response upon SAMs. By shallow penetration and sliding using a repulsive indenter, the SAMs under positive electrical fields exhibit a level of frictional response that is comparatively lower than those under zero and negative potentials, which may be attributed to reduced interchain space for deformation, limited conformational transition, and less energy absorption. The simulation results demonstrate that with appropriate selection of functional end groups attached to SAM backbone chains it is possible to modulate frictional performance of densely packed SAMs via electrostatic stimuli.
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Affiliation(s)
- Xiao Ma
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Pranav Shrotriya
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
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27
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Zhu D, Bungart BL, Yang X, Zhumadilov Z, Lee JCM, Askarova S. Role of membrane biophysics in Alzheimer's-related cell pathways. Front Neurosci 2015; 9:186. [PMID: 26074758 PMCID: PMC4444756 DOI: 10.3389/fnins.2015.00186] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/11/2015] [Indexed: 01/04/2023] Open
Abstract
Cellular membrane alterations are commonly observed in many diseases, including Alzheimer's disease (AD). Membrane biophysical properties, such as membrane molecular order, membrane fluidity, organization of lipid rafts, and adhesion between membrane and cytoskeleton, play an important role in various cellular activities and functions. While membrane biophysics impacts a broad range of cellular pathways, this review addresses the role of membrane biophysics in amyloid-β peptide aggregation, Aβ-induced oxidative pathways, amyloid precursor protein processing, and cerebral endothelial functions in AD. Understanding the mechanism(s) underlying the effects of cell membrane properties on cellular processes should shed light on the development of new preventive and therapeutic strategies for this devastating disease.
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Affiliation(s)
- Donghui Zhu
- Department of Chemical, Biological and Bioengineering, North Carolina A&T State UniversityGreensboro, NC, USA
| | - Brittani L. Bungart
- Indiana University School of Medicine Medical Scientist Training Program, Indiana University School of MedicineIndianapolis, IN, USA
| | - Xiaoguang Yang
- Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of GothenburgGothenburg, Sweden
- The Hope Center for Neurological Disorders and Department of Neurology, Washington University School of MedicineSt. Louis, MO, USA
| | - Zhaxybay Zhumadilov
- Department of Bioengineering and Regenerative Medicine, Center for Life Sciences, Nazarbayev UniversityAstana, Kazakhstan
| | - James C-M. Lee
- Department of Bioengineering, University of Illinois at ChicagoChicago, IL, USA
| | - Sholpan Askarova
- Department of Bioengineering and Regenerative Medicine, Center for Life Sciences, Nazarbayev UniversityAstana, Kazakhstan
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28
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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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29
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Sun Y, Xi W, Wei G. Atomic-Level Study of the Effects of O4 Molecules on the Structural Properties of Protofibrillar Aβ Trimer: β-Sheet Stabilization, Salt Bridge Protection, and Binding Mechanism. J Phys Chem B 2015; 119:2786-94. [DOI: 10.1021/jp508122t] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yunxiang Sun
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
| | - Wenhui Xi
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
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30
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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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31
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Tsigelny IF, Sharikov Y, Kouznetsova VL, Greenberg JP, Wrasidlo W, Gonzalez T, Desplats P, Michael SE, Trejo-Morales M, Overk CR, Masliah E. Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation. J Alzheimers Dis 2014; 39:583-600. [PMID: 24240640 DOI: 10.3233/jad-131589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteristics. Then we selected the dimers that would evolve to membranephilic annular oligomers. Nearly one third of the 28 evaluated annular oligomers had the dimer interfaces between the neighboring Aβ42 monomers with possible salt bridges between the residue K28 from one side and either residue E22 or D23 on the other. Based on these results, key amino acids were identified for point mutations that either enhanced or suppressed the formation and toxicity of oligomer rings. Our studies suggest a greater diversity of Aβ dimers. Understanding the structure of Aβ dimers might be important for the rationale design of small molecules that block formation of toxic oligomers.
