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Xu Z, Tang J, Gong Y, Zhang J, Zou Y. Atomistic Insights into the Stabilization of TDP-43 Protofibrils by ATP. J Chem Inf Model 2024. [PMID: 39292611 DOI: 10.1021/acs.jcim.4c01140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
The aberrant accumulation of the transactive response deoxyribonucleic acid (DNA)-binding protein of 43 kDa (TDP-43) aggregates in the cytoplasm of motor neurons is the main pathological hallmark of amyotrophic lateral sclerosis (ALS). Previous experiments reported that adenosine triphosphate (ATP), the universal energy currency for all living cells, could induce aggregation and enhance the folding of TDP-43 fibrillar aggregates. However, the significance of ATP on TDP-43 fibrillation and the mechanism behind it remain elusive. In this work, we conducted multiple atomistic molecular dynamics (MD) simulations totaling 20 μs to search the critical nucleus size of TDP-43282-360 and investigate the impact of ATP molecules on preformed protofibrils. The results reveal that the trimer is the critical nucleus for TDP-43282-360 fibril formation and the tetramer is the minimal stable nucleus. When ATP molecules bind to the TDP-43282-360 trimer and tetramer, they can consolidate the TDP-43282-360 protofibrils by increasing the content of the β-sheet structure and promoting the formation of hydrogen bonds (H-bonds). Binding site analyses show that the N-terminus of TDP-43282-360 protofibrils is the main binding site of ATP, and R293 dominates the direct binding of ATP. Further analyses reveal that the π-π, cation-π, salt bridge, and H-bonding interactions together contribute to the binding of ATP to TDP-43282-360 protofibrils. This study decoded the detailed stabilization mechanism of protofibrillar TDP-43282-360 oligomers by ATP, and may provide new avenues for the development of drug design against ALS.
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Affiliation(s)
- Zhengdong Xu
- Department of Physical Education, Shanghai University of Engineering Science, 333 Long Teng Road, Shanghai 201620, People's Republic of China
| | - Jiaxing Tang
- College of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Yehong Gong
- General Education Center, Westlake University, 600 Dunyu Road, Hangzhou 310030, People's Republic of China
| | - Jianxin Zhang
- Department of Physical Education, Shanghai University of Engineering Science, 333 Long Teng Road, Shanghai 201620, People's Republic of China
| | - Yu Zou
- Department Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310007, People's Republic of China
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2
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Nie RZ, Zhang SS, Yan XK, Feng K, Lao YJ, Bao YR. Molecular insights into the structure destabilization effects of ECG and EC on the Aβ protofilament: An all-atom molecular dynamics simulation study. Int J Biol Macromol 2023; 253:127002. [PMID: 37729983 DOI: 10.1016/j.ijbiomac.2023.127002] [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: 05/04/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
The formation of Aβ into amyloid fibrils was closely connected to AD, therefore, the Aβ aggregates were the primary therapeutic targets against AD. Previous studies demonstrated that epicatechin-3-gallate (ECG), which possessed a gallate moiety, exhibited a greater ability to disrupt the preformed Aβ amyloid fibrils than epicatechin (EC), indicating that the gallate moiety was crucial. In the present study, the molecular mechanisms were investigated. Our results demonstrated that ECG had more potent disruptive impacts on the β-sheet structure and K28-A42 salt bridges than EC. We found that ECG significantly interfered the interactions between Peptide-4 and Peptide-5. However, EC could not. The disruption of K28-A42 salt bridges by ECG was mainly due to the interactions between ECG and the hydrophobic residues located at C-terminus. Interestingly, EC disrupted the K28-A42 salt bridges by the interactions with C-terminal hydrophobic residues and the cation-π interactions with K28. Moreover, our results indicated that hydrophobic interactions, H-bonds, π-π interactions and cation-π interactions between ECG and the bend of L-shaped region caused the disaggregation of interactions between Peptide-4 and Peptide-5. Significantly, gallate moiety in ECG had contributed tremendously to the disaggregation. We believed that our findings could be useful for designing prospective drug candidates targeting AD.
