1
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Huang F, Fan X, Wang Y, Zou Y, Lian J, Wang C, Ding F, Sun Y. Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease. Brief Bioinform 2024; 25:bbad526. [PMID: 38271485 PMCID: PMC10810335 DOI: 10.1093/bib/bbad526] [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] [Received: 11/08/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The aggregation of medin forming aortic medial amyloid is linked to arterial wall degeneration and cerebrovascular dysfunction. Elevated levels of arteriolar medin are correlated with an increased presence of vascular amyloid-β (Aβ) aggregates, a hallmark of Alzheimer's disease (AD) and vascular dementia. The cross-interaction between medin and Aβ results in the formation of heterologous fibrils through co-aggregation and cross-seeding processes both in vitro and in vivo. However, a comprehensive molecular understanding of the cross-interaction between medin and Aβ-two intrinsically disordered proteins-is critically lacking. Here, we employed atomistic discrete molecular dynamics simulations to systematically investigate the self-association, co-aggregation and also the phenomenon of cross-seeding between these two proteins. Our results demonstrated that both Aβ and medin were aggregation prone and their mixture tended to form β-sheet-rich hetero-aggregates. The formation of Aβ-medin hetero-aggregates did not hinder Aβ and medin from recruiting additional Aβ and medin peptides to grow into larger β-sheet-rich aggregates. The β-barrel oligomer intermediates observed in the self-aggregations of Aβ and medin were also present during their co-aggregation. In cross-seeding simulations, preformed Aβ fibrils could recruit isolated medin monomers to form elongated β-sheets. Overall, our comprehensive simulations suggested that the cross-interaction between Aβ and medin may contribute to their pathological aggregation, given the inherent amyloidogenic tendencies of both medin and Aβ. Targeting medin, therefore, could offer a novel therapeutic approach to preserving brain function during aging and AD by improving vascular health.
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Affiliation(s)
- Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Jiangfang Lian
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Chuang Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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2
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Wang F, Xia W, Zhang M, Wu R, Song X, Hao Y, Feng Y, Zhang L, Li D, Kang W, Liu C, Liu L. Engineering of antimicrobial peptide fibrils with feedback degradation of bacterial-secreted enzymes. Chem Sci 2023; 14:10914-10924. [PMID: 37829030 PMCID: PMC10566480 DOI: 10.1039/d3sc01089a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
Proteins and peptides can assemble into functional amyloid fibrils with distinct architectures. These amyloid fibrils can fulfil various biological functions in living organisms, and then be degraded. By incorporating an amyloidogenic segment and enzyme-cleavage segment together, we designed a peptide (enzyme-cleavage amyloid peptides (EAP))-based functional fibril which could be degraded specifically by gelatinase. To gain molecular insights into the assembly and degradation of EAP fibrils, we determined the atomic structure of the EAP fibril using cryo-electron microscopy. The amyloidogenic segment of EAP adopted a β-strand conformation and mediated EAP-fibril formation mainly via steric zipper-like interactions. The enzyme-cleavage segment was partially involved in self-assembly, but also exhibited high flexibility in the fibril structure, with accessibility to gelatinase binding and degradation. Moreover, we applied the EAP fibril as a tunable scaffold for developing degradable self-assembled antimicrobial fibrils (SANs) by integrating melittin and EAP together. SANs exhibited superior activity for killing bacteria, and significantly improved the stability and biocompatibility of melittin. SANs were eliminated automatically by the gelatinase secreted from targeted bacteria. Our work provides a new strategy for rational design of functional fibrils with a feedback regulatory loop for optimizing the biocompatibility and biosafety of designed fibrils. Our work may aid further developments of "smart" peptide-based biomaterials for biomedical applications.
