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Srivastava A, Al Adem K, Shanti A, Lee S, Abedrabbo S, Homouz D. Inhibition of the Early-Stage Cross-Amyloid Aggregation of Amyloid-β and IAPP via EGCG: Insights from Molecular Dynamics Simulations. ACS OMEGA 2024; 9:30256-30269. [PMID: 39035938 PMCID: PMC11256295 DOI: 10.1021/acsomega.4c00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024]
Abstract
Amyloid-β (Aβ) and islet amyloid polypeptide (IAPP) are small peptides that have the potential to not only self-assemble but also cross-assemble and form cytotoxic amyloid aggregates. Recently, we experimentally investigated the nature of Aβ-IAPP coaggregation and its inhibition by small polyphenolic molecules. Notably, we found that epigallocatechin gallate (EGCG) had the ability to reduce heteroaggregate formation. However, the precise molecular mechanism behind the reduction of heteroaggregates remains unclear. In this study, the dimerization processes of Aβ40 and IAPP peptides with and without EGCG were characterized by the enhanced sampling technique. Our results showed that these amyloid peptides exhibited a tendency to form a stable heterodimer, which represented the first step toward coaggregation. Furthermore, we also found that the EGCG regulated the dimerization process. In the presence of EGCG, well-tempered metadynamics simulation indicated a notable shift in the bound state toward a greater center of mass (COM) distance. Additionally, the presence of EGCG led to a significant increase in the free energy barrier height (∼15k B T) along the COM distance, and we observed a transition state between the bound and unbound states. Our findings also unveiled that the EGCG formed a greater number of hydrogen bonds with Aβ40, effectively obstructing the dimer formation. In addition, we carried out microseconds of all-atom conventional molecular dynamics (cMD) simulations to investigate the formation of both hetero- and homo-oligomer states by these peptides. MD simulations illustrated that EGCG played a significant role in preventing oligomer formation by reducing the content of β-sheets in the peptide. Collectively, our results offered valuable insight into the mechanism of cross-amyloid aggregation between Aβ40 and IAPP and the inhibition effect of EGCG on the heteroaggregation process.
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Affiliation(s)
- Amit Srivastava
- Department
of Physics, Khalifa University of Science
and Technology, Abu Dhabi 127788, UAE
| | - Kenana Al Adem
- Chair
of Biological Imaging, Central Institute for Translational Cancer
Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich 81675, Germany
- Institute
of Biological and Medical Imaging, Helmholtz
Zentrum München, Neuherberg 81675, Germany
| | - Aya Shanti
- Department
of Biological Sciences, Khalifa University
of Science and Technology, Abu
Dhabi 127788, UAE
| | - Sungmun Lee
- Department
of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi 127788, UAE
- Khalifa University’s
Center for Biotechnology, Khalifa University
of Science and Technology, Abu
Dhabi 127788, UAE
| | - Sufian Abedrabbo
- Department
of Physics, Khalifa University of Science
and Technology, Abu Dhabi 127788, UAE
| | - Dirar Homouz
- Department
of Physics, Khalifa University of Science
and Technology, Abu Dhabi 127788, UAE
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2
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Fan X, Zhang X, Yan J, Xu H, Zhao W, Ding F, Huang F, Sun Y. Computational Investigation of Coaggregation and Cross-Seeding between Aβ and hIAPP Underpinning the Cross-Talk in Alzheimer's Disease and Type 2 Diabetes. J Chem Inf Model 2024; 64:5303-5316. [PMID: 38921060 PMCID: PMC11339732 DOI: 10.1021/acs.jcim.4c00859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The coexistence of amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) in the brain and pancreas is associated with an increased risk of Alzheimer's disease (AD) and type 2 diabetes (T2D) due to their coaggregation and cross-seeding. Despite this, the molecular mechanisms underlying their interaction remain elusive. Here, we systematically investigated the cross-talk between Aβ and hIAPP using atomistic discrete molecular dynamics (DMD) simulations. Our results revealed that the amyloidogenic core regions of both Aβ (Aβ10-21 and Aβ30-41) and hIAPP (hIAPP8-20 and hIAPP22-29), driving their self-aggregation, also exhibited a strong tendency for cross-interaction. This propensity led to the formation of β-sheet-rich heterocomplexes, including potentially toxic β-barrel oligomers. The formation of Aβ and hIAPP heteroaggregates did not impede the recruitment of additional peptides to grow into larger aggregates. Our cross-seeding simulations demonstrated that both Aβ and hIAPP fibrils could mutually act as seeds, assisting each other's monomers in converting into β-sheets at the exposed fibril elongation ends. The amyloidogenic core regions of Aβ and hIAPP, in both oligomeric and fibrillar states, exhibited the ability to recruit isolated peptides, thereby extending the β-sheet edges, with limited sensitivity to the amino acid sequence. These findings suggest that targeting these regions by capping them with amyloid-resistant peptide drugs may hold potential as a therapeutic approach for addressing AD, T2D, and their copathologies.
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Affiliation(s)
- Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Xiaohan Zhang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Huan Xu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Wenhui Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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3
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Liu X, Li X, Qiao Q, Li F, Wei G. ALS-Linked A315T and A315E Mutations Enhance β-Barrel Formation of the TDP-43 307-319 Hexamer: A REST2 Simulation Study. ACS Chem Neurosci 2023; 14:1310-1320. [PMID: 36888995 DOI: 10.1021/acschemneuro.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Pathogenic mutations of transactivation response element DNA-binding protein 43 (TDP-43) are closely linked with amyotrophic lateral sclerosis (ALS). It was recently reported that two ALS-linked familial mutants A315T and A315E of TDP-43307-319 peptides can self-assemble into oligomers including tetramers, hexamers, and octamers, among which hexamers were suggested to form the β-barrel structure. However, due to the transient nature of oligomers, their conformational properties and the atomic mechanisms underlying the β-barrel formation remain largely elusive. Herein, we investigated the hexameric conformational distributions of the wild-type (WT) TDP-43307-319 fragment and its A315T and A315E mutants by performing all-atom explicit-solvent replica exchange with solute tempering 2 simulations. Our simulations reveal that each peptide can self-assemble into diverse conformations including ordered β-barrels, bilayer β-sheets and/or monolayer β-sheets, and disordered complexes. A315T and A315E mutants display higher propensity to form β-barrel structures than the WT, which provides atomic explanation for their enhanced neurotoxicity reported previously. Detailed interaction analysis shows that A315T and A315E mutations increase inter-molecular interactions. Also, the β-barrel structures formed by the three different peptides are stabilized by distinct inter-peptide side-chain hydrogen bonding, hydrophobic, and aromatic stacking interactions. This study demonstrates the enhanced β-barrel formation of the TDP-43307-319 hexamer by the pathogenic A315T and A315E mutations and reveals the underlying molecular determinants, which may be helpful for in-depth understanding of the ALS-mutation-induced neurotoxicity of TDP-43 protein.
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Affiliation(s)
- Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.,Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
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4
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Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 2023; 18:315-333. [PMID: 36715303 PMCID: PMC10149343 DOI: 10.1080/17460441.2023.2171396] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
BACKGROUND Protein-protein interactions (PPIs) are intriguing targets for designing novel small-molecule inhibitors. The role of PPIs in various infectious and neurodegenerative disorders makes them potential therapeutic targets . Despite being portrayed as undruggable targets, due to their flat surfaces, disorderedness, and lack of grooves. Recent progresses in computational biology have led researchers to reconsider PPIs in drug discovery. AREAS COVERED In this review, we introduce in-silico methods used to identify PPI interfaces and present an in-depth overview of various computational methodologies that are successfully applied to annotate the PPIs. We also discuss several successful case studies that use computational tools to understand PPIs modulation and their key roles in various physiological processes. EXPERT OPINION Computational methods face challenges due to the inherent flexibility of proteins, which makes them expensive, and result in the use of rigid models. This problem becomes more significant in PPIs due to their flexible and flat interfaces. Computational methods like molecular dynamics (MD) simulation and machine learning can integrate the chemical structure data into biochemical and can be used for target identification and modulation. These computational methodologies have been crucial in understanding the structure of PPIs, designing PPI modulators, discovering new drug targets, and predicting treatment outcomes.
