1
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Kumar N, Khatua P, Sinha SK. Can local heating and molecular crowders disintegrate amyloid aggregates? Chem Sci 2024; 15:6095-6105. [PMID: 38665536 PMCID: PMC11040654 DOI: 10.1039/d4sc00103f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
The present study employs a blend of molecular dynamics simulations and a theoretical model to explore the potential disintegration mechanism of a matured Aβ octamer, aiming to offer a strategy to combat Alzheimer's disease. We investigate local heating and crowding effects on Aβ disintegration by selectively heating key Aβ segments and varying the concentration of sodium dodecyl sulphate (SDS), respectively. Despite initiation of disruption, Aβ aggregates resist complete disintegration during local heating due to rapid thermal energy distribution to the surrounding water. Conversely, although SDS molecules effectively inhibit Aβ aggregation at higher concentration through micelle formation, they fail to completely disintegrate the aggregate due to the exceedingly high energy barrier. To address the sampling challenge posed by the formidable energy barrier, we have performed well-tempered metadynamics simulations. Simulations reveal a multi-step disintegration mechanism for the Aβ octamer, suggesting a probable sequence: octamer → pentamer/hexamer ⇌ tetramer → monomer, with a rate-determining step constituting 45 kJ mol-1 barrier during the octamer to pentamer/hexamer transition. Additionally, we have proposed a novel two-state mean-field model based on Ising spins that offers an insight into the kinetics of the Aβ growth process and external perturbation effects on disintegration. Thus, the current simulation study, coupled with the newly introduced mean-field model, offers an insight into the detailed mechanisms underlying the Aβ aggregation process, guiding potential strategies for effective disintegration of Aβ aggregates.
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Affiliation(s)
- Naresh Kumar
- Department of Chemistry, Theoretical and Computational Biophysical Chemistry Group, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India +91-01881-232066
| | - Prabir Khatua
- Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University) Bengaluru 562163 India
| | - Sudipta Kumar Sinha
- Department of Chemistry, Theoretical and Computational Biophysical Chemistry Group, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India +91-01881-232066
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2
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Lee HY, Baek S, Cha M, Yang SH, Cho I, Shin H, Lee S, Kim HY, Lee S, Shin J, Lee D, Kim K, Park I, Yoon S, Kim J, Park SJ, Kim SM, Kim KE, Kim HJ, Oh MS, Lee GH, Yu BY, Kannan P, Park K, Kim Y. Amyloid Against Amyloid: Dimeric Amyloid Fragment Ameliorates Cognitive Impairments by Direct Clearance of Oligomers and Plaques. Angew Chem Int Ed Engl 2023; 62:e202210209. [PMID: 36316282 DOI: 10.1002/anie.202210209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/07/2022] [Accepted: 10/26/2022] [Indexed: 01/13/2023]
Abstract
Amyloid-β (Aβ) in the form of neurotoxic aggregates is regarded as the main pathological initiator and key therapeutic target of Alzheimer's disease. However, anti-Aβ drug development has been impeded by the lack of a target needed for structure-based drug design and low permeability of the blood-brain barrier (BBB). An attractive therapeutic strategy is the development of amyloid-based anti-Aβ peptidomimetics that exploit the self-assembling nature of Aβ and penetrate the BBB. Herein, we designed a dimeric peptide drug candidate based on the N-terminal fragment of Aβ, DAB, found to cross the BBB and solubilize Aβ oligomers and fibrils. Administration of DAB reduced amyloid burden in 5XFAD mice, and downregulated neuroinflammation and prevented memory impairment in the Y-maze test. Peptide mapping assays and molecular docking studies were utilized to elucidate DAB-Aβ interaction. To further understand the active regions of DAB, we assessed the dissociative activity of DAB with sequence modifications.