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Affiliation(s)
- Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Yuriy Sharikov
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jerry P Greenberg
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Wolfgang Wrasidlo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Tania Gonzalez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Paula Desplats
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Sarah E Michael
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Cassia R Overk
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA Department of Pathology, University of California, San Diego, La Jolla, CA, USA
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32
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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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33
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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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34
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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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35
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Ragaliauskas T, Mickevicius M, Budvytyte R, Niaura G, Carbonnier B, Valincius G. Adsorption of β-amyloid oligomers on octadecanethiol monolayers. J Colloid Interface Sci 2014; 425:159-67. [PMID: 24776678 DOI: 10.1016/j.jcis.2014.03.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 10/25/2022]
Abstract
HYPOTHESIS β-Amyloid oligomers of different aggregation and physiological functions exhibit distinct adsorption behavior allowing them to be discriminated in preparations. EXPERIMENTS Two forms of amyloid oligomers, small 1-4 nm and large 5-10nm were formulated using synthetic 42 amino acids β-amyloid peptide. Forms differ in their size and physiological function. A systematic study of adsorption of these amyloid species on self-assembled monolayers of octadecanethiol on gold was performed. Structural changes upon adsorption of oligomers were interrogated by the reflection absorption infrared spectroscopy. FINDINGS The amount of adsorbed peptide material, as detected by surface plasmon resonance spectroscopy, is similar in case of both small and large oligomers. However, adsorption of small oligomers leads to a transformation from beta sheet rich to beta sheet depleted secondary structure. These changes were accompanied by the unique morphology patterns detectable by atomic force microscopy (AFM), while the quartz microbalance with dissipation indicated a formation of a compact adsorbate layer in case of small oligomers. These effects may be integrated and utilized in bioanalytical systems for sensing and detection of Alzheimer's disease related peptide forms in artificial, and possibly, real preparations.
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Affiliation(s)
- Tadas Ragaliauskas
- Institute of Biochemistry, Vilnius University, Mokslininku 12, LT-08662 Vilnius, Lithuania.
| | - Mindaugas Mickevicius
- Institute of Biochemistry, Vilnius University, Mokslininku 12, LT-08662 Vilnius, Lithuania.
| | - Rima Budvytyte
- Institute of Biochemistry, Vilnius University, Mokslininku 12, LT-08662 Vilnius, Lithuania.
| | - Gediminas Niaura
- Institute of Biochemistry, Vilnius University, Mokslininku 12, LT-08662 Vilnius, Lithuania.
| | - Benjamin Carbonnier
- Institut de Chimie et des Matériaux Paris-Est, Université Paris-Est, 2 rue Henri Dunant, 94320 Thiais, France.
| | - Gintaras Valincius
- Institute of Biochemistry, Vilnius University, Mokslininku 12, LT-08662 Vilnius, Lithuania.
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36
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Yu G, Liu J, Zhou J. Mesoscopic coarse-grained simulations of lysozyme adsorption. J Phys Chem B 2014; 118:4451-60. [PMID: 24785197 DOI: 10.1021/jp409326f] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a "top end-on" orientation, while they are exposed to the liquid phase on the hydrophilic surface with a "back-on" orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale.
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Affiliation(s)
- Gaobo Yu
- School of Chemistry and Chemical Engineering, South China University of Technology , Guangzhou, Guangdong 510640, China
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37
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Liu J, Wang W, Zhang Q, Zhang S, Yuan Z. Study on the Efficiency and Interaction Mechanism of a Decapeptide Inhibitor of β-Amyloid Aggregation. Biomacromolecules 2014; 15:931-9. [DOI: 10.1021/bm401795e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jing Liu
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Wei Wang
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Qian Zhang
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Saihui Zhang
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Zhi Yuan
- Key Laboratory
of Functional
Polymer Materials of Ministry of Education, and Institute of Polymer
Chemistry, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
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38
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Smith MD, Srinivasa Rao J, Cruz L. Spontaneous dimer states of the Aβ21–30decapeptide. Phys Chem Chem Phys 2014; 16:13069-73. [DOI: 10.1039/c4cp01090f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Computational examination of the spontaneous dimerization of Aβ21–30and stability measures of the resulting parallel and anti-parallel aligned dimers.