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Affiliation(s)
- Ashfaq Ur Rehman
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Ho-Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, Zhejiang, China
| | - Zhiqiang Wei
- Medicinal Chemistry and Bioinformatics Center, Ocean University of China, Qingdao, Shandong, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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5
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Insights into Non-Proteolytic Inhibitory Mechanisms of Polymorphic Early-Stage Amyloid β Oligomers by Insulin Degrading Enzyme. Biomolecules 2022; 12:biom12121886. [PMID: 36551314 PMCID: PMC9776231 DOI: 10.3390/biom12121886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Insulin degrading enzyme (IDE) has been detected in the cerebrospinal fluid media and plays a role in encapsulating and degrading the amyloid β (Aβ) monomer, thus regulating the levels of Aβ monomers. The current work illustrates a first study by which IDE encapsulates polymorphic early-stage Aβ oligomers. The main goal of this study was to investigate the molecular mechanisms of IDE activity on the encapsulated early-stage Aβ dimers: fibril-like and random coil/α-helix dimers. Our work led to several findings. First, when the fibril-like Aβ dimer interacts with IDE-C domain, IDE does not impede the contact between the monomers, but plays a role as a 'dead-end' chaperone protein. Second, when the fibril-like Aβ dimer interacts with the IDE-N domain, IDE successfully impedes the contacts between monomers. Third, the inhibitory activity of IDE on random coil/α-helix dimers depends on the stability of the dimer. IDE could impede the contacts between monomers in relatively unstable random coil/α-helix dimers, but gets hard to impede in stable dimers. However, IDE encapsulates stable dimers and could serve as a 'dead-end' chaperone. Our results examine the molecular interactions between IDE and the dimers, and between the monomers within the dimers. Hence, this study provides insights into the inhibition mechanisms of the primary nucleation of Aβ aggregation and the basic knowledge for rational design to inhibit Aβ aggregation.
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6
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Liu X, Lao Z, Li X, Dong X, Wei G. ALS-associated A315E and A315pT variants exhibit distinct mechanisms in inducing irreversible aggregation of TDP-43 312-317 peptides. Phys Chem Chem Phys 2022; 24:16263-16273. [PMID: 35758309 DOI: 10.1039/d2cp01625g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is intensively associated with insoluble aggregates formed by transactivation response element DNA-binding protein 43 (TDP-43) in the cytoplasm of neuron cells. A recent experimental study reported that two ALS-linked familial variants, A315E and A315pT (pT, phosphorylated threonine), can induce irreversible aggregation of the TDP-43 312NFGAFS317 segment (TDP-43312-317). However, the underlying molecular mechanism remains largely elusive. Here, we investigated the early aggregation process of the wild type (WT) 312NFGAFS317 segment and its A315E and A315pT variants by performing multiple microsecond all-atom molecular dynamics simulations. Our simulations show that the two variants display lower fluidity than WT, consistent with their decreased labilities observed in previous denaturation assay experiments. Despite each of the two variants carrying one negative charge, unexpectedly, we find that both A315E mutation and A315pT phosphorylation enhance intermolecular interactions and result in the formation of more compact oligomers. Compared to WT, A315E oligomers possess low β-sheet content but a compact hydrophobic core, while A315pT oligomers have high β-sheet content and large β-sheets. Side chain hydrogen-bonding and hydrophobic interactions as well as N312-E315 salt bridges contribute most to the increased aggregation propensity of the A315E mutant. By contrast, main chain and side chain hydrogen-bonding interactions, side chain hydrophobic and aromatic interactions, are crucial to the enhanced aggregation capability of the A315pT variant. These results indicate that glutamate mutation and phosphorylation at position 315 induce the irreversible aggregation of TDP-43312-317 peptides through differential mechanisms, which remind us that we should be careful in the investigation of the phosphorylation effect on protein aggregation by using phosphomimetic substitutions. This study provides mechanistic insights into the A315E/A315pT-induced irreversible aggregation of TDP-43312-317, which may be helpful for the in-depth understanding of ALS-mutation/phosphorylation-associated liquid-to-solid phase transition of TDP-43 protein aggregates.
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Affiliation(s)
- Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
| | - Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, P. R. China.
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7
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Patel VN, Chorawala MR, Shah MB, Shah KC, Dave BP, Shah MP, Patel TM. Emerging Pathophysiological Mechanisms Linking Diabetes Mellitus and Alzheimer’s Disease: An Old Wine in a New Bottle. J Alzheimers Dis Rep 2022; 6:349-357. [PMID: 35891636 PMCID: PMC9277673 DOI: 10.3233/adr-220021] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/30/2022] [Indexed: 01/15/2023] Open
Abstract
Type-2 diabetes mellitus (T2DM) is a chronic immuno-inflammatory and metabolic disease characterized by hyperglycemia and insulin resistance with corresponding hyperinsulinemia. On the other hand, Alzheimer’s disease (AD) is a neurodegenerative disease involving cognitive impairment, neuronal dysfunction, and memory loss. Several recently published literatures suggest a causal relationship between T2DM and AD. In this review, we have discussed several potential mechanisms underlying diabetes-induced cognitive impairment which include, abnormal insulin signaling, amyloid-β accumulation, oxidative stress, immuno-inflammation, mitochondrial dysfunction, advanced glycation end products, acetylcholinesterase and butyrylcholinesterase, advanced lipid peroxidation products, and apolipoprotein E. All these interconnected mechanisms may act either individually or synergistically which eventually leads to neurodegeneration and AD.
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Affiliation(s)
- Vishvas N. Patel
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Mehul R. Chorawala
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Maitri B. Shah
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Kashvi C. Shah
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Bhavarth P. Dave
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Manal P. Shah
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Tanvi M. Patel
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, Gujarat, India
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8
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Simulations of Cross-Amyloid Aggregation of Amyloid-β and Islet Amyloid Polypeptide Fragments. Biophys J 2022; 121:2002-2013. [PMID: 35538665 DOI: 10.1016/j.bpj.2022.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
Amyloid-beta (Aβ) and islet amyloid polypeptide (IAPP) are small peptides, classified as amyloids, that have the potential to self-assemble and form cytotoxic species, such as small soluble oligomers and large insoluble fibrils. The formation of Aβ aggregates facilitates the progression of Alzheimer's disease (AD), while IAPP aggregates induce pancreatic β-cell apoptosis, leading to exacerbation of Type 2 diabetes (T2D). Cross-amyloid interactions between Aβ and IAPP have been described both in vivo and in vitro, implying the role of Aβ or IAPP as modulators of cytotoxic self-aggregation of each species, and suggesting that Aβ-IAPP interactions are a potential molecular link between AD and T2D. Using molecular dynamics simulations, "hot spot" regions of the two peptides were studied to understand the formation of hexamers in a heterogenous and homogenous peptide-containing environment. Systems of only Aβ(16-22) peptides formed antiparallel, β-barrel-like structures, while systems of only IAPP(20-29) peptides formed stacked, parallel beta sheets and had relatively unstable aggregation structures after 2 μs of simulation time. Systems containing both Aβ and IAPP (1:1 ratio) hexamers showed antiparallel, β-barrel-like structures, with an interdigitated arrangement of Aβ(16-22) and IAPP(20-29). These β-barrel structures have features of cytotoxic amyloid species identified in previous literature. Ultimately, this work seeks to provide atomistic insight into both the mechanism behind cross-amyloid interactions and structural morphologies of these toxic amyloid species.
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9
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Dharmaraj GL, Arigo FD, Young KA, Martins R, Mancera RL, Bharadwaj P. Novel Amylin Analogues Reduce Amyloid-β Cross-Seeding Aggregation and Neurotoxicity. J Alzheimers Dis 2022; 87:373-390. [PMID: 35275530 DOI: 10.3233/jad-215339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Type 2 diabetes related human islet amyloid polypeptide (hIAPP) plays a dual role in Alzheimer's disease (AD). hIAPP has neuroprotective effects in AD mouse models whereas, high hIAPP concentrations can promote co-aggregation with amyloid-β (Aβ) to promote neurodegeneration. In fact, both low and high plasma hIAPP concentration has been associated with AD. Therefore, non-aggregating hIAPP analogues have garnered interest as a treatment for AD. The aromatic amino acids F23 and I26 in hIAPP have been identified as the key residues involved in self-aggregation and Aβ cross-seeding. OBJECTIVE Three novel IAPP analogues with single and double alanine mutations (A1 = F23, A2 = I26, and A3 = F23 + I26) were assessed for their ability to aggregate, modulate Aβ oligomer formation, and alter neurotoxicity. METHODS A range of biophysical methods including Thioflavin-T, gel electrophoresis, photo-crosslinking, circular dichroism combined with cell viability assays were utilized to assess protein aggregation and toxicity. RESULTS All IAPP analogues showed significantly less self-aggregation than hIAPP. Co-aggregated Aβ 42-A2 and A3 also showed reduced aggregation compared to Aβ 42-hIAPP mixtures. Self- and co-oligomerized A1, A2, and A3 exhibited random coil conformations with reduced beta sheet content compared to hIAPP and Aβ 42-hIAPP aggregates. A1 was toxic at high concentrations compared to A2 and A3. However, co-aggregated Aβ 42-A1, A2, or A3 showed reduced neurotoxicity compared to Aβ 42, hIAPP, and Aβ 42-hIAPP aggregates. CONCLUSION These findings confirm that hIAPP analogues with non-aromatic residues at positions 23 and 26 have reduced self-aggregation and the ability to neutralize Aβ 42 toxicity. This warrants further characterization of their protective effects in pre-clinical AD models.