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Affiliation(s)
- Hee Yang Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Seungyeop Baek
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Minhae Cha
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Seung-Hoon Yang
- Department of Medical Biotechnology, Dongguk University Jung-gu, Seoul, 04620, South Korea
| | - Illhwan Cho
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Heewon Shin
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Sejin Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Hye Yun Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Songmin Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Jisu Shin
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Donghee Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Kyeonghwan Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - InWook Park
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Soljee Yoon
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea.,Department of Integrative Biotechnology and Translational Medicine, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea
| | - Jiyoon Kim
- Brain Science Institute, Korea Institute of Science and Technology Seongbuk-gu, Seoul, 02792, South Korea
| | - Seong Jeong Park
- Amyloid Solution Bundang-gu, Seongnam-si, Gyeonggi-do, 13486, South Korea
| | - Seong Muk Kim
- Amyloid Solution Bundang-gu, Seongnam-si, Gyeonggi-do, 13486, South Korea
| | - Ko Eun Kim
- Amyloid Solution Bundang-gu, Seongnam-si, Gyeonggi-do, 13486, South Korea
| | - Hye Ju Kim
- Amyloid Solution Bundang-gu, Seongnam-si, Gyeonggi-do, 13486, South Korea
| | - Min-Seok Oh
- Advanced Analysis and data Center, Korea Institute of Science and Technology Seongbuk-gu, Seoul, 02792, South Korea.,Department of Stem Cell Biology, Konkuk University Gwangjin-Gu, Seoul, 05029, South Korea
| | - Gwan-Ho Lee
- Advanced Analysis and data Center, Korea Institute of Science and Technology Seongbuk-gu, Seoul, 02792, South Korea
| | - Byung-Yong Yu
- Advanced Analysis and data Center, Korea Institute of Science and Technology Seongbuk-gu, Seoul, 02792, South Korea
| | - Priyadharshini Kannan
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, 25457, South Korea.,Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangwon-do, 25451, South Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangwon-do, 25451, South Korea
| | - YoungSoo Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea.,Department of Integrative Biotechnology and Translational Medicine, Yonsei University Yeonsu-gu, Incheon, 21983, South Korea.,Amyloid Solution Bundang-gu, Seongnam-si, Gyeonggi-do, 13486, South Korea
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3
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Lee HY, Baek S, Cha M, Yang S, Cho I, Shin H, Lee S, Kim HY, Lee S, Shin J, Lee D, Kim K, Park I, Yoon S, Kim J, Park SJ, Kim SM, Kim KE, Kim HJ, Oh M, Lee G, Yu B, Kannan P, Park K, Kim Y. Amyloid Against Amyloid: Dimeric Amyloid Fragment Ameliorates Cognitive Impairments by Direct Clearance of Oligomers and Plaques. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202210209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Hee Yang Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Seungyeop Baek
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Minhae Cha
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Seung‐Hoon Yang
- Department of Medical Biotechnology Dongguk University Jung-gu Seoul 04620 South Korea
| | - Illhwan Cho
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Heewon Shin
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Sejin Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Hye Yun Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Songmin Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Jisu Shin
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Donghee Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Kyeonghwan Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - InWook Park
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Soljee Yoon
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
- Department of Integrative Biotechnology and Translational Medicine Yonsei University Yeonsu-gu Incheon 21983 South Korea
| | - Jiyoon Kim
- Brain Science Institute Korea Institute of Science and Technology Seongbuk-gu Seoul 02792 South Korea
| | - Seong Jeong Park
- Amyloid Solution Bundang-gu Seongnam-si Gyeonggi-do 13486 South Korea
| | - Seong Muk Kim
- Amyloid Solution Bundang-gu Seongnam-si Gyeonggi-do 13486 South Korea
| | - Ko Eun Kim
- Amyloid Solution Bundang-gu Seongnam-si Gyeonggi-do 13486 South Korea
| | - Hye Ju Kim
- Amyloid Solution Bundang-gu Seongnam-si Gyeonggi-do 13486 South Korea
| | - Min‐Seok Oh
- Advanced Analysis and data Center Korea Institute of Science and Technology Seongbuk-gu Seoul 02792 South Korea
- Department of Stem Cell Biology Konkuk University Gwangjin-Gu Seoul 05029 South Korea
| | - Gwan‐Ho Lee
- Advanced Analysis and data Center Korea Institute of Science and Technology Seongbuk-gu Seoul 02792 South Korea
| | - Byung‐Yong Yu
- Advanced Analysis and data Center Korea Institute of Science and Technology Seongbuk-gu Seoul 02792 South Korea
| | - Priyadharshini Kannan
- Department of Biochemical Engineering Gangneung-Wonju National University Gangneung 25457 South Korea
- Natural Product Informatics Research Center Korea Institute of Science and Technology Gangwon-do 25451 South Korea
| | - Keunwan Park
- Natural Product Informatics Research Center Korea Institute of Science and Technology Gangwon-do 25451 South Korea
| | - YoungSoo Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences Yonsei University Yeonsu-gu Incheon 21983 South Korea
- Department of Integrative Biotechnology and Translational Medicine Yonsei University Yeonsu-gu Incheon 21983 South Korea
- Amyloid Solution Bundang-gu Seongnam-si Gyeonggi-do 13486 South Korea
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4
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Khan AN, Nabi F, Ajmal MR, Ali SM, Almutairi FM, Alalawy AI, Khan RH. Moxifloxacin Disrupts and Attenuates Aβ42 Fibril and Oligomer Formation: Plausibly Repositioning an Antibiotic as Therapeutic against Alzheimer's Disease. ACS Chem Neurosci 2022; 13:2529-2539. [PMID: 35930676 DOI: 10.1021/acschemneuro.2c00371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The aggregation of Aβ42 is established as a key factor in the development of Alzheimer's disease (AD). Consequently, molecules that inhibit aggregation of peptide may lead to therapies to prevent or control AD. Several studies suggest that oligomeric intermediates present during aggregation may be more cytotoxic than fibrils themselves. In this work, we examine the inhibitory activity of an antibiotic MXF on aggregation (fibrils and oligomers) and disaggregation of Aβ42 using various biophysical and microscopic studies. Computational analysis was done to offer mechanistic insight. The amyloid formation of Aβ42 is suppressed by MXF, as demonstrated by the decrease in both the corresponding ThT fluorescence intensity and other biophysical techniques. The lag phase of amyloid formation doubled from 4.53 to 9.66 h in the presence of MXF. The addition of MXF at the completion of the fibrillation reaction, as monitored by ThT, led to a rapid, concentration dependent, exponential decrease in fluorescence signal that was consistent with loss of fibrils. We used TEM to directly demonstrate that MXF caused fibrils to disassemble. Our docking results show that MXF binds to both monomeric and fibrillar forms of Aβ42 with significant affinities. We also observed breaking of fibrils in the presence of MXF through molecular dynamics simulation. These findings suggest that antibiotic MXF could be a promising lead compound with dual role as fibril/oligomer inhibitor and disaggregase for further development as potential repurposed therapeutic against AD.
