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Li X, Chen Y, Yang Z, Zhang S, Wei G, Zhang L. Structural insights into the co-aggregation of Aβ and tau amyloid core peptides: Revealing potential pathological heterooligomers by simulations. Int J Biol Macromol 2024; 254:127841. [PMID: 37924907 DOI: 10.1016/j.ijbiomac.2023.127841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
The self-aggregation of amyloid-β (Aβ) and tau proteins are closely implicated in Alzheimer's disease (AD). Recent evidence indicates that Aβ and tau proteins can cross-interact to form co-aggregates, which aggravates the development of AD. However, their transient heterooligomer conformations and co-aggregation molecular mechanisms are largely unknown. Herein, we utilize replica exchange molecular dynamics simulations to investigate the conformational ensembles formed by the central hydrophobic core of Aβ (Aβ16-22) and each of two fibril-nucleating core segments of tau (PHF6* and PHF6). Both PHF6 and PHF6* are found to co-aggregate with Aβ16-22 into β-sheet-rich heterooligomers. Intriguingly, PHF6 and Aβ16-22 peptides formed closed β-barrels, while PHF6* and Aβ16-22 formed open β-barrels, implying their distinct co-aggregation property. Compared to Aβ16-22-PHF6*, Aβ16-22-PHF6 heterooligomers have higher β-sheet content, and contain longer β-strands and larger β-sheets, indicative of stronger co-aggregation ability of PHF6 with Aβ16-22. Further analyses reveal that hydrophobic and π-π stacking interactions between Y310 of PHF6 and Aβ16-22 are crucial for the closed β-barrel/larger β-sheet formation in Aβ16-22-PHF6 heterooligomers. These results highlight the paramount importance of PHF6 fragment, particularly Y310 residue, as a potential target for inhibiting Aβ-tau co-aggregation, which could help for effective therapeutic design in mitigating Aβ-tau co-aggregation related amyloidogenesis.
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Affiliation(s)
- Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China; State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yujie Chen
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China..
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, China.
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2
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Alraawi Z, Banerjee N, Mohanty S, Kumar TKS. Amyloidogenesis: What Do We Know So Far? Int J Mol Sci 2022; 23:ijms232213970. [PMID: 36430450 PMCID: PMC9695042 DOI: 10.3390/ijms232213970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.
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Affiliation(s)
- Zeina Alraawi
- Department of Chemistry and Biochemistry, Fulbright College of Art and Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Nayan Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Srujana Mohanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
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3
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Wang Y, Liu Y, Zhang Y, Wei G, Ding F, Sun Y. Molecular insights into the oligomerization dynamics and conformations of amyloidogenic and non-amyloidogenic amylin from discrete molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:21773-21785. [PMID: 36098068 PMCID: PMC9623603 DOI: 10.1039/d2cp02851d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The amyloid aggregation of human islet amyloid polypeptide (hIAPP) is associated with pancreatic β-cell death in type 2 diabetes. The S20G substitution of hIAPP (hIAPP(S20G)), found in Japanese and Chinese people, is more amyloidogenic and cytotoxic than wild-type hIAPP. Rat amylin (rIAPP) does not have aggregation propensity or cytotoxicity. Mounting evidence suggests that soluble low-molecular-weight amyloid oligomers formed during early aggregation are more cytotoxic than mature fibrils. The self-assembly dynamics and oligomeric conformations remain unknown because the oligomers are heterogeneous and transient. The molecular mechanism of sequence-variation rendering dramatically different aggregation propensity and cytotoxicity is also elusive. Here, we investigate the oligomerization dynamics and conformations of amyloidogenic hIAPP, hIAPP(S20G), and non-amyloidogenic rIAPP using atomistic discrete molecular dynamics (DMD) simulations. Our simulation results demonstrated that all three monomeric amylin peptides mainly adopted an unstructured formation with partial dynamical helices near the N-terminus. Relatively transient β-hairpins were more abundant in hIAPP and hIAPP(S20G) than in rIAPP. The S20G-substituting mutant of hIAPP altered the turn region of the β-hairpin motif, resulting in more hydrophobic residue-pairwise contacts within the β-hairpin. Oligomerization dynamic investigation revealed that all three peptides spontaneously accumulated into helix-populated oligomers. The conformational conversion to form β-sheet-rich oligomers was only observed in hIAPP and hIAPP(S20G). The population of high-β-sheet-content oligomers was enhanced by S20G substitution. Interestingly, both hIAPP and hIAPP(S20G) could form β-barrel formations, and the β-barrel propensity of hIAPP(S20G) was three times larger than that of hIAPP. No β-sheet-rich or β-barrel formations were observed in rIAPP. Our direct observation of the correlation between β-barrel oligomer formation and cytotoxicity suggests that β-barrels might play a critically important role in the cytotoxicity of amyloidosis.
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Affiliation(s)
- Ying Wang
- Department of Physics, Ningbo University, Ningbo 315211, China.
| | - Yuying Liu
- Department of Physics, Ningbo University, Ningbo 315211, China.
| | - Yu Zhang
- Department of Physics, Ningbo University, Ningbo 315211, China.
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China.
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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Zhang Y, Zhu Y, Yue H, Zhao Q, Li H. Exploring the misfolding and self-assembly mechanism of TTR (105–115) peptides by all-atom molecular dynamics simulation. Front Mol Biosci 2022; 9:982276. [PMID: 36120541 PMCID: PMC9473747 DOI: 10.3389/fmolb.2022.982276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Pathological aggregation of essentially dissociative Transthyretin (TTR) monomers protein, driven by misfolded and self-interaction, is connected with Amyloid Transthyretin amyloidosis (ATTR) disease. The TTR monomers protein contains several fragments that tend to self-aggregate, such as residue 105–115 sequence [TTR (105–115)]. However, the misfolding and aggregation mechanisms of TTR are still unknown. In this study, we explored the misfolding and self-assembly of TTR (105–115) peptides by all-atom molecular dynamics simulation. Our results indicated that the conformation of the two-peptides appears unstable. In the tetramerization and hexamerization simulations, the results are reversed. When the number of peptides increases, the probability and the length of β-Sheet contents increase. Our results show that that the four- and six-peptides both can form β-Barrel intermediates and then aggregate into fibers. The critical nucleation for the formation of fibril should be larger than four-peptides. The interactions between hydrophobic residues I107-L111 play an important role in the formation of stable fibrils at an early stage. Our results on the structural ensembles and early aggregation dynamics of TTR (105–115) will be useful to comprehend the nucleation and fibrillization of TTR (105–115).