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Affiliation(s)
- Fenghua Wang
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University Zhenjiang Jiangsu 212013 China
- College of Aeronautical Engineering, Jiangsu Aviation Vocational and Technical College Zhenjiang Jiangsu 212134 China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
| | - Mingming Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
| | - Rongrong Wu
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University Zhenjiang Jiangsu 212013 China
| | - Xiaolu Song
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University Zhenjiang Jiangsu 212013 China
| | - Yun Hao
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University Zhenjiang Jiangsu 212013 China
| | - Yonghai Feng
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University Zhenjiang Jiangsu 212013 China
| | - Liwei Zhang
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University Zhenjiang Jiangsu 212013 China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University Shanghai 200030 China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University Shanghai 200240 China
| | - Wenyan Kang
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
- Department of Neurology, Ruijin Hainan Hospital, Shanghai Jiao Tong University School of Medicine (Boao Research Hospital) Hainan 571434 China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- Department of Neurology, Ruijin Hainan Hospital, Shanghai Jiao Tong University School of Medicine (Boao Research Hospital) Hainan 571434 China
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences Shanghai 200032 China
| | - Lei Liu
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University Zhenjiang Jiangsu 212013 China
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3
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Jia X, Liu Y, Qu Y, Li YQ, Liu X, Liu P, Li W. Electric Field-Controlled Peptide Self-Assembly through Funnel-Shaped Two-Dimensional Nanopores. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51183-51189. [PMID: 36329605 DOI: 10.1021/acsami.2c13590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Self-assembly of biomolecules is critical for the realization of biological functions. Thus, the precise control of self-assembly has great significance in the design of biochips and biomedical agents. In this report, we design a Y-shaped funnel on a two-dimensional (2D) heterostructure, called 2D funnel, based on monolayered polyaniline carbon nitride (C3N) and boron carbide (BC3), and study its application in the self-assembly state regulation of the peptide oligomer, using Aβ16-21 as the representative model. Structurally, the 2D funnel is composed of three regions: channel area, triangle area, and barrier area. The channel and triangle areas show higher binding affinity to the peptide than that of the barrier area, which leads to the confinement of the peptide in the 2D funnel. Our results show that when an external electric field is applied along the 2D funnel, the oligomer is driven to migrate across the funnel. Its trajectory is confined inside the narrow channel area, which effectively causes peptide dissociation into the individual peptide chains. Then, when the external electric field is turned off, the separated peptide chains spontaneously assemble in the triangle area and tend to reunite. Our present findings propose a novel heterostructure platform, which enables the manipulation of the self-assembly state of peptides by switching the electric field, which could guide the design and fabrication of nanodevices for sensing and sequencing applications.
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Affiliation(s)
- Xiao Jia
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yang Liu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Yong-Qiang Li
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Xiangdong Liu
- School of Physics, Shandong University, Jinan, Shandong 250100, China
| | - Peng Liu
- Institute of Frontier and Interdisciplinary Science and Key Laboratory of Particle Physics and Particle Irradiation (MOE), Shandong University, Qingdao, Shandong 266237, China
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, Shandong 250100, China
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4
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Jorgenson TD, Zareie HM, Sarikaya M, Overney RM. Symbiotic assembly of peptide nano-mosaics at solid interfaces. NANOSCALE 2021; 13:7735-7743. [PMID: 33928951 DOI: 10.1039/d0nr07208g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The spontaneous co-organization of distinct biomolecules at interfaces enables many of Nature's hierarchical organizations involving both hard and soft materials. Engineering efforts to mimic such hybrid complexes rely on our ability to rationally structure biomolecules at inorganic interfaces. Control over the nanoscale structure of patterned biomolecules remains challenging due to difficulties in controlling the multifarious interactions involved. This work discusses binary peptide assembly as a means to fabricate biomolecular nano-mosaics at graphite surfaces with predictable structures. Distinct peptide-substrate interactions lead to divergent crystallographic growth directions, molecular scale immiscibility, and a symbiotic assembly phenomenon. We present a symbiotic assembly model that accurately predicts the binary assembly structure relying solely on the constituent peptide nucleation kinetics and molar fractions. The ability to tune such biomolecular nano-mosaic structures facilitates the bottom up fabrication of high-density, multifunctional interfaces for nanotechnology.