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Affiliation(s)
- Rong-Zu Nie
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Shan-Shuo Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Xiao-Ke Yan
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Kun Feng
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Yan-Jing Lao
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Ya-Ru Bao
- Science and Technology Division, Zhengzhou University of Light Industry, Zhengzhou 450002, China.
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3
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Nie RZ, Cai S, Yu B, Fan WY, Li HH, Tang SW, Huo YQ. Molecular insights into the very early steps of Aβ1-42 pentameric protofibril disassembly by PGG: A molecular dynamics simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Zou Y, Qi B, Tan J, Sun Y, Gong Y, Zhang Q. Mechanistic insight into the disruption of Tau R3-R4 protofibrils by curcumin and epinephrine: an all-atom molecular dynamics study. Phys Chem Chem Phys 2022; 24:20454-20465. [PMID: 35993190 DOI: 10.1039/d2cp02353a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The accumulation of Tau protein aggregates is a pathological hallmark of tauopathy, including chronic traumatic encephalopathy (CTE). Inhibiting Tau aggregation or disrupting preformed Tau fibrils is considered one of the rational therapeutic strategies to combat tauopathy. Previous studies reported that curcumin (Cur, a molecule of a labile natural product) and epinephrine (EP, an important neurotransmitter) could effectively inhibit the formation of Tau fibrillar aggregates and disassociate preformed fibrils. However, the underlying molecular mechanisms remain elusive. In this study, we performed multiple molecular dynamics simulations for 17.5 μs in total to investigate the influence of Cur and EP on the C-shaped Tau protofibril associated with CTE. Our simulations show that the protofibrillar pentamer is the smallest stable Tau R3-R4 protofibril. Taking the pentamer as a protofibril model, we found that both Cur and EP molecules could affect the shape of the Tau pentamer by changing the β2-β3 and β7-β8 angles, leading to a more extended structure. Cur and EP display a disruptive effect on the local β-sheets and the formation of hydrogen bonds, and thus destabilize the global protofibril structure. The contact number analysis shows that Cur has a higher binding affinity with the Tau pentamer than EP, especially in the nucleating segment PHF6. Hydrophobic, π-π and cation-π interactions together facilitate the binding of Cur and EP with the Tau pentamer. Cur exhibits stronger hydrophobic and π-π interactions with Tau than EP, and EP displays a stronger cation-π interaction. Our findings provide molecular insights into the disruptive mechanisms of the Tau R3-R4 protofibrils by curcumin and epinephrine, which may be useful for the design of effective drug candidates for the treatment of CTE.
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Affiliation(s)
- Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China.
| | - Bote Qi
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China.
| | - Jingwang Tan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang, P. R. China.
| | - Yunxiang Sun
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China.,Department of Physics, Ningbo University, 818 Fenghua Road, Ningbo 315211, Zhejiang, P. R. China
| | - Yehong Gong
- School of Sports Science and Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, P. R. China
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5
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Triterpenoids impede the fibrillation and cytotoxicity of human islet amyloid polypeptide. Int J Biol Macromol 2022; 199:189-200. [PMID: 34973981 DOI: 10.1016/j.ijbiomac.2021.12.127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 01/05/2023]
Abstract
The inhibition of human islet amyloid polypeptide (hIAPP) deposition to block its toxicity is an important strategy for the prevention and treatment of type II diabetes mellitus (T2DM).Natural compounds with pharmacological properties and low toxicity can serve as a good point to discover potential inhibitors of protein misfolding, which may be useful for the treatment of various amyloidosis-related diseases. Previous studies have reported that triterpenoids, such as maslinic acid (MA) and momordicin I (MI), can modulate glucose metabolism partially by reducing insulin resistance. However, the internal antidiabetic mechanism of these triterpenoids remains unclear. In this study, we examined the inhibition and disaggregation of MAandits isomer MI on the fibrillation of hIAPP using various experimental and computational approaches. The assembly behaviors and peptide-induced cytotoxicity of hIAPP could be effectively resisted by MA and MI. Moreover, the interaction of the two triterpenoids with hIAPP displayed a spontaneous and exothermic process. Moreover, molecular dynamics simulation results of different peptides revealed that MA and MI could bind to Asn and other non-polar residues near the core C-terminal region and reduce the oligomerization of hIAPP. The binding affinity was predominantly contributed by hydrophobic, electrostatic and hydrogen bonding interactions. The present work provides valuable data for MA and MI to treat T2DM and amyloidosis-related diseases.