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Affiliation(s)
- Yuqi Zhang
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, China
| | - Yanyan Zhu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, China
| | - Haiyan Yue
- Naval Medical Center of PLA, Department of Digestive Diseases, Naval Medical University, Shanghai, China
| | - Qingjie Zhao
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Qingjie Zhao, ; Huiyu Li,
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, China
- *Correspondence: Qingjie Zhao, ; Huiyu Li,
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Zou Y, Guan L. Unraveling the Influence of K280 Acetylation on the Conformational Features of Tau Core Fragment: A Molecular Dynamics Simulation Study. Front Mol Biosci 2021; 8:801577. [PMID: 34966788 PMCID: PMC8710698 DOI: 10.3389/fmolb.2021.801577] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 01/16/2023] Open
Abstract
Abnormal aggregation of the microtubule-associated protein Tau is closely associated with tauopathies, including Alzheimer's disease and chronic traumatic encephalopathy. The hexapeptide 275VQIINK280 (PHF6*), a fibril-nucleating core motif of Tau, has been shown to play a vital role in the aggregation of Tau. Mounting experiment evidence demonstrated the acetylation of a single-lysine residue K280 in the PHF6* was a critical event for the formation of pathological Tau amyloid deposits. However, the underlying mechanisms by which K280 acetylation affects Tau aggregation at the atomic level remain elusive. In this work, we performed replica exchange molecular dynamics simulations to investigate the influence of acetylation of K280 on the aggregation of PHF6*. Our simulations show that acetylation of K280 not only enhances the self-assembly capability of PHF6* peptides but also increases the β-sheet structure propensity of the PHF6*. The inter-molecular interactions among PHF6* peptides are strengthened by the acetylation of K280, resulting in an increased ordered β-sheet-rich conformations of the PHF6* assemblies along with a decrease of the structural diversity. The residue-pairwise contact frequency analysis shows that K280 acetylation increases the interactions among the hydrophobic chemical groups from PHF6* peptides, which promotes the aggregation of PHF6*. This study offers mechanistic insights into the effects of acetylation on the aggregation of PHF6*, which will be helpful for an in-depth understanding of the relationship between acetylation and Tau aggregation at the molecular level.
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Affiliation(s)
- Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, Hangzhou, China
| | - Lulu Guan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, Hangzhou, China
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6
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Li F, Zhan C, Dong X, Wei G. Molecular mechanisms of resveratrol and EGCG in the inhibition of Aβ 42 aggregation and disruption of Aβ 42 protofibril: similarities and differences. Phys Chem Chem Phys 2021; 23:18843-18854. [PMID: 34612422 DOI: 10.1039/d1cp01913a] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The aggregation of amyloid-β protein (Aβ) into fibrillary deposits is implicated in Alzheimer's disease (AD), and inhibiting Aβ aggregation and clearing Aβ fibrils are considered as promising strategies to treat AD. It has been reported that resveratrol (RSV) and epigallocatechin-3-gallate (EGCG), two of the most extensively studied natural polyphenols, are able to inhibit Aβ fibrillization and remodel the preformed fibrillary aggregates into amorphous, non-toxic species. However, the mechanisms by which RSV inhibits Aβ42 aggregation and disrupts Aβ42 protofibril, as well as the inhibitory/disruptive mechanistic similarities and differences between RSV and EGCG, remain mostly elusive. Herein, we performed extensive all-atom molecular dynamics (MD) simulations on Aβ42 dimers (the early aggregation state of Aβ42) and protofibrils (the intermediate of Aβ42 fibril formation and elongation) in the absence/presence of RSV or EGCG molecules. Our simulations show that both RSV and EGCG can bind with Aβ42 monomers and inhibit the dimerization of Aβ42. The binding of RSV with Aβ42 peptide is mostly viaπ-π stacking interactions, while the binding of EGCG with Aβ42 is mainly through hydrophobic, π-π stacking, and hydrogen-bonding interactions. Moreover, both RSV and EGCG disrupt the β-sheet structure and K28-A42 salt bridges, leading to a disruption of Aβ42 protofibril structure. RSV mainly binds with residues whose side-chains point inwards from the surface of the protofibril, while EGCG mostly binds with residues whose side-chains point outwards from the surface of the protofibril. Furthermore, RSV interacts with Aβ42 protofibrils mostly viaπ-π stacking interactions, while EGCG interacts with Aβ42 protofibrils mainly via hydrogen-bonding and hydrophobic interactions. For comparison, we also explore the effects of RSV/EGCG molecules on the aggregation inhibition and protofibril disruption of the Iowa mutant (D23N) Aβ. Our findings may pave the way for the design of more effective drug candidates as well as the utilization of cocktail therapy using RSV and EGCG for the treatment of AD.
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Affiliation(s)
- Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, 200438, People's Republic of China.
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7
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Sun Y, Kakinen A, Wan X, Moriarty N, Hunt CP, Li Y, Andrikopoulos N, Nandakumar A, Davis TP, Parish CL, Song Y, Ke PC, Ding F. Spontaneous Formation of β-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta. NANO TODAY 2021; 38:101125. [PMID: 33936250 PMCID: PMC8081394 DOI: 10.1016/j.nantod.2021.101125] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Soluble low-molecular-weight oligomers formed during the early aggregation of amyloid peptides have been hypothesized as a major toxic species of amyloidogenesis. Herein, we performed the first synergic in silico, in vitro and in vivo validations of the structure, dynamics and toxicity of Aβ42 oligomers. Aβ peptides readily assembled into β-rich oligomers comprised of extended β-hairpins and β-strands. Nanosized β-barrels were observed with certainty with simulations, transmission electron microscopy and Fourier transform infrared spectroscopy, corroborated by immunohistochemistry, cell viability, apoptosis, inflammation, autophagy and animal behavior assays. Secondary and tertiary structural proprieties of these oligomers, such as the sequence regions with high β-sheet propensities and inter-residue contact frequency patterns, were similar to the properties known for Aβ fibrils. The unambiguous spontaneous formation of β-barrels in the early aggregation of Aβ42 supports their roles as the common toxic intermediates in Alzheimer's pathobiology and a target for Alzheimer's therapeutics.