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Affiliation(s)
| | - J. Srinivasa Rao
- Department of Physics
- New Jersey Institute of Technology
- University Heights
- Newark, USA
| | - Luis Cruz
- Department of Physics
- Drexel University
- Philadelphia, USA
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39
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Poojari C, Strodel B. Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations. PLoS One 2013; 8:e78399. [PMID: 24244308 PMCID: PMC3820573 DOI: 10.1371/journal.pone.0078399] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022] Open
Abstract
Interactions of the amyloid β-protein (Aβ) with neuronal cell membranes, leading to the disruption of membrane integrity, are considered to play a key role in the development of Alzheimer’s disease. Natural mutations in Aβ42, such as the Arctic mutation (E22G) have been shown to increase Aβ42 aggregation and neurotoxicity, leading to the early-onset of Alzheimer’s disease. A correlation between the propensity of Aβ42 to form protofibrils and its effect on neuronal dysfunction and degeneration has been established. Using rational mutagenesis of the Aβ42 peptide it was further revealed that the aggregation of different Aβ42 mutants in lipid membranes results in a variety of polymorphic aggregates in a mutation dependent manner. The mutant peptides also have a variable ability to disrupt bilayer integrity. To further test the connection between Aβ42 mutation and peptide–membrane interactions, we perform molecular dynamics simulations of membrane-inserted Aβ42 variants (wild-type and E22G, D23G, E22G/D23G, K16M/K28M and K16M/E22G/D23G/K28M mutants) as β-sheet monomers and tetramers. The effects of charged residues on transmembrane Aβ42 stability and membrane integrity are analyzed at atomistic level. We observe an increased stability for the E22G Aβ42 peptide and a decreased stability for D23G compared to wild-type Aβ42, while D23G has the largest membrane-disruptive effect. These results support the experimental observation that the altered toxicity arising from mutations in Aβ is not only a result of the altered aggregation propensity, but also originates from modified Aβ interactions with neuronal membranes.
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Affiliation(s)
- Chetan Poojari
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail:
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40
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Deighan M, Pfaendtner J. Exhaustively sampling peptide adsorption with metadynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7999-8009. [PMID: 23706011 DOI: 10.1021/la4010664] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Simulating the adsorption of a peptide or protein and obtaining quantitative estimates of thermodynamic observables remains challenging for many reasons. One reason is the dearth of molecular scale experimental data available for validating such computational models. We also lack simulation methodologies that effectively address the dual challenges of simulating protein adsorption: overcoming strong surface binding and sampling conformational changes. Unbiased classical simulations do not address either of these challenges. Previous attempts that apply enhanced sampling generally focus on only one of the two issues, leaving the other to chance or brute force computing. To improve our ability to accurately resolve adsorbed protein orientation and conformational states, we have applied the Parallel Tempering Metadynamics in the Well-Tempered Ensemble (PTMetaD-WTE) method to several explicitly solvated protein/surface systems. We simulated the adsorption behavior of two peptides, LKα14 and LKβ15, onto two self-assembled monolayer (SAM) surfaces with carboxyl and methyl terminal functionalities. PTMetaD-WTE proved effective at achieving rapid convergence of the simulations, whose results elucidated different aspects of peptide adsorption including: binding free energies, side chain orientations, and preferred conformations. We investigated how specific molecular features of the surface/protein interface change the shape of the multidimensional peptide binding free energy landscape. Additionally, we compared our enhanced sampling technique with umbrella sampling and also evaluated three commonly used molecular dynamics force fields.