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Affiliation(s)
| | - Fraulein Denise Arigo
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
| | - Kimberly A Young
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
| | - Ralph Martins
- Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Perth WA, Australia.,School of Biomedical Science, Macquarie University, Sydney, NSW, Australia
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
| | - Prashant Bharadwaj
- Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Perth WA, Australia.,Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
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10
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Orr AA, Kuhlmann SK, Tamamis P. Computational design of a β-wrapin's N-terminal domain with canonical and non-canonical amino acid modifications mimicking curcumin's proposed inhibitory function. Biophys Chem 2022; 286:106805. [DOI: 10.1016/j.bpc.2022.106805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/14/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
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11
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Salimi A, Chatterjee S, Lee JY. Mechanistic Insights into the Polymorphic Associations and Cross-Seeding of Aβ and hIAPP in the Presence of Histidine Tautomerism: An All-Atom Molecular Dynamic Study. Int J Mol Sci 2022; 23:1930. [PMID: 35216047 PMCID: PMC8878669 DOI: 10.3390/ijms23041930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
Hundreds of millions of people around the world have been affected by Type 2 diabetes (T2D) which is a metabolic disorder. Clinical research has revealed T2D as a possible risk factor for Alzheimer's disease (AD) development (and vice versa). Amyloid-β (Aβ) and human islet amyloid polypeptide are the main pathological species in AD and T2D, respectively. However, the mechanisms by which these two amyloidogenic peptides co-aggregate are largely uninvestigated. Herein, for the first time, we present the cross-seeding between Amylin1-37 and Aβ40 considering the particular effect of the histidine tautomerism at atomic resolution applying the all-atom molecular dynamics (MD) simulations for heterodimeric complexes. The results via random seed MD simulations indicated that the Aβ40(δδδ) isomer in cross-talking with Islet(ε) and Islet(δ) isomers could retain or increase the β-sheet content in its structure that may make it more prone to further aggregation and exhibit higher toxicity. The other tautomeric isomers which initially did not have a β-sheet structure in their monomeric forms did not show any generated β-sheet, except for one seed of the Islet(ε) and Aβ40(εεε) heterodimers complex that displayed a small amount of formed β-sheet. This computational research may provide a different point of view to examine all possible parameters that may contribute to the development of AD and T2D and provide a better understanding of the pathological link between these two severe diseases.
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Affiliation(s)
| | | | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Korea; (A.S.); (S.C.)
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12
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Tang Y, Zhang D, Gong X, Zheng J. A mechanistic survey of Alzheimer's disease. Biophys Chem 2021; 281:106735. [PMID: 34894476 DOI: 10.1016/j.bpc.2021.106735] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most common, age-dependent neurodegenerative disorder. While AD has been intensively studied from different aspects, there is no effective cure for AD, largely due to a lack of a clear mechanistic understanding of AD. In this mini-review, we mainly focus on the discussion and summary of mechanistic causes of Alzheimer's disease (AD). While different AD mechanisms illustrate different molecular and cellular pathways in AD pathogenesis, they do not necessarily exclude each other. Instead, some of them could work together to initiate, trigger, and promote the onset and development of AD. In a broader viewpoint, some AD mechanisms (e.g., amyloid aggregation mechanism, microbial infection/neuroinflammation mechanism, and amyloid cross-seeding mechanism) could also be applicable to other amyloid diseases including type II diabetes, Parkinson's disease, and prion disease. Such common mechanisms for AD and other amyloid diseases explain not only the pathogenesis of individual amyloid diseases, but also the spreading of pathologies between these diseases, which will inspire new strategies for therapeutic intervention and prevention for AD.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, OH, United States of America
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America.
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13
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Miller Y. Advancements and future directions in research of the roles of insulin in amyloid diseases. Biophys Chem 2021; 281:106720. [PMID: 34823073 DOI: 10.1016/j.bpc.2021.106720] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/02/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022]
Abstract
Amyloid diseases, such as type 2 diabetes, Alzheimer's disease and Parkinson's disease are characterized by amyloid aggregates. Insulin is released from the pancreas, and it is known that insulin downstream signaling molecules are located majorly in the regions of cortex and hippocampus. Therefore, insulin plays crucial roles not only in the pancreas, but also in the brain. Recent studies have focused on the role of insulin in amyloid diseases. This review demonstrates the recent studies in which insulin affects amyloid aggregation. Specifically, molecular modeling studies provide insights into the molecular mechanisms of the effects of insulin in amyloid aggregates. Still, experimental studies are required to provide insights into the kinetics effects. This review opens new avenues for future studies on insulin molecules and amyloid aggregation.
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Affiliation(s)
- Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be'er Sheva 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel.
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14
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Abramov-Harpaz K, Pollock-Gagolashvili M, Miller Y. Insights into the Mechanistic Perspective Effect of Insulin on the Nonamyloidogenic Component (NAC) and α-Synuclein Aggregation. ACS Chem Neurosci 2021; 12:3266-3276. [PMID: 34406742 DOI: 10.1021/acschemneuro.1c00445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Insulin plays important functions in the brain, such as neuroprotective effects on neurons, and it is also involved in cognitive functions (e.g., attention, learning and memory). It is proposed that a lack of insulin in the brain may initiate development of neurodegenerative diseases. Herein, we examined the effect of insulin on aggregates of α-synuclein (AS), a protein that is related to Parkinson's disease (PD), and its segment nonamyloidogenic component (NAC), which is known to play a crucial role in AS aggregation. The molecular modeling tools assist us to provide insights into the molecular mechanism of the effect of insulin on fibrillation of NAC and AS. Our research leads to three conclusions. First, the preferred interactions between insulin chain B and the "zipper domain" sequence within both NAC and AS appear at the central domain across the fibril axis or at the edge of the fibril. Second, these interactions do not disrupt the cross-β structure of NAC fibril-like oligomers but disrupt the cross-β structure of AS fibril-like oligomers. Thus, insulin does not inhibit the fibrillation of NAC but may inhibit AS fibrillation. Third, some of the polymorphic NAC and AS fibril-like oligomers bind to chain A in insulin. This is the first study that demonstrates that insulin chain A can also participate in the interactions with amyloid fibril-like oligomers. Our study proposes that insulin plays a crucial role in impeding AS aggregation in the brain and consequently could inhibit the development of PD.
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Affiliation(s)
- Karina Abramov-Harpaz
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva84105, Israel
| | - Maya Pollock-Gagolashvili
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva84105, Israel
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15
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Li X, Lao Z, Zou Y, Dong X, Li L, Wei G. Mechanistic Insights into the Co-Aggregation of Aβ and hIAPP: An All-Atom Molecular Dynamic Study. J Phys Chem B 2021; 125:2050-2060. [PMID: 33616398 DOI: 10.1021/acs.jpcb.0c11132] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Patients with Alzheimer's disease (AD) have a high risk of developing Type II diabetes (T2D). The co-aggregation of the two disease-related proteins, Aβ and hIAPP, has been proposed as a potential molecular mechanism. However, the detailed Aβ-hIAPP interactions and structural characteristics of co-aggregates are mostly unknown at atomic level. Here, we explore the conformational ensembles of the Aβ-hIAPP heterodimer and Aβ or hIAPP homodimer by performing all-atom explicit-solvent replica exchange molecular dynamic simulations. Our simulations show that the interaction propensity of Aβ-hIAPP in the heterodimer is comparable with that of Aβ-Aβ/hIAPP-hIAPP in the homodimer. Similar hot spot residues of Aβ/hIAPP in the homodimer and heterodimer are identified, indicating that both Aβ and hIAPP have similar molecular recognition sites for self-aggregation and co-aggregation. Aβ in the heterodimer possesses three high β-sheet probability regions: the N-terminal region E3-H6, the central hydrophobic core region K16-E22, and the C-terminal hydrophobic region I31-A41, which is highly similar to Aβ in the homodimer. More importantly, in the heterodimer, the regions E3-H6, F19-E22, and I31-M35 of Aβ and the amyloid core region N20-T30 of hIAPP display higher β-sheet probability than they do in homodimer, implying their crucial roles in the formation of β-sheet-rich co-aggregates. Our study sheds light on the co-aggregation of Aβ and hIAPP at an atomic level, which will be helpful for an in-depth understanding of the molecular mechanism for epidemiological correlation of AD and T2D.
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Affiliation(s)
- Xuhua Li
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China.,MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zenghui Lao
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310007 Zhejiang, China
| | - Xuewei Dong
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Le Li
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
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16
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Zhang Y, Zhang M, Liu Y, Zhang D, Tang Y, Ren B, Zheng J. Dual amyloid cross-seeding reveals steric zipper-facilitated fibrillization and pathological links between protein misfolding diseases. J Mater Chem B 2021; 9:3300-3316. [PMID: 33651875 DOI: 10.1039/d0tb02958k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amyloid cross-seeding, as a result of direct interaction and co-aggregation between different disease-causative peptides, is considered as a main mechanism for the spread of the overlapping pathology across different cells and tissues between different protein-misfolding diseases (PMDs). Despite the biomedical significance of amyloid cross-seeding in amyloidogenesis, it remains a great challenge to discover amyloid cross-seeding systems and reveal their cross-seeding structures and mechanisms. Herein, we are the first to report that GNNQQNY - a short fragment from yeast prion protein Sup35 - can cross-seed with both amyloid-β (Aβ, associated with Alzheimer's disease) and human islet amyloid polypeptide (hIAPP, associated with type II diabetes) to form β-structure-rich assemblies and to accelerate amyloid fibrillization. Dry, steric β-zippers, formed by the two β-sheets of different amyloid peptides, provide generally interactive and structural motifs to facilitate amyloid cross-seeding. The presence of different steric β-zippers in a variety of GNNQQNY-Aβ and GNNQQNY-hIAPP assemblies also explains amyloid polymorphism. In addition, alteration of steric zipper formation by single-point mutations of GNNQQNY and interactions of GNNQQNY with different Aβ and hIAPP seeds leads to different amyloid cross-seeding efficiencies, further confirming the existence of cross-seeding barriers. This work offers a better structural-based understanding of amyloid cross-seeding mechanisms linked to different PMDs.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering The University of Akron, Ohio, USA.