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Affiliation(s)
- 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
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Xulin Wan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Food Science, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
| | - Niamh Moriarty
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Cameron P.J. Hunt
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Yuhuan Li
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas P. Davis
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Clare L. Parish
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Yang Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Pu Chun Ke
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
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Kanchi PK, Dasmahapatra AK. Enhancing the binding of the β-sheet breaker peptide LPFFD to the amyloid-β fibrils by aromatic modifications: A molecular dynamics simulation study. Comput Biol Chem 2021; 92:107471. [PMID: 33706107 DOI: 10.1016/j.compbiolchem.2021.107471] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 11/25/2022]
Abstract
Alzheimer's is a fatal neurodegenerative disease for which there is no cure at present. The disease is characterized by the presence of plaques in the brains of a patient, which are composed mainly of aggregates of the amyloid-β peptide in the form of β-sheet fibrils. Here, we investigated the possibility of exploiting the superior binding ability of aromatic amino acids to a particular model of the amyloid-β fibrils. which is a difficult target for drug design. The β-sheet breaker peptide LPFFD was modified with aromatic amino acids and its binding to these fibrils was studied. We found that the orientation and the electrostatic complementarity of the modified peptide with respect to the fibrils played a crucial role in determining whether its binding was improved by the aromatic amino acids. The modified LPFFD peptides were able to bind to those fibril residues. which are important in the aggregation of amyloid-β peptides and thus can potentially inhibit the further aggregation of the amyloid-beta peptides by blocking their interactions. We found that the tryptophan modified LPFFD peptides had the best binding affinities. In most cases, the aromatic amino acids in the N-terminus of the modified peptides made more contacts with the fibrils than those in the C-terminus. We also found that increasing the aromatic content did not significantly improve the binding of the LPFFD peptide to the fibrils. Our study can serve as a basis for the design of novel peptide-based drugs for Alzheimer's disease in which aromatic interactions play an important role.
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Affiliation(s)
- Pavan Krishna Kanchi
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Sun Y, Huang J, Duan X, Ding F. Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD1 28-38 and Absence in Nontoxic Glycine Mutants. J Chem Inf Model 2021; 61:966-975. [PMID: 33445870 DOI: 10.1021/acs.jcim.0c01319] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Soluble low-molecular-weight oligomers formed during the early stage of amyloid aggregation are considered the major toxic species in amyloidosis. The structure-function relationship between oligomeric assemblies and the cytotoxicity in amyloid diseases are still elusive due to the heterogeneous and transient nature of these aggregation intermediates. To uncover the structural characteristics of toxic oligomeric intermediates, we compared the self-assembly dynamics and structures of SOD128-38, a cytotoxic fragment of the superoxide dismutase 1 (SOD1) associated with the amyotrophic lateral sclerosis, with its two nontoxic mutants G33V and G33W using molecular dynamics simulations. Single-point glycine substitutions in SOD128-38 have been reported to abolish the amyloid toxicity. Our simulation results showed that the toxic SOD128-38 and its nontoxic mutants followed different aggregation pathways featuring distinct aggregation intermediates. Specifically, wild-type SOD128-38 initially self-assembled into random-coil-rich oligomers, among which fibrillar aggregates composed of well-defined curved single-layer β-sheets were nucleated via coil-to-sheet conversions and the formation of β-barrels as intermediates. In contrast, the nontoxic G33V/G33W mutants readily assembled into small β-sheet-rich oligomers and then coagulated with each other into cross-β fibrils formed by two-layer β-sheets without forming β-barrels as the intermediates. The direct observation of β-barrel oligomers during the assembly of toxic SOD128-38 fragments but not the nontoxic glycine-substitution mutants strongly supports β-barrels as the toxic oligomers in amyloidosis, probably via interactions with the cell membrane and forming amyloid pores. With well-defined structures, the β-barrel might serve as a novel therapeutic target against amyloid-related diseases.
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Affiliation(s)
- Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.,Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Junchao Huang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.,Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Xiangmei Duan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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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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11
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Sun Y, Kakinen A, Xing Y, Faridi P, Nandakumar A, Purcell AW, Davis TP, Ke PC, Ding F. Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805166. [PMID: 30908844 PMCID: PMC6499678 DOI: 10.1002/smll.201805166] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/21/2019] [Indexed: 05/19/2023]
Abstract
The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet-rich nanofibrils is associated with the pathogeny of type 2 diabetes. Soluble hIAPP is intrinsically disordered with N-terminal residues 8-17 as α-helices. To understand the contribution of the N-terminal helix to the aggregation of full-length hIAPP, here the oligomerization dynamics of the hIAPP fragment 8-20 (hIAPP8-20) are investigated with combined computational and experimental approaches. hIAPP8-20 forms cross-β nanofibrils in silico from isolated helical monomers via the helical oligomers and α-helices to β-sheets transition, as confirmed by transmission electron microscopy, atomic force microscopy, circular dichroism spectroscopy, Fourier transform infrared spectroscopy, and reversed-phase high performance liquid chromatography. The computational results also suggest that the critical nucleus of aggregation corresponds to hexamers, consistent with a recent mass-spectroscopy study of hIAPP8-20 aggregation. hIAPP8-20 oligomers smaller than hexamers are helical and unstable, while the α-to-β transition starts from the hexamers. Converted β-sheet-rich oligomers first form β-barrel structures as intermediates before aggregating into cross-β nanofibrils. This study uncovers a complete picture of hIAPP8-20 peptide oligomerization, aggregation nucleation via conformational conversion, formation of β-barrel intermediates, and assembly of cross-β protofibrils, thereby shedding light on the aggregation of full-length hIAPP, a hallmark of pancreatic beta-cell degeneration.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics, Faculty of Science, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pouya Faridi
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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12
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Som Chaudhury S, Sannigrahi A, Nandi M, Mishra VK, De P, Chattopadhyay K, Mishra S, Sil J, Das Mukhopadhyay C. A Novel PEGylated Block Copolymer in New Age Therapeutics for Alzheimer’s Disease. Mol Neurobiol 2019; 56:6551-6565. [DOI: 10.1007/s12035-019-1542-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022]
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13
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Zhao X, Liao C, Ma YT, Ferrell JB, Schneebeli ST, Li J. Top-down Multiscale Approach To Simulate Peptide Self-Assembly from Monomers. J Chem Theory Comput 2019; 15:1514-1522. [PMID: 30677300 DOI: 10.1021/acs.jctc.8b01025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modeling peptide assembly from monomers on large time and length scales is often intractable at the atomistic resolution. To address this challenge, we present a new approach which integrates coarse-grained (CG), mixed-resolution, and all-atom (AA) modeling in a single simulation. We simulate the initial encounter stage with the CG model, while the further assembly and reorganization stages are simulated with the mixed-resolution and AA models. We have implemented this top-down approach with new tools to automate model transformations and to monitor oligomer formations. Further, a theory was developed to estimate the optimal simulation length for each stage using a model peptide, melittin. The assembly level, the oligomer distribution, and the secondary structures of melittin simulated by the optimal protocol show good agreement with prior experiments and AA simulations. Finally, our approach and theory have been successfully validated with three amyloid peptides (β-amyloid 16-22, GNNQQNY fragment from the yeast prion protein SUP35, and α-synuclein fibril 35-55), which highlight the synergy from modeling at multiple resolutions. This work not only serves as proof of concept for multiresolution simulation studies but also presents practical guidelines for further self-assembly simulations at more physically and chemically relevant scales.