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Affiliation(s)
- Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
| | - Mohammad Rehan Ajmal
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Syed Moasfar Ali
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
| | - Fahad M Almutairi
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Adel I Alalawy
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
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5
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Xu S, Sun Y, Dong X. Design of Gallic Acid-Glutamine Conjugate and Chemical Implications for Its Potency Against Alzheimer's Amyloid-β Fibrillogenesis. Bioconjug Chem 2022; 33:677-690. [PMID: 35380783 DOI: 10.1021/acs.bioconjchem.2c00073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) has been widely recognized as a potent inhibitor of Alzheimer's amyloid-β (Aβ) fibrillogenesis. We found that gallic acid (GA) has superior inhibitory effects over EGCG at the same mass concentrations and assumed the pivotal role of the carboxyl group in GA. Therefore, we designed five GA-derivatives to investigate the significance of carboxyl groups in modulating Aβ fibrillogenesis, including carboxyl-amidated GA (GA-NH2), GA-glutamic acid conjugate (GA-E), and GA-E derivatives with amidated either of the two carboxyl groups (GA-Q and GA-E-NH2) or with two amidated-carboxyl groups (GA-Q-NH2). Intriguingly, only GA-Q shows significantly stronger potency than GA and extends the life span of the AD transgenic nematode by over 30%. Thermodynamic studies reveal that GA-Q has a strong binding affinity for Aβ42 with two binding sites, one stronger (site 1, Ka1 = 3.1 × 106 M-1) and the other weaker (site 2, Ka2 = 0.8 × 106 M-1). In site 1, hydrogen bonding, electrostatic interactions, and hydrophobic interactions all have contributions, while in site 2, only hydrogen bonding and electrostatic interactions work. The two sites are confirmed by molecular simulations, and the computations specified the key residues. GA-Q has strong binding to Asp23, Gly33, Gly38, Ala30, Ile31, and Leu34 via hydrogen bonding and electrostatic interactions, while it interacts with Phe19, Ala21 Gly25, and Asn27 via hydrophobic interactions. Consequently, GA-Q destroys Asp23-Lys28 salt bridges and restricts β-sheet/bridge structures. The thermodynamic and molecular insight into the GA-Q functions on inhibiting Aβ fibrillogenesis would pave a new way to the design of potent molecules against Alzheimer's amyloid.
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Affiliation(s)
- Shaoying Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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6
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Hu Q, Jayasinghe‐Arachchige VM, Sharma G, Serafim LF, Paul TJ, Prabhakar R. Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Gaurav Sharma
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Thomas J. Paul
- Department of Chemistry, University of Miami Coral Gables Florida
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami Coral Gables Florida
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7
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Iscen A, Brue CR, Roberts KF, Kim J, Schatz GC, Meade TJ. Inhibition of Amyloid-β Aggregation by Cobalt(III) Schiff Base Complexes: A Computational and Experimental Approach. J Am Chem Soc 2019; 141:16685-16695. [DOI: 10.1021/jacs.9b06388] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Aysenur Iscen
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Christopher R. Brue
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Kaleigh F. Roberts
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Joy Kim
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - George C. Schatz
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Thomas J. Meade
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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8
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Amini Z, Fatemi MH, Rauk A. Molecular dynamics studies of a β-sheet blocking peptide with the full-length amyloid beta peptide of Alzheimer’s disease. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The region encompassing residues 13–23 of the amyloid beta peptide (Aβ(13–23)) of Alzheimer’s disease is the self-recognition site that initiates toxic oligomerization and fibrillization. A number of pseudopeptides have been designed to bind to Aβ(13–23) and been computationally shown to do so with high affinity. More interactions are available in full-length Aβ than are available in the shorter peptide. We describe herein a study by molecular dynamics (MD) of nine distinct complexes formed by one such pseudopeptide, SGA1, with full-length beta amyloid, Aβ(1–42). The relative stabilities of the Aβ–SGA1 complexes were estimated by a combination of MD and ab initio methods. The most stable complex, designated AB1, was found to be one in which SGA1 is bound to the self-recognition site of Aβ(1–42) in an antiparallel β-sheet fashion. Another complex, designated AB3, also involved SGA1 binding to the self-recognition region of Aβ(1–42), albeit with lower affinity. In both AB1 and AB3, SGA1 formed antiparallel β-sheets but to opposite edges of Aβ. A complex, AB4, with similar stability to AB3, was found with a parallel β-sheet in the self-recognition site. A fourth complex, AB7, also with similar stability, formed a parallel β-sheet in the hydrophobic central region of Aβ. In all cases, complexation of SGA1 induced extensive β-sheet structure in Aβ(1–42).
