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Wu M, Wille H, Stepanova M. Essential collective dynamics analysis reveals nonlocal interactions of alpha-synuclein 38-95 monomers with fibrillar seeds. J Chem Phys 2022; 157:235101. [PMID: 36550041 DOI: 10.1063/5.0116032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Alpha-synuclein (α-syn) is a cytoplasmic protein commonly found in the nervous system. In solution, α-syn adopts disordered unfolded conformations, although it can also form α-helices upon binding to lipid membranes. Under conditions that are not yet fully understood, α-syn can misfold and aggregate, giving rise to β-sheet rich amyloid fibrils, which then tend to accumulate in degenerating neurons. This leads to Parkinson's disease (PD) and several other conditions collectively termed synucleinopathies. Development of disease-modifying treatments requires detailed understanding of structure and dynamics of α-syn's misfolded aggregates. We have employed 1000 ns long, all-atom molecular dynamics simulations to investigate the interaction of monomeric α-syn38-95 fragments, which contain the most important amyloidogenic regions, with preformed fibrillar seeds composed of staggered, β-sheet rich α-syn chains of matching length. The simulations indicate that α-syn38-95 monomers tend to form aggregates with the fibrillar seeds, although we have not observed alignment of the monomeric chains with β-strands of the fibril. To analyze the stability of these aggregates, we have employed the essential collective dynamics method, which allows making accurate assessment of dynamical coupling across individual atoms in macromolecules and supramolecular complexes. The analysis revealed extensive dynamical coupling across initially monomeric α-syn chains and the fibrillar seeds including distal regions thereof that did not contact the monomer directly. We have discussed structural origins of these long-range interactions, their impacts for the stability of α-syn aggregates, and potential implications for the development of anti-PD treatments.
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Affiliation(s)
- Min Wu
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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Significance of native PLGA nanoparticles in the treatment of Alzheimer's disease pathology. Bioact Mater 2022; 17:506-525. [PMID: 36330076 PMCID: PMC9614411 DOI: 10.1016/j.bioactmat.2022.05.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 04/26/2022] [Accepted: 05/23/2022] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is believed to be triggered by increased levels/aggregation of β-amyloid (Aβ) peptides. At present, there is no effective disease-modifying treatment for AD. Here, we evaluated the therapeutic potential of FDA-approved native poly(d,l-lactide-co-glycolide) (PLGA) nanoparticles on Aβ aggregation and in cellular/animal models of AD. Our results showed that native PLGA can not only suppress the spontaneous aggregation but can also trigger disassembly of preformed Aβ aggregates. Spectroscopic studies, molecular dynamics simulations and biochemical analyses revealed that PLGA, by interacting with the hydrophobic domain of Aβ1-42, prevents a conformational shift towards the β-sheet structure, thus precluding the formation and/or triggering disassembly of Aβ aggregates. PLGA-treated Aβ samples can enhance neuronal viability by reducing phosphorylation of tau protein and its associated signaling mechanisms. Administration of PLGA can interact with Aβ aggregates and attenuate memory deficits as well as Aβ levels/deposits in the 5xFAD mouse model of AD. PLGA can also protect iPSC-derived neurons from AD patients against Aβ toxicity by decreasing tau phosphorylation. These findings provide unambiguous evidence that native PLGA, by targeting different facets of the Aβ axis, can have beneficial effects in mouse neurons/animal models as well as on iPSC-derived AD neurons - thus signifying its unique therapeutic potential in the treatment of AD pathology. PLGA nanoparticles by interacting with hydrophobic domain inhibit Aβ aggregation. PLGA-mediated inhibition of Aβ aggregation can increase viability of mouse neurons. PLGA administration can attenuate cognitive deficits/pathology in 5xFAD AD mouse model. PLGA can protect iPSC-derived neurons from AD patients against Aβ toxicity.