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Affiliation(s)
- Tyler D Jorgenson
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
| | - Hadi M Zareie
- Department of Material Science and Engineering, University of Washington, Seattle, WA, USA
| | - Mehmet Sarikaya
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA. and Department of Material Science and Engineering, University of Washington, Seattle, WA, USA
| | - René M Overney
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA. and Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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5
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Feng Q, Hong Y, Pradeep Nidamanuri N, Yang C, Li Q, Dong M. Identification and Nanomechanical Characterization of the HIV Tat-Amyloid β Peptide Multifibrillar Structures. Chemistry 2020; 26:9449-9453. [PMID: 32167218 DOI: 10.1002/chem.201905715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/29/2020] [Indexed: 12/25/2022]
Abstract
HIV transactivator of transcription (Tat) protein could interact with amyloid β (Aβ) peptide which cause the growth of Aβ plaques in the brain and result in Alzheimer's disease in HIV-infected patients. Herein, we employ high-resolution atomic force microscopy and quantitative nanomechanical mapping to investigate the effects of Tat protein in Aβ peptide aggregation. Our results demonstrate that the Tat protein could bind to the Aβ fibril surfaces and result in the formation of Tat-Aβ multifibrillar structures. The resultant Tat-Aβ multifibrillar aggregates represent an increase in stiffness compared with Aβ fibrils due to the increase in β-sheet formation. The identification and characterization of the Tat-Aβ intermediate aggregates is important to understanding the interactions between Tat protein and Aβ peptide, and the development of novel therapeutic strategy for Alzheimer's disease-like disorder in HIV infected individuals.
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Affiliation(s)
- Qiying Feng
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Yue Hong
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Naga Pradeep Nidamanuri
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Chuanxu Yang
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Mingdong Dong
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
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6
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Chen Y, Peng F, Su T, Yang H, Qiu F. Direct Identification of Amyloid Peptide Fragments in Human α-Synuclein Based on Consecutive Hydrophobic Amino Acids. ACS OMEGA 2020; 5:11677-11686. [PMID: 32478258 PMCID: PMC7254785 DOI: 10.1021/acsomega.0c00979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/04/2020] [Indexed: 02/08/2023]
Abstract
![]()
Formation of amyloid fibrils by misfolding
α-synuclein is
a characteristic feature of Parkinson’s disease, but the exact
molecular mechanism of this process has long been an unresolved mystery.
Identification of critical amyloid peptide fragments from α-synuclein
may hold the key to decipher this mystery. Focusing on consecutive
hydrophobic amino acids (CHAA) in the protein sequence, in this study
we proposed a sequence-based strategy for direct identification of
amyloid peptide fragments in α-synuclein. We picked out three
CHAA fragments (two hexapeptides and one tetrapeptide) from α-synuclein
and studied their amyloidogenic property. The thioflavin-T binding
test, transmission electron microscopy, Congo red staining, and Fourier
transform infrared spectroscopy revealed that although only hexapeptides
could undergo amyloid aggregation on their own, extended peptide fragments
based on any of the three peptides could form typical amyloid fibrils.
Primary amyloidogenic fragments based on the three peptides showed
synergetic aggregation behavior and could accelerate the aggregation
of full-length α-synuclein. It was proved that hydrophobic interaction
played a predominant role for the aggregation of these peptides and
full-length α-synuclein. A central alanine-to-lysine substitution
in each hydrophobic fragment completely eliminated the peptides’
amyloidogenic property, and alanine-to-lysine substitutions at corresponding
sites in full-length α-synuclein also decreased the protein’s
amyloidogenic potency. These findings suggested that CHAA fragments
were potentially amyloidogenic and played an important role for the
aggregation of α-synuclein. The identification of these fragments
might provide helpful information for eventually clarifying the molecular
mechanism of α-synuclein aggregation. On the other hand, our
study suggested that the CHAA fragment might be a simple motif for
direct sequence-based identification of amyloid peptides.
