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Dey A, Patil A, Arumugam S, Maiti S. Single-Molecule Maps of Membrane Insertion by Amyloid-β Oligomers Predict Their Toxicity. J Phys Chem Lett 2024; 15:6292-6298. [PMID: 38855822 DOI: 10.1021/acs.jpclett.4c01048] [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: 06/11/2024]
Abstract
The interaction of small Amyloid-β (Aβ) oligomers with the lipid membrane is an important component of the pathomechanism of Alzheimer's disease (AD). However, oligomers are heterogeneous in size. How each type of oligomer incorporates into the membrane, and how that relates to their toxicity, is unknown. Here, we employ a single molecule technique called Q-SLIP (Quencher-induced Step Length Increase in Photobleaching) to measure the membrane insertion of each monomeric unit of individual oligomers of Aβ42, Aβ40, and Aβ40-F19-Cyclohexyl alanine (Aβ40-F19Cha), and correlate it with their toxicity. We observe that the N-terminus of Aβ42 inserts close to the center of the bilayer, the less toxic Aβ40 inserts to a shallower depth, and the least toxic Aβ40-F19Cha has no specific distribution. This oligomer-specific map provides a mechanistic representation of membrane-mediated Aβ toxicity and should be a valuable tool for AD research.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Abhishek Patil
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Senthil Arumugam
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia
- European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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2
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Rahman MU, Song K, Da LT, Chen HF. Early aggregation mechanism of Aβ 16-22 revealed by Markov state models. Int J Biol Macromol 2022; 204:606-616. [PMID: 35134456 DOI: 10.1016/j.ijbiomac.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 12/19/2022]
Abstract
Aβ16-22 is believed to have critical role in early aggregation of full length amyloids that are associated with the Alzheimer's disease and can aggregate to form amyloid fibrils. However, the early aggregation mechanism is still unsolved. Here, multiple long-term molecular dynamics simulations combining with Markov state model were used to probe the early oligomerization mechanism of Aβ16-22 peptides. The identified dimeric form adopted either globular random-coil or extended β-strand like conformations. The observed dimers of these variants shared many overall conformational characteristics but differed in several aspects at detailed level. In all cases, the most common type of secondary structure was intermolecular antiparallel β-sheets. The inter-state transitions were very frequent ranges from few to hundred nanoseconds. More strikingly, those states which contain fraction of β secondary structure and significant amount of extended coiled structures, therefore exposed to the solvent, were majorly participated in aggregation. The assembly of low-energy dimers, in which the peptides form antiparallel β sheets, occurred by multiple pathways with the formation of an obligatory intermediates. We proposed that these states might facilitate the Aβ16-22 aggregation through a significant component of the conformational selection mechanism, because they might increase the aggregates population by promoting the inter-chain hydrophobic and the hydrogen bond contacts. The formation of early stage antiparallel β sheet structures is critical for oligomerization, and at the same time provided a flat geometry to seed the ordered β-strand packing of the fibrils. Our findings hint at reorganization of this part of the molecule as a potentially critical step in Aβ aggregation and will insight into early oligomerization for large β amyloids.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaiyuan Song
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Center for Bioinformation Technology, Shanghai, 200235, China.
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3
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Gomes GN, Levine ZA. Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments. J Phys Chem B 2021; 125:1974-1996. [PMID: 33464098 PMCID: PMC8362740 DOI: 10.1021/acs.jpcb.0c09193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
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Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
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4
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Sequeira MA, Herrera MG, Dodero VI. Modulating amyloid fibrillation in a minimalist model peptide by intermolecular disulfide chemical reduction. Phys Chem Chem Phys 2019; 21:11916-11923. [PMID: 31125036 DOI: 10.1039/c9cp01846h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptide structural transformation and aggregation is associated with a large number of outsider aetiology diseases, and it is intrinsically linked to amyloid peptide aggregation. Diphenylalanine self-assembled structures are used as robust minimalist beta amyloids not only to elucidate protein aggregation but also to generate hydrogels. Herein, we employed a neutral model peptide Ac-Phe-Phe-Cys-NH2 (Ac-FFC-NH2) to elucidate the role of intermolecular disulfide bonds in protein fibrillation. The Ac-FFC-NH2 peptide initially self-assembles into nanospheres that evolve to amyloid type fibrils under mild oxidative conditions. Incubation of the peptide in the presence of the chemical reduction agent TCEP inhibits the formation of the fibrils, detecting only spherical nanostructures with no secondary structure. Importantly, we triggered the transformation of the preformed linear straight amyloid fibrils to non-fibrillar structures by TCEP treatment. Under this condition, the amyloid bundles are transformed into rings, which evolve to a new spherical microstructure. We showed that the chemical reduction of intermolecular S-S in internal amyloid sequences might favour the off-path intermediates of amyloid fibril growth, even when the fibrils are formed. Our findings demonstrated that in internal amyloid sequences, the formation of intermolecular S-S promotes the formation of amyloid type fibrils; meanwhile, its reduction stabilises non-fibrillar structures. Altogether, this work provides fundamental understanding at the molecular and supramolecular level, thus facilitating the rational design of therapeutic tools for protein aggregation diseases.
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Affiliation(s)
- María Alejandra Sequeira
- Instituto de Química del Sur (INQUISUR-CONICET), Departamento de Química, Universidad Nacional del Sur, 8000FTN Bahía Blanca, Argentina
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5
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Blinov N, Wishart DS, Kovalenko A. Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation. J Phys Chem B 2019; 123:2491-2506. [PMID: 30811210 DOI: 10.1021/acs.jpcb.9b00480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural characterization of amyloid (A)β peptides implicated in Alzheimer's disease is a challenging problem due to their intrinsically disordered nature and their high propensity for aggregation. Only limited information is currently available from experiments on conformational properties and aggregation pathways of the peptides in cellular environments. In silico modeling complements experimental information, providing atomistic insight into structure and dynamics of different Aβ species. All-atom explicit solvent molecular dynamics (MD) simulations with a properly selected force field can deliver reliable structural and dynamic information. In the case of intrinsically disordered Aβ peptides, enhanced sampling simulations beyond the nanosecond time scale are required to obtain statistically meaningful results even for simple solvent conditions. To overcome the challenges of conformational sampling in crowded cellular environments, alternative approaches have to be used, including postprocessing of MD data. In this study, we employ the statistical-mechanical, three-dimensional reference interaction site model with the Kovalenko-Hirata closure integral equation molecular theory of solvation to describe solvent composition effects on the conformational equilibrium in a structural ensemble of the Aβ42 (covering residues 1-42) monomer based on a statistical reweighting technique. The methodology enables a computationally efficient prediction on how different factors in the cellular environment, such as solvent composition, nonpolar solvation, and macromolecular crowding, affect the structural properties of the monomer. Similarities have been identified between changes in the structural ensemble caused by nonpolar solvation and crowded environments modeled by ionic solution with large negative ions. In particular, both solvent conditions reduce the random coil content and enhance the helical structure content of the monomer. In contrast to the previous studies, which reported increased α-helical content of peptides in crowded environments, this work attributes these structural features to the difference in solvent exposure of hydrophilic residues of the monomer for different secondary structure elements, rather than to (entropic) excluded volume effects.