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Kaumbekova S, Torkmahalleh MA, Shah D. Impact of ultrafine particles and secondary inorganic ions on early onset and progression of amyloid aggregation: Insights from molecular simulations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117147. [PMID: 33894535 DOI: 10.1016/j.envpol.2021.117147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder, associated with the aggregation of amyloid beta (Aβ) peptides and formation of plaques. The impact of airborne particulate matter (PM) and ultrafine particles (UFPs), on early onset and progression of AD has been recently hypothesized. Considering their small size, carbon black nanoparticles and UFPs can penetrate into human organism and affect Alzheimer's progression. While experiments show that the exposure of PM and UFPs can lead to enhanced concentrations of Aβ peptides, the interactions between the peptides and UFPs remain obscured. Particularly, the impact of UFPs on the initial rate of aggregation of the peptides is ambiguous. Herein, we perform molecular dynamics simulations to investigate the aggregation of Aβ16-21 peptides, an aggregation-prone segment of Aβ, in the presence of UFPs, mimicked by C60, under different salt solutions suggesting the presence of the inorganic constituents of PM in the blood. In particular, the simulations were performed in the presence of Na+, Cl- and CO3-2 ions to characterize typical buffer environments and electrolytes present in human blood. Furthermore, NH4+, NO3- and SO4-2 ions, found in PM, were used in the simulations. The results revealed high propensity for the aggregation of Aβ16-21 peptides. Moreover, the peptides made clusters with C60 molecules, that would be expected to act as a nucleation site for the formation of amyloid plaques. Taken together, the results showed that UFPs affected the peptide aggregation differently, depending on the type of ions present in the simulation environment. In the presence of C60, SO4-2 and NO3- ions accelerated the aggregation of Aβ16-21 peptides, however, NH4+ ions decelerated their aggregation. In addition, UFP lowered β-sheets amounts at all environments, except NaCl solution.
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Affiliation(s)
- Samal Kaumbekova
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kazakhstan
| | - Mehdi Amouei Torkmahalleh
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kazakhstan
| | - Dhawal Shah
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kazakhstan.
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Wu M, Dorosh L, Schmitt-Ulms G, Wille H, Stepanova M. Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations. PLoS Comput Biol 2021; 17:e1008771. [PMID: 33711010 PMCID: PMC7990313 DOI: 10.1371/journal.pcbi.1008771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/24/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14’s presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42–SST14, Aβ42–AVP, and Aβ40–SST14. The Aβ42–SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42–SST14 system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ42–SST14 oligomerization. Improper folding of proteins causes disorders known as protein misfolding diseases. Under normal conditions most proteins adopt particular folds, which allow them functioning properly. However, for reasons that are not yet fully understood, proteins may misfold and aggregate, forming deposits known as amyloid fibrils, which accumulate in the brain or other tissues. This process affects functioning of the nervous system, gradually causing loss of cognitive abilities. Alzheimer’s disease is one of the most common diseases from this group. A better understanding of the aggregation of peptides implicated in Alzheimer’s disease, known as amyloid beta (Aβ) peptides, may facilitate the development of treatments that ameliorate or prevent the disease. We use detailed molecular dynamics simulations to investigate the influence of somatostatin-14 (SST14), a cyclic neuropeptide that might be involved in the amyloidogenic aggregation of Aβ, on molecular processes occurring at the onset of Aβ aggregation. Results of these simulations explain how the presence of SST14 might alter pathways of aggregation of Aβ, shedding light upon the possible role of extrinsic factors in the aggregation at a molecular level.
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Affiliation(s)
- Min Wu
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada
- Centre for Prions and Protein Folding Diseases, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
- * E-mail:
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Shojapour M, Fatemi F, Farahmand S, Shasaltaneh MD. Investigation of Cyc 1 protein structure stability after H53I mutation using computational approaches to improve redox potential. J Mol Graph Model 2021; 105:107864. [PMID: 33647753 DOI: 10.1016/j.jmgm.2021.107864] [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] [Received: 11/10/2020] [Revised: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
Acidithiobacillus ferrooxidans (Af) is an acidophilic bacterium that grows in rigid surroundings and gets its own energy from the oxidation of Fe2+ to Fe3+. These bacteria are involved in the bioleaching process. Cyc1 is a periplasmic protein with a crucial role in electron transportation in the respiratory chain. His53 of the Cyc1 protein, involved in electron transfer to CoxB, was selected for mutation and bioinformatics studies. His53 was substituted by Ile using PyMol software. Molecular dynamics simulations were performed for wild and mutant types of Cyc1 protein. The conformational changes of mutated protein were studied by analyzing RMSD, RMSF, SASA, Rg, H Bond, and DSSP. The results of the RMSF analysis indicated an increase in the flexibility of the ligand in the mutant. Finally, active site instability leads to an increase in the value of E0 at the mutation point and improving electron transfer. On the other, His53 in Cyc1 is interconnected to Glu126 in CoxB through the water molecule (W76) and hydrogen bonding. In the H53I mutation, there was a decrease in the distance between H2O 2030, 2033, and isoleucine 53, and subsequently, the distance to the water molecule 76 between the two proteins was reduced and strengthens the hydrogen bond between Cyc1 and CoxB, finally improves electron transfer and the bioleaching process.