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17
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 386] [Impact Index Per Article: 128.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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18
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Ivanova MI, Lin Y, Lee YH, Zheng J, Ramamoorthy A. Biophysical processes underlying cross-seeding in amyloid aggregation and implications in amyloid pathology. Biophys Chem 2021; 269:106507. [PMID: 33254009 PMCID: PMC10317075 DOI: 10.1016/j.bpc.2020.106507] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/18/2022]
Abstract
Abnormal aggregation of proteins into filamentous aggregates commonly associates with many diseases, such as Alzheimer's disease, Parkinson's disease and type-2 diabetes. These filamentous aggregates, also known as amyloids, can propagate their abnormal structures to either the same precursor molecules (seeding) or other protein monomers (cross-seeding). Cross-seeding has been implicated in the abnormal protein aggregation and has been found to facilitate the formation of physiological amyloids. It has risen to be an exciting area of research with a high volume of published reports. In this review article, we focus on the biophysical processes underlying the cross-seeding for some of the most commonly studied amyloid proteins. Here we will discuss the relevant literature related to cross-seeded polymerization of amyloid-beta, human islet amyloid polypeptide (hIAPP, or also known as amylin) and alpha-synuclein. SEVI (semen-derived enhancer of viral infection) amyloid formation by the cross-seeding between the bacterial curli protein and PAP248-286 is also briefly discussed.
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Affiliation(s)
- Magdalena I Ivanova
- Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea; Research headquarters, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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19
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Zhang Y, Tang Y, Zhang D, Liu Y, He J, Chang Y, Zheng J. Amyloid cross-seeding between Aβ and hIAPP in relation to the pathogenesis of Alzheimer and type 2 diabetes. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.09.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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20
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Konstantoulea K, Louros N, Rousseau F, Schymkowitz J. Heterotypic interactions in amyloid function and disease. FEBS J 2021; 289:2025-2046. [PMID: 33460517 DOI: 10.1111/febs.15719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 11/27/2022]
Abstract
Amyloid aggregation results from the self-assembly of identical aggregation-prone sequences into cross-beta-sheet structures. The process is best known for its association with a wide range of human pathologies but also as a functional mechanism in all kingdoms of life. Less well elucidated is the role of heterotypic interactions between amyloids and other proteins and macromolecules and how this contributes to disease. We here review current data with a focus on neurodegenerative amyloid-associated diseases. Evidence indicates that heterotypic interactions occur in a wide range of amyloid processes and that these interactions modify fundamental aspects of amyloid aggregation including seeding, aggregation rates and toxicity. More work is required to understand the mechanistic origin of these interactions, but current understanding suggests that both supersaturation and sequence-specific binding can contribute to heterotypic amyloid interactions. Further unravelling these mechanisms may help to answer outstanding questions in the field including the selective vulnerability of cells types and tissues and the stereotypical spreading patterns of amyloids in disease.
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Affiliation(s)
- Katerina Konstantoulea
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolaos Louros
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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21
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Milardi D, Gazit E, Radford SE, Xu Y, Gallardo RU, Caflisch A, Westermark GT, Westermark P, Rosa CL, Ramamoorthy A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 2021; 121:1845-1893. [PMID: 33427465 DOI: 10.1021/acs.chemrev.0c00981] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.
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Affiliation(s)
- Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Gunilla T Westermark
- Department of Medical Cell Biology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 41809-1055, United States
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22
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Nisar O, Pervez H, Mandalia B, Waqas M, Sra HK. Type 3 Diabetes Mellitus: A Link Between Alzheimer's Disease and Type 2 Diabetes Mellitus. Cureus 2020; 12:e11703. [PMID: 33391936 PMCID: PMC7769816 DOI: 10.7759/cureus.11703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chronic diseases, as their name suggests, are progressive and can have overlapping features. Similar to this, Alzheimer's disease (AD) and diabetes mellitus (DM) fall into the category of chronic degenerative diseases. The global burden of these two ailments is manifold; hence, it seems important to view the pathophysiologic mechanisms of DM in the worsening of AD. Genetic as well as environmental factors are seen to play a role in the disease pathogenesis. Several genes, metabolic pathways, electrolytes, and dietary habits are seen to hasten brain atrophy. Lying behind this is the accumulation of amyloid precursor and tau - the misfolded proteins - within the brain substance. This mechanism is usually innate to AD itself, but the impact of insulin resistance, disturbing the homeostatic milieu, is seen as a powerful contributing factor aggravating the neuronal loss impairing an individual's memory. Since this neuronal loss is permanent, it may lead to complications as seen with AD. To reach a consensus, we conducted an electronic literature review search using different databases. This aided us in understanding the common aspects between AD and DM on genetic, molecular, cellular levels, as well as the impact of minerals and diet on the disease manifestation. We also found that despite exceptional work, additional efforts are needed to explore the relationship between the two entities. This will help physicians, researchers, and pharmaceuticals to frame remedies targeting the cause and avoid the progression of AD.
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Affiliation(s)
- Omar Nisar
- Internal Medicine, Shalamar Medical and Dental College, Lahore, PAK
| | - Hira Pervez
- Internal Medicine/Cardiology, Dow University of Health Sciences, Karachi, PAK
| | | | - Muhammad Waqas
- Internal Medicine, Liaquat University of Medical and Health Sciences, Hyderabad, PAK
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23
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Abstract
In systemic amyloidosis, serum amyloid A (SAA) fibril deposits cause widespread damages to tissues and organs that eventually may lead to death. A therapeutically intervention therefore has either to dissolve these fibrils or inhibit their formation. However, only recently has the human SAA fibril structure been resolved at a resolution that is sufficient for development of drug candidates. Here, we use molecular dynamic simulations to probe the factors that modulate the stability of this fibril model. Our simulations suggest that fibril formation starts with the stacking of two misfolded monomers into metastable dimers, with the stacking depending on the N-terminal amyloidogenic regions of different chains forming anchors. The resulting dimers pack in a second step into a 2-fold two-layer tetramer that is stable enough to nucleate fibril formation. The stability of the initial dimers is enhanced under acidic conditions by a strong salt bridge and side-chain hydrogen bond network in the C-terminal cavity (residues 23-51) but is not affected by the presence of the disordered C-terminal tail.
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Affiliation(s)
- Wenhua Wang
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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24
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Tang Y, Zhang D, Zhang Y, Liu Y, Gong X, Chang Y, Ren B, Zheng J. Introduction and Fundamentals of Human Islet Amyloid Polypeptide Inhibitors. ACS APPLIED BIO MATERIALS 2020; 3:8286-8308. [DOI: 10.1021/acsabm.0c01234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325-3906, United States
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325-3906, United States
| | - Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325-3906, United States
| | - Yonglan Liu
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325-3906, United States
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, Akron, Ohio 44325-0301, United States
| | - Yung Chang
- Department of Chemical Engineering, R&D Center for Membrane Technology, Chung Yuan Christian University, Taoyuan 320, Taiwan
| | - Baiping Ren
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325-3906, United States
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325-3906, United States
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25
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Are Heat Shock Proteins an Important Link between Type 2 Diabetes and Alzheimer Disease? Int J Mol Sci 2020; 21:ijms21218204. [PMID: 33147803 PMCID: PMC7662599 DOI: 10.3390/ijms21218204] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Type 2 diabetes (T2D) and Alzheimer’s disease (AD) are growing in prevalence worldwide. The development of T2D increases the risk of AD disease, while AD patients can show glucose imbalance due to an increased insulin resistance. T2D and AD share similar pathological features and underlying mechanisms, including the deposition of amyloidogenic peptides in pancreatic islets (i.e., islet amyloid polypeptide; IAPP) and brain (β-Amyloid; Aβ). Both IAPP and Aβ can undergo misfolding and aggregation and accumulate in the extracellular space of their respective tissues of origin. As a main response to protein misfolding, there is evidence of the role of heat shock proteins (HSPs) in moderating T2D and AD. HSPs play a pivotal role in cell homeostasis by providing cytoprotection during acute and chronic metabolic stresses. In T2D and AD, intracellular HSP (iHSP) levels are reduced, potentially due to the ability of the cell to export HSPs to the extracellular space (eHSP). The increase in eHSPs can contribute to oxidative damage and is associated with various pro-inflammatory pathways in T2D and AD. Here, we review the role of HSP in moderating T2D and AD, as well as propose that these chaperone proteins are an important link in the relationship between T2D and AD.