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Affiliation(s)
- Zohreh Amini
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar, Mazandaran 47416-95447, Iran
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mohammad Hossein Fatemi
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar, Mazandaran 47416-95447, Iran
| | - Arvi Rauk
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
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9
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Investigation of the effect of erythrosine B on amyloid beta peptide using molecular modeling. J Mol Model 2016; 22:92. [DOI: 10.1007/s00894-016-2960-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/07/2016] [Indexed: 12/11/2022]
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10
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Tran L, Ha-Duong T. Exploring the Alzheimer amyloid-β peptide conformational ensemble: A review of molecular dynamics approaches. Peptides 2015; 69:86-91. [PMID: 25908410 DOI: 10.1016/j.peptides.2015.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease is one of the most common dementia among elderly worldwide. There is no therapeutic drugs until now to treat effectively this disease. One main reason is due to the poorly understood mechanism of Aβ peptide aggregation, which plays a crucial role in the development of Alzheimer's disease. It remains challenging to experimentally or theoretically characterize the secondary and tertiary structures of the Aβ monomer because of its high flexibility and aggregation propensity, and its conformations that lead to the aggregation are not fully identified. In this review, we highlight various structural ensembles of Aβ peptide revealed and characterized by computational approaches in order to find converging structures of Aβ monomer. Understanding how Aβ peptide forms transiently stable structures prior to aggregation will contribute to the design of new therapeutic molecules against the Alzheimer's disease.
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Affiliation(s)
- Linh Tran
- BioCIS, UMR CNRS 8076, LabEx LERMIT, Faculty of Pharmacy, University Paris Sud, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France
| | - Tâp Ha-Duong
- BioCIS, UMR CNRS 8076, LabEx LERMIT, Faculty of Pharmacy, University Paris Sud, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France.
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Jana AK, Sengupta N. Surface induced collapse of Aβ1-42 with the F19A replacement following adsorption on a single walled carbon nanotube. Biophys Chem 2013; 184:108-15. [DOI: 10.1016/j.bpc.2013.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/25/2013] [Accepted: 09/28/2013] [Indexed: 12/12/2022]
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12
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Chong SH, Ham S. Assessing the influence of solvation models on structural characteristics of intrinsically disordered protein. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Chong SH, Yim J, Ham S. Structural heterogeneity in familial Alzheimer's disease mutants of amyloid-beta peptides. MOLECULAR BIOSYSTEMS 2013; 9:997-1003. [DOI: 10.1039/c2mb25457c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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Ozbil M, Barman A, Bora RP, Prabhakar R. Computational Insights into Dynamics of Protein Aggregation and Enzyme-Substrate Interactions. J Phys Chem Lett 2012; 3:3460-3469. [PMID: 26290973 DOI: 10.1021/jz301597k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this Perspective, the roles of protein dynamics have been discussed in the aggregation of amyloid beta (Aβ) peptides and formation of enzyme-substrate complexes of beta-secretase (BACE1) and insulin-degrading enzyme (IDE). The studies regarding the influence of individual amino acid residues and specific regions on the structures and oligomerization of early Aβ aggregates and computations of their translational and rotational diffusion coefficients and order parameters exhibited that even the short-time-scale molecular dynamics simulations can reproduce certain experimental parameters with reasonable accuracy. The simulations elucidating the enzyme-substrate interactions of BACE1 and IDE successfully showed that the chemical nature and length of the substrates influence the dynamics and plasticity of both the enzyme and substrate. An atomic-level understanding of these processes will advance our efforts to develop therapeutic strategies for several deadly diseases through the design of small molecules with antiaggregation properties and substrate-specific "designer" forms of enzymes.