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Affiliation(s)
- Mahnaz Shojapour
- Department of Biology, Faculty of Sciences, Payame Noor University, Tehran, Iran.
| | - Faezeh Fatemi
- Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Somayeh Farahmand
- Department of Biology, Faculty of Sciences, Payame Noor University, Tehran, Iran
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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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Ahamad S, Hema K, Gupta D. Structural stability predictions and molecular dynamics simulations of RBD and HR1 mutations associated with SARS-CoV-2 spike glycoprotein. J Biomol Struct Dyn 2021; 40:6697-6709. [PMID: 33618621 DOI: 10.1080/07391102.2021.1889671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The COVID-19 pandemic is caused by human transmission and infection of Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2). There is no trusted drug against the virus; hence, efforts are on discovering novel inhibitors for the virus. The entry of a SARS-CoV-2 virus particle into a host cell is initiated by its spike glycoprotein and host Angiotensin-Converting Enzyme 2 (ACE2) receptor interaction. Spike glycoprotein domains, namely, the Receptor Binding Domain (RBD) and Heptad Repeat (HR) domains, are essential for this activity. We have studied the impact of mutations such as A348T, N354D, D364Y, G476S, V483A, S494D in the RBD (319-591), and S939F, S940T, T941A, S943P (912-984) in the HR1 domains of spike glycoprotein. Summarily, we utilized the computational screening algorithms to rank the deleterious, damaging and disease-associated spike glycoprotein mutations. Subsequently, to understand the changes in conformation, flexibility and function of the spike glycoprotein mutants, Molecular Dynamics (MD) simulations were performed. The computational predictions and analysis of the MD trajectories suggest that the RBD and HR1 mutations induce significant phenotypic effects on the pre-binding spike glycoprotein structure, which are presumably consequential to its binding to the receptor and provides lead to design inhibitors against the binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Kanipakam Hema
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Ahamad S, Kanipakam H, Kumar V, Gupta D. A molecular journey to check the conformational dynamics of tau tubulin kinase 2 mutations associated with Alzheimer's disease. RSC Adv 2021; 11:1320-1331. [PMID: 35424125 PMCID: PMC8693565 DOI: 10.1039/d0ra07659g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/28/2020] [Indexed: 01/25/2023] Open
Abstract
Proteins are one of the most vital components of biological functions. Proteins have evolutionarily conserved structures as the shape and folding pattern predominantly determine their function. Considerable research efforts have been made to study the protein folding mechanism. The misfolding of protein intermediates of large groups form polymers with unwanted aggregates that may initiate various diseases. Amongst the diseases caused by misfolding of proteins, Alzheimer's disease (AD) is one of the most prevalent neuro-disorders which has a worldwide impact on human health. The disease is associated with several vital proteins and single amino acid mutations. Tau tubulin kinase 2 (TTBK2) is one of the kinases which is known to phosphorylate tau and tubulin. The literature strongly supports that the mutations-K50E, D163A, R181E, A184E and K143E are associated with multiple important cellular processes of TTBK2. In this study, to understand the molecular basis of the functional effects of the mutations, we have performed structural modeling for TTBK2 and its mutations, using computational prediction algorithms and Molecular Dynamics (MD) simulations. The MD simulations highlighted the impact of the mutations on the Wild Type (WT) by the conformational dynamics, Free Energy Landscape (FEL) and internal molecular motions, indicating the structural de-stabilization which may lead to the disruption of its biological functions. The destabilizing effect of TTBK2 upon mutations provided valuable information about individuals carrying this mutant which could be used as a diagnostic marker in AD.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) Aruna Asaf Ali Marg New Delhi 110067 India +919312304662 +91 1126742184
| | - Hema Kanipakam
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) Aruna Asaf Ali Marg New Delhi 110067 India +919312304662 +91 1126742184
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University Noida UP India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) Aruna Asaf Ali Marg New Delhi 110067 India +919312304662 +91 1126742184