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Affiliation(s)
- Michael Deighan
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
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41
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O'Mahony S, O'Dwyer C, Nijhuis CA, Greer JC, Quinn AJ, Thompson D. Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7271-7282. [PMID: 23301836 DOI: 10.1021/la304545n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Atomic-scale molecular dynamics computer simulations are used to probe the structure, dynamics, and energetics of alkylamine self-assembled monolayer (SAM) films on graphene and to model the formation of molecular bilayers and protein complexes on the films. Routes toward the development and exploitation of functionalized graphene structures are detailed here, and we show that the SAM architecture can be tailored for use in emerging applications (e.g., electrically stimulated nerve fiber growth via the targeted binding of specific cell surface peptide sequences on the functionalized graphene scaffold). The simulations quantify the changes in film physisorption on graphene and the alkyl chain packing efficiency as the film surface is made more polar by changing the terminal groups from methyl (-CH3) to amine (-NH2) to hydroxyl (-OH). The mode of molecule packing dictates the orientation and spacing between terminal groups on the surface of the SAM, which determines the way in which successive layers build up on the surface, whether via the formation of bilayers of the molecule or the immobilization of other (macro)molecules (e.g., proteins) on the SAM. The simulations show the formation of ordered, stable assemblies of monolayers and bilayers of decylamine-based molecules on graphene. These films can serve as protein adsorption platforms, with a hydrophobin protein showing strong and selective adsorption by binding via its hydrophobic patch to methyl-terminated films and binding to amine-terminated films using its more hydrophilic surface regions. Design rules obtained from modeling the atomic-scale structure of the films and interfaces may provide input into experiments for the rational design of assemblies in which the electronic, physicochemical, and mechanical properties of the substrate, film, and protein layer can be tuned to provide the desired functionality.
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Affiliation(s)
- S O'Mahony
- Theory Modelling and Design Centre, Tyndall National Institute, University College Cork, Cork, Ireland
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42
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Jose JC, Sengupta N. Molecular dynamics simulation studies of the structural response of an isolated Aβ1–42 monomer localized in the vicinity of the hydrophilic TiO2 surface. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:487-94. [DOI: 10.1007/s00249-013-0900-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/21/2013] [Accepted: 03/21/2013] [Indexed: 12/12/2022]
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43
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Yu X, Wang Q, Pan Q, Zhou F, Zheng J. Molecular interactions of Alzheimer amyloid-β oligomers with neutral and negatively charged lipid bilayers. Phys Chem Chem Phys 2013; 15:8878-89. [PMID: 23493873 DOI: 10.1039/c3cp44448a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Interaction of p3 (Aβ(17-42)) peptides with cell membranes is crucial for the understanding of amyloid toxicity associated with Alzheimer's disease (AD). Such p3-membrane interactions are considered to induce the disruption of membrane permeability and integrity, but the exact mechanisms of how p3 aggregates, particularly small p3 oligomers, induce receptor-independent membrane disruption are not yet completely understood. Here, we investigate the adsorption, orientation, and surface interaction of the p3 pentamer with lipid bilayers composed of both pure zwitterionic POPC (palmitoyl-oleoyl-phosphatidylcholine) and mixed anionic POPC-POPG (palmitoyl-oleoyl-phosphatidylglycerol) (3 : 1) lipids using explicit-solvent molecular dynamics (MD) simulations. MD simulation results show that the p3 pentamer has much stronger interactions with mixed POPC-POPG lipids than pure POPC lipids, consistent with experimental observation that Aβ adsorption and fibrillation are enhanced on anionic lipid bilayers. Although electrostatic interactions are main attractive forces to drive the p3 pentamer to adsorb on the bilayer surface, the adsorption of the p3 pentamer on the lipid bilayer with C-terminal β-strands facing toward the bilayer surface is a net outcome of different competitions between p3 peptides-lipid bilayer and ions-p3-bilayer interactions. More importantly, Ca(2+) ions are found to form ionic bridges to associate negatively charged residues of p3 with anionic headgroups of the lipid bilayer, resulting in Aβ-Ca(2+)-PO4(-) complexes. Intensive Ca(2+) bound to the lipid bilayer and Ca(2+) ionic bridges may lead to Ca(2+) hemostasis responsible for neuronal dysfunction and death. This work provides insights into the mutual structure, dynamics, and interactions of both Aβ peptides and lipid bilayers at the atomic level, which expand our understanding of the complex behavior of amyloid-induced membrane disruption.