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Affiliation(s)
- Yongzhu Chen
- Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
- Periodical Press of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fei Peng
- Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Su
- West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Yang
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Qiu
- Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
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7
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Feng M, Bell DR, Wang Z, Zhang W. Length-Dependent Structural Transformations of Huntingtin PolyQ Domain Upon Binding to 2D-Nanomaterials. Front Chem 2020; 8:299. [PMID: 32391325 PMCID: PMC7189795 DOI: 10.3389/fchem.2020.00299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/26/2020] [Indexed: 11/13/2022] Open
Abstract
There is a strong negative correlation between the polyglutamine (polyQ) domain length (Q-length) in the intrinsically disordered Huntingtin protein (Htt) exon-1 and the age of onset of Huntington's disease (HD). PolyQ of Q-length longer than 40 has the propensity of forming very compact aggregate structures, leading to HD at full penetrance. Recent advances in nanobiotechnology provided a new platform for the development of novel diagnosis and therapeutics. Here, we explore the possibility of utilizing 2D-nanomaterials to inhibit the formation of supercompact polyQ structures through the so-called “folding-upon-binding” where the protein structure is dependent on the binding substrate. Using molecular dynamics simulations, we characterize two polyQ peptides with Q-length of 22 (Q22, normal length) and 46 (Q46, typical length causing HD) binding to both graphene and molybdenum disulfide (MoS2) nanosheets, which have been applied as antibacterial or anticancer agents. Upon binding, Q22 unfolds and elongates on both grapheme and MoS2 surfaces, regardless of its initial conformation, with graphene showing slightly stronger effect. In contrast, initially collapsed Q46 remains mostly collapsed within our simulation time on both nanosheets even though they do provide some “stretching” to Q46 as well. Further analyses indicate that the hydrophobic nature of graphene/MoS2 promotes the stretching of polyQ on nanosheets. However, there is strong competition with the intra-polyQ interactions (mainly internal hydrogen bonds) leading to the disparate folding/binding behaviors of Q22 and Q46. Our results present distinct Q-length specific behavior of the polyQ domain upon binding to two types of 2D-nanomaterials which holds clinical relevance for Huntington's disease.
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Affiliation(s)
- Mei Feng
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - David R Bell
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, United States
| | - Zhenhua Wang
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - Wei Zhang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou, China
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8
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Hao S, Li X, Han A, Yang Y, Fang G, Liu J, Wang S. CLVFFA-Functionalized Gold Nanoclusters Inhibit Aβ40 Fibrillation, Fibrils' Prolongation, and Mature Fibrils' Disaggregation. ACS Chem Neurosci 2019; 10:4633-4642. [PMID: 31637909 DOI: 10.1021/acschemneuro.9b00469] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The abnormal aggregation of amyloid beta (Aβ or A beta) from monomeric proteins into amyloid fibrils is an important pathological contact to Alzheimer's disease (AD). Amyloid beta 40 (Aβ40), the pivotal biomarker of AD, aggregates to form amyloid plaques. For this reason, inhibition of amyloid fibrillation had become a crucial prevention and therapeutic strategy. Usually, LVFFA is the central hydrophobic fragment of Aβ and can inhibit the aggregation of Aβ40. In this work, in order to improve the inhibitory ability of LVFFA, hexapeptide CLVFFA were conjugated at the surface of Au clusters (AuNCs) to manufacture a nanosized inhibitor, AuNCs-CLVFFA. Thioflavin T fluorescence and transmission electron microscope results showed that AuNCs-CLVFFA inhibited Aβ40 fibrillogenesis, fibrils' prolongation, and mature fibrils' disaggregation. Furthermore, AuNCs as the backbone of the inhibitor showed extraordinary inhibition ability for Aβ40 aggregation at a low AuNCs-CLVFFA concentration. Free hexapeptide CLVFFA, at the same concentration, showed almost no inhibition. Additionally, the inhibitor could maintain the optical properties of nanoclusters, and the cell viability demonstrated that the inhibitor had good biocompatibility and may potentially be applied into AD therapy or treatment.