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Affiliation(s)
- Mehmet Ozbil
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Arghya Barman
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Ram Prasad Bora
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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15
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Lin YS, Bowman GR, Beauchamp KA, Pande VS. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. Biophys J 2012; 102:315-24. [PMID: 22339868 DOI: 10.1016/j.bpj.2011.12.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/12/2011] [Accepted: 12/01/2011] [Indexed: 12/21/2022] Open
Abstract
The aggregation of amyloid beta (Aβ) peptides plays an important role in the development of Alzheimer's disease. Despite extensive effort, it has been difficult to characterize the secondary and tertiary structure of the Aβ monomer, the starting point for aggregation, due to its hydrophobicity and high aggregation propensity. Here, we employ extensive molecular dynamics simulations with atomistic protein and water models to determine structural ensembles for Aβ(42), Aβ(40), and Aβ(42)-E22K (the Italian mutant) monomers in solution. Sampling of a total of >700 microseconds in all-atom detail with explicit solvent enables us to observe the effects of peptide length and a pathogenic mutation on the disordered Aβ monomer structural ensemble. Aβ(42) and Aβ(40) have crudely similar characteristics but reducing the peptide length from 42 to 40 residues reduces β-hairpin formation near the C-terminus. The pathogenic Italian E22K mutation induces helix formation in the region of residues 20-24. This structural alteration may increase helix-helix interactions between monomers, resulting in altered mechanism and kinetics of Aβ oligomerization.
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Affiliation(s)
- Yu-Shan Lin
- Department of Chemistry, Stanford University, Stanford, California, USA
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16
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Wang SH, Dong XY, Sun Y. Thermodynamic analysis of the molecular interactions between amyloid β-protein fragments and (-)-epigallocatechin-3-gallate. J Phys Chem B 2012; 116:5803-9. [PMID: 22536844 DOI: 10.1021/jp209406t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(-)-Epigallocatechin-3-gallate (EGCG) has been proven effective in preventing the aggregation of amyloid β-protein 42 (Aβ42), and the thermodynamic interactions between Aβ42 and EGCG have been studied in our previous work ( J. Phys. Chem. B 2010, 114, 11576). Herein, to further probe the interactions between different regions of Aβ42 and EGCG, three Aβ42 fragments (i.e., Aβ1-16, Aβ1-30, and Aβ31-42) were synthesized, and the thermodynamic interactions between each of the fragments and EGCG at different EGCG and salt concentrations were investigated by isothermal titration calorimetry. The results indicate that, although hydrogen bonding and hydrophobic interaction are both involved in the interactions between Aβ42 and EGCG, hydrogen bonding mainly happens in Aβ1-16 while hydrophobic interaction mainly happens in Aβ17-42. It is found that when Aβ42 and its fragments are saturated by EGCG, their thermodynamic parameters have linear relationships. The saturated binding stoichiometry (N(s)) for Aβ42 is the sum of the N(s) values for Aβ1-30 and Aβ31-42, while ΔH(s), ΔS(s), and ΔG(s) for Aβ42 are half the sum of the values for Aβ1-30 and Aβ31-42. The result suggests that there are no specific interactions and binding sites in the Aβ42 and EGCG binding. The orders of ΔH(s) and TΔS(s) values for the Aβ fragments are determined as Aβ17-42 > Aβ31-42 > Aβ1-30 > Aβ1-16. Moreover, there is significant enthalpy-entropy compensation in the binding of EGCG to Aβ42 and its fragments, resulting in insignificant change of ΔG with the change of the solution environment. The research has shed new light on the molecular mechanisms of the interactions between EGCG and Aβ42.
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Affiliation(s)
- Shi-Hui Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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17
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Zhu X, Bora RP, Barman A, Singh R, Prabhakar R. Dimerization of the Full-Length Alzheimer Amyloid β-Peptide (Aβ42) in Explicit Aqueous Solution: A Molecular Dynamics Study. J Phys Chem B 2012; 116:4405-16. [DOI: 10.1021/jp210019h] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Rajiv Singh
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146,
United States
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18
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Effects of ligands on unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. PLoS One 2012; 7:e30510. [PMID: 22291970 PMCID: PMC3264620 DOI: 10.1371/journal.pone.0030510] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 12/22/2011] [Indexed: 11/28/2022] Open
Abstract
Polymerization of the amyloid β-peptide (Aβ), a process which requires that the helical structure of Aβ unfolds beforehand, is suspected to cause neurodegeneration in Alzheimer's disease. According to recent experimental studies, stabilization of the Aβ central helix counteracts Aβ polymerization into toxic assemblies. The effects of two ligands (Dec-DETA and Pep1b), which were designed to bind to and stabilize the Aβ central helix, on unfolding of the Aβ central helix were investigated by molecular dynamics simulations. It was quantitatively demonstrated that the stability of the Aβ central helix is increased by both ligands, and more effectively by Pep1b than by Dec-DETA. In addition, it was shown that Dec-DETA forms parallel conformations with β-strand-like Aβ, whereas Pep1b does not and instead tends to bend unwound Aβ. The molecular dynamics results correlate well with previous experiments for these ligands, which suggest that the simulation method should be useful in predicting the effectiveness of novel ligands in stabilizing the Aβ central helix. Detailed Aβ structural changes upon loss of helicity in the presence of the ligands are also revealed, which gives further insight into which ligand may lead to which path subsequent to unwinding of the Aβ central helix.