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Affiliation(s)
- Xiang Yu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA
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44
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Poojari C, Kukol A, Strodel B. How the amyloid-β peptide and membranes affect each other: An extensive simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:327-39. [DOI: 10.1016/j.bbamem.2012.09.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022]
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45
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Verma S, Singh A, Mishra A. The effect of fulvic acid on pre‐ and postaggregation state of Aβ17–42: Molecular dynamics simulation studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:24-33. [DOI: 10.1016/j.bbapap.2012.08.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/25/2012] [Accepted: 08/20/2012] [Indexed: 11/25/2022]
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46
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Zhao J, Luo Y, Jang H, Yu X, Wei G, Nussinov R, Zheng J. Probing ion channel activity of human islet amyloid polypeptide (amylin). BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:3121-30. [PMID: 22935354 PMCID: PMC3455117 DOI: 10.1016/j.bbamem.2012.08.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 08/14/2012] [Accepted: 08/16/2012] [Indexed: 01/14/2023]
Abstract
Interactions of human islet amyloid polypeptide (hIAPP or amylin) with the cell membrane are correlated with the dysfunction and death of pancreatic islet β-cells in type II diabetes. Formation of receptor-independent channels by hIAPP in the membrane is regarded as one of the membrane-damaging mechanisms that induce ion homeostasis and toxicity in islet β-cells. Here, we investigate the dynamic structure, ion conductivity, and membrane interactions of hIAPP channels in the DOPC bilayer using molecular modeling and molecular dynamics simulations. We use the NMR-derived β-strand-turn-β-strand motif as a building block to computationally construct a series of annular-like hIAPP structures with different sizes and topologies. In the simulated lipid environments, the channels lose their initial continuous β-sheet network and break into oligomeric subunits, which are still loosely associated to form heterogeneous channel conformations. The channels' shapes, morphologies and dimensions are compatible with the doughnut-like images obtained by atomic force microscopy, and with those of modeled channels for Aβ, the β(2)-microglobulin-derived K3 peptides, and the β-hairpin-based channels of antimicrobial peptide PG-1. Further, all channels induce directional permeability of multiple ions across the bilayers from the lower to the upper leaflet. This similarity suggests that loosely-associated β-structure motifs can be a general feature of toxic, unregulated channels. In the absence of experimental high-resolution atomic structures of hIAPP channels in the membrane, this study represents a first attempt to delineate some of the main structural features of the hIAPP channels, for a better understanding of the origin of amyloid toxicity and the development of pharmaceutical agents.