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Niu H, Hou X, Zhang Y, Wu X, Deng F, Huang F, Shi L, Ma R. Self-Assembled Nanochaperones Inhibit the Aggregation of Human Islet Amyloid Polypeptide Associated with Type 2 Diabetes. ACS Macro Lett 2021; 10:662-670. [PMID: 35549098 DOI: 10.1021/acsmacrolett.1c00200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) aggregation is closely associated with dysfunction and apoptosis of pancreatic β-cells in type 2 diabetes (T2D). Accordingly, hIAPP amyloid inhibitors have shown promise against T2D. Here, by mimicking the function of natural molecular chaperones, nanochaperones (nChaps) based on self-assembled polymeric micelles with tunable surface microdomains for T2D treatment are reported. By capturing the aggregation-prone species of hIAPP onto the hydrophobic microdomains and segregating them by hydrophilic PEG chains, this kind of nChaps could effectively prevent hIAPP aggregation, block cell adhesion of hIAPP, facilitate hIAPP aggregates degradation and reduce hIAPP-related cytotoxicity. Therefore, our work will provide useful insights to develop a biomimetic strategy for the treatment of T2D.
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Affiliation(s)
- Haihong Niu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiaoxue Hou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Yanli Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiaohui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Fei Deng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Fan Huang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rujiang Ma
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, China
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7
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Nie RZ, Dang MZ, Ge ZZ, Huo YQ, Yu B, Tang SW. Influence of the gallate moiety on the interactions between green tea polyphenols and lipid membranes elucidated by molecular dynamics simulations. Biophys Chem 2021; 274:106592. [PMID: 33887572 DOI: 10.1016/j.bpc.2021.106592] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 02/09/2023]
Abstract
Previous studies suggested that naturally occurring EGCG primarily acted on the bacterial cell membrane then damaged the membrane and the gallate moiety in EGCG was very important to its anti-bacterial activity. However, the detailed mechanisms were still poorly understood. In this paper, EGCG and EGC were selected to study the great contribution of gallate moiety on the anti-bacterial activities of polyphenols. The results indicated that EGCG could penetrate deeper into the POPG lipid bilayer and possess more potent structure-perturbing potency on the POPG lipid bilayer than EGC. We also found that EGCG had the ability to form hydrogen bonds with the deeper inside oxygen atoms in the POPG lipid bilayer and the gallate moiety was the key functional group for EGCG forming hydrogen bonds with the POPG lipid bilayer. Moreover, results from the binding free energy analysis demonstrated that the gallate moiety made great contribution to the high affinity between EGCG and the POPG lipid bilayer. We believed that these findings could yield useful insights into the influence mechanisms of gallate moiety on the anti-bacterial activities of polyphenols.
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Affiliation(s)
- Rong-Zu Nie
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Mei-Zhu Dang
- School of Energy and Intelligence Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450002, China
| | - Zhen-Zhen Ge
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Yin-Qiang Huo
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Bo Yu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China
| | - Shang-Wen Tang
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, Xiangyang 441053, China.