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Affiliation(s)
- Xiaochuan Zhao
- Department of Chemistry , The University of Vermont , Burlington , Vermont 05405 , United States
| | - Chenyi Liao
- Department of Chemistry , The University of Vermont , Burlington , Vermont 05405 , United States
| | - Yong-Tao Ma
- Department of Chemistry , The University of Vermont , Burlington , Vermont 05405 , United States
| | - Jonathon B Ferrell
- Department of Chemistry , The University of Vermont , Burlington , Vermont 05405 , United States
| | - Severin T Schneebeli
- Department of Chemistry , The University of Vermont , Burlington , Vermont 05405 , United States
| | - Jianing Li
- Department of Chemistry , The University of Vermont , Burlington , Vermont 05405 , United States
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14
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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15
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Sun Y, Kakinen A, Xing Y, Pilkington EH, Davis TP, Ke PC, Ding F. Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide. Biochim Biophys Acta Mol Basis Dis 2018; 1865:434-444. [PMID: 30502402 DOI: 10.1016/j.bbadis.2018.11.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/10/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet rich amyloid aggregates is associated with pancreatic β-cell death in type 2 diabetes (T2D). Prior experimental studies of hIAPP aggregation reported the early accumulation of α-helical intermediates before the rapid conversion into β-sheet rich amyloid fibrils, as also corroborated by our experimental characterizations with transmission electron microscopy and Fourier transform infrared spectroscopy. Although increasing evidence suggests that small oligomers populating early hIAPP aggregation play crucial roles in cytotoxicity, structures of these oligomer intermediates and their conformational conversions remain unknown, hindering our understanding of T2D disease mechanism and therapeutic design targeting these early aggregation species. We further applied large-scale discrete molecule dynamics simulations to investigate the oligomerization of full-length hIAPP, employing multiple molecular systems of increasing number of peptides. We found that the oligomerization process was dynamic, involving frequent inter-oligomeric exchanges. On average, oligomers had more α-helices than β-sheets, consistent with ensemble-based experimental measurements. However, in ~4-6% independent simulations, β-rich oligomers expected as the fibrillization intermediates were observed, especially in the pentamer and hexamer simulations. These β-rich oligomers could adopt β-barrel conformations, recently postulated to be the toxic oligomer species but only observed computationally in the aggregates of short amyloid protein fragments. Free-energy analysis revealed high energies of these β-rich oligomers, supporting the nucleated conformational changes of oligomers in amyloid aggregation. β-barrel oligomers of full-length hIAPP with well-defined three-dimensional structures may play an important pathological role in T2D etiology and may be a therapeutic target for the disease.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emily H Pilkington
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Thomas P Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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16
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Carballo-Pacheco M, Ismail AE, Strodel B. On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6063-6075. [PMID: 30336669 DOI: 10.1021/acs.jctc.8b00579] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aβ16-22 peptide and two of its mutants: Aβ16-22(F19V,F20V), which does not form fibrils, and Aβ16-22(F19L) which forms fibrils faster than the wild type. We observe that while oligomer formation kinetics depends strongly on the force field, structural properties, such as the most relevant protein-protein contacts, are similar between them. The oligomer formation kinetics obtained with different force fields differ more from each other than the kinetics between aggregating and nonaggregating peptides simulated with a single force field. We discuss the difficulties in comparing atomistic simulations of amyloid oligomer formation with experimental observables.
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Affiliation(s)
- Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Ahmed E Ismail
- AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany.,Aachener Verfahrenstechnik, Faculty of Mechanical Engineering , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , 40225 Düsseldorf , Germany
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17
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Zhang M, Zheng J, Nussinov R, Ma B. Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates. Antibodies (Basel) 2018; 7:E25. [PMID: 31544877 PMCID: PMC6640678 DOI: 10.3390/antib7030025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Aβ is the toxic amyloid polypeptide responsible for Alzheimer's disease (AD). Prevention and elimination of the Aβ misfolded aggregates are the promising therapeutic strategies for the AD treatments. Gammabody, the Aβ-Specific Single-domain (VH) antibody, recognizes Aβ aggregates with high affinity and specificity and reduces their toxicities. Employing the molecular dynamics simulations, we studied diverse gammabody-Aβ recognition complexes to get insights into their structural and dynamic properties and gammabody-Aβ recognitions. Among many heterogeneous binding modes, we focused on two gammabody-Aβ recognition scenarios: recognition through Aβ β-sheet backbone and on sidechain surface. We found that the gammabody primarily uses the complementarity-determining region 3 (CDR3) loop with the grafted Aβ sequence to interact with the Aβ fibril, while CDR1/CDR2 loops have very little contact. The gammabody-Aβ complexes with backbone binding mode are more stable, explaining the gammabody's specificity towards the C-terminal Aβ sequence.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, OH 44325, USA.
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, OH 44325, USA.
| | - Ruth Nussinov
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 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.
| | - Buyong Ma
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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18
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β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates. Sci Rep 2018; 8:10353. [PMID: 29985420 PMCID: PMC6037789 DOI: 10.1038/s41598-018-28649-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/22/2018] [Indexed: 12/22/2022] Open
Abstract
Oligomers populated during the early amyloid aggregation process are more toxic than mature fibrils, but pinpointing the exact toxic species among highly dynamic and heterogeneous aggregation intermediates remains a major challenge. β-barrel oligomers, structurally-determined recently for a slow-aggregating peptide derived from αB crystallin, are attractive candidates for exerting amyloid toxicity due to their well-defined structures as therapeutic targets and compatibility to the "amyloid-pore" hypothesis of toxicity. To assess whether β-barrel oligomers are common intermediates to amyloid peptides - a necessary step toward associating β-barrel oligomers with general amyloid cytotoxicity, we computationally studied the oligomerization and fibrillization dynamics of seven well-studied fragments of amyloidogenic proteins with different experimentally-determined aggregation morphologies and cytotoxicity. In our molecular dynamics simulations, β-barrel oligomers were only observed in five peptides self-assembling into the characteristic cross-β aggregates, but not the other two that formed polymorphic β-rich aggregates as reported experimentally. Interestingly, the latter two peptides were previously found nontoxic. Hence, the observed correlation between β-barrel oligomers formation and cytotoxicity supports the hypothesis of β-barrel oligomers as the common toxic intermediates of amyloid aggregation.