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19
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Chong SH, Park M, Ham S. Structural and Thermodynamic Characteristics That Seed Aggregation of Amyloid-β Protein in Water. J Chem Theory Comput 2012; 8:724-34. [DOI: 10.1021/ct200757a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Song-Ho Chong
- Department
of Chemistry, Sookmyung Women’s University,
Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
| | - Mirae Park
- Department
of Chemistry, Sookmyung Women’s University,
Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
| | - Sihyun Ham
- Department
of Chemistry, Sookmyung Women’s University,
Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
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20
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Computational insights into the development of novel therapeutic strategies for Alzheimer's disease. Future Med Chem 2011; 1:119-35. [PMID: 21426072 DOI: 10.4155/fmc.09.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND β-amyloidosis and oxidative stress have been implicated as root causes of Alzheimer's disease (AD). Current potential therapeutic strategies for the treatment of AD include inhibition of amyloid β (Aβ) production, stimulation of Aβ degradation and prevention of Aβ oligomerization. However, efforts in this direction are hindered by the lack of understanding of the biochemical processes occurring at the atomic level in AD. DISCUSSION A radically different approach to achieve this goal would be the application of comprehensive theoretical and computational techniques such as molecular dynamics, quantum mechanics, hybrid quantum mechanics/molecular mechanics, bioinformatics and rotational spectroscopy to investigate complex chemical and physical processes in β-amyloidosis and the oxidative stress mechanism. CONCLUSION Results obtained from these studies will provide an atomic level understanding of biochemical processes occurring in AD and advance efforts to develop effective therapeutic strategies for this disease.
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21
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Velez-Vega C, Escobedo FA. Characterizing the structural behavior of selected Aβ-42 monomers with different solubilities. J Phys Chem B 2011; 115:4900-10. [PMID: 21486050 DOI: 10.1021/jp1086575] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conformational behavior of the wild-type amyloid β-42 (Aβ-42) monomer and two of its mutants was explored via all-atom replica exchange molecular dynamics simulations in explicit solvent, to identify structural features that may promote or deter early-stage oligomerization. The markers used for this purpose indicate that while the three peptides are relatively flexible they have distinct preferential structures and degree of rigidity. In particular, we found that one mutant that remains in the monomeric state in experiments displays a characteristic N-terminal structure that significantly enhances its rigidity. This finding is consistent with various studies that have detected a reduction in oligomerization frequency and Aβ-related toxicity upon sequence-specific antibody or ligand binding to the N-terminal tail of wild-type monomers, likely leading to the stabilization of this region. In general, our results highlight a potential role of the N-terminal segment on Aβ oligomerization and give insights into specific interactions that may be responsible for promoting the pronounced structural changes observed upon introducing point mutations on the wild-type Aβ-42 peptide.
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Affiliation(s)
- Camilo Velez-Vega
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
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22
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Ito M, Johansson J, Strömberg R, Nilsson L. Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. PLoS One 2011; 6:e17587. [PMID: 21408230 PMCID: PMC3049775 DOI: 10.1371/journal.pone.0017587] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 02/05/2011] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) pathogenesis is associated with formation of amyloid fibrils caused by polymerization of the amyloid β-peptide (Aβ), which is a process that requires unfolding of the native helical structure of Aβ. According to recent experimental studies, stabilization of the Aβ central helix is effective in preventing Aβ polymerization into toxic assemblies. To uncover the fundamental mechanism of unfolding of the Aβ central helix, we performed molecular dynamics simulations for wild-type (WT), V18A/F19A/F20A mutant (MA), and V18L/F19L/F20L mutant (ML) models of the Aβ central helix. It was quantitatively demonstrated that the stability of the α-helical conformation of both MA and ML is higher than that of WT, indicating that the α-helical propensity of the three nonpolar residues (18, 19, and 20) is the main factor for the stability of the whole Aβ central helix and that their hydrophobicity plays a secondary role. WT was found to completely unfold by a three-step mechanism: 1) loss of α-helical backbone hydrogen bonds, 2) strong interactions between nonpolar sidechains, and 3) strong interactions between polar sidechains. WT did not completely unfold in cases when any of the three steps was omitted. MA and ML did not completely unfold mainly due to the lack of the first step. This suggests that disturbances in any of the three steps would be effective in inhibiting the unfolding of the Aβ central helix. Our findings would pave the way for design of new drugs to prevent or retard AD.