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Affiliation(s)
- Nikolay Blinov
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
| | - David S Wishart
- Departments of Computing Science and Biological Sciences , University of Alberta , Edmonton , Alberta T6G 2E8 , Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
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6
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Structure of amyloid β 25-35 in lipid environment and cholesterol-dependent membrane pore formation. Sci Rep 2019; 9:2689. [PMID: 30804528 PMCID: PMC6389947 DOI: 10.1038/s41598-019-38749-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/08/2019] [Indexed: 01/14/2023] Open
Abstract
The amyloid β (Aβ) peptide and its shorter variants, including a highly cytotoxic Aβ25–35 peptide, exert their neurotoxic effect during Alzheimer’s disease by various mechanisms, including cellular membrane permeabilization. The intrinsic polymorphism of Aβ has prevented the identification of the molecular basis of Aβ pore formation by direct structural methods, and computational studies have led to highly divergent pore models. Here, we have employed a set of biophysical techniques to directly monitor Ca2+-transporting Aβ25–35 pores in lipid membranes, to quantitatively characterize pore formation, and to identify the key structural features of the pore. Moreover, the effect of membrane cholesterol on pore formation and the structure of Aβ25–35 has been elucidated. The data suggest that the membrane-embedded peptide forms 6- or 8-stranded β-barrel like structures. The 8-stranded barrels may conduct Ca2+ ions through an inner cavity, whereas the tightly packed 6-stranded barrels need to assemble into supramolecular structures to form a central pore. Cholesterol affects Aβ25–35 pore formation by a dual mechanism, i.e., by direct interaction with the peptide and by affecting membrane structure. Collectively, our data illuminate the molecular basis of Aβ membrane pore formation, which should advance both basic and clinical research on Alzheimer’s disease and membrane-associated pathologies in general.
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7
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Jin Y, Sun Y, Lei J, Wei G. Dihydrochalcone molecules destabilize Alzheimer's amyloid-β protofibrils through binding to the protofibril cavity. Phys Chem Chem Phys 2018; 20:17208-17217. [DOI: 10.1039/c8cp01631c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dihydrochalcone molecules destabilize Aβ17–42protofibrils by disrupting the N-terminal β1 region and the turn region through binding to the protofibril cavity.
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Affiliation(s)
- Yibo Jin
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Yunxiang Sun
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Jiangtao Lei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Guanghong Wei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
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8
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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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9
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Söldner CA, Sticht H, Horn AHC. Role of the N-terminus for the stability of an amyloid-β fibril with three-fold symmetry. PLoS One 2017; 12:e0186347. [PMID: 29023579 PMCID: PMC5638522 DOI: 10.1371/journal.pone.0186347] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/01/2017] [Indexed: 12/28/2022] Open
Abstract
A key player in Alzheimer’s disease is the peptide amyloid-beta (Aβ), whose aggregation into small soluble oligomers, protofilaments, and fibrils finally leads to plaque deposits in human brains. The aggregation behavior of Aβ is strongly modulated by the nature and composition of the peptide’s environment and by its primary sequence properties. The N-terminal residues of Aβ play an important role, because they are known to change the peptide’s aggregation propensity. Since these residues are for the first time completely resolved at the molecular level in a three-fold symmetric fibril structure derived from a patient, we chose that system as template for a systematic investigation of the influence of the N-terminus upon structural stability. Using atomistic molecular dynamics simulations, we examined several fibrillar systems comprising three, six, twelve and an infinite number of layers, both with and without the first eight residues. First, we found that three layers are not sufficient to stabilize the respective Aβ topology. Second, we observed a clear stabilizing effect of the N-terminal residues upon the overall fibril fold: truncated Aβ systems were less stable than their full-length counterparts. The N-terminal residues Arg5, Asp7, and Ser8 were found to form important interfilament contacts stabilizing the overall fibril structure of three-fold symmetry. Finally, similar structural rearrangements of the truncated Aβ species in different simulations prompted us to suggest a potential mechanism involved in the formation of amyloid fibrils with three-fold symmetry.
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Affiliation(s)
- Christian A. Söldner
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anselm H. C. Horn
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- * E-mail:
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10
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Dorosh L, Stepanova M. Probing oligomerization of amyloid beta peptide in silico. MOLECULAR BIOSYSTEMS 2017; 13:165-182. [PMID: 27844078 DOI: 10.1039/c6mb00441e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aggregation of amyloid β (Aβ) peptide is implicated in fatal Alzheimer's disease, for which no cure is available. Understanding the mechanisms responsible for this aggregation is required in order for therapies to be developed. In an effort to better understand the molecular mechanisms involved in spontaneous aggregation of Aβ peptide, extensive molecular dynamics simulations are reported, and the results are analyzed through a combination of structural biology tools and a novel essential collective dynamics method. Several model systems composed of ten or twelve Aβ17-42 chains in water are investigated, and the influence of metal ions is probed. The results suggest that Aβ monomers tend to aggregate into stable globular-like oligomers with 13-23% of β-sheet content. Two stages of oligomer formation have been identified: quick collapse within the first 40 ns of the simulation, characterized by a decrease in inter-chain separation and build-up of β-sheets, and the subsequent slow relaxation of the oligomer structure. The resulting oligomers comprise a stable, coherently moving sub-aggregate of 6-9 strongly inter-correlated chains. Cu2+ and Fe2+ ions have been found to develop coordination bonds with carboxylate groups of E22, D23 and A42, which remain stable during 200 ns simulations. The presence of Fe2+, and particularly Cu2+ ions, in negatively charged cavities has been found to cause significant changes in the structure and dynamics of the oligomers. The results indicate, in particular, that formation of non-fibrillar oligomers might be involved in early template-free aggregation of Aβ17-42 monomers, with charged species such as Cu2+ or Fe2+ ions playing an important role.
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Affiliation(s)
- L Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada
| | - M Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada and Department of Physics, Astronomy, and Materials Science, Missouri State University, Springfield, MO, USA
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11
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Menon S, Sengupta N. Influence of Hyperglycemic Conditions on Self-Association of the Alzheimer's Amyloid β (Aβ 1-42) Peptide. ACS OMEGA 2017; 2:2134-2147. [PMID: 30023655 PMCID: PMC6044820 DOI: 10.1021/acsomega.7b00018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/08/2017] [Indexed: 06/08/2023]
Abstract
Clinical studies have identified a correlation between type-2 diabetes mellitus and cognitive decrements en route to the onset of Alzheimer's disease (AD). Recent studies have established that post-translational modifications of the amyloid β (Aβ) peptide occur under hyperglycemic conditions; particularly, the process of glycation exacerbates its neurotoxicity and accelerates AD progression. In view of the assertion that macromolecular crowding has an altering effect on protein self-assembly, it is crucial to characterize the effects of hyperglycemic conditions via crowding on Aβ self-assembly. Toward this purpose, fully atomistic molecular dynamics simulations were performed to study the effects of glucose crowding on Aβ dimerization, which is the smallest known neurotoxic species. The dimers formed in the glucose-crowded environment were found to have weaker associations as compared to that of those formed in water. Binding free energy calculations show that the reduced binding strength of the dimers can be mainly attributed to the overall weakening of the dispersion interactions correlated with substantial loss of interpeptide contacts in the hydrophobic patches of the Aβ units. Analysis to discern the differential solvation pattern in the glucose-crowded and pure water systems revealed that glucose molecules cluster around the protein, at a distance of 5-7 Å, which traps the water molecules in close association with the protein surface. This preferential exclusion of glucose molecules and resulting hydration of the Aβ peptides has a screening effect on the hydrophobic interactions, which in turn diminishes the binding strength of the resulting dimers. Our results imply that physical effects attributed to crowded hyperglycemic environments are incapable of solely promoting Aβ self-assembly, indicating that further mechanistic studies are required to provide insights into the self-assembly of post-translationally modified Aβ peptides, known to possess aggravated toxicity, under these conditions.