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26
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de Matos AM, Blázquez-Sánchez MT, Bento-Oliveira A, de Almeida RFM, Nunes R, Lopes PEM, Machuqueiro M, Cristóvão JS, Gomes CM, Souza CS, El Idrissi IG, Colabufo NA, Diniz A, Marcelo F, Oliveira MC, López Ó, Fernandez-Bolaños JG, Dätwyler P, Ernst B, Ning K, Garwood C, Chen B, Rauter AP. Glucosylpolyphenols as Inhibitors of Aβ-Induced Fyn Kinase Activation and Tau Phosphorylation: Synthesis, Membrane Permeability, and Exploratory Target Assessment within the Scope of Type 2 Diabetes and Alzheimer's Disease. J Med Chem 2020; 63:11663-11690. [PMID: 32959649 DOI: 10.1021/acs.jmedchem.0c00841] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite the rapidly increasing number of patients suffering from type 2 diabetes, Alzheimer's disease, and diabetes-induced dementia, there are no disease-modifying therapies that are able to prevent or block disease progress. In this work, we investigate the potential of nature-inspired glucosylpolyphenols against relevant targets, including islet amyloid polypeptide, glucosidases, and cholinesterases. Moreover, with the premise of Fyn kinase as a paradigm-shifting target in Alzheimer's drug discovery, we explore glucosylpolyphenols as blockers of Aβ-induced Fyn kinase activation while looking into downstream effects leading to Tau hyperphosphorylation. Several compounds inhibit Aβ-induced Fyn kinase activation and decrease pTau levels at 10 μM concentration, particularly the per-O-methylated glucosylacetophloroglucinol and the 4-glucosylcatechol dibenzoate, the latter inhibiting also butyrylcholinesterase and β-glucosidase. Both compounds are nontoxic with ideal pharmacokinetic properties for further development. This work ultimately highlights the multitarget nature, fine structural tuning capacity, and valuable therapeutic significance of glucosylpolyphenols in the context of these metabolic and neurodegenerative disorders.
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Affiliation(s)
- Ana M de Matos
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - M Teresa Blázquez-Sánchez
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Andreia Bento-Oliveira
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Rodrigo F M de Almeida
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Rafael Nunes
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.,Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Pedro E M Lopes
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Miguel Machuqueiro
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Joana S Cristóvão
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Cláudio M Gomes
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Cleide S Souza
- Department of Chemistry, The University of Sheffield, Dainton Building, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - Imane G El Idrissi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "A. Moro", Via Orabona, 4, 70125 Bari, Italy
| | - Nicola A Colabufo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "A. Moro", Via Orabona, 4, 70125 Bari, Italy
| | - Ana Diniz
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - M Conceição Oliveira
- Mass Spectrometry Facility at CQE, Insituto Superior Técnico, Av. Rovisco Pais, Lisboa 1049-001, Portugal
| | - Óscar López
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 1203, Sevilla E-41071, Spain
| | - José G Fernandez-Bolaños
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 1203, Sevilla E-41071, Spain
| | - Philipp Dätwyler
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel CH-4056, Switzerland
| | - Beat Ernst
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel CH-4056, Switzerland
| | - Ke Ning
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - Claire Garwood
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - Beining Chen
- Department of Chemistry, The University of Sheffield, Dainton Building, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - Amélia P Rauter
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
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27
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Pandey P, Nguyen N, Hansmann UHE. d-Retro Inverso Amylin and the Stability of Amylin Fibrils. J Chem Theory Comput 2020; 16:5358-5368. [PMID: 32667784 DOI: 10.1021/acs.jctc.0c00523] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Motivated by the role that amylin aggregates play in type-II diabetes, we compare the stability of regular amylin fibrils with the stability of fibrils where l-amino acid chains are replaced by d-retro inverso (DRI) amylin, that is, peptides where the sequence of amino acids is reversed, and at the same time, the l-amino acids are replaced by their mirror images. Our molecular dynamics simulations show that despite leading to only a marginal difference in the fibril structure and stability, aggregating DRI-amylin peptides have different patterns of contacts and hydrogen bonding. Because of these differences, DRI-amylin, when interacting with regular (l) amylin, alters the elongation process and lowers the stability of hybrid amylin fibrils. Our results not only suggest the potential use of DRI-amylin as an inhibitor of amylin fibril formation but also point to the possibility of using the insertion of DRI proteins in l-assemblies as a way to probe the role of certain kinds of hydrogen bonds in supramolecular assemblies or aggregates.
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Affiliation(s)
- Preeti Pandey
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Natalie Nguyen
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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28
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Bharadwaj P, Solomon T, Sahoo BR, Ignasiak K, Gaskin S, Rowles J, Verdile G, Howard MJ, Bond CS, Ramamoorthy A, Martins RN, Newsholme P. Amylin and beta amyloid proteins interact to form amorphous heterocomplexes with enhanced toxicity in neuronal cells. Sci Rep 2020; 10:10356. [PMID: 32587390 PMCID: PMC7316712 DOI: 10.1038/s41598-020-66602-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/10/2020] [Indexed: 01/09/2023] Open
Abstract
Human pancreatic islet amyloid polypeptide (hIAPP) and beta amyloid (Aβ) can accumulate in Type 2 diabetes (T2D) and Alzheimer's disease (AD) brains and evidence suggests that interaction between the two amyloidogenic proteins can lead to the formation of heterocomplex aggregates. However, the structure and consequences of the formation of these complexes remains to be determined. The main objective of this study was to characterise the different types and morphology of Aβ-hIAPP heterocomplexes and determine if formation of such complexes exacerbate neurotoxicity. We demonstrate that hIAPP promotes Aβ oligomerization and formation of small oligomer and large aggregate heterocomplexes. Co-oligomerized Aβ42-hIAPP mixtures displayed distinct amorphous structures and a 3-fold increase in neuronal cell death as compared to Aβ and hIAPP alone. However, in contrast to hIAPP, non-amyloidogenic rat amylin (rIAPP) reduced oligomer Aβ-mediated neuronal cell death. rIAPP exhibited reductions in Aβ induced neuronal cell death that was independent of its ability to interact with Aβ and form heterocomplexes; suggesting mediation by other pathways. Our findings reveal distinct effects of IAPP peptides in modulating Aβ aggregation and toxicity and provide new insight into the potential pathogenic effects of Aβ-IAPP hetero-oligomerization and development of IAPP based therapies for AD and T2D.
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Affiliation(s)
- Prashant Bharadwaj
- School of Pharmacy and Biomedical Sciences, Curtin Health and Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, WA, 6107, Australia.
- Centre of Excellence for Alzheimer's disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia.