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Affiliation(s)
- Sijia Hao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xia Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Ailing Han
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yayu Yang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Guozhen Fang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jifeng Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shuo Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China
- Research Center of Food Science and Human Health, School of Medicine, Nankai University, Tianjin 300071, PR China
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9
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He Z, Li J, Chen SH, Zhou R. Surface Inhomogeneity of Graphene Oxide Influences Dissociation of Aβ 16-21 Peptide Assembly. J Phys Chem B 2019; 123:9098-9103. [PMID: 31566974 DOI: 10.1021/acs.jpcb.9b07359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abnormal peptide assembly and aggregation is associated with an array of neurodegenerative diseases including Alzheimer's disease (AD). A detailed understanding of how nanostructured materials such as oxidized graphene perturb the peptide assembly and subsequently induce fibril dissociation may open new directions for the development of potential AD treatments. Here, we investigate the impact of surface inhomogeneity of graphene oxide (GO) on the assembly of amyloid-beta Aβ16-21 peptides on GO surfaces with different degrees of oxidation using molecular dynamics simulations. Interestingly, nonuniform GO nanosheets (in terms of oxidation sites) have a much stronger perturbation effect on the structure of Aβ16-21 assembly. The Aβ peptides exhibit a remarkable tendency in binding to the scattered interfaces between unoxidized and oxidized regions, which induces the dissociation of Aβ amyloid fibril. These findings should deepen our understanding of surface-induced peptide dissociation and stimulate discovery of alternative AD treatments.
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Affiliation(s)
| | | | - Serena H Chen
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
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10
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Liu F, Wang W, Sang J, Jia L, Lu F. Hydroxylated Single-Walled Carbon Nanotubes Inhibit Aβ 42 Fibrillogenesis, Disaggregate Mature Fibrils, and Protect against Aβ 42-Induced Cytotoxicity. ACS Chem Neurosci 2019; 10:588-598. [PMID: 30335950 DOI: 10.1021/acschemneuro.8b00441] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The fibrillogenesis of amyloid-β protein (Aβ) is considered a crucial factor in the pathogenesis of Alzheimer's disease (AD). Hence, inhibiting Aβ fibrillogenesis is regarded as the primary therapeutic strategy for the prevention and treatment of AD. However, the development of effective inhibitors against Aβ fibrillogenesis has faced significant challenges. Previous studies have shown that pristine single-walled carbon nanotubes (SWNTs) can inhibit fibrillogenesis of some amyloid proteins. However, the poor dispersibility of SWNTs in an aqueous environment greatly hinders their inhibitory efficacy. Here, we examined the inhibitory activity of hydroxylated SWNTs (SWNT-OH) on the aggregation and cytotoxicity of Aβ42 using thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), cellular viability assays, and molecular dynamics (MD) simulations. ThT and AFM results showed that SWNT-OH inhibits Aβ42 fibrillogenesis and disaggregates preformed amyloid fibrils in a dose-dependent manner. Furthermore, the ratio of hydroxyl groups in SWNT-OH is crucial for their effect against Aβ42 aggregation. SWNT-OH exerted cytoprotective effects against Aβ42 fibrillation-induced cytotoxicity. The results of free-energy decomposition studies based on MD simulations revealed that nonpolar interactions, and especially van der Waals forces, contributed most of the free energy of binding in the SWNT-OH-Aβ complex. Two regions of the Aβ pentamer were identified to interact with SWNT-OH, spanning H13-Q15 and V36-G38. The findings presented here will contribute to a comprehensive understanding of the inhibitory effect of hydroxylated nanoparticles against Aβ fibrillogenesis, which is critical for the search for more effective agents that can counteract amyloid-mediated pathologies.