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8
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Chowdhary S, Moschner J, Mikolajczak DJ, Becker M, Thünemann AF, Kästner C, Klemczak D, Stegemann A, Böttcher C, Metrangolo P, Netz RR, Koksch B. The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation. Chembiochem 2020; 21:3544-3554. [PMID: 33405360 PMCID: PMC7756607 DOI: 10.1002/cbic.202000373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/31/2020] [Indexed: 12/12/2022]
Abstract
The hexapeptide hIAPP22-27 (NFGAIL) is known as a crucial amyloid core sequence of the human islet amyloid polypeptide (hIAPP) whose aggregates can be used to better understand the wild-type hIAPP's toxicity to β-cell death. In amyloid research, the role of hydrophobic and aromatic-aromatic interactions as potential driving forces during the aggregation process is controversially discussed not only in case of NFGAIL, but also for amyloidogenic peptides in general. We have used halogenation of the aromatic residue as a strategy to modulate hydrophobic and aromatic-aromatic interactions and prepared a library of NFGAIL variants containing fluorinated and iodinated phenylalanine analogues. We used thioflavin T staining, transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) to study the impact of side-chain halogenation on NFGAIL amyloid formation kinetics. Our data revealed a synergy between aggregation behavior and hydrophobicity of the phenylalanine residue. This study introduces systematic fluorination as a toolbox to further investigate the nature of the amyloid self-assembly process.
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Affiliation(s)
- Suvrat Chowdhary
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Johann Moschner
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Dorian J. Mikolajczak
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Maximilian Becker
- Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Andreas F. Thünemann
- Federal Institute for Materials Research and Testing (BAM)Unter den Eichen 8712205BerlinGermany
| | - Claudia Kästner
- Federal Institute for Materials Research and Testing (BAM)Unter den Eichen 8712205BerlinGermany
| | - Damian Klemczak
- Institute of PharmacyFreie Universität BerlinKönigin-Luise-Str. 2–414195BerlinGermany
| | - Anne‐Katrin Stegemann
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Christoph Böttcher
- Institute of Chemistry and Biochemistry and Core Facility BioSupraMolFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Pierangelo Metrangolo
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanItaly
| | - Roland R. Netz
- Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Beate Koksch
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
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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
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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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Nie RZ, Huo YQ, Yu B, Liu CJ, Zhou R, Bao HH, Tang SW. Molecular insights into the inhibitory mechanisms of gallate moiety on the Aβ 1-40 amyloid aggregation: A molecular dynamics simulation study. Int J Biol Macromol 2020; 156:40-50. [PMID: 32275992 DOI: 10.1016/j.ijbiomac.2020.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease is the most common form of neurodegenerative disease and the formation of Aβ amyloid aggregates has been widely demonstrated to be the principal cause of Alzheimer's disease. Our previous study and other studies suggested that the gallate moiety played an obligatory role in the inhibition process of naturally occurring polyphenols on Aβ amyloid fibrils formation. However, the detailed mechanisms were still unknown. Thus, in the present study, the gallic acid (GA) was specially selected and the molecular recognition mechanisms between GA molecules and Aβ1-40 monomer were examined and analyzed by molecular dynamics simulation. The in silico experiments revealed that GA significantly prevented the conformational changes of Aβ1-40 monomer with no β-sheet structure during the whole 100 ns. By analyzing the binding sites of GA molecules to Aβ1-40 monomer, we found that both hydrophilic and hydrophobic amino acid residues were participated in the binding of GA molecules to Aβ1-40 monomer. Moreover, results from the binding free energy analysis further demonstrated that the strength of polar interactions was significantly stronger than that of nonpolar interactions. We believed that our results could help to elucidate the underlying mechanisms of gallate moiety on the anti-amyloidogenic effects of polyphenols at the atomic level.
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Affiliation(s)
- Rong-Zu Nie
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Yin-Qiang Huo
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Bo Yu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Chuan-Ju Liu
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Rui Zhou
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Hong-Hui Bao
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China
| | - Shang-Wen Tang
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China; Food Ingredients Engineering Technology Research Center of Hubei, China.
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11
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Kumar AP, Lee S, Lukman S. Computational and Experimental Approaches to Design Inhibitors of Amylin Aggregation. Curr Drug Targets 2019; 20:1680-1694. [DOI: 10.2174/1389450120666190719164316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023]
Abstract
Amylin is a neuroendocrine peptide hormone secreted by pancreatic ß-cells; however,
amylin is toxic to ß-cells when it is aggregated in type 2 diabetes mellitus (T2DM). It is important to
understand amylin’s structures and aggregation mechanism for the discovery and design of effective
drugs to inhibit amylin aggregation. In this review, we investigated experimental and computational
studies on amylin structures and inhibitors. Our review provides some novel insights into amylin, particularly
for the design of its aggregation inhibitors to treat T2DM. We detailed the potential inhibitors
that have been studied hitherto and highlighted the neglected need to consider different amylin attributes
that depend on the presence/absence of physiologically relevant conditions, such as membranes.