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19
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Xi W, Hansmann UHE. Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant Aβ 40 fibrils. J Chem Phys 2018; 148:045103. [PMID: 29390821 DOI: 10.1063/1.5016166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Using a variant of Hamilton-replica-exchange, we study for wild type and Iowa mutant Aβ40 the conversion between fibrils with antiparallel β-sheets and such with parallel β-sheets. We show that wild type and mutant form distinct salt bridges that in turn stabilize different fibril organizations. The conversion between the two fibril forms leads to the release of small aggregates that in the Iowa mutant may shift the equilibrium from fibrils to more toxic oligomers.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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20
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Chen Y, Chen Z, Sun Y, Lei J, Wei G. Mechanistic insights into the inhibition and size effects of graphene oxide nanosheets on the aggregation of an amyloid-β peptide fragment. NANOSCALE 2018; 10:8989-8997. [PMID: 29725676 DOI: 10.1039/c8nr01041b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The aggregation of amyloid-β (Aβ), which involves the formation of small oligomers and mature fibrils, has received considerable attention in the past few decades due to its close link with Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. In this respect, graphene oxide (GO) has gained significant attention because of its high solubility, good biocompatibility and inhibitory effect on the aggregation of Aβ and the 33-42 fragment (Aβ33-42). However, the inhibitory mechanism at the atomic level remains elusive. Herein, we investigated the oligomerization of Aβ33-42 by performing replica exchange molecular dynamics simulations on four Aβ33-42 peptide chains in the absence and presence of two different sizes of GO. Our simulations show that isolated Aβ33-42 can form fibril-prone extended β-sheets and barrel-like structures, whereas they are suppressed in the presence of GO nanosheets. Our data reveal that GO inhibits Aβ33-42 oligomerization by making Aβ33-42 peptides separate from each other through strong interactions with M35. With the same total number of atoms, GO120 displays better inhibitory effect than GO60 by providing a larger effective contact surface area. This study provides the molecular mechanism of GO in inhibiting the aggregation of Aβ33-42, which might offer a theoretical insight into the design of drugs against AD at the atomic level.
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Affiliation(s)
- Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People's Republic of China.
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21
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Brown N, Lei J, Zhan C, Shimon LJW, Adler-Abramovich L, Wei G, Gazit E. Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System. ACS NANO 2018; 12:3253-3262. [PMID: 29558116 PMCID: PMC6333291 DOI: 10.1021/acsnano.7b07723] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.
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Affiliation(s)
- Noam Brown
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Chemical Physics, School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jiangtao Lei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People’s Republic of China
| | - Chendi Zhan
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People’s Republic of China
| | - Linda J. W. Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, the Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People’s Republic of China
- Corresponding Authors: .
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding Authors: .
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22
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Ge X, Sun Y, Ding F. Structures and dynamics of β-barrel oligomer intermediates of amyloid-beta16-22 aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1687-1697. [PMID: 29550287 DOI: 10.1016/j.bbamem.2018.03.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 01/13/2023]
Abstract
Accumulating evidence suggests that soluble oligomers are more toxic than final fibrils of amyloid aggregations. Among the mixture of inter-converting intermediates with continuous distribution of sizes and secondary structures, oligomers in the β-barrel conformation - a common class of protein folds with a closed β-sheet - have been postulated as the toxic species with well-defined three-dimensional structures to perform pathological functions. A common mechanism for amyloid toxicity, therefore, implies that all amyloid peptides should be able to form β-barrel oligomers as the aggregation intermediates. Here, we applied all-atom discrete molecular dynamics (DMD) simulations to evaluate the formation of β-barrel oligomers and characterize their structures and dynamics in the aggregation of a seven-residue amyloid peptide, corresponding to the amyloid core of amyloid-β with a sequence of 16KLVFFAE22 (Aβ16-22). We carried out aggregation simulations with various numbers of peptides to study the size dependence of aggregation dynamics and assembly structures. Consistent with previous computational studies, we observed the formation of β-barrel oligomers in all-atom DMD simulations. Using a network-based approach to automatically identify β-barrel conformations, we systematically characterized β-barrels of various sizes. Our simulations revealed the conformational inter-conversion between β-barrels and double-layer β-sheets due to increased structural strains upon forming a closed β-barrel while maximizing backbone hydrogen bonds. The potential of mean force analysis further characterized the free energy barriers between these two states. The obtained structural and dynamic insights of β-barrel oligomers may help better understand the molecular mechanism of oligomer toxicities and design novel therapeutics targeting the toxic β-barrel oligomers. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Xinwei Ge
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States.
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23
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Qian Z, Zhang Q, Liu Y, Chen P. Assemblies of amyloid-β30-36 hexamer and its G33V/L34T mutants by replica-exchange molecular dynamics simulation. PLoS One 2017; 12:e0188794. [PMID: 29186195 PMCID: PMC5706729 DOI: 10.1371/journal.pone.0188794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/13/2017] [Indexed: 02/02/2023] Open
Abstract
The aggregation of amyloid-β peptides is associated with the pathogenesis of Alzheimer’s disease, in which the 30–36 fragments play an important part as a fiber-forming hydrophobic region. The fibrillar structure of Aβ30–36 has been detected by means of X-ray diffraction, but its oligomeric structural determination, biophysical characterization, and pathological mechanism remain elusive. In this study, we have investigated the structures of Aβ30–36 hexamer as well as its G33V and L34T mutants in explicit water environment using replica-exchange molecular dynamics (REMD) simulations. Our results show that the wild-type (WT) Aβ30–36 hexamer has a preference to form β-barrel and bilayer β-sheet conformations, while the G33V or L34T mutation disrupts the β-barrel structures: the G33V mutant is homogenized to adopt β-sheet-rich bilayers, and the structures of L34T mutant on the contrary get more diverse. The hydrophobic interaction plays a critical role in the formation and stability of oligomeric assemblies among all the three systems. In addition, the substitution of G33 by V reduces the β-sheet content in the most populated conformations of Aβ30–36 oligomers through a steric effect. The L34T mutation disturbs the interpeptide hydrogen bonding network, and results in the increased coil content and morphological diversity. Our REMD runs provide structural details of WT and G33V/L34T mutant Aβ30–36 oligomers, and molecular insight into the aggregation mechanism, which will be helpful for designing novel inhibitors or amyloid-based materials.
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Affiliation(s)
- Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai, China
- * E-mail: (ZQ); (PC)
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, Shanghai, China
| | - Yu Liu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Peijie Chen
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai, China
- * E-mail: (ZQ); (PC)
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24
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Sun Y, Wang B, Ge X, Ding F. Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide. Phys Chem Chem Phys 2017; 19:28414-28423. [PMID: 29038815 PMCID: PMC5657190 DOI: 10.1039/c7cp05695h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A direct observation of amyloid aggregation from isolated peptides to cross-β fibrils is crucial for understanding the nucleation-dependence process, but the corresponding macroscopic timescales impose a major computational challenge. Using rapid all-atom discrete molecular dynamics simulations, we capture the oligomerization and fibrillization dynamics of the amyloid core sequences of amyloid-β (Aβ) in Alzheimer's disease and islet amyloid polypeptide (IAPP) in type-2 diabetes, namely Aβ16-22 and IAPP22-28. Both peptides and their mixture spontaneously assemble into cross-β aggregates in silico, but follow distinct pathways. Aβ16-22 is highly aggregation-prone with a funneled free energy basin toward multi-layer β-sheet aggregates. IAPP22-28, on the other hand, features the accumulation of unstructured oligomers before the nucleation of β-sheets and growth into double-layer β-sheet aggregates. In the presence of Aβ16-22, the aggregation of IAPP22-28 is promoted by forming co-aggregated multi-layer β-sheets. Our study offers a detailed molecular insight to the long-postulated oligomerization-nucleation process in the amyloid aggregations.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA.