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Affiliation(s)
- Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry
of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, P. R. China
| | - Wenjuan Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Jingcheng Sang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Longgang Jia
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry
of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, P. R. China
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11
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Li S, Lin D, Hu X, Yang X. Directly probing the dissociation effects of graphene oxide nanosheets on hIAPP fibrils. NANOTECHNOLOGY 2018; 29:495102. [PMID: 30211692 DOI: 10.1088/1361-6528/aae143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The aggregation of human islet amyloid polypeptides (hIAPP) to mature fibrils is considered as the main cause of type II diabetes. Therefore destroying the pre-formed hIAPP fibrils is expected to be a promising strategy for therapeutic treatments. In this work, the dissociation effects of graphene oxide (GO) nanosheets on hIAPP mature fibrils are investigated. The results clearly demonstrate that hIAPP fibrils can be quickly adsorbed on the GO surface and efficiently broken into short fragments. Meanwhile, the β-sheet structures of hIAPP fibrils are greatly destroyed. Particularly, in situ atomic force microscopy was applied to monitor the real-time interaction between hIAPP fibrils and GO nanosheets. It provides distinct evidence that the disruption of hIAPP fibrils by GO nanosheets mainly occurs at the GO edges. Size-dependent experiments further justify the interfere of edge contribution, which suggest small-sized GO nanosheets exhibit better dissociation ability than large-sized ones. Therefore, this study not only provides valuable information that GO nanosheets (especially small-sized ones) can act as efficient nanoblades to break hIAPP fibrils, but also suggests a powerful and widely available methodology for investigating real-time interaction between nanomaterials and biomolecules.
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Affiliation(s)
- Shujie Li
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, People's Republic of China. Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, People's Republic of China
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12
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Brahmkhatri VP, Sharma N, Sunanda P, D’Souza A, Raghothama S, Atreya HS. Curcumin nanoconjugate inhibits aggregation of N-terminal region (Aβ-16) of an amyloid beta peptide. NEW J CHEM 2018. [DOI: 10.1039/c8nj03541e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A highly stable system of a polymeric nanoparticle-encapsulated curcumin with gold nanoparticles decorated on the surface for inhibition of Aβ1–16 aggregation.
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Affiliation(s)
- Varsha P. Brahmkhatri
- NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- Centre for Nano and Material Sciences
| | - Naveen Sharma
- Division of Pharmaceutical Science
- Shri Guru Raam Rai Institute of Technology and Science
- Dehradun
- India
| | | | - Aviva D’Souza
- Centre for Nano and Material Sciences
- Jain University
- Jain Global Campus
- Bengaluru 562 112
- India
| | | | - Hanudatta S. Atreya
- NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- Solid State Structural Chemistry Unit
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13
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Tian R, Luo M, Li J. Spontaneous protein desorption from self-assembled monolayer (SAM)-coated gold nanoparticles. Phys Chem Chem Phys 2018; 20:68-74. [DOI: 10.1039/c7cp05515c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Interfacial water molecules and lateral diffusion of protein reduce the adsorption affinity of protein and promote protein desorption.
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Affiliation(s)
- Ranran Tian
- Department of Physics
- Zhejiang University
- Hangzhou
- China
| | - Mengbo Luo
- Department of Physics
- Zhejiang University
- Hangzhou
- China
| | - Jingyuan Li
- Department of Physics
- Zhejiang University
- Hangzhou
- China
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14
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Božinovski DM, Petrović PV, Belić MR, Zarić SD. Insight into the Interactions of Amyloid β-Sheets with Graphene Flakes: Scrutinizing the Role of Aromatic Residues in Amyloids that Interact with Graphene. Chemphyschem 2017; 19:1226-1233. [DOI: 10.1002/cphc.201700847] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dragana M. Božinovski
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building Education City Doha Qatar
| | - Predrag V. Petrović
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building Education City Doha Qatar
| | - Milivoj R. Belić
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building Education City Doha Qatar
| | - Snežana D. Zarić
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building Education City Doha Qatar
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15
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Song M, Zhu Y, Wei G, Li H. Carbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1321757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Menghua Song