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Affiliation(s)
- Sneha Menon
- Physical
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Training and Development Complex, CSIR Campus,
CSIR Road, Chennai 600113, India
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
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12
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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13
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Chi H, Keiderling TA. Structural Rearrangement from Oligomer to Fibril Detected with FRET in a Designed Amphiphilic Peptide. Chembiochem 2016; 18:195-205. [DOI: 10.1002/cbic.201600436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Heng Chi
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
- Department of Pharmacy; Jiangsu Food and Pharmaceutical Science College; 4 E. Meicheng Rd. Huai'an Jiangsu Province 223005 China
| | - Timothy A. Keiderling
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
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14
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Cheon M, Kang M, Chang I. Polymorphism of fibrillar structures depending on the size of assembled Aβ 17-42 peptides. Sci Rep 2016; 6:38196. [PMID: 27901087 PMCID: PMC5128875 DOI: 10.1038/srep38196] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/04/2016] [Indexed: 01/16/2023] Open
Abstract
The size of assembled Aβ17-42 peptides can determine polymorphism during oligomerization and fibrillization, but the mechanism of this effect is unknown. Starting from separate random monomers, various fibrillar oligomers with distinct structural characteristics were identified using discontinuous molecular dynamics simulations based on a coarse-grained protein model. From the structures observed in the simulations, two characteristic oligomer sizes emerged, trimer and paranuclei, which generated distinct structural patterns during fibrillization. A majority of the simulations for trimers and tetramers formed non-fibrillar oligomers, which primarily progress to off-pathway oligomers. Pentamers and hexamers were significantly converted into U-shape fibrillar structures, meaning that these oligomers, called paranuclei, might be potent on-pathway intermediates in fibril formation. Fibrillar oligomers larger than hexamers generated substantial polymorphism in which hybrid structures were readily formed and homogeneous fibrillar structures appeared infrequently.
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Affiliation(s)
- Mookyung Cheon
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea.,Department of Neural Development and Disease, Korea Brain Research Institute, Daegu 41068, Korea
| | - Mooseok Kang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
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15
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Zhang M, Ren B, Chen H, Sun Y, Ma J, Jiang B, Zheng J. Molecular Simulations of Amyloid Structures, Toxicity, and Inhibition. Isr J Chem 2016. [DOI: 10.1002/ijch.201600075] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Hong Chen
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology Tianjin University Tianjin 300072 P. R. China
| | - Jie Ma
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
- State Key Laboratory of Pollution Control and Resource Reuse School of Environmental Science and Engineering Tongji University Shanghai 200092 P. R. China
| | - Binbo Jiang
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
- College of Chemical and Biological Engineering Zhejiang University Hangzhou Zhejiang 310027 P. R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
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16
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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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17
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Jang H, Arce FT, Lee J, Gillman AL, Ramachandran S, Kagan BL, Lal R, Nussinov R. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels. Methods Mol Biol 2016; 1345:251-68. [PMID: 26453217 PMCID: PMC7511997 DOI: 10.1007/978-1-4939-2978-8_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
| | - Fernando Teran Arce
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Joon Lee
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alan L Gillman
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90024, USA
| | - Ratnesh Lal
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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18
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Lugli F, Toschi F, Biscarini F, Zerbetto F. Electric Field Effects on Short Fibrils of Aβ Amyloid Peptides. J Chem Theory Comput 2015; 6:3516-26. [PMID: 26617101 DOI: 10.1021/ct1001335] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid fibrils are highly ordered protein aggregates, which are associated with many neurodegenerative diseases. The assembling dynamics of monomeric beta-amyloid peptides, Aβ, into small aggregates (and then into long fibrils) is still debated and has become a hot topic. In this study, we conducted molecular dynamics simulations in explicit water of small Aβ protofibrils (from monomer to pentamer) under the perturbation of an externally applied electric field with the aim of investigating the fundamental molecular interactions involved in the aggregation mechanism. Dynamics of small adducts of Aβ(16-42) in the presence of an electric field, which was shown before to accelerate the conformational change of a single molecule, indicate that the structural resilience increases with the number of molecules in the aggregate. In particular, for 50 ns, the pentamer shows an enhanced stability in secondary structure, number of hydrogen bonds, and number of salt bridges, even in the presence of the field perturbation. The resilience to the field perturbation is linked to the variation of the induced dipole moment of the aggregates that tends to level off very rapidly with the growing number of molecules, thereby reducing the energy available per molecule to produce structural changes. The results also show that in the presence of the field the stability of the hydrophobic second β-sheet (β2, residues 31-42) is higher than that of the first one (β1, residues 18-26). In particular, we identify Gly33, Gly37, and Met35 as the most important residues that stabilize the intermolecular packing and may act as nucleation sites for fibrillization. Furthermore, dynamics of the full-length Aβ(1-42) pentameric aggregate, which include the highly charged random coil residues 1-15, confirmed the key role of the second hydrophobic core in the protofibril structure.
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Affiliation(s)
- Francesca Lugli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Francesca Toschi
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Fabio Biscarini
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
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19
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Cheon M, Hall CK, Chang I. Structural Conversion of Aβ17-42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways. PLoS Comput Biol 2015; 11:e1004258. [PMID: 25955249 PMCID: PMC4425657 DOI: 10.1371/journal.pcbi.1004258] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/29/2015] [Indexed: 11/18/2022] Open
Abstract
Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer's and Parkinson's. The goal of this work is to provide insights into the structural changes that characterize the kinetic pathways by which amyloid-β peptides convert from monomers to oligomers to fibrils. By applying discontinuous molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physical aspects of protein aggregation, we have been able to trace out the entire aggregation process for a system containing 8 Aβ17-42 peptides. We uncovered two fibrillization mechanisms that govern the structural conversion of Aβ17-42 peptides from disordered oligomers into protofilaments. The first mechanism is monomeric conversion templated by a U-shape oligomeric nucleus into U-shape protofilament. The second mechanism involves a long-lived and on-pathway metastable oligomer with S-shape chains, having a C-terminal turn, en route to the final U-shape protofilament. Oligomers with this C-terminal turn have been regarded in recent experiments as a major contributing element to cell toxicity in Alzheimer's disease. The internal structures of the U-shape protofilaments from our PRIME20/DMD simulation agree well with those from solid state NMR experiments. The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer's disease in particular.