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25
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Wang B, Pilkington EH, Sun Y, Davis TP, Ke PC, Ding F. Modulating protein amyloid aggregation with nanomaterials. ENVIRONMENTAL SCIENCE. NANO 2017; 4:1772-1783. [PMID: 29230295 PMCID: PMC5722024 DOI: 10.1039/c7en00436b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Direct exposure or intake of nanopaticles (NPs) to the human body can invoke a series of biological responses, some of which are deleterious, and as such the role of NPs in vivo requires thorough examination. Over the past decade, it has been established that biomolecules such as proteins can bind NPs to form a 'corona', where the structures and dynamics of NP-associated proteins can assign new functionality, systemic distribution and toxicity. However, the behavior and fate of NPs in biological systems are still far from being fully understood. Growing evidence has shown that some natural or artificial NPs could either up- or down-regulate protein amyloid aggregation, which is associated with neurodegenerative diseases like Alzheimer's and Parkinson's diseases, as well as metabolic diseases such as type 2 diabetes. These effects can be either indirect (e.g., through a crowding effect) or direct, depending on the NP composition, size, shape and surface chemistry. However, efforts to design anti-amyloid NPs for biomedical applications have been largely hindered by insufficient understanding of the complex processes, even though proof-of-concept experiments have been conducted. Therefore, exploring the general mechanisms of NP-meditated protein aggregation marks an emerging field in bio-nano research and a new stage of handling nanotechnology that not only aids in elucidating the origin of nanotoxicity, but also provides a foundation for engineering de novo anti-amyloid nanomedicines. In this review, we summarize research on NP-mediated protein amyloid aggregation, with the goal of contributing to sustained nanotechnology and safe nanomedicine against amyloid diseases.
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Affiliation(s)
- Bo Wang
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA
| | - Emily H Pilkington
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade Parkville, VIC 3052, Australia
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA
| | - Thomas P Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade Parkville, VIC 3052, Australia
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade Parkville, VIC 3052, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC, USA
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26
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Abstract
Living systems contain remarkable functional capability built within sophisticated self-organizing frameworks. Defining the assembly codes that coordinate these systems could greatly extend nanobiotechnology. To that end, we have highlighted the self-assembling architecture of the chlorosome antenna arrays and report the emulation and extension of their features for the development of cell-compatible photoredox materials. We specifically review work on amyloid peptide scaffolds able to (1) organize light-harvesting chromophores, (2) break peptide bilayer symmetry for directional energy and electron transfer, and (3) incorporate redox active metal ions at high density for energy storage.
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Affiliation(s)
- Rolando F Rengifo
- Emory University, Departments of Biology and Chemistry, 1515 Dickey Dr. NE, Atlanta, GA 30322, USA.
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27
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EGCG inhibits the oligomerization of amyloid beta (16-22) hexamer: Theoretical studies. J Mol Graph Model 2017; 76:1-10. [PMID: 28658644 DOI: 10.1016/j.jmgm.2017.06.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 11/21/2022]
Abstract
An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the inhibition of (-)-epigallocatechin-3-gallate (EGCG) on the Aβ16-22 hexamer. Structural variations of the oligomers without and with EGCG were monitored and analyzed in detail. It has been found that EGCG prevents the formation of Aβ oligomer through two different ways by either accelerating the Aβ oligomerization or reducing the β-content of the hexamer. It also decreases the potential "highly toxic" conformations of Aβ oligomer, which is related to the conformations having high order β-sheet sizes. Both electrostatic and van der Waals interaction energies are found to be involved to the binding process. Computed results using quantum chemical methods show that the π-π stacking is a critical factor of the interaction between EGCG and the peptides. As a result, the binding free energy of the EGCG to the Aβ peptides is slightly larger than that of the curcumin.
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28
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Wu R, Liu J, Qiu X, Deng M. Molecular dynamics simulation of the nanofibrils formed by amyloid-based peptide amphiphiles. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1321758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rongliang Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Jun Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Xinlong Qiu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Manli Deng
- Key Laboratory of Colloid and Interface Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, P.R. China
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29
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Wang J, Tao K, Zhou P, Pambou E, Li Z, Xu H, Rogers S, King S, Lu JR. Tuning self-assembled morphology of the Aβ(16-22) peptide by substitution of phenylalanine residues. Colloids Surf B Biointerfaces 2016; 147:116-123. [PMID: 27497075 DOI: 10.1016/j.colsurfb.2016.07.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 11/25/2022]
Abstract
The effects of the two phenylalanine (Phe) residues in the blocked Aβ(16-22) peptide on its self-assembly have been investigated by replacing both of them with two cyclohexylalanines (Chas) or two phenylglycines (Phgs). TEM and SANS studies revealed that the flat and wide nanoribbons of Aβ(16-22) were transformed into thin nanotubes when replaced with Chas, and thinner and twisted nanofibrils when replaced with Phgs. The red-shifting degree of characteristic CD peaks suggested an increased twisting in the self-assembly of the derivative peptides, especially in the case of Ac-KLV(Phg)(Phg)AE-NH2. Furthermore, molecular dynamics (MD) simulations also indicated the increasing trend in twisting when Chas or Phgs were substituted for Phes. These results demonstrated that the hydrophobic interactions and spatial conformation between Cha residues were sufficient to cause lateral association of β-sheets to twisted/helical nanoribbons, which finally developed into nanotubes, while for Phg residue, the loss of the rotational freedom of the aromatic ring induced much stronger steric hindrance for the lateral stacking of Ac-KLV(Phg)(Phg)AE-NH2 β-sheets, eventually leading to the nanofibril formation. This study thus demonstrates that both the aromatic structure and the steric conformation of Phe residues are crucial in Aβ(16-22) self-assembly, especially in the significant lateral association of β-sheets.