These conditions and the experimental methods can greatly influence the results of studies on amylininhibitor
complexes. Text-mining over 3,000 amylin-related PubMed abstracts suggests the combined
therapeutic potential of amylin with leptin and glucagon-like peptide-1, which are two key hormones
in obesity. The results also suggest that targeting amylin aggregation can contribute to therapeutic efforts
for Alzheimer’s disease (AD). Therefore, we have also reviewed the role of amylin in other conditions
including obesity and AD. Finally, we provided insights for designing inhibitors of different
types (small molecules, proteins, peptides/mimetics, metal ions) to inhibit amylin aggregation.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Sungmun Lee
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, College of Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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12
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Role of physical nucleation theory in understanding conformational conversion between pathogenic and nonpathogenic aggregates of low-complexity amyloid peptides. RESEARCH ON CHEMICAL INTERMEDIATES 2019. [DOI: 10.1007/s11164-019-03974-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Xin Y, Zhang H, Hu Q, Tian S, Wang C, Luo L, Meng F. Oligotyrosines Inhibit Amyloid Formation of Human Islet Amyloid Polypeptide in a Tyrosine-Number-Dependent Manner. ACS Biomater Sci Eng 2018; 5:1092-1099. [DOI: 10.1021/acsbiomaterials.8b01384] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yanru Xin
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huazhi Zhang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qigang Hu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Sidan Tian
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chenhui Wang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Liang Luo
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Fanling Meng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Wuhan Institute of Biotechnology, Wuhan 430075, China
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14
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Ning L, Mu Y. Aggregation of PrP106-126 on surfaces of neutral and negatively charged membranes studied by molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1936-1948. [PMID: 29550288 DOI: 10.1016/j.bbamem.2018.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 01/28/2023]
Abstract
Prion diseases are neurodegenerative disorders characterized by the aggregation of an abnormal form of prion protein. The interaction of prion protein and cellular membrane is crucial to elucidate the occurrence and development of prion diseases. Its fragment, residues 106-126, has been proven to maintain the pathological properties of misfolded prion and was used as a model peptide. In this study, explicit solvent molecular dynamics (MD) simulations were carried out to investigate the adsorption, folding and aggregation of PrP106-126 with different sizes (2-peptides, 4-peptides and 6-peptides) on the surface of both pure neutral POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and negatively charged POPC/POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol) (3:1) lipids. MD simulation results show that PrP106-126 display strong affinity with POPC/POPG but does not interact with pure POPC. The positively charged and polar residues participating hydrogen bonding with membrane promote the adsorption of PrP106-126. The presence of POPC and POPC/POPG exert limited influence on the secondary structures of PrP106-126 and random coil structures are predominant in all simulation systems. Upon the adsorption on the POPC/POPG surface, the aggregation states of PrP106-126 have been changed and more small oligomers were observed. This work provides insights into the interactions of PrP106-126 and membranes with different compositions in atomic level, which expand our understanding the role membrane plays in the development of prion diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Lulu Ning
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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15
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Lagarias P, Elkhou Y, Vedad J, Konstantinidi A, Profit AA, Kellici TF, Kolocouris A, Desamero RZB, Mavromoustakos T. Molecular Dynamics Simulations on the Bioactive Molecule of hIAPP22-29 (NFGAILSS) and Rational Drug Design. Methods Mol Biol 2018; 1824:1-16. [PMID: 30039398 DOI: 10.1007/978-1-4939-8630-9_1] [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] [Indexed: 06/08/2023]
Abstract
This chapter includes information about the structure in equilibrium of the bioactive molecule hIAPP22-29 (NFGAILSS). The experimental structure was derived using X-ray and its 2D NOESY NMR experiments in d 6-DMSO and d-HFIP solvents. This molecule contains eight of the ten amino acids of the 20-29 region of the human islet amyloid polypeptide (hIAPP) often referred as the "amyloidogenic core." Amyloid deposits are well-known to cause as many as 20 pathological neurodegenerative disorders such as Alzheimer, Parkinson, Huntington, and Creutzfeldt-Jakob. The experimental structure was relaxed using molecular dynamics (MD) in simulation boxes consisting in DMSO and HFIP; the latter not provided by the applied software. The calculations were performed in GPUs and supercomputers, and some basic scripting is described for reference. The simulations confirmed the inter- and intramolecular forces that led to an "amyloidogenic core" observed from NOE experiments. The results showed that in DMSO and HFIP environment, Phe is not in spatial proximity with Leu or Ile, and this is consistent with an amyloidogenic core. However, in an amphipathic environment such as the model lipid bilayers, this communication is possible and may influence peptide amyloidogenic properties. The knowledge gained through this study may contribute to the rational drug design of novel peptides or organic molecules acting by modifying preventing amyloidogenic properties of the hIAPP peptide.