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Affiliation(s)
- Mookyung Cheon
- Center for Proteome Biophysics, Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (CKH); (IC)
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
- * E-mail: (CKH); (IC)
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20
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Zhang M, Zhao J, Zheng J. Molecular understanding of a potential functional link between antimicrobial and amyloid peptides. SOFT MATTER 2014; 10:7425-7451. [PMID: 25105988 DOI: 10.1039/c4sm00907j] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antimicrobial and amyloid peptides do not share common sequences, typical secondary structures, or normal biological activity but both the classes of peptides exhibit membrane-disruption ability to induce cell toxicity. Different membrane-disruption mechanisms have been proposed for antimicrobial and amyloid peptides, individually, some of which are not exclusive to either peptide type, implying that certain common principles may govern the folding and functions of different cytolytic peptides and associated membrane disruption mechanisms. Particularly, some antimicrobial and amyloid peptides have been identified to have dual complementary amyloid and antimicrobial properties, suggesting a potential functional link between amyloid and antimicrobial peptides. Given that some similar structural and membrane-disruption characteristics exist between the two classes of peptides, this review summarizes major findings, recent advances, and future challenges related to antimicrobial and amyloid peptides and strives to illustrate the similarities, differences, and relationships in the sequences, structures, and membrane interaction modes between amyloid and antimicrobial peptides, with a special focus on direct interactions of the peptides with the membranes. We hope that this review will stimulate further research at the interface of antimicrobial and amyloid peptides - which has been studied less intensively than either type of peptides - to decipher a possible link between both amyloid pathology and antimicrobial activity, which can guide drug design and peptide engineering to influence peptide-membrane interactions important in human health and diseases.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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21
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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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22
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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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23
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Cheng H, Huang WYC, Tsai TWT, Mou Y, Chao JCH, Chan JCC. Depletion of Water Molecules Near the End Stage of Steric Zipper Formation. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300073] [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)
- Hsin‐Mei Cheng
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - William Y. C. Huang
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Tim W. T. Tsai
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - John Chin Hao Chao
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Jerry C. C. Chan
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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24
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Autiero I, Saviano M, Langella E. In silico investigation and targeting of amyloid β oligomers of different size. MOLECULAR BIOSYSTEMS 2013; 9:2118-24. [PMID: 23708585 DOI: 10.1039/c3mb70086k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Aggregation of amyloid β (Aβ) peptides into fibrils has been implicated in the pathogenesis of Alzheimer's disease (AD). As a result, in recent years, substantial efforts have been expended in the study of the mechanism of aggregation of the Aβ peptide as well as of its inhibition by potential drug molecules. In this context, we have built a model of the Aβ(17-42) deca-oligomer using the solid-state NMR (ssNMR) structure of the Aβ(17-42) penta-oligomer as a reference. Both the penta- and deca-oligomer systems have been studied by all-atom molecular dynamics (MD) simulations and used as target systems for the investigation of the mechanism of action of a trehalose-derived Aβ aggregation inhibitor. In the deca-oligomer all the main structural features of the putative fibrillar state are retained. Moreover, the simulations reveal a remarkable gain in stability as the oligomer grows. MD studies of the inhibitor in complex with the penta- and deca-oligomers indicate a significant destabilization of the structure beyond the hampering of the addition of successive Aβ peptides at the ends of the fibril due to the presence of the inhibitor molecule. Our work provides an easy and effective approach which could be useful for the in silico development of potential drug molecules acting at different stages of the progression of Aβ-related diseases.
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Affiliation(s)
- Ida Autiero
- National Research Council, Institute of Biostructures and Bioimaging, 80138 Naples, Italy
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25
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Zhang L, Tang R, Bai S, Connors NK, Lua LHL, Chuan YP, Middelberg APJ, Sun Y. Molecular Energetics in the Capsomere of Virus-Like Particle Revealed by Molecular Dynamics Simulations. J Phys Chem B 2013; 117:5411-21. [DOI: 10.1021/jp311170w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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, China
| | - Ronghong Tang
- 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
| | - Shu Bai
- 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
| | - Natalie K. Connors
- Australian Institute for Bioengineering
and Nanotechnology, Centre for Biomolecular Engineering, The University of Queensland, St Lucia, QLD, 4072,
Australia
| | - Linda H. L. Lua
- Protein Expression
Facility, The University of Queensland,
St Lucia, QLD, 4072,
Australia
| | - Yap P. Chuan
- Australian Institute for Bioengineering
and Nanotechnology, Centre for Biomolecular Engineering, The University of Queensland, St Lucia, QLD, 4072,
Australia
| | - Anton P. J. Middelberg
- Australian Institute for Bioengineering
and Nanotechnology, Centre for Biomolecular Engineering, The University of Queensland, St Lucia, QLD, 4072,
Australia
| | - 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
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26
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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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27
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Comparative docking and ADMET study of some curcumin derivatives and herbal congeners targeting β-amyloid. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13721-012-0021-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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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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29
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Norlin N, Hellberg M, Filippov A, Sousa AA, Gröbner G, Leapman RD, Almqvist N, Antzutkin ON. Aggregation and fibril morphology of the Arctic mutation of Alzheimer's Aβ peptide by CD, TEM, STEM and in situ AFM. J Struct Biol 2012; 180:174-89. [PMID: 22750418 PMCID: PMC3466396 DOI: 10.1016/j.jsb.2012.06.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/10/2012] [Accepted: 06/14/2012] [Indexed: 10/28/2022]
Abstract
Morphology of aggregation intermediates, polymorphism of amyloid fibrils and aggregation kinetics of the "Arctic" mutant of the Alzheimer's amyloid β-peptide, Aβ((1-40))(E22G), in a physiologically relevant Tris buffer (pH 7.4) were thoroughly explored in comparison with the human wild type Alzheimer's amyloid peptide, wt-Aβ((1-40)), using both in situ atomic force and electron microscopy, circular dichroism and thioflavin T fluorescence assays. For arc-Aβ((1-40)) at the end of the 'lag'-period of fibrillization an abrupt appearance of ≈ 3 nm size 'spherical aggregates' with a homogeneous morphology, was identified. Then, the aggregation proceeds with a rapid growth of amyloid fibrils with a variety of morphologies, while the spherical aggregates eventually disappeared during in situ measurements. Arc-Aβ((1-40)) was also shown to form fibrils at much lower concentrations than wt-Aβ((1-40)): ≤ 2.5 μM and 12.5 μM, respectively. Moreover, at the same concentration, 50 μM, the aggregation process proceeds more rapidly for arc-Aβ((1-40)): the first amyloid fibrils were observed after c.a. 72 h from the onset of incubation as compared to approximately 7 days for wt-Aβ((1-40)). Amyloid fibrils of arc-Aβ((1-40)) exhibit a large variety of polymorphs, at least five, both coiled and non-coiled distinct fibril structures were recognized by AFM, while at least four types of arc-Aβ((1-40)) fibrils were identified by TEM and STEM and their mass-per-length statistics were collected suggesting supramolecular structures with two, four and six β-sheet laminae. Our results suggest a pathway of fibrillogenesis for full-length Alzheimer's peptides with small and structurally ordered transient spherical aggregates as on-pathway immediate precursors of amyloid fibrils.