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Ahamad S, Kanipakam H, Birla S, Ali MS, Gupta D. Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 M pro, using molecular docking and dynamics simulation studies. Eur J Pharmacol 2020; 890:173664. [PMID: 33131721 PMCID: PMC7584923 DOI: 10.1016/j.ejphar.2020.173664] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) Main protease (Mpro) is one of the vital drug targets amongst all the coronaviruses, as the protein is indispensable for virus replication. The study aimed to identify promising lead molecules against Mpro enzyme through virtual screening of Malaria Venture (MMV) Malaria Box (MB) comprising of 400 experimentally proven compounds. The binding affinities were studied using virtual screening based molecular docking, which revealed five molecules having the highest affinity scores compared to the reference molecules. Utilizing the established 3D structure of Mpro the binding affinity conformations of the docked complexes were studied by Molecular Dynamics (MD) simulations. The MD simulation trajectories were analysed to monitor protein deviation, relative fluctuation, atomic gyration, compactness covariance, residue-residue map and free energy landscapes. Based on the present study outcome, we propose three Malaria_box (MB) compounds, namely, MB_241, MB_250 and MB_266 to be the best lead compounds against Mpro activity. The compounds may be evaluated for their inhibitory activities using experimental techniques.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Hema Kanipakam
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Shweta Birla
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Md Shaukat Ali
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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11
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Xing X, Liu C, Yang H, Nouman MF, Ai H. Folding dynamics of Aβ42 monomer at pH 4.0–7.5 with and without physiological salt conditions – does the β1 or β2 region fold first? NEW J CHEM 2020. [DOI: 10.1039/d0nj01090a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The seeding region of Aβ42 monomer is jointly affected by the solution acidity, ionic distribution of the salt, and charged residues.
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Affiliation(s)
- Xiaofeng Xing
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | | | - Hongqi Ai
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
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12
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Liu C, Zhao W, Xing X, Shi H, Kang B, Liu H, Li P, Ai H. An Original Monomer Sampling from a Ready‐Made Aβ
42
NMR Fibril Suggests a Turn‐β‐Strand Synergetic Seeding Mechanism. Chemphyschem 2019; 20:1649-1660. [DOI: 10.1002/cphc.201801137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Chengqiang Liu
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Wei Zhao
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Xiaofeng Xing
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Hu Shi
- School of Chemistry and Chemical EngineeringShanxi University Taiyuan 030006 China
| | - Baotao Kang
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Haiying Liu
- School of PhysicsUniversity of Jinan Jinan 250022 China
| | - Ping Li
- Key Laboratory of Life-Organic Analysis, School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165 China
| | - Hongqi Ai
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
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13
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Xing X, Zhao W, Hu D, Kang B, Shi H, Lee JY, Ai H. Tautomerization Effect of Histidines on Oligomer Aggregation of β-Amyloid(1-40/42) during the Early Stage: Tautomerism Hypothesis for Misfolding Protein Aggregation. ACS Chem Neurosci 2019; 10:2602-2608. [PMID: 30813720 DOI: 10.1021/acschemneuro.9b00094] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
As the intrinsic origin of the hypothesis for β-amyloid (Aβ) from Alzheimer's disease, histidine behaviors were found to play a crucial role in Aβ aggregation. To investigate the histidine behaviors during the early stage of aggregation, Aβ40/42 pentamers with different histidine isomer states were simulated at the atomic level. Results show that five Aβ40 (δδδ) and Aβ42 (εδδ) monomers can rapidly decrease the aggregation threshold, promote stable pentamer formation, and increase pentamer contents by 51.8% and 56.7%, respectively, as compared with the values of their wild-type (εεε) counterparts. Additionally, pentamers of Aβ40 (δδδ) and Aβ42 (εδδ) have different aggregation pathways and disassembly species, Tr+D and Te+M, during the growth of the pentamer. This work discloses the significance of histidine tautomerization in Aβ aggregation, implying a potential way to control Aβ aggregation and develop the assembly inhibitors.