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Affiliation(s)
- Jiqian Wang
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China.
| | - Kai Tao
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Peng Zhou
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Elias Pambou
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Schuster Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Zongyi Li
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Schuster Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Hai Xu
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China.
| | - Sarah Rogers
- ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Didcot, Oxon OX11 0QZ, United Kingdom
| | - Stephen King
- ISIS Pulsed Neutron Source, Rutherford Appleton Laboratory, Didcot, Oxon OX11 0QZ, United Kingdom
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Schuster Building, Oxford Road, Manchester M13 9PL, United Kingdom
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30
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Bellucci L, Ardèvol A, Parrinello M, Lutz H, Lu H, Weidner T, Corni S. The interaction with gold suppresses fiber-like conformations of the amyloid β (16-22) peptide. NANOSCALE 2016; 8:8737-8748. [PMID: 27064268 DOI: 10.1039/c6nr01539e] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Inorganic surfaces and nanoparticles can accelerate or inhibit the fibrillation process of proteins and peptides, including the biomedically relevant amyloid β peptide. However, the microscopic mechanisms that determine such an effect are still poorly understood. By means of large-scale, state-of-the-art enhanced sampling molecular dynamics simulations, here we identify an interaction mechanism between the segments 16-22 of the amyloid β peptide, known to be fibrillogenic by itself, and the Au(111) surface in water that leads to the suppression of fiber-like conformations from the peptide conformational ensemble. Moreover, thanks to advanced simulation analysis techniques, we characterize the conformational selection vs. induced fit nature of the gold effect. Our results disclose an inhibition mechanism that is rooted in the details of the microscopic peptide-surface interaction rather than in general phenomena such as peptide sequestration from the solution.
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Affiliation(s)
- Luca Bellucci
- Dipartimento FIM, Università di Modena e Reggio Emilia, I-41125, Modena, Italy. and Centro S3, CNR-NANO Istituto Nanoscienze, I-41125, Modena, Italy.
| | - Albert Ardèvol
- Department of Chemistry and Applied Biosciences, ETH-Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900, Lugano, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH-Zurich, Switzerland and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900, Lugano, Switzerland
| | - Helmut Lutz
- Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - Hao Lu
- Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - Stefano Corni
- Centro S3, CNR-NANO Istituto Nanoscienze, I-41125, Modena, Italy. and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900, Lugano, Switzerland
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31
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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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32
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Wei J, Antzutkin ON, Filippov AV, Iuga D, Lam PY, Barrow MP, Dupree R, Brown SP, O'Connor PB. Amyloid Hydrogen Bonding Polymorphism Evaluated by (15)N{(17)O}REAPDOR Solid-State NMR and Ultra-High Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Biochemistry 2016; 55:2065-8. [PMID: 26983928 DOI: 10.1021/acs.biochem.5b01095] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A combined approach, using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and solid-state NMR (Nuclear Magnetic Resonance), shows a high degree of polymorphism exhibited by Aβ species in forming hydrogen-bonded networks. Two Alzheimer's Aβ peptides, Ac-Aβ(16-22)-NH2 and Aβ(11-25), selectively labeled with (17)O and (15)N at specific amino acid residues were investigated. The total amount of peptides labeled with (17)O as measured by FTICR-MS enabled the interpretation of dephasing observed in (15)N{(17)O}REAPDOR solid-state NMR experiments. Specifically, about one-third of the Aβ peptides were found to be involved in the formation of a specific >C═(17)O···H-(15)N hydrogen bond with their neighbor peptide molecules, and we hypothesize that the rest of the molecules undergo ± n off-registry shifts in their hydrogen bonding networks.
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Affiliation(s)
| | - Oleg N Antzutkin
- Chemistry of Interfaces, Luleå University of Technology , SE-971 87, Luleå, Sweden
| | - Andrei V Filippov
- Chemistry of Interfaces, Luleå University of Technology , SE-971 87, Luleå, Sweden
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33
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Sun Y, Qian Z, Guo C, Wei G. Amphiphilic Peptides A6K and V6K Display Distinct Oligomeric Structures and Self-Assembly Dynamics: A Combined All-Atom and Coarse-Grained Simulation Study. Biomacromolecules 2015; 16:2940-9. [PMID: 26301845 DOI: 10.1021/acs.biomac.5b00850] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amphiphilic peptides can self-assemble into ordered nanostructures with different morphologies. However, the assembly mechanism and the structures of the early assemblies prior to nanostructure formation remain elusive. In this study, we investigated the oligomeric structures of two amphiphilic heptapeptides A6K and V6K by all-atom explicit-solvent replica-exchange molecular dynamics (REMD) simulations, and then examined the assembly dynamics of large aggregates by coarse-grained (CG) MD simulations. Our 200 ns REMD simulations show that A6K peptides predominantly adopt loosely packed disordered coil aggregates, whereas V6K peptides mostly assemble into compact β-sheet-rich conformations, consistent with the signal measured experimentally in aqueous solution. Well-organized β-sheet-rich conformations, albeit with low population, are also populated for V6K octamers, including bilayer β-sheets and β-barrels. These ordered β-sheet-rich conformations are observed for the first time for amphiphilic peptides. Our 10-μs CG-MD simulations on 200 peptide chains demonstrate that A6K and V6K peptides follow two different self-assembly processes, and the former form monolayer lamellas while the latter assemble into plate-like assemblies. CG-MD simulations also show that V6K peptides display higher assembly capability than A6K, in support of our all-atom REMD simulation results. Interpeptide interaction analyses reveal that the marked differences in oligomeric structures and assembly dynamics between A6K and V6K result from the subtle interplay of competition among hydrophobic, hydrogen-bonding, and electrostatic interactions of the two peptides. Our study provides structural and mechanistic insights into the initial self-assembly process of A6K and V6K at the molecular level.