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Affiliation(s)
- Nils Norlin
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Magnus Hellberg
- Division of Physics, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Andrei Filippov
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden
- Department of Physics, Kazan State University, 420008, Kazan, Russia
| | - Alioscka A. Sousa
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892-5766, USA
| | - Gerhard Gröbner
- Department of Biological Chemistry, Institute of Chemistry, Umeå University, SE-90187, Umeå, Sweden
| | - Richard D. Leapman
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892-5766, USA
| | - Nils Almqvist
- Division of Physics, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Oleg N. Antzutkin
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden
- Department of Physics, Warwick University, Coventry, CV4 7AL, United Kingdom
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30
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Pires RH, Karsai Á, Saraiva MJ, Damas AM, Kellermayer MSZ. Distinct annular oligomers captured along the assembly and disassembly pathways of transthyretin amyloid protofibrils. PLoS One 2012; 7:e44992. [PMID: 22984597 PMCID: PMC3440338 DOI: 10.1371/journal.pone.0044992] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 08/15/2012] [Indexed: 11/20/2022] Open
Abstract
Background Defects in protein folding may lead to severe degenerative diseases characterized by the appearance of amyloid fibril deposits. Cytotoxicity in amyloidoses has been linked to poration of the cell membrane that may involve interactions with amyloid intermediates of annular shape. Although annular oligomers have been detected in many amyloidogenic systems, their universality, function and molecular mechanisms of appearance are debated. Methodology/Principal Findings We investigated with high-resolution in situ atomic force microscopy the assembly and disassembly of transthyretin (TTR) amyloid protofibrils formed of the native protein by pH shift. Annular oligomers were the first morphologically distinct intermediates observed in the TTR aggregation pathway. Morphological analysis suggests that they can assemble into a double-stack of octameric rings with a 16±2 nm diameter, and displaying the tendency to form linear structures. According to light scattering data coupled to AFM imaging, annular oligomers appeared to undergo a collapse type of structural transition into spheroid oligomers containing 8–16 monomers. Disassembly of TTR amyloid protofibrils also resulted in the rapid appearance of annular oligomers but with a morphology quite distinct from that observed in the assembly pathway. Conclusions/Significance Our observations indicate that annular oligomers are key dynamic intermediates not only in the assembly but also in the disassembly of TTR protofibrils. The balance between annular and more compact forms of aggregation could be relevant for cytotoxicity in amyloidogenic disorders.
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Affiliation(s)
- Ricardo H. Pires
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
- * E-mail: (RHP); (AMD); (MSZK)
| | - Árpád Karsai
- Department of Biophysics, University of Pécs, Pécs, Hungary
| | - Maria J. Saraiva
- Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar, University of Porto, Porto, Portugal
| | - Ana M. Damas
- Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar, University of Porto, Porto, Portugal
- * E-mail: (RHP); (AMD); (MSZK)
| | - Miklós S. Z. Kellermayer
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- * E-mail: (RHP); (AMD); (MSZK)
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31
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Li J, Zhang L, Sun Y. Molecular basis of the initial platelet adhesion in arterial thrombosis: Molecular dynamics simulations. J Mol Graph Model 2012; 37:49-58. [DOI: 10.1016/j.jmgm.2012.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 03/17/2012] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
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32
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Wang SH, Dong XY, Sun Y. Thermodynamic analysis of the molecular interactions between amyloid β-protein fragments and (-)-epigallocatechin-3-gallate. J Phys Chem B 2012; 116:5803-9. [PMID: 22536844 DOI: 10.1021/jp209406t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(-)-Epigallocatechin-3-gallate (EGCG) has been proven effective in preventing the aggregation of amyloid β-protein 42 (Aβ42), and the thermodynamic interactions between Aβ42 and EGCG have been studied in our previous work ( J. Phys. Chem. B 2010, 114, 11576). Herein, to further probe the interactions between different regions of Aβ42 and EGCG, three Aβ42 fragments (i.e., Aβ1-16, Aβ1-30, and Aβ31-42) were synthesized, and the thermodynamic interactions between each of the fragments and EGCG at different EGCG and salt concentrations were investigated by isothermal titration calorimetry. The results indicate that, although hydrogen bonding and hydrophobic interaction are both involved in the interactions between Aβ42 and EGCG, hydrogen bonding mainly happens in Aβ1-16 while hydrophobic interaction mainly happens in Aβ17-42. It is found that when Aβ42 and its fragments are saturated by EGCG, their thermodynamic parameters have linear relationships. The saturated binding stoichiometry (N(s)) for Aβ42 is the sum of the N(s) values for Aβ1-30 and Aβ31-42, while ΔH(s), ΔS(s), and ΔG(s) for Aβ42 are half the sum of the values for Aβ1-30 and Aβ31-42. The result suggests that there are no specific interactions and binding sites in the Aβ42 and EGCG binding. The orders of ΔH(s) and TΔS(s) values for the Aβ fragments are determined as Aβ17-42 > Aβ31-42 > Aβ1-30 > Aβ1-16. Moreover, there is significant enthalpy-entropy compensation in the binding of EGCG to Aβ42 and its fragments, resulting in insignificant change of ΔG with the change of the solution environment. The research has shed new light on the molecular mechanisms of the interactions between EGCG and Aβ42.
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Affiliation(s)
- Shi-Hui Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Chebaro Y, Jiang P, Zang T, Mu Y, Nguyen PH, Mousseau N, Derreumaux P. Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure. J Phys Chem B 2012; 116:8412-22. [PMID: 22283547 DOI: 10.1021/jp2118778] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The amyloid-β protein (Aβ) oligomers are believed to be the main culprits in the cytoxicity of Alzheimer's disease (AD) and p3 peptides (Aβ17-42 fragments) are present in AD amyloid plaques. Many small-molecule or peptide-based inhibitors are known to slow down Aβ aggregation and reduce the toxicity in vitro, but their exact modes of action remain to be determined since there has been no atomic level of Aβ(p3)-drug oligomers. In this study, we have determined the structure of Aβ17-42 trimers both in aqueous solution and in the presence of five small-molecule inhibitors using a multiscale computational study. These inhibitors include 2002-H20, curcumin, EGCG, Nqtrp, and resveratrol. First, we used replica exchange molecular dynamics simulations coupled to the coarse-grained (CG) OPEP force field. These CG simulations reveal that the conformational ensemble of Aβ17-42 trimer can be described by 14 clusters with each peptide essentially adopting turn/random coil configurations, although the most populated cluster is characterized by one peptide with a β-hairpin at Phe19-Leu31. Second, these 14 dominant clusters and the less-frequent fibril-like state with parallel register of the peptides were subjected to atomistic Autodock simulations. Our analysis reveals that the drugs have multiple binding modes with different binding affinities for trimeric Aβ17-42 although they interact preferentially with the CHC region (residues 17-21). The compounds 2002-H20 and Nqtrp are found to be the worst and best binders, respectively, suggesting that the drugs may interfere at different stages of Aβ oligomerization. Finally, explicit solvent molecular dynamics of two predicted Nqtrp-Aβ17-42 conformations describe at atomic level some possible modes of action for Nqtrp.