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Affiliation(s)
- Panagiotis Lagarias
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Youness Elkhou
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Jayson Vedad
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Athina Konstantinidi
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Adam A Profit
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Tahsin F Kellici
- Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Antonios Kolocouris
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Ruel Z B Desamero
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Thomas Mavromoustakos
- Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
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16
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Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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17
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Capping effects on polymorphic Aβ 16-21 amyloids depend on their size: A molecular dynamics simulation study. Biophys Chem 2017; 232:1-11. [PMID: 29046256 DOI: 10.1016/j.bpc.2017.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 11/24/2022]
Abstract
Understanding Aβ amyloid oligomers associated with neuro-degenerative diseases is needed due to their toxic characteristics and mediation of amyloid fibril growth. Depending on various physiological circumstances such as ionic strength, metal ion, and point-residue mutation, oligomeric amyloids exhibit polymorphic behavior and structural stabilities, i.e. showing different conformation and stabilities. Specifically, experimental and computational researchers have found that the capping modulates the physical and chemical properties of amyloids by preserving electrostatic energy interactions, which is one of the dominant factors for amyloid stability. Still, there is no detailed knowledge for the polymorphic amyloids with reflecting the terminal capping effects. In the present study, we investigated the role of terminal capping (i.e. N-terminal acetylation and C-terminal amidation) on polymorphic Aβ16-21 amyloid oligomer and protofibrils via molecular dynamics (MD) simulations. We found that the capping effects have differently altered the conformation of polymorphic antiparallel-homo and -hetero Aβ16-21 amyloid oligomer, but not Aβ16-21 amyloid protofibrils. However, regardless of polymorphic composition of the amyloids, the capping induces the thermodynamic instabilities of Aβ16-21 amyloid oligomers, but does not show any distinct affect on Aβ16-21 amyloid protofibrils. Specifically, among the molecular mechanic factors, electrostatic energy dominantly contributes the thermodynamic stability of the Aβ16-21 amyloids. We hope that our computation study about the role of the capping effects on the polymorphic amyloids will facilitate additional efforts to enhance degradation of amyloids and to design a selective drug in the future.
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18
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Chang HJ, Lee M, Kim JI, Yoon G, Na S. Mechanical and vibrational characterization of amyloid-like HET-s nanosheets based on the skewed plate theory. Phys Chem Chem Phys 2017; 19:11492-11501. [PMID: 28425516 DOI: 10.1039/c7cp01418j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pathological amyloidogenic prion proteins have a toxic effect on functional cells in the human cerebrum because of poor degradability and the tendency to accumulate in an uncontrolled manner under physiological conditions. HET-s, a fungal prion protein, is known to undergo conformational variations from fibrillar to nanosheet structures during a change from low to high pH conditions. It has been said that this conformational change can lead to self-propagation by nucleating on the lateral surface of singlet fibrils. Efforts have been made toward the mechanical characterization of fibrillar amyloids, but a global understanding of amyloid-like HET-s nanosheet structures is lacking. In this study, we analyzed the mechanical and vibrational characteristics of the skewed HET-s nanosheet structures that developed under neutral pH conditions by performing various molecular dynamics simulations. By applying the skewed plate theory to HET-s nanosheets for various length scales with numerous pores inside the structures, we found that the skewed HET-s nanosheet structure has mechanical properties comparable to those of previously reported biological film materials and nanomaterials. Considering the inherent characteristics of structural stability, our observation provides valuable and detailed structural information on skewed amyloid-like HET-s nanosheets.