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Affiliation(s)
- Mika Ito
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jan Johansson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, the Biomedical Centre, Uppsala, Sweden
- Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet Alzheimer Disease Research Center (KI-ADRC), Huddinge, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- * E-mail:
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23
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Bora RP, Prabhakar R. Translational, rotational and internal dynamics of amyloid beta-peptides (Abeta40 and Abeta42) from molecular dynamics simulations. J Chem Phys 2010; 131:155103. [PMID: 20568886 DOI: 10.1063/1.3249609] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In this study, diffusion constants [translational (D(T)) and rotational (D(R))], correlation times [rotational (tau(rot)) and internal (tau(int))], and the intramolecular order parameters (S(2)) of the Alzheimer amyloid-beta peptides Abeta40 and Abeta42 have been calculated from 150 ns molecular dynamics simulations in aqueous solution. The computed parameters have been compared with the experimentally measured values. The calculated D(T) of 1.61 x 10(-6) cm(2)/s and 1.43 x 10(-6) cm(2)/s for Abeta40 and Abeta42, respectively, at 300 K was found to follow the correct trend defined by the Debye-Stokes-Einstein relation that its value should decrease with the increase in the molecular weight. The estimated D(R) for Abeta40 and Abeta42 at 300 K are 0.085 and 0.071 ns(-1), respectively. The rotational (C(rot)(t)) and internal (C(int)(t)) correlation functions of Abeta40 and Abeta42 were observed to decay at nano- and picosecond time scales, respectively. The significantly different time decays of these functions validate the factorization of the total correlation function (C(tot)(t)) of Abeta peptides into C(rot)(t) and C(int)(t). At both short and long time scales, the Clore-Szabo model that was used as C(int)(t) provided the best behavior of C(tot)(t) for both Abeta40 and Abeta42. In addition, an effective rotational correlation time of Abeta40 is also computed at 18 degrees C and the computed value (2.30 ns) is in close agreement with the experimental value of 2.45 ns. The computed S(2) parameters for the central hydrophobic core, the loop region, and C-terminal domains of Abeta40 and Abeta42 are in accord with the previous studies.
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Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA
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24
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Lee C, Ham S. Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water. J Comput Chem 2010; 32:349-55. [DOI: 10.1002/jcc.21628] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 05/12/2010] [Accepted: 06/14/2010] [Indexed: 12/21/2022]
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25
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Bora RP, Prabhakar R. Elucidation of Interactions of Alzheimer Amyloid β Peptides (Aβ40 and Aβ42) with Insulin Degrading Enzyme: A Molecular Dynamics Study. Biochemistry 2010; 49:3947-56. [DOI: 10.1021/bi1002103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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26
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Barman A, Taves W, Prabhakar R. Insights into the mechanism of methionine oxidation catalyzed by metal (Cu(2+), Zn(2+), and Fe(3+)) - amyloid beta (Abeta) peptide complexes: A computational study. J Comput Chem 2009; 30:1405-13. [PMID: 19037857 DOI: 10.1002/jcc.21167] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this DFT study, a mechanism of the oxidation of methionine (Met) amino acid residue catalyzed by the metal (Cu(2+), Zn(2+), and Fe(3+)) bound amyloid beta (Abeta) peptide has been proposed. Based on experimental information, two different mechanisms: (1) stepwise and (2) concerted mechanisms for this important process have been investigated. The B3LYP calculations suggest that in the stepwise mechanism, the two separate pathways leading to the same sulfoxide product [Met(O)] go through prohibitively high barriers of 27.3 and 35.1 kcal/mol, therefore it is ruled out. In the concerted mechanism, the Cu(2+)-Abeta complex has been found to be the most efficient catalyst with the computed barrier of 14.3 kcal/mol. The substitutions of Cu(2+) by Zn(2+) and Fe(3+) increase barriers to 19.6 and 16.9 kcal/mol, respectively and make the reaction thermodynamically less favorable. It was also found that, in comparison with the cysteine (Cys) residue, Met is more susceptible toward oxidation. Its substitution with Cys slightly increased the barrier to 15.8 kcal/mol for the Cu(2+)-Abeta complex.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA
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27
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Xu W, Ping J, Li W, Mu Y. Assembly dynamics of two-beta sheets revealed by molecular dynamics simulations. J Chem Phys 2009; 130:164709. [PMID: 19405618 DOI: 10.1063/1.3123532] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The assembly dynamics of two beta sheets with different initial separation distances are explored by multiple all-atom molecular dynamics simulations with the presence of explicit water solvent. The beta sheet is composed of seven identical peptides in an antiparallel fashion. The peptide sequence is the 20-29 segment of human Islet amyloid polypeptide. Our simulations show that the assembly occurs not only in the lateral direction but also along the longitudinal direction, which provides a new insight into the assembly pathway at the early stage of fibril elongation. Based on Poisson-Boltzmann free energy analysis and quasiharmonic configuration entropy estimation, the entropic contribution is found to play an important role in the longitudinal assembly. Moreover, a possible oligomeric state with cyclic form is suggested based on one assembly model found in the simulations, illustrating the polymorphic nature of aggregation of the amyloidogenic peptide.