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Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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Abstract
In this chapter we provided the overall background to the subject of protein aggregation and fibrillogenesis in amyloidogenesis, with introduction and brief discussion of the various topics that are included with the coming chapters. The division of the book into basic science and clinical science sections enables correlation of the topics to be made. The many proteins and peptides that have currently been found to undergo fibrillogenesis are tabulated. A broad technical survey is made, to indicate the vast array of techniques currently available to study aspects of protein oligomerization, aggregation and fibrillogenesis. These are split into three groups and tabulated, as the microscopical techniques, the analytical and biophysical methods, and the biochemical and cellular techniques. A few techniques are discussed, but in most cases only a link to relevant recent literature is provided.
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35
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Polymorphic structures of Alzheimer's β-amyloid globulomers. PLoS One 2011; 6:e20575. [PMID: 21687730 PMCID: PMC3110195 DOI: 10.1371/journal.pone.0020575] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 05/04/2011] [Indexed: 01/25/2023] Open
Abstract
Background Misfolding and self-assembly of Amyloid-β (Aβ) peptides into amyloid fibrils is pathologically linked to the development of Alzheimer's disease. Polymorphic Aβ structures derived from monomers to intermediate oligomers, protofilaments, and mature fibrils have been often observed in solution. Some aggregates are on-pathway species to amyloid fibrils, while the others are off-pathway species that do not evolve into amyloid fibrils. Both on-pathway and off-pathway species could be biologically relevant species. But, the lack of atomic-level structural information for these Aβ species leads to the difficulty in the understanding of their biological roles in amyloid toxicity and amyloid formation. Methods and Findings Here, we model a series of molecular structures of Aβ globulomers assembled by monomer and dimer building blocks using our peptide-packing program and explicit-solvent molecular dynamics (MD) simulations. Structural and energetic analysis shows that although Aβ globulomers could adopt different energetically favorable but structurally heterogeneous conformations in a rugged energy landscape, they are still preferentially organized by dynamic dimeric subunits with a hydrophobic core formed by the C-terminal residues independence of initial peptide packing and organization. Such structural organizations offer high structural stability by maximizing peptide-peptide association and optimizing peptide-water solvation. Moreover, curved surface, compact size, and less populated β-structure in Aβ globulomers make them difficult to convert into other high-order Aβ aggregates and fibrils with dominant β-structure, suggesting that they are likely to be off-pathway species to amyloid fibrils. These Aβ globulomers are compatible with experimental data in overall size, subunit organization, and molecular weight from AFM images and H/D amide exchange NMR. Conclusions Our computationally modeled Aβ globulomers provide useful insights into structure, dynamics, and polymorphic nature of Aβ globulomers which are completely different from Aβ fibrils, suggesting that these globulomers are likely off-pathway species and explaining the independence of the aggregation kinetics between Aβ globulomers and fibrils.
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36
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Nasica-Labouze J, Meli M, Derreumaux P, Colombo G, Mousseau N. A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35. PLoS Comput Biol 2011; 7:e1002051. [PMID: 21625573 PMCID: PMC3098217 DOI: 10.1371/journal.pcbi.1002051] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 03/28/2011] [Indexed: 12/17/2022] Open
Abstract
The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided. The formation of amyloid fibrils is associated with many neurodegenerative diseases such as Alzheimer's, Creutzfeld-Jakob, Parkinson's, the Prion disease and diabetes mellitus. In all cases, proteins misfold to form highly ordered insoluble aggregates called amyloid fibrils that deposit intra- and extracellularly and are resistant to proteases. All proteins are believed to have the instrinsic capability of forming amyloid fibrils that share common specific structural properties that have been observed by X-ray crystallography and by NMR. However, little is known about the aggregation dynamics of amyloid assemblies, and their toxicity mechanism is therefore poorly understood. It is believed that small amyloid oligomers, formed on the aggregation pathway of full amyloid fibrils, are the toxic species. A detailed atomic characterization of the oligomerization process is thus necessary to further our understanding of the amyloid oligomer's toxicity. Our approach here is to study the aggregation dynamics of a 7-residue amyloid peptide GNNQQNY through a combination of numerical techniques. Our results suggest that this amyloid sequence can form fibril-like structures and is polymorphic, which agrees with recent experimental observations. The ability to fully characterize and describe the aggregation pathway of amyloid sequences numerically is key to the development of future drugs to target amyloid oligomers.
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Affiliation(s)
| | - Massimiliano Meli
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Institut de Biologie Physico-Chimique, Université Paris 7, and Institut Universitaire de France, Paris, France
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
- * E-mail: (GC); (NM)
| | - Normand Mousseau
- Département de Physique and GEPROM, Université de Montréal, Montréal, Québec, Canada
- * E-mail: (GC); (NM)
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37
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Zhao J, Yu X, Liang G, Zheng J. Heterogeneous Triangular Structures of Human Islet Amyloid Polypeptide (Amylin) with Internal Hydrophobic Cavity and External Wrapping Morphology Reveal the Polymorphic Nature of Amyloid Fibrils. Biomacromolecules 2011; 12:1781-94. [DOI: 10.1021/bm2001507] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Xiang Yu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Guizhao Liang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- Key Laboratory of Biorheological Science and Technology Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
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38
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Buch I, Tsai CJ, Wolfson HJ, Nussinov R. Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers. Protein Pept Lett 2011; 18:362-72. [PMID: 21222638 PMCID: PMC7316382 DOI: 10.2174/092986611794653996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 12/15/2010] [Indexed: 11/22/2022]
Abstract
We construct nanotubes using native protein structures and their native associations from structural databases. The construction is based on a shape-guided symmetric self-assembly concept. Our strategy involves fusing judiciously-selected oligomerization domains via peptide linkers. Linkers are inherently flexible, hence their choice is critical: they should position the domains in three-dimensional space in the desired orientation while retaining their own natural conformational tendencies; however, at the same time, retain the construct stability. Here we outline a design scheme which accounts for linker flexibility considerations, and present two examples. The first is HIV-1 capsid protein, which in vitro self-assembles into nanotubes and conical capsids, and its linker exists as a short flexible loop. The second involves novel nanotubes construction based on antimicrobial homodimer Magainin 2, employing linkers of distinct lengths and flexibility levels. Our strategy utilizes the abundance of unique shapes and sizes of proteins and their building blocks which can assemble into a vast number of combinations, and consequently, nanotubes of distinct morphologies and diameters. Computational design and assessment methodologies can help reduce the number of candidates for experimental validation. This is an invited paper for a special issue on protein dynamics, here focusing on flexibility in nanotube design based on protein building blocks.