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, P.R. China
- College of Energy and Mechanical Engineering, Shanghai University of Electric Power, Shanghai, P.R. China
| | - Yanyan Zhu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, P.R. China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences(Ministry of Education), and Department of Physics, Fudan University, Shanghai, P.R. China
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, P.R. China
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences(Ministry of Education), and Department of Physics, Fudan University, Shanghai, P.R. China
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16
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Zhang Y, Hashemi M, Lv Z, Lyubchenko YL. Self-assembly of the full-length amyloid Aβ42 protein in dimers. NANOSCALE 2016; 8:18928-18937. [PMID: 27714140 PMCID: PMC5114164 DOI: 10.1039/c6nr06850b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The self-assembly of amyloid (Aβ) proteins into nano-aggregates is a hallmark of Alzheimer's disease (AD) development, yet the mechanism of how disordered monomers assemble into aggregates remains elusive. Here, we applied long-time molecular dynamics simulations to fully characterize the assembly of Aβ42 monomers into dimers. Monomers undergo conformational changes during their interaction, but the resulting dimer structures do not resemble those found in fibril structures. To identify natural conformations of dimers among a set of simulated ones, validation approaches were developed and applied, and a subset of dimer conformations were characterized. These dimers do not contain long β-strands that are usually found in fibrils. The dimers are stabilized primarily by interactions within the central hydrophobic regions and the C-terminal regions, with a contribution from local hydrogen bonding. The dimers are dynamic, as evidenced by the existence of a set of conformations and by the quantitative analyses of the dimer dissociation process.
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Affiliation(s)
- Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 69198, USA.
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17
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Sun Y, Qian Z, Wei G. The inhibitory mechanism of a fullerene derivative against amyloid-β peptide aggregation: an atomistic simulation study. Phys Chem Chem Phys 2016; 18:12582-91. [PMID: 27091578 DOI: 10.1039/c6cp01014h] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease (AD) is associated with the pathological self-assembly of amyloid-β (Aβ) peptides into β-sheet enriched fibrillar aggregates. Aβ dimers formed in the initial step of Aβ aggregation were reported to be the smallest toxic species. Inhibiting the formation of β-sheet-rich oligomers and fibrils is considered as the primary therapeutic strategy for AD. Previous studies reported that fullerene derivatives strongly inhibit Aβ fibrillation. However, the underlying inhibitory mechanism remains elusive. As a first step to understand fullerene-modulated full-length Aβ aggregation, we investigated the conformational ensemble of the Aβ1-42 dimer with and without 1,2-(dimethoxymethano)fullerene (DMF) - a more water-soluble fullerene derivative - by performing a 340 ns explicit-solvent replica exchange molecular dynamics simulation. Our simulations show that although disordered states are the most abundant conformations of the Aβ1-42 dimer, conformations containing diverse extended β-hairpins are also populated. The first most-populated β-hairpins involving residues L17-D23 and A30-V36 strongly resemble the engineered β-hairpin which is a building block of toxic Aβ oligomers. We find that the interaction of DMFs with Aβ peptides greatly impedes the formation of such β-hairpins and inter-peptide β-sheets. Binding energy analyses demonstrate that DMF preferentially binds not only to the central hydrophobic motif LVFFA of the Aβ peptide as suggested experimentally, but also to the aromatic residues including F4 and Y10 and the C-terminal hydrophobic region I31-V40. This study reveals a complete picture of the inhibitory mechanism of full-length Aβ1-42 aggregation by fullerenes, providing theoretical insights into the development of drug candidates against AD.
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Affiliation(s)
- Yunxiang Sun
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China.
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18
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Bag S, Sett A, DasGupta S, Dasgupta S. Hydropathy: the controlling factor behind the inhibition of Aβ fibrillation by graphene oxide. RSC Adv 2016. [DOI: 10.1039/c6ra23570k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Fibrillation of Aβ25–35 peptide is inhibited in presence of graphene oxide.
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Affiliation(s)
- Sudipta Bag
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Ayantika Sett
- Department of Chemical Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Sunando DasGupta
- Department of Chemical Engineering
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
| | - Swagata Dasgupta
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur 721302
- India
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