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Affiliation(s)
- Weixin Xu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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28
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29
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Brovchenko I, Burri RR, Krukau A, Oleinikova A, Winter R. Intrinsic thermal expansivity and hydrational properties of amyloid peptide Aβ42 in liquid water. J Chem Phys 2008; 129:195101. [DOI: 10.1063/1.3012562] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Inclusion Body Myositis: A View from the Caenorhabditis elegans Muscle. Mol Neurobiol 2008; 38:178-98. [DOI: 10.1007/s12035-008-8041-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 08/16/2008] [Indexed: 01/09/2023]
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31
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Hung A, Griffin MDW, Howlett GJ, Yarovsky I. Effects of oxidation, pH and lipids on amyloidogenic peptide structure: implications for fibril formation? EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:99-110. [PMID: 18769912 DOI: 10.1007/s00249-008-0363-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 08/01/2008] [Accepted: 08/04/2008] [Indexed: 10/21/2022]
Abstract
We have performed experimental and computational studies to investigate the influences of phospholipids, methionine oxidation and acidic pH on amyloid fibril formation by a peptide derived from human apolipoprotein C-II (apoC-II), a known component of proteinaceous atherosclerotic plaques. Fibril growth monitored by thioflavin T fluorescence revealed inhibition under lipid-rich and oxidising conditions. We subsequently performed fully-solvated atomistic molecular dynamics (MD) simulations of the peptide monomer to study its conformations under both fibril favouring (neutral and low pH) and inhibiting (lipid-rich and oxidising) conditions. Examination of the chain topology, backbone hydrogen-bonding patterns and aromatic sidechain orientations of the peptide under different conditions reveals that, while the peptide adopts similar structures under the fibril-favouring conditions, significantly different structures are obtained under fibril-disruptive conditions. Based on our results, we advance hypotheses for the roles of peptide conformation on aggregation and fibrillisation propensities.
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Affiliation(s)
- Andrew Hung
- School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, VIC 3001, Australia
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32
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Computational study of the binding of CuII to Alzheimer’s amyloid-β peptide: Do Aβ42 and Aβ40 bind copper in identical fashion? J Biol Inorg Chem 2008; 13:1197-204. [DOI: 10.1007/s00775-008-0403-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 06/25/2008] [Indexed: 12/31/2022]
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33
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Triguero L, Singh R, Prabhakar R. Comparative molecular dynamics studies of wild-type and oxidized forms of full-length Alzheimer amyloid beta-peptides Abeta(1-40) and Abeta(1-42). J Phys Chem B 2008; 112:7123-31. [PMID: 18476733 DOI: 10.1021/jp801168v] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this study, all-atom 50 ns molecular dynamics simulations are performed on the full-length amyloid beta (Abeta) monomers (WT-Abeta(1-40) and WT-Abeta(1-42)) and their oxidized forms (Met35(O)-Abeta(1-40) and Met35(O)-Abeta(1-42)) in aqueous solution. The effects of the oxidation state of Met35 and the presence of dipeptide (Ile41-Ala42) on the secondary structures of the three distinct regions (the central hydrophobic core region 17-21 (LVFFA), the loop 23-28 (DVGSNK), and the second hydrophobic domain 29-35 (GAIIGLM)) of all monomers have been analyzed in detail, and results are compared with the available experimental information. Our simulations indicate that the WT-Abeta(1-40) monomer adopts an overall beta-hairpin-like structure, which is promoted by the turn region (24-27). This turn region is stabilized through salt-bridge formation between the Asp23 and Lys28 residues. In contrast, the overall structure of the oxidized (Met35(O)-Abeta(1-40)) monomer can be divided into three well-defined bend regions separated by coil segments. These structural differences may be critical for the measured decrease in the rate of aggregation of Met35(O)-Abeta(1-40) peptide. In the WT-Abeta(1-42) monomer, in comparison to the WT-Abeta(1-40), the Asp23-Lys28 salt bridge is absent, and consequently, the turn in the middle (24-27) region has a smaller curvature. The observed difference in the aggregation rates of these two peptides may be related to the opening of the turn (24-27) stabilized by the Asp23-Lys28 salt bridge. For WT-Abeta(1-42), in the absence of this salt bridge, the unfolding and aggregation events may be more favorable than for WT-Abeta(1-40).
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Affiliation(s)
- Luciano Triguero
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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