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Affiliation(s)
- Idit Buch
- Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI – Frederick, Bldg 469, Frederick, MD 21702, USA
| | - Haim J. Wolfson
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Nussinov
- Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI – Frederick, Bldg 469, Frederick, MD 21702, USA
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39
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Takeda T, Chang WE, Raman EP, Klimov DK. Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril. Proteins 2011; 78:2849-60. [PMID: 20635343 DOI: 10.1002/prot.22804] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nonsteroidal anti-inflammatory drugs are considered as potential therapeutic agents against Alzheimer's disease. Using replica exchange molecular dynamics and atomistic implicit solvent model, we studied the mechanisms of binding of naproxen and ibuprofen to the Abeta fibril derived from solid-state NMR measurements. The binding temperature of naproxen is found to be almost 40 K higher than of ibuprofen implicating higher binding affinity of naproxen. The key factor, which enhances naproxen binding, is strong interactions between ligands bound to the surface of the fibril. The naphthalene ring in naproxen appears to provide a dominant contribution to ligand-ligand interactions. In contrast, ligand-fibril interactions cannot explain differences in the binding affinities of naproxen and ibuprofen. The concave fibril edge with the groove is identified as the primary binding location for both ligands. We show that confinement of the ligands to the groove facilitates ligand-ligand interactions that lowers the energy of the ligands bound to the concave edge compared with those bound to the convex edge. Our simulations appear to provide microscopic rationale for the differing binding affinities of naproxen and ibuprofen observed experimentally.
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Affiliation(s)
- Takako Takeda
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia 20110, USA
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40
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Zhao J, Yu X, Liang G, Zheng J. Structural Polymorphism of Human Islet Amyloid Polypeptide (hIAPP) Oligomers Highlights the Importance of Interfacial Residue Interactions. Biomacromolecules 2010; 12:210-20. [DOI: 10.1021/bm101159p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
| | - Xiang Yu
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
| | - Guizhao Liang
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, United States, and Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P.R. China
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41
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Murciano-Calles J, Cobos ES, Mateo PL, Camara-Artigas A, Martinez JC. An oligomeric equilibrium intermediate as the precursory nucleus of globular and fibrillar supramacromolecular assemblies in a PDZ domain. Biophys J 2010; 99:263-72. [PMID: 20655855 DOI: 10.1016/j.bpj.2010.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/26/2010] [Accepted: 04/01/2010] [Indexed: 11/26/2022] Open
Abstract
The equilibrium unfolding at neutral pH of the third PDZ domain of PSD95, as followed by DSC, is characterized by the presence of an equilibrium intermediate with clear signs of oligomerization. DLS and SEC measurements indicate that at 60-70 degrees C small oligomers populate, showing a typical beta-sheet far-UV CD spectrum. These intermediate species lead to the formation of rodlike particulates of approximately 12 nm, which remain in solution after 2 weeks incubation and grow until they adopt annular/spherical shapes of approximately 50 nm and protofibrils, which are subsequently fully transformed into fibrils. The fibrils can also disaggregate after the addition of 1:1 buffer dilution followed by cooling to room temperature, thus returning to the initial monomeric state. Growth kinetics, as shown by ThT and ANS fluorescence, show that the organization of the different supramacromolecular structures comes from a common nucleation unit, the small oligomers, which organize themselves before reaching the incubation temperature of 60 degrees C. Our experiments point toward the existence of a well-defined reversible, stepwise, and downhill organization of the processes involved in the association-dissociation of the intermediate. We estimate the enthalpy change accompanying the association-dissociation equilibria to be 130 kJ x mol(-1). Furthermore, the coalescence under essentially reversible conditions of different kinds of supramacromolecular assemblies renders this protein system highly interesting for biophysical studies aimed at our further understanding of amyloid pathological conditions.
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Affiliation(s)
- Javier Murciano-Calles
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, Granada, Spain
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42
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Yu X, Wang Q, Zheng J. Structural determination of Abeta25-35 micelles by molecular dynamics simulations. Biophys J 2010; 99:666-74. [PMID: 20643087 DOI: 10.1016/j.bpj.2010.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022] Open
Abstract
Amyloid-beta (Abeta) peptides and other amyloidogenic proteins can form a wide range of soluble oligomers of varied morphologies at the early aggregation stage, and some of these oligomers are biologically relevant to the pathogenesis of Alzheimer's disease. Spherical micelle-like oligomers have been often observed for many different types of amyloids. Here, we report a hybrid computational approach to systematically construct, search, optimize, and rank soluble micelle-like Abeta25-35 structures with different side-chain packings at the atomic level. Simulations reveal for the first time, to our knowledge, that two Abeta micelles with antiparallel peptide organization and distinct surface hydrophobicity display high structural stability. Stable micelles experience a slow secondary structural transition from turn to alpha-helix. Energetic analysis coupled with computational mutagenesis reveals that van der Waals and solvation energies play a more pronounced role in stabilizing the micelles, whereas the electrostatic energies present a stable but minor energetic contribution to peptide assemblies. Modeled Abeta micelles with shapes and dimensions similar to those of experimentally derived spherical structures also provide detailed information about the roles of structural dynamics and transition in the formation of amyloid fibrils. The strong binding affinity of our micelles to antibodies implies that micelles may be a biologically relevant species.
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Affiliation(s)
- Xiang Yu
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio, USA
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43
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Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010; 110:4820-38. [PMID: 20402519 PMCID: PMC2920034 DOI: 10.1021/cr900377t] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Indexed: 01/13/2023]
Affiliation(s)
| | | | - Ruth Nussinov
- To whom correspondence should be addressed. Tel.: (301) 846-5579. Fax: (301) 846-5598. E-mail:
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44
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Jang H, Teran Arce F, Ramachandran S, Capone R, Lal R, Nussinov R. Structural convergence among diverse, toxic beta-sheet ion channels. J Phys Chem B 2010; 114:9445-51. [PMID: 20608696 PMCID: PMC2908347 DOI: 10.1021/jp104073k] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/22/2010] [Indexed: 12/11/2022]
Abstract
Recent studies show that an array of beta-sheet peptides, including N-terminally truncated Abeta peptides (Abeta(11-42/17-42)), K3 (a beta(2)-microglobulin fragment), and protegrin-1 (PG-1) peptides form ion channel-like structures and elicit single channel ion conductance when reconstituted in lipid bilayers and induce cell damage through cell calcium overload. Striking similarities are observed in the dimensions of these toxic channels irrespective of their amino acid sequences. However, the intriguing question of preferred channel sizes is still unresolved. Here, exploiting ssNMR-based, U-shaped, beta-strand-turn-beta-strand coordinates, we modeled truncated Abeta peptide (p3) channels with different sizes (12- to 36-mer). Molecular dynamics (MD) simulations show that optimal channel sizes of the ion channels presenting toxic ionic flux range between 16- and 24-mer. This observation is in good agreement with channel dimensions imaged by AFM for Abeta(9-42), K3 fragment, and PG-1 channels and highlights the bilayer-supported preferred toxic beta-channel sizes and organization, regardless of the peptide sequence.