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Affiliation(s)
- Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea.
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19
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Xu ZX, Ma GL, Zhang Q, Chen CH, He YM, Xu LH, Zhou GR, Li ZH, Yang HJ, Zhou P. Inhibitory Mechanism of Epigallocatechin Gallate on Fibrillation and Aggregation of Amidated Human Islet Amyloid Polypeptide. Chemphyschem 2017; 18:1611-1619. [PMID: 28297133 DOI: 10.1002/cphc.201700057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 01/06/2023]
Abstract
The abnormal fibrillation of human islet amyloid polypeptide (hIAPP) is associated with development of type II diabetes mellitus (T2DM). (-)-Epigallocatechin gallate (EGCG) can bind amyloid proteins to inhibit the fibrillation of these proteins. However, the mechanic detail of EGCG inhibiting amyloid formation is still unclear at the molecular level. In the present work, we sought to investigate the effect of EGCG on amidated hIAPP (hIAPP-NH2 ) fibrillation and aggregation by using spectroscopic and microscopic techniques, and also sought to gain insights into the interaction of EGCG and hIAPP22-27 by using spectroscopic experiments and quantum chemical calculations. ThT fluorescence, real-time NMR, and TEM studies demonstrated that EGCG inhibits the formation of hIAPP-NH2 fibrils, while promoting the formation of hIAPP-NH2 amorphous aggregates. Phenylalanine intrinsic fluorescence and NMR studies of the EGCG/hIAPP22-27 complex revealed three important binding sites including the A ring of EGCG, residue Phe23, and residue Ile26. DFT calculations identified the dominant binding structures of EGCG/Phe23 and EGCG/Ile26 complexes, named structure I and structure II, respectively. Our study demonstrates the inhibitory mechanism of EGCG on fibrillation and aggregation of hIAPP-NH2 in which EGCG interacts with hIAPP-NH2 through hydrogen bonding and π-π interactions between the A ring and residue Phe23 as well as hydrophobic interactions between the A ring and residue Ile26, which can thus inhibit the interpeptide interaction between hIAPP-NH2 monomers and finally inhibit fibrillation of hIAPP-NH2 . This study agrees with and reinforces previous studies and offers an intuitive explanation at both the atomic and molecular levels. Our findings may provide an invaluable reference for the future development of new drugs in the management of diabetes.
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Affiliation(s)
- Zhi-Xue Xu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Gong-Li Ma
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Qiang Zhang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, P. R. China
| | - Cong-Heng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Yan-Ming He
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, P. R. China
| | - Li-Hui Xu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Guang-Rong Zhou
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
| | - Zhen-Hua Li
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Hong-Jie Yang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, P. R. China
| | - Ping Zhou
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China), Fax: (+86) 21-55664038
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20
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Zhou S, Wang Q, Ren M, Zhang A, Liu H, Yao X. Molecular dynamics simulation on the inhibition mechanism of peptide-based inhibitor of islet amyloid polypeptide (IAPP) to islet amyloid polypeptide (IAPP22-28) oligomers. Chem Biol Drug Des 2017; 90:31-39. [DOI: 10.1111/cbdd.12924] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/18/2016] [Accepted: 11/27/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Shuangyan Zhou
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry; Lanzhou University; Lanzhou China
- School of Pharmacy; Lanzhou University; Lanzhou China
| | - Qianqian Wang
- State Key Laboratory of Quality Research in Chinese Medicine; Macau Institute for Applied Research in Medicine and Health; Macau University of Science and Technology; Taipa Macau China
| | - Mengdan Ren
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry; Lanzhou University; Lanzhou China
| | - Ai Zhang
- School of Pharmacy; Lanzhou University; Lanzhou China
| | - Huanxiang Liu
- School of Pharmacy; Lanzhou University; Lanzhou China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry; Lanzhou University; Lanzhou China
- State Key Laboratory of Quality Research in Chinese Medicine; Macau Institute for Applied Research in Medicine and Health; Macau University of Science and Technology; Taipa Macau China
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21