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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
| | - Zhenyu Qian
- 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
| | - Cong Guo
- 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
| | - Guanghong Wei
- 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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34
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Abraham JN, Gour N, Bolisetty S, Mezzenga R, Nardin C. Controlled aggregation of peptide–DNA hybrids into amyloid-like fibrils. Eur Polym J 2015. [DOI: 10.1016/j.eurpolymj.2015.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Sun Y, Xi W, Wei G. Atomic-Level Study of the Effects of O4 Molecules on the Structural Properties of Protofibrillar Aβ Trimer: β-Sheet Stabilization, Salt Bridge Protection, and Binding Mechanism. J Phys Chem B 2015; 119:2786-94. [DOI: 10.1021/jp508122t] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yunxiang Sun
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
| | - Wenhui Xi
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), Department of Physics, Fudan University, 220 Handan
Road, Shanghai 200433, China
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36
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Xie L, Lin D, Luo Y, Li H, Yang X, Wei G. Effects of hydroxylated carbon nanotubes on the aggregation of Aβ16-22 peptides: a combined simulation and experimental study. Biophys J 2014; 107:1930-1938. [PMID: 25418174 PMCID: PMC4213673 DOI: 10.1016/j.bpj.2014.08.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/27/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
The pathogenesis of Alzheimer's disease (AD) is associated with the aggregation of amyloid-β (Aβ) peptides into toxic aggregates with ?-sheet character. In a previous computational study, we showed that pristine single-walled carbon nanotubes (SWCNTs) can inhibit the formation of β-sheet-rich oligomers in the central hydrophobic core fragment of Aβ (Aβ16-22). However, the poor solubility of SWCNTs in water hinders their use in biomedical applications and nanomedicine. Here, we investigate the influence of hydroxylated SWCNT, a water-soluble SWCNT derivative, on the aggregation of Aβ16-22 peptides using all-atom explicit-water replica exchange molecular dynamics simulations. Our results show that hydroxylated SWCNTs can significantly inhibit β-sheet formation and shift the conformations of Aβ16-22 oligomers from ordered β-sheet-rich structures toward disordered coil aggregates. Detailed analyses of the SWCNT-Aβ interaction reveal that the inhibition of β-sheet formation by hydroxylated SWCNTs mainly results from strong electrostatic interactions between the hydroxyl groups of SWCNTs and the positively charged residue K16 of Aβ16-22 and hydrophobic and aromatic stacking interactions between SWCNTs and F19 and F20. In addition, our atomic force microscopy and thioflavin T fluorescence experiments confirm the inhibitory effect of both pristine and hydroxylated SWCNTs on Aβ16-22 fibrillization, in support of our previous and present replica exchange molecular dynamics simulation results. These results demonstrate that hydroxylated SWCNTs efficiently inhibit the aggregation of Aβ16-22; in addition, they offer molecular insight into the inhibition mechanism, thus providing new clues for the design of therapeutic drugs against amyloidosis.
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Affiliation(s)
- Luogang Xie
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Dongdong Lin
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Yin Luo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Huiyu Li
- Department of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, China
| | - Xinju Yang
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China.
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37
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Berhanu WM, Hansmann UHE. Stability of amyloid oligomers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:113-41. [PMID: 25443956 DOI: 10.1016/bs.apcsb.2014.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Molecular simulations are now commonly used to complement experimental techniques in investigating amyloids and their role in human diseases. In this chapter, we will summarize techniques and approaches often used in amyloid simulations and will present recent success stories. Our examples will be focused on lessons learned from molecular dynamics simulations in aqueous environments that start from preformed aggregates. These studies explore the limitations that arise from the choice of force field, the role of mutations in the growth of amyloid aggregates, segmental polymorphism, and the importance of cross-seeding. Furthermore, they give evidence for potential toxicity mechanisms. We finally discuss the role of molecular simulations in the search for aggregation inhibitors.
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Affiliation(s)
- Workalemahu M Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA.
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38
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Xie L, Luo Y, Lin D, Xi W, Yang X, Wei G. The molecular mechanism of fullerene-inhibited aggregation of Alzheimer's β-amyloid peptide fragment. NANOSCALE 2014; 6:9752-62. [PMID: 25004796 DOI: 10.1039/c4nr01005a] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Amyloid deposits are implicated in the pathogenesis of many neurodegenerative diseases such as Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. Increasing data show that nanoparticles can retard or promote the fibrillation of amyloid-β (Aβ) peptides depending on the physicochemical properties of nanoparticles, however, the underlying molecular mechanism remains elusive. In this study, our replica exchange molecular dynamics (REMD) simulations show that fullerene nanoparticle - C60 (with a fullerene : peptide molar ratio greater than 1 : 8) can dramatically prevent β-sheet formation of Aβ(16-22) peptides. Atomic force microscopy (AFM) experiments further confirm the inhibitory effect of C60 on Aβ(16-22) fibrillation, in support of our REMD simulations. An important finding from our REMD simulations is that fullerene C180, albeit with the same number of carbon atoms as three C60 molecules (3C60) and smaller surface area than 3C60, displays an unexpected stronger inhibitory effect on the β-sheet formation of Aβ(16-22) peptides. A detailed analysis of the fullerene-peptide interaction reveals that the stronger inhibition of β-sheet formation by C180 results from the strong hydrophobic and aromatic-stacking interactions of the fullerene hexagonal rings with the Phe rings relative to the pentagonal rings. The strong interactions between the fullerene nanoparticles and Aβ(16-22) peptides significantly weaken the peptide-peptide interaction that is important for β-sheet formation, thus retarding Aβ(16-22) fibrillation. Overall, our studies reveal the significant role of fullerene hexagonal rings in the inhibition of Aβ(16-22) fibrillation and provide novel insight into the development of drug candidates against Alzheimer's disease.
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Affiliation(s)
- Luogang Xie
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China.
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Bocchinfuso G, Conflitti P, Raniolo S, Caruso M, Mazzuca C, Gatto E, Placidi E, Formaggio F, Toniolo C, Venanzi M, Palleschi A. Aggregation propensity of Aib homo-peptides of different length: an insight from molecular dynamics simulations. J Pept Sci 2014; 20:494-507. [DOI: 10.1002/psc.2648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Gianfranco Bocchinfuso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Paolo Conflitti
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Stefano Raniolo
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Mario Caruso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Claudia Mazzuca
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Emanuela Gatto
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Ernesto Placidi
- Department of Physics; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
- CNR-ISM; Via Fosso del Cavaliere 100 I-00133 Roma Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
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Barz B, Wales DJ, Strodel B. A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly. J Phys Chem B 2014; 118:1003-11. [PMID: 24401100 PMCID: PMC3908877 DOI: 10.1021/jp412648u] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is generally accepted that oligomers of aggregating proteins play an important role in the onset of neurodegenerative diseases. While in silico aggregation studies of full length amyloidogenic proteins are computationally expensive, the assembly of short protein fragments derived from these proteins with similar aggregating properties has been extensively studied. In the present work, molecular dynamics simulations are performed to follow peptide aggregation on the microsecond time scale. By defining aggregation states, we identify transition networks, disconnectivity graphs, and first passage time distributions to describe the kinetics of the assembly process. This approach unravels differences in the aggregation into hexamers of two peptides with different primary structures. The first is GNNQQNY, a hydrophilic fragment from the prion protein Sup35, and the second is KLVFFAE, a fragment from amyloid-β protein, with a hydrophobic core delimited by two charged amino acids. The assembly of GNNQQNY suggests a mechanism of monomer addition, with a bias toward parallel peptide pairs and a gradual increase in the amount of β-strand content. For KLVFFAE, a mechanism involving dimers rather than monomers is revealed, involving a generally higher β-strand content and a transition toward a larger number of antiparallel peptide pairs during the rearrangement of the hexamer. The differences observed for the aggregation of the two peptides suggests the existence of a sequence-aggregation relationship.
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Affiliation(s)
- Bogdan Barz
- Forschungszentrum Jülich GmbH Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
| | - David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK
| | - Birgit Strodel
- Forschungszentrum Jülich GmbH Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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