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Affiliation(s)
| | | | | | | | - Ratnesh Lal
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
| | - Ruth Nussinov
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
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45
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De Simone A, Derreumaux P. Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent. J Chem Phys 2010; 132:165103. [DOI: 10.1063/1.3385470] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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46
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Miyashita N, Straub JE, Thirumalai D. Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc 2010; 131:17843-52. [PMID: 19995075 DOI: 10.1021/ja905457d] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aggregation of Amyloid beta (Abeta) peptide has been linked to the neurodegenerative Alzheimer's Disease and implicated in other amyloid diseases including cerebral amyloid angiopathy. Abeta peptide is generated by cleavage of the amyloid precursor protein (APP) by transmembrane proteases. It is crucial to determine the structures of beta-amyloid peptides in a membrane to provide a molecular basis for the cleavage mechanism. We report the structures of amyloid beta peptide (Abeta(1-40) and Abeta(1-42)) as well as the 672-726 fragment of APP (referred to as Abeta(1-55)) in a membrane environment determined by replica-exchange molecular dynamics simulation. Abeta(1-40) is found to have two helical domains A (13-22) and B(30-35) and a type I beta-turn at 23-27. The peptide is localized at the interface between membrane and solvent. Substantial fluctuations in domain A are observed. The dominant simulated tertiary structure of Abeta(1-40) is observed to be similar to the simulated Abeta(1-42) structure. However, there are differences observed in the overall conformational ensemble, as characterized by the two-dimensional free energy surfaces. The fragment of APP (Abeta(1-55)) is observed to have a long transmembrane helix. The position of the transmembrane region and ensemble of membrane structures are elucidated. The conformational transition between the transmembrane Abeta(1-55) structure, prior to cleavage, and the Abeta(1-40) structure, following cleavage, is proposed.
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Affiliation(s)
- Naoyuki Miyashita
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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Zheng J, Yu X, Wang J, Yang JC, Wang Q. Molecular modeling of two distinct triangular oligomers in amyloid beta-protein. J Phys Chem B 2010; 114:463-70. [PMID: 20014755 DOI: 10.1021/jp907608s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-beta (Abeta) peptides exhibit many distinct structural morphology at the early aggregate stage, some of which are biological relevant to the pathogenesis of Alzheimer's disease (AD). Atomic-resolution structures of the early Abeta aggregates and their conformational changes in amyloid aggregation remain elusive. Here, we perform all-atom molecular modeling and dynamics simulations to obtain two stable triangular-like Abeta structures with the lowest packing energy, one corresponding to the Tycko's model (Paravastu, A.; Leapman, R.; Yau, W.; Tycko, R. Proc. Nat. Acad. Soc. U.S.A. 2008, 105, 18349-18354) (referred to C-WT model) and the other corresponding to computational model (N-WT model). Both models have the same 3-fold symmetry but distinct beta-sheet organizations in which three Abeta hexamers pack together via either C-terminal beta-strand residues or N-terminal beta-strand residues forming distinct hydrophobic cross section. Structural and energetic comparisons of two 3-fold Abeta oligomers, coupled with structural changes upon the mutations occurring at the interacting interfaces, reveal that although hydrophobic interactions are still dominant forces, electrostatic interactions are more favorable in the N-WT model due to the formation of more and stable intersheet salt bridges, while solvation energy is more favorable in the C-WT model due to more exposed hydrophilic residues to solvent. Both models display many common features similar to other amyloid oligomers and therefore are likely to be biologically relevant.
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Affiliation(s)
- Jie Zheng
- Department of Chemical and Biomolecular Engineering, University of Akron, Akron, Ohio 44325, USA.
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Tsai HHG, Lee JB, Tseng SS, Pan XA, Shih YC. Folding and membrane insertion of amyloid-beta (25-35) peptide and its mutants: Implications for aggregation and neurotoxicity. Proteins 2010; 78:1909-25. [DOI: 10.1002/prot.22705] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Jang H, Arce FT, Capone R, Ramachandran S, Lal R, Nussinov R. Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels. Biophys J 2010; 97:3029-37. [PMID: 19948133 DOI: 10.1016/j.bpj.2009.09.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 08/31/2009] [Accepted: 09/10/2009] [Indexed: 02/05/2023] Open
Abstract
In Alzheimer's disease, calcium permeability through cellular membranes appears to underlie neuronal cell death. It is increasingly accepted that calcium permeability involves toxic ion channels. We modeled Alzheimer's disease ion channels of different sizes (12-mer to 36-mer) in the lipid bilayer using molecular dynamics simulations. Our Abeta channels consist of the solid-state NMR-based U-shaped beta-strand-turn-beta-strand motif. In the simulations we obtain ion-permeable channels whose subunit morphologies and shapes are consistent with electron microscopy/atomic force microscopy. In agreement with imaged channels, the simulations indicate that beta-sheet channels break into loosely associated mobile beta-sheet subunits. The preferred channel sizes (16- to 24-mer) are compatible with electron microscopy/atomic force microscopy-derived dimensions. Mobile subunits were also observed for beta-sheet channels formed by cytolytic PG-1 beta-hairpins. The emerging picture from our large-scale simulations is that toxic ion channels formed by beta-sheets spontaneously break into loosely interacting dynamic units that associate and dissociate leading to toxic ionic flux. This sharply contrasts intact conventional gated ion channels that consist of tightly interacting alpha-helices that robustly prevent ion leakage, rather than hydrogen-bonded beta-strands. The simulations suggest why conventional gated channels evolved to consist of interacting alpha-helices rather than hydrogen-bonded beta-strands that tend to break in fluidic bilayers. Nature designs folded channels but not misfolded toxic channels.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, NCI-Frederick, SAIC-Frederick, Frederick, Maryland, USA.
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Vitagliano L, Stanzione F, De Simone A, Esposito L. Dynamics and stability of amyloid-like steric zipper assemblies with hydrophobic dry interfaces. Biopolymers 2010; 91:1161-71. [PMID: 19280623 DOI: 10.1002/bip.21182] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent seminal investigations have suggested that the basic structural motif of amyloid fibers may be constituted by a tight association of two facing beta-sheets (steric zipper). Although this model has been derived from crystal structures of small peptide models, several theoretical investigations, essentially focused on steric zipper interface containing large polar and/or aromatic side chains, have confirmed the stability of this motif in a crystal-free context. To analyze the general validity of these findings, we carried out molecular dynamics (MD) simulations on aggregates stabilized by steric zipper interfaces made also of small or hydrophobic residues. In particular, we here characterized assemblies formed by the peptides SSTSAA and VQIVYK, whose structures have been recently solved at high resolution. In contrast to previous results obtained for polar/aromatic aggregates of the same size and with similar interface area, steric zipper assemblies composed of a pair of 10-stranded beta-sheets show high fluctuations and significant distortions in the simulation timescales (40-60 ns). Taking into account the crystal packing, the effect of the addition of an extra sheet to the assemblies was also evaluated. The MD results indicate that this addition does not provide extra-stabilization to the pair of sheet models. Although present data do not preclude the possibility that the steric zipper association identified in the crystal structure is the basic motif of SSTSAA and VQIVYK fibers, our findings highlight the importance of the nature of residues directly involved in the motif. Indeed, polar and aromatic residues that may form intrasheet and intersheet interactions likely provide a strong contribution to the steric zipper motif stability. Along this line, assemblies endowed with hydrophobic residues presumably require larger interfaces. In line with this suggestion, MD analysis of the HET-s(218-289) prion models composed of a similar number of strands shows that the assembly is endowed with a remarkable stability.
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Affiliation(s)
- Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy.
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