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Lee M, Chang HJ, Baek I, Na S. Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations. Proteins 2016; 85:580-592. [PMID: 28019690 DOI: 10.1002/prot.25232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/12/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Because of its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aβ amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aβ amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aβ pair amyloids based on the facing β-strand directions between the amyloid pairs. As a result, we were able to observe the varying effects of mutation, polymorphism, and protofibril lengths on the structural stability of pair amyloids. Furthermore, we have also found that opposite structural stability exists on a certain polymorphic Aβ pair amyloids depending on its oligomeric or protofibrillar state, which can be helpful for understanding the amyloid growth mechanism via repetitive fragmentation and elongation mechanism. Proteins 2017; 85:580-592. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Myeongsang Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Inchul Baek
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
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22
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Protective V127 prion variant prevents prion disease by interrupting the formation of dimer and fibril from molecular dynamics simulations. Sci Rep 2016; 6:21804. [PMID: 26906032 PMCID: PMC4764842 DOI: 10.1038/srep21804] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/01/2016] [Indexed: 12/12/2022] Open
Abstract
Recent studies uncovered a novel protective prion protein variant: V127 variant, which was reported intrinsically resistant to prion conversion and propagation. However, the structural basis of its protective effect is still unknown. To uncover the origin of the protective role of V127 variant, molecular dynamics simulations were performed to explore the influence of G127V mutation on two key processes of prion propagation: dimerization and fibril formation. The simulation results indicate V127 variant is unfavorable to form dimer by reducing the main-chain H-bond interactions. The simulations of formed fibrils consisting of β1 strand prove V127 variant will make the formed fibril become unstable and disorder. The weaker interaction energies between layers and reduced H-bonds number for V127 variant reveal this mutation is unfavorable to the formation of stable fibril. Consequently, we find V127 variant is not only unfavorable to the formation of dimer but also unfavorable to the formation of stable core and fibril, which can explain the mechanism on the protective role of V127 variant from the molecular level. Our findings can deepen the understanding of prion disease and may guide the design of peptide mimetics or small molecule to mimic the protective effect of V127 variant.
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23
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Baek I, Lee M, Na S. Understanding structural characteristics of out-of-register hIAPP amyloid proteins via molecular dynamics. RSC Adv 2016. [DOI: 10.1039/c6ra19100b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We investigated characteristics of out-of-register (OOR) hIAPP amyloids. By varying the length size of OOR hIAPP, we found 8 layers is most stable. In addition, OOR hIAPP has relative structural instability than in-register hAIPP.
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Affiliation(s)
- Inchul Baek
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
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24
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Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation. Int J Mol Sci 2015; 16:14291-304. [PMID: 26114384 PMCID: PMC4519842 DOI: 10.3390/ijms160714291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 01/22/2023] Open
Abstract
The dimeric structure of the N-terminal 12 residues drives the interaction of α-synuclein protein with membranes. Moreover, experimental studies indicated that the aggregation of α-synuclein is faster at low pH than neutral pH. Nevertheless, the effects of different pH on the structural characteristics of the α-syn12 dimer remain poorly understood. We performed 500 ns temperature replica exchange molecular dynamics (T-REMD) simulations of two α-syn12 peptides in explicit solvent. The free energy surfaces contain ten highly populated regions at physiological pH, while there are only three highly populated regions contained at acidic pH. The anti-parallel β-sheet conformations were found as the lowest free energy state. Additionally, these states are nearly flat with a very small barrier which indicates that these states can easily transit between themselves. The dimer undergoes a disorder to order transition from physiological pH to acidic pH and the α-syn12 dimer at acidic pH involves a faster dimerization process. Further, the Lys6–Asp2 contact may prevent the dimerization.
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25
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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