| | - Tanya Solomon
- School of Pharmacy and Biomedical Sciences, Curtin Health and Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, WA, 6107, Australia
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Katarzyna Ignasiak
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Scott Gaskin
- School of Pharmacy and Biomedical Sciences, Curtin Health and Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, WA, 6107, Australia
| | - Joanne Rowles
- School of Pharmacy and Biomedical Sciences, Curtin Health and Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, WA, 6107, Australia
| | - Giuseppe Verdile
- School of Pharmacy and Biomedical Sciences, Curtin Health and Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, WA, 6107, Australia
- Centre of Excellence for Alzheimer's disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Mark J Howard
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Crawley, WA, 6009, Australia
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Ralph N Martins
- Centre of Excellence for Alzheimer's disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
- School of Biomedical Science, Macquarie University, Sydney, NSW, Australia
| | - Philip Newsholme
- School of Pharmacy and Biomedical Sciences, Curtin Health and Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, WA, 6107, Australia
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29
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Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020; 8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
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Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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30
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Jash K, Gondaliya P, Kirave P, Kulkarni B, Sunkaria A, Kalia K. Cognitive dysfunction: A growing link between diabetes and Alzheimer's disease. Drug Dev Res 2020; 81:144-164. [DOI: 10.1002/ddr.21579] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/12/2019] [Accepted: 06/30/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Kavya Jash
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Ahmedabad Gandhinagar Gujarat India
| | - Piyush Gondaliya
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Ahmedabad Gandhinagar Gujarat India
| | - Prathibha Kirave
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Ahmedabad Gandhinagar Gujarat India
| | - Bhagyashri Kulkarni
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Ahmedabad Gandhinagar Gujarat India
| | - Aditya Sunkaria
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Ahmedabad Gandhinagar Gujarat India
| | - Kiran Kalia
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Ahmedabad Gandhinagar Gujarat India
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31
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Sun Y, Ding F. Thermo- and pH-responsive fibrillization of squid suckerin A1H1 peptide. NANOSCALE 2020; 12:6307-6317. [PMID: 32108838 PMCID: PMC7083694 DOI: 10.1039/c9nr09271d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Stimuli-responsive smart materials have attracted considerable attention with numerous applications in nanotechnology, sensing, and biomedicine. Suckerin family proteins found in squid ring teeth represent such a class of peptide-based smart materials with their self-assemblies featuring excellent thermo-plasticity and pH-dependence. Similar to block copolymers, suckerin proteins are comprised of two repeating sequence motifs, where M1 motifs are abundant in alanine and histidine residues and M2 are rich in glycine. Experimental studies of suckerin assemblies suggested that M1 regions mainly formed nano-confined β-sheets within an amorphous matrix made of M2 modules stabilizing these β-rich nano-assemblies. The histidine-containing M1 modules are believed to govern the pH- and temperature-sensitive properties of suckerin assemblies. To better understand the stimuli-responsive properties of suckerin assemblies at the molecular level, we systematically studied the self-assembly dynamics of A1H1 peptides - a representative M1 sequence - at different temperatures and pH conditions with atomistic discrete molecular dynamic simulations. Our simulations with twenty A1H1 peptides demonstrated that below the transition temperature Tagg, they could readily self-assemble from isolated monomers into well-defined β-sheet nanostructures by both primary and secondary nucleation of β-sheets and subsequent aggregation growth via elongation and coagulation. Interestingly, the dissociation of pre-formed A1H1 β-sheet nanostructures featured a melting temperature Tm higher than Tagg, exhibiting the thermal hysteresis that is characteristic of first-order phase transitions with high energy barriers. In acidic environments where all histidine residues were protonated, the stability of the A1H1 β-sheet nano-assemblies was reduced and the β-rich assemblies easily dissociated into unstructured monomers at significantly lower temperatures than in the neutral solution. The computationally derived molecular mechanisms for pH- and temperature-dependent A1H1 self-assembly will help to understand the supramolecular assembly structures and functions of the large suckerin family and aid in the future design of peptide-based stimuli-responsive smart materials.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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32
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Baram M, Miller Y. Inhibitory Activity of Insulin on Aβ Aggregation Is Restricted Due to Binding Selectivity and Specificity to Polymorphic Aβ States. ACS Chem Neurosci 2020; 11:445-452. [PMID: 31899862 PMCID: PMC7467570 DOI: 10.1021/acschemneuro.9b00645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
![]()
Clinical
trials of intranasal insulin treatment for Alzheimer’s
patients have shown cognitive and memory improvement, but the effect
of insulin has shown a limitation. It was suggested that insulin molecule
binds to Aβ aggregates and impedes Aβ aggregation. Yet,
the specific interactions between insulin molecule and Aβ aggregates
at atomic resolution are still elusive. Three main conclusions are
observed in this work. First, insulin can interact across the fibril
only to “U-shape” Aβ fibrils and not to “S-shape”
Aβ fibrils. Therefore, insulin is not expected to influence
the “S-shape” Aβ fibrils. Second, insulin disrupts
β-strands along Aβ fibril-like oligomers via interaction
with chain A, which is not a part of the recognition motif. It is
suggested that insulin affects as an inhibitor of Aβ fibrillation,
but it is limited due to the specificity of the polymorphic Aβ
fibril-like oligomer. Third, the current work proposes that insulin
promotes Aβ aggregation, when interacting along the fibril axis
of Aβ fibril-like oligomer. The coaggregation could be initiated
via the recognition motif. The lack of the interactions of insulin
in the recognition motif impede the coaggregation of insulin and Aβ.
The current work reports the specific binding domains between insulin
molecule and polymorphic Aβ fibril-like oligomers. This research
provides insights into the molecular mechanisms of the functional
activity of insulin on Aβ aggregation that strongly depends
on the particular polymorphic Aβ aggregates.
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Affiliation(s)
- Michal Baram
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
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33
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Li L, Li X, Tang Y, Lao Z, Lei J, Wei G. Common cancer mutations R175H and R273H drive the p53 DNA-binding domain towards aggregation-prone conformations. Phys Chem Chem Phys 2020; 22:9225-9232. [DOI: 10.1039/c9cp06671c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cancer mutations R175H and R273H induce p53C towards aggregation-prone conformations by increasing their SASA, water exposure of H-bonds and flexibility of loop2.
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Affiliation(s)
- Le Li
- Department of Physics
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Multiscale Research Institute of Complex Systems
- Fudan University
- Shanghai 200438
| | - Xuhua Li
- Department of Physics
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Multiscale Research Institute of Complex Systems
- Fudan University
- Shanghai 200438
| | - Yiming Tang
- Department of Physics
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Multiscale Research Institute of Complex Systems
- Fudan University
- Shanghai 200438
| | - Zenghui Lao
- Department of Physics
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Multiscale Research Institute of Complex Systems
- Fudan University
- Shanghai 200438
| | - Jiangtao Lei
- Department of Physics
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Multiscale Research Institute of Complex Systems
- Fudan University
- Shanghai 200438
| | - Guanghong Wei
- Department of Physics
- State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Multiscale Research Institute of Complex Systems
- Fudan University
- Shanghai 200438
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34
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Jonnalagadda SVR, Gerace AJ, Thai K, Johnson J, Tsimenidis K, Jakubowski JM, Shen C, Henderson KJ, Tamamis P, Gkikas M. Amyloid Peptide Scaffolds Coordinate with Alzheimer’s Disease Drugs. J Phys Chem B 2019; 124:487-503. [DOI: 10.1021/acs.jpcb.9b10368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | - Andrew James Gerace
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Kathleen Thai
- Department of Biology, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Jonathan Johnson
- Department of Biology, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Kostas Tsimenidis
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Joseph M. Jakubowski
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Christina Shen
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Kendal J. Henderson
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Phanourios Tamamis
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Manos Gkikas
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
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35
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Kokotidou C, Jonnalagadda SVR, Orr AA, Vrentzos G, Kretsovali A, Tamamis P, Mitraki A. Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles. Biomolecules 2019; 10:E7. [PMID: 31861408 PMCID: PMC7023140 DOI: 10.3390/biom10010007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Cell-penetrating peptides are used extensively to deliver molecules into cells due to their unique characteristics such as rapid internalization, charge, and non-cytotoxicity. Amyloid fibril biomaterials were reported as gene transfer or retroviral infection enhancers; no cell internalization of the peptides themselves is reported so far. In this study, we focus on two rationally and computationally designed peptides comprised of β-sheet cores derived from naturally occurring protein sequences and designed positively charged and aromatic residues exposed at key residue positions. The β-sheet cores bestow the designed peptides with the ability to self-assemble into amyloid fibrils. The introduction of positively charged and aromatic residues additionally promotes DNA condensation and cell internalization by the self-assembled material formed by the designed peptides. Our results demonstrate that these designer peptide fibrils can efficiently enter mammalian cells while carrying packaged luciferase-encoding plasmid DNA, and they can act as a protein expression enhancer. Interestingly, the peptides additionally exhibited strong antimicrobial activity against the enterobacterium Escherichia coli.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - George Vrentzos
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Androniki Kretsovali
- Institute of Molecular Biology and Biotechnology (IMBB) FORTH, 70013 Heraklion, Crete, Greece; (G.V.); (A.K.)
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University College Station, TX 77843-3251, USA; (S.V.R.J.); (A.A.O.)
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Grete, Greece;
- Institute of Electronic Structure and Laser (IESL) FORTH, 70013 Heraklion, Crete, Greece
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Ren B, Zhang Y, Zhang M, Liu Y, Zhang D, Gong X, Feng Z, Tang J, Chang Y, Zheng J. Fundamentals of cross-seeding of amyloid proteins: an introduction. J Mater Chem B 2019; 7:7267-7282. [PMID: 31647489 DOI: 10.1039/c9tb01871a] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Misfolded protein aggregates formed by the same (homologous) or different (heterologous/cross) sequences are the pathological hallmarks of many protein misfolding diseases (PMDs) including Alzheimer's disease (AD) and type 2 diabetes (T2D). Different from homologous-amyloid aggregation that is solely associated with a specific PMD, cross-amyloid aggregation (i.e. cross-seeding) of different amyloid proteins is more fundamentally and biologically important for understanding and untangling not only the pathological process of each PMD, but also a potential molecular cross-talk between different PMDs. However, the cross-amyloid aggregation is still a subject poorly explored and little is known about its sequence/structure-dependent aggregation mechanisms, as compared to the widely studied homo-amyloid aggregation. Here, we review the most recent and important findings of amyloid cross-seeding behaviors from in vitro, in vivo, and in silico studies. Some typical cross-seeding phenomena between Aβ/hIAPP, Aβ/tau, Aβ/α-synuclein, and tau/α-synuclein are selected and presented, and the underlying specific or general cross-seeding mechanisms are also discussed to better reveal their sequence-structure-property relationships. The potential use of the cross-seeding concept to design amyloid inhibitors is also proposed. Finally, we offer some personal perspectives on current major challenges and future research directions in this less-studied yet important field, and hopefully this work will stimulate more research to explore all possible fundamental and practical aspects of amyloid cross-seeding.