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Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, The University of Akron Akron, Ohio 44325
| | - Yin Luo
- Department of Chemical and Biomolecular Engineering, The University of Akron Akron, Ohio 44325
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P.R. China
| | - Hyunbum Jang
- Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute, Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Xiang Yu
- Department of Chemical and Biomolecular Engineering, The University of Akron Akron, Ohio 44325
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P.R. China
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute, Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron Akron, Ohio 44325
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47
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Hung SW, Hsiao PY, Lu MC, Chieng CC. Thermodynamic Investigations Using Molecular Dynamics Simulations with Potential of Mean Force Calculations for Cardiotoxin Protein Adsorption on Mixed Self-Assembled Monolayers. J Phys Chem B 2012; 116:12661-8. [DOI: 10.1021/jp304695w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Shih-Wei Hung
- Department of Engineering
and
System Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Pai-Yi Hsiao
- Department of Engineering
and
System Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Chang Lu
- Department
of Mechanical Engineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Ching-Chang Chieng
- Department of Engineering
and
System Science, National Tsing Hua University, Hsinchu, Taiwan
- Department
of Mechanical and Biomedical
Engineering, City University of Hong Kong, Kowloon, Hong Kong
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48
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Jiang D, Rauda I, Han S, Chen S, Zhou F. Aggregation pathways of the amyloid β(1-42) peptide depend on its colloidal stability and ordered β-sheet stacking. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12711-12721. [PMID: 22870885 PMCID: PMC3464049 DOI: 10.1021/la3021436] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Amyloid β (Aβ) fibrils are present as a major component in senile plaques, the hallmark of Alzheimer's disease (AD). Diffuse plaques (nonfibrous, loosely packed Aβ aggregates) containing amorphous Aβ aggregates are also formed in brain. This work examines the influence of Cu(2+) complexation by Aβ on the aggregation process in the context of charge and structural variations. Changes in the surface charges of Aβ molecules due to Cu(2+) binding, measured with a ζ-potential measurement device, were correlated with the aggregate morphologies examined by atomic force microscopy. As a result of the charge variation, the "colloid-like" stability of the aggregation intermediates, which is essential to the fibrillation process, is affected. Consequently, Cu(2+) enhances the amorphous aggregate formation. By monitoring variations in the secondary structures with circular dichroism spectroscopy, a direct transformation from the unstructured conformation to the β-sheet structure was observed for all types of aggregates observed (oligomers, fibrils, and/or amorphous aggregates). Compared to the Aβ aggregation pathway in the absence of Cu(2+) and taking other factors affecting Aβ aggregation (i.e., pH and temperature) into account, our investigation indicates that formations of amorphous and fibrous aggregates diverge from the same β-sheet-containing partially folded intermediate. This study suggests that the hydrophilic domain of Aβ also plays a role in the Aβ aggregation process. A kinetic model was proposed to account for the effects of the Cu(2+) binding on these two aggregation pathways in terms of charge and structural variations.
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Affiliation(s)
| | | | - Shubo Han
- Department of Natural Sciences, Fayetteville State University, Fayetteville, NC
| | | | - Feimeng Zhou
- Corresponding author. Phone: 323-343-2390. Fax: 323-343-6490.
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49
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Hamley IW. The Amyloid Beta Peptide: A Chemist’s Perspective. Role in Alzheimer’s and Fibrillization. Chem Rev 2012; 112:5147-92. [DOI: 10.1021/cr3000994] [Citation(s) in RCA: 670] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- I. W. Hamley
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD,
U.K
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50
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Liu J, Chen M, Qian DJ. Copper(II)-mediated layer-by-layer assembly of viologenthiol-functionalized carbon nanotube hybrid multilayers: preparation, characterization, morphology, and electrochemical properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:9496-9505. [PMID: 22624584 DOI: 10.1021/la3010954] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The metal-mediated self-assembly of coordination polymers, building blocks, and metal-organic frameworks has been widely used to construct multifunctional novel materials on the molecular level. Here, we developed this technique to build up multilayers of functionalized carbon nanotubes on the basis of both intermolecular electrostatic and coordinative interactions. Positively charged electroactive viologenthiol (VSH) was first immobilized on multiwalled carbon nanotubes (MWNTs) to form MWNT-VSH hybrids with a relative content of ∼9% by weight. Field emission transmission electron microscopy images revealed that the VSH molecules randomly covered the surfaces of MWNTs with a thickness of 1 to 2 nm. Then, the MWNT-VSH hybrids were used as nanoscale multidentate "ligands" (linkers) to construct metal-mediated multilayers with the use of CuAc(2) as the connectors by the layer-by-layer (LBL) method. The assembly process was monitored by absorption and X-ray photoelectron spectroscopy as well as scanning electron and atomic force microscopy after each assembly of Cu(II) ions and MWNT-VSH hybrids. Finally, the electrochemical behaviors of the viologens in the MWNT-VS/Cu LBL multilayers were investigated.
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Affiliation(s)
- Jiang Liu
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
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