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Affiliation(s)
- Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Yonglan Liu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Dong Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, Ohio, USA
| | - Zhangqi Feng
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Jianxin Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Yung Chang
- Department of Chemical Engineering, R&D Center for Membrane Technology, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
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Alves NA, Dias LG, Frigori RB. Synergistic long-range effects of mutations underlie aggregation propensities of amylin analogues. J Mol Model 2019; 25:263. [PMID: 31428870 DOI: 10.1007/s00894-019-4137-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/14/2019] [Indexed: 12/16/2022]
Abstract
The USFDA has approved pramlintide, commercially named Symlin (sIAPP), as adjunctive therapy for type 2 diabetes (T2D). This analogue of the human amylin peptide (hIAPP) has triple proline substitutions typical of the rat isoform (rIAPP). Recently, it was proposed that pramlintide solubility and aggregation resistance might be improved by incorporating further mutations, as S20R, screened from the wild-type porcine isoform (pIAPP), which leads to the variant named sIAPP+. To better elucidate how such properties might be systematically induced in rationally designed analogues, we performed comparative assessments of rIAPP, sIAPP, and sIAPP+ using replica-exchange molecular dynamics (REMD) with an accurate combination of force field Charmm22* and explicit aqueous solvation TIP4P/Ew. Our thermo-structural analyses show that sIAPP exhibits a thermal conversion channel of helices[Formula: see text]-sheets resembling hIAPP. This channel is depleted in rIAPP and is absent in sIAPP+. As a consequence, sIAPP+ presents an overall decrease of β-like secondary structures and an overstabilization of α-helices. Additionally, we observed in rIAPP and sIAPP+ an increase in the backbone RMSF of molecular terminals and the exposed area of key residues. These structural features of sIAPP+ suggest a nonamyloidogenic character, which is corroborated by our judicious estimate of the electrostatic component of the solvation free energy using a generalized Born model, and so it may constitute an alternative strategy to sIAPP as a peptide analogue of hIAPP. Furthermore, our findings confirm that different aggregation propensities of amylin and its analogues are synergistically modulated by long-range effects of key mutations. Graphical Abstract S20R-Pramlintide.
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Affiliation(s)
- Nelson A Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, 14040-901, SP, Brazil.
| | - Luis G Dias
- Departamento de Química, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, 14040-901, SP, Brazil
| | - Rafael B Frigori
- Universidade Tecnológica Federal do Paraná, Rua Cristo Rei 19, Toledo, 85902-490, PR, Brazil
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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Atsmon-Raz Y, Wineman-Fisher V, Baram M, Miller Y. Unique Inversion Events of Residues around the Backbone in the Turn Domain of β-Arches in Amylin Fibrils. ACS Chem Neurosci 2019; 10:1209-1213. [PMID: 30565922 DOI: 10.1021/acschemneuro.8b00554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Orientational inversion events of residues along the turn domains of amylin fibrils have been detected. This exceptional phenomenon has been observed in isolated amylin fibrils and in the cross-seeding amylin-Aβ and amylin-NAC fibrils. These new findings provide new avenues for detection of side chain flipping and side chain inversion events in turn domains and loops of various proteins.
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Affiliation(s)
- Yoav Atsmon-Raz
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Vered Wineman-Fisher
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Michal Baram
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
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40
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Amundarain MJ, Herrera MG, Zamarreño F, Viso JF, Costabel MD, Dodero VI. Molecular mechanisms of 33-mer gliadin peptide oligomerisation. Phys Chem Chem Phys 2019; 21:22539-22552. [DOI: 10.1039/c9cp02338k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The 33-mer gliadin peptide oligomerizes driven by its non-ionic polar character, flexible PPII secondary structure and stable glutamine H-bonds.
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Affiliation(s)
- María Julia Amundarain
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | | | - Fernando Zamarreño
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Juan Francisco Viso
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Marcelo D. Costabel
- Grupo de Biofísica
- Instituto de Física del Sur
- Universidad Nacional del Sur
- Bahía Blanca
- Argentina
| | - Verónica I. Dodero
- Universität Bielefeld
- Fakultät für Chemie
- Organische Chemie
- 33615 Bielefeld
- Germany
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41
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Alves NA, Frigori RB. In Silico Comparative Study of Human and Porcine Amylin. J Phys Chem B 2018; 122:10714-10721. [DOI: 10.1021/acs.jpcb.8b09363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nelson A. Alves
- Departamento de Fı́sica, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes, 3900. Ribeirão Preto 14040-901, SP Brazil
| | - Rafael B. Frigori
- Universidade Tecnológica Federal do Paraná, Rua Cristo Rei 19, Toledo 85902-490, PR Brazil
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42
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Miao H, Klein T, Kouřil D, Mindek P, Schatz K, Gröller ME, Kozlíková B, Isenberg T, Viola I. Multiscale Molecular Visualization. J Mol Biol 2018; 431:1049-1070. [PMID: 30227136 DOI: 10.1016/j.jmb.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023]
Abstract
We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field.
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43
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Moore SJ, Sonar K, Bharadwaj P, Deplazes E, Mancera RL. Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies. Molecules 2018; 23:E2142. [PMID: 30149632 PMCID: PMC6225196 DOI: 10.3390/molecules23092142] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/26/2022] Open
Abstract
Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer's disease. The soluble, oligomeric forms of hIAPP are the most toxic to β-cells in the pancreas. However, the structure of these oligomeric forms is difficult to characterise because of their intrinsic disorder and their tendency to rapidly aggregate into insoluble fibrils. Experimental studies of hIAPP have generally used non-physiological conditions to prevent aggregation, and they have been unable to describe its soluble monomeric and oligomeric structure at physiological conditions. Molecular dynamics (MD) simulations offer an alternative for the detailed characterisation of the monomeric structure of hIAPP and its aggregation in aqueous solution. This paper reviews the knowledge that has been gained by the use of MD simulations, and its relationship to experimental data for both hIAPP and rat IAPP. In particular, the influence of the choice of force field and water models, the choice of initial structure, and the configurational sampling method used, are discussed in detail. Characterisation of the solution structure of hIAPP and its mechanism of oligomerisation is important to understanding its cellular toxicity and its role in disease states, and may ultimately offer new opportunities for therapeutic interventions.
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Affiliation(s)
- Sandra J Moore
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Krushna Sonar
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Prashant Bharadwaj
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
- Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, 270 Joondalup Drive, Edith Cowan University, Joondalup, WA 6027, Australia.
| | - Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
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44
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Macalino SJY, Basith S, Clavio NAB, Chang H, Kang S, Choi S. Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. Molecules 2018; 23:E1963. [PMID: 30082644 PMCID: PMC6222862 DOI: 10.3390/molecules23081963] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The advent of advanced molecular modeling software, big data analytics, and high-speed processing units has led to the exponential evolution of modern drug discovery and better insights into complex biological processes and disease networks. This has progressively steered current research interests to understanding protein-protein interaction (PPI) systems that are related to a number of relevant diseases, such as cancer, neurological illnesses, metabolic disorders, etc. However, targeting PPIs are challenging due to their "undruggable" binding interfaces. In this review, we focus on the current obstacles that impede PPI drug discovery, and how recent discoveries and advances in in silico approaches can alleviate these barriers to expedite the search for potential leads, as shown in several exemplary studies. We will also discuss about currently available information on PPI compounds and systems, along with their usefulness in molecular modeling. Finally, we conclude by presenting the limits of in silico application in drug discovery and offer a perspective in the field of computer-aided PPI drug discovery.
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Affiliation(s)
- Stephani Joy Y Macalino
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Shaherin Basith
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Nina Abigail B Clavio
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Hyerim Chang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Soosung Kang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea.
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45
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Nizynski B, Nieznanska H, Dec R, Boyko S, Dzwolak W, Nieznanski K. Amyloidogenic cross-seeding of Tau protein: Transient emergence of structural variants of fibrils. PLoS One 2018; 13:e0201182. [PMID: 30024984 PMCID: PMC6053212 DOI: 10.1371/journal.pone.0201182] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
Amyloid aggregates of Tau protein have been implicated in etiology of many neurodegenerative disorders including Alzheimer's disease (AD). When amyloid growth is induced by seeding with preformed fibrils assembled from the same protein, structural characteristics of the seed are usually imprinted in daughter generations of fibrils. This so-called conformational memory effect may be compromised when the seeding involves proteins with non-identical sequences leading to the emergence of distinct structural variants of fibrils (amyloid ‘strains’). Here, we investigate cross-seeding of full-length human Tau (FL Tau) with fibrils assembled from K18 and K18ΔK280 fragments of Tau in the presence of poly-L-glutamate (poly-Glu) as an enhancer of Tau aggregation. To study cross-seeding between Tau polypeptides and the role of the conformational memory effect in induction of Tau amyloid polymorphism, kinetic assays, transmission electron microscopy, infrared spectroscopy and limited proteolysis have been employed. The fastest fibrillization was observed for FL Tau monomers seeded with preformed K18 amyloid yielding daughter fibrils with unique trypsin digestion patterns. Morphological features of daughter FL Tau fibrils induced by K18 and K18ΔK280 seeds were reminiscent of the mother fibrils (i.e. straight paired fibrils and paired helical filaments (PHFs), respectively) but disappeared in the following generations which became similar to unpaired FL Tau amyloid fibrils formed de novo. The structural evolution observed in our study was accompanied by disappearance of the unique proteolysis profile originated from K18. Our findings may have implications for understanding molecular mechanisms of the emergence and stability of Tau amyloid strains.
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Affiliation(s)
- Bartosz Nizynski
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, Warsaw, Poland.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Hanna Nieznanska
- Department of Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Solomiia Boyko
- Department of Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Krzysztof Nieznanski
- Department of Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
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46
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Mietlicki-Baase EG. Amylin in Alzheimer's disease: Pathological peptide or potential treatment? Neuropharmacology 2018; 136:287-297. [PMID: 29233636 PMCID: PMC5994175 DOI: 10.1016/j.neuropharm.2017.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/06/2017] [Accepted: 12/07/2017] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease for which we currently lack effective treatments or a cure. The pancreatic peptide hormone amylin has recently garnered interest as a potential pharmacological target for the treatment of AD. A number of studies have demonstrated that amylin and amylin analogs like the FDA-approved diabetes drug pramlintide can reduce amyloid burden in the brain and improve cognitive symptoms of AD. However, other data suggest that amylin may have pathological effects in AD due to its propensity to misfold and aggregate under certain conditions. Here, the literature supporting a beneficial versus harmful role of amylin in AD is reviewed. Additionally, several critical gaps in the literature are discussed, such as our limited understanding of the amylin system during aging and in disease states, as well as complexities of amylin receptor signaling and of changing pathophysiology during AD progression that might underlie the seemingly conflicting or contradictory results in the amylin/AD literature. This article is part of the Special Issue entitled 'Metabolic Impairment as Risk Factors for Neurodegenerative Disorders.'
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Affiliation(s)
- Elizabeth G Mietlicki-Baase
- Department of Exercise and Nutrition Sciences, School of Public Health and Health Professions, State University of New York at Buffalo, Buffalo, NY 14214, USA.
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47
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Ge X, Yang Y, Sun Y, Cao W, Ding F. Islet Amyloid Polypeptide Promotes Amyloid-Beta Aggregation by Binding-Induced Helix-Unfolding of the Amyloidogenic Core. ACS Chem Neurosci 2018; 9:967-975. [PMID: 29378116 DOI: 10.1021/acschemneuro.7b00396] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Amyloid aggregation of amyloid-beta (Aβ) and islet amyloid polypeptide (IAPP) is associated with Alzheimer's disease (AD) and type-2 diabetes (T2D), respectively. With T2D being the risk factor for AD and the ability of IAPP to cross the blood-brain barrier, the coaggregation of Aβ and IAPP has been explored to understand the cross-talk between the two diseases. Recent studies demonstrated that soluble IAPP could significantly accelerate the aggregation of Aβ while preformed amyloids of IAPP were poor "seeds" for Aβ aggregation. Here, we apply all-atom discrete molecular dynamics simulations to investigate possible molecular mechanisms for the accelerated coaggregation of IAPP and Aβ42 comparing to Aβ42 aggregation alone, which was confirmed by the complementary thioflavin-T fluorescence assay. Our simulation results suggest that peptides in the mixture tend to form heterodimers as the first step toward their coaggregation. Strong interpeptide interactions with IAPP in the heterodimer shift the helical conformation of Aβ42 in its amyloidogenic central hydrophobic core, residues 16-22 (Aβ16-22), to the extended conformation ready to form β-sheets. Our study suggests that the unfolding of Aβ16-22 helix contributes to the aggregation free-energy barrier and corresponds to the rate-limiting conformational change for Aβ42 aggregation. Therefore, we propose that soluble IAPP promotes the aggregation of Aβ42 by binding-induced conformational change of Aβ42 in its amyloidogenic core and thus reduced aggregation free-energy barrier.
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48
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Jana AK, Batkulwar KB, Kulkarni MJ, Sengupta N. Glycation induces conformational changes in the amyloid-β peptide and enhances its aggregation propensity: molecular insights. Phys Chem Chem Phys 2018; 18:31446-31458. [PMID: 27827482 DOI: 10.1039/c6cp05041g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cytotoxicity of the amyloid beta (Aβ) peptide, implicated in the pathogenesis of Alzheimer's disease (AD), can be enhanced by its post-translational glycation, a series of non-enzymatic reactions with reducing sugars and reactive dicarbonyls. However, little is known about the underlying mechanisms that potentially enhance the cytotoxicity of the advanced glycation modified Aβ. In this work, fully atomistic molecular dynamics (MD) simulations are exploited to obtain direct molecular insights into the process of early Aβ self-assembly in the presence and absence of glycated lysine residues. Analyses of data exceeding cumulative timescales of 1 microsecond for each system reveal that glycation results in a stronger enthalpy of association between Aβ monomers and lower conformational entropy, in addition to a sharp overall increase in the beta-sheet content. Further analyses reveal that the enhanced interactions originate, in large part, due to markedly stronger, as well as new, inter-monomer salt bridging propensities in the glycated variety. Interestingly, these conformational and energetic effects are broadly reflected in preformed protofibrillar forms of Aβ small oligomers modified with glycation. Our combined results imply that glycation consolidates Aβ self-assembly regardless of its point of occurrence in the pathway. They provide a basis for further mechanistic studies and therapeutic endeavors that could potentially result in novel ways of combating AGE related AD progression.
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Affiliation(s)
- Asis K Jana
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India and Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Kedar B Batkulwar
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India and Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - Mahesh J Kulkarni
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India and Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - Neelanjana Sengupta
- Dept. of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741 246, W. Bengal, India.
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Tofoleanu F, Yuan Y, Pickard FC, Tywoniuk B, Brooks BR, Buchete NV. Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018; 122:5657-5665. [PMID: 29406755 DOI: 10.1021/acs.jpcb.7b12083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37-amino-acid peptide, co-secreted with insulin, and widely found in fibril form in type-2 diabetes patients. By using all-atom molecular dynamics simulations, we study hIAPP fibril segments (i.e., fibrillar oligomers) formed with sequences of naturally occurring variants from cat, rat, and pig, presenting different aggregation propensities. We characterize the effect of mutations on the structural dynamics of solution-formed hIAPP fibril models built from solid-state NMR data. Results from this study are in agreement with experimental observations regarding their respective relative aggregation propensities. We analyze in detail the specific structural characteristics and infer mechanisms that modulate the conformational stability of amylin fibrils. Results provide a platform for further studies and the design of new drugs that could interfere with amylin aggregation and its cytotoxicity. One particular mutation, N31K, has fibril-destabilizing properties, and could potentially improve the solubility of therapeutic amylin analogs.
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Affiliation(s)
- Florentina Tofoleanu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States
| | - Ye Yuan
- Institute for Discovery , University College Dublin , Belfield, Dublin 4 , Ireland.,School of Physics , University College Dublin , Dublin 4 , Ireland
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Bartłomiej Tywoniuk
- Institute for Discovery , University College Dublin , Belfield, Dublin 4 , Ireland.,School of Physics , University College Dublin , Dublin 4 , Ireland
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Nicolae-Viorel Buchete
- Institute for Discovery , University College Dublin , Belfield, Dublin 4 , Ireland.,School of Physics , University College Dublin , Dublin 4 , Ireland
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Frigori RB. Be positive: optimizing pramlintide from microcanonical analysis of amylin isoforms. Phys Chem Chem Phys 2018; 19:25617-25633. [PMID: 28905065 DOI: 10.1039/c7cp04074a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amylin, or human islet amyloid polypeptide (hIAPP), is a 37-residue hormone synergistic to insulin and co-secreted with it by β-cells in the pancreas. The deposition of its cytotoxic amyloid fibrils is strongly related to the progression of Type II diabetes (T2D) and islet graft failures. Notably, isoforms from some mammalian species, such as rats (rIAPP) and porcine (pIAPP), present a few key mutations preventing aggregation. This has lead to biotechnological development of drugs for adjunct therapies of T2D, such as pramlintide, a variant of hIAPP inspired by rIAPP whose proline substitutions have β-strand fibril-breaking properties. Ideally, such a drug should be formulated with insulin and co-administered, but this has been prevented by a poor solubility profile at the appropriate pH. Hopefully, this could be improved with appropriate point mutations, increasing the molecular net charge. Despite experimental progress, preliminary screening during rational drug design can greatly benefit from thermodynamic insight derived from molecular simulations. So we introduce microcanonical thermostatistics analysis of multicanonical (MUCA) simulations of wild-type amylin isoforms as a systematic assessment of protein thermostability. As a consequence of this comprehensive investigation, the most suitable single-point mutations able to optimize pramlintide are located among the wild-type amylin isoforms. In particular, we find that aggregation inhibition and increased solubility are inherited by pramlintide through further S20R substitution typical of pIAPP. Thus, we provide a consistent thermostatistical methodology to aid the design of improved adjunct therapies for T2D according to current clinical knowledge.
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Affiliation(s)
- Rafael B Frigori
- Universidade Tecnológica Federal do Paraná, Rua Cristo Rei 19, 85902-490, Toledo, PR, Brazil.
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