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Affiliation(s)
- Xiaofeng Xing
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Wei Zhao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Dingkun Hu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, P. R. China
| | - Jin Yong Lee
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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14
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Salimi A, Li H, Shi H, Lee JY. Intrinsic origin of amyloid aggregation: Behavior of histidine (εεε) and (δδδ) tautomer homodimers of Aβ (1–40). Biochim Biophys Acta Gen Subj 2019; 1863:795-801. [DOI: 10.1016/j.bbagen.2019.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 02/08/2023]
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15
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Saracino GAA, Fontana F, Jekhmane S, Silva JM, Weingarth M, Gelain F. Elucidating Self-Assembling Peptide Aggregation via Morphoscanner: A New Tool for Protein-Peptide Structural Characterization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800471. [PMID: 30128255 PMCID: PMC6097002 DOI: 10.1002/advs.201800471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/11/2018] [Indexed: 05/13/2023]
Abstract
Self-assembling and molecular folding are ubiquitous in Nature: they drive the organization of systems ranging from living creatures to DNA molecules. Elucidating the complex dynamics underlying these phenomena is of crucial importance. However, a tool for the analysis of the various phenomena involved in protein/peptide aggregation is still missing. Here, an innovative software is developed and validated for the identification and visualization of b-structuring and b-sheet formation in both simulated systems and crystal structures of proteins and peptides. The novel software suite, dubbed Morphoscanner, is designed to identify and intuitively represent b-structuring and b-sheet formation during molecular dynamics trajectories, paying attention to temporary strand-strand alignment, suboligomer formation and evolution of local order. Self-assembling peptides (SAPs) constitute a promising class of biomaterials and an interesting model to study the spontaneous assembly of molecular systems in vitro. With the help of coarse-grained molecular dynamics the self-assembling of diverse SAPs is simulated into molten aggregates. When applied to these systems, Morphoscanner highlights different b-structuring schemes and kinetics related to SAP sequences. It is demonstrated that Morphoscanner is a novel versatile tool designed to probe the aggregation dynamics of self-assembling systems, adaptable to the analysis of differently coarsened simulations of a variety of biomolecules.
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Affiliation(s)
- Gloria A. A. Saracino
- Center for Nanomedicine and Tissue Engineering (CNTE)ASST Ospedale Niguarda Cà GrandaPiazza dell'Ospedale Maggiore 320162MilanItaly
| | - Federico Fontana
- IRCCS Casa Sollievo della SofferenzaOpera di San Pio da PietralcinaViale Capuccini 171013San Giovanni RotondoItaly
| | - Shehrazade Jekhmane
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - João Medeiros Silva
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Fabrizio Gelain
- IRCCS Casa Sollievo della SofferenzaOpera di San Pio da PietralcinaViale Capuccini 171013San Giovanni RotondoItaly
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16
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Zhao W, Ai H. Effect of pH on Aβ 42 Monomer and Fibril-like Oligomers-Decoding in Silico of the Roles of pK Values of Charged Residues. Chemphyschem 2018; 19:1103-1116. [PMID: 29380494 DOI: 10.1002/cphc.201701384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 01/10/2023]
Abstract
Amyloid beta-peptide (Aβ) is the key to developing Alzheimer's disease. Experiments have confirmed that different acidity influences directly not only the structural morphology and population of Aβ oligomers, but also the toxicity. The atomic-level association between the pH, charged residues, and Aβ properties remains obscure. Herein, conformational changes of Aβ42 monomer, fibril-like trimer, and pentamer in the medium pH range of 4.0-7.5 are studied. The results reveal that, as the pH changes from 7.5 to the isoelectric pH, His6, His13, and His14 are protonated in turn, successively approach the center of mass of folded Aβ monomer, trigger ionic interactions and changes of neighboring turns (Asp7-Ser8, His14-Lys16) and even a distant one (Leu34-Met35), as well as concomitant changes of secondary structure, and promote the conformation transition from unfolded to folded. This observation discloses that protonation can convert these charged residues from originally hydrophilic to "hydrophobic-like". For fibril-like oligomers, the pH susceptibility essentially stems from the pK values of charged residues in the context of the Aβ fibril, and in turn one can predict the dynamic behavior of these residues in the processes of dissociation or stabilization of a fibril by comparing the pK values of residues involved in salt bridges in the normal state with those in the current context. This idea is justified by two fibril models and appears to be applicable to other peptides and their fibril systems.
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Affiliation(s)
- Wei Zhao
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
| | - Hongqi Ai
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
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17
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Rivera I, Capone R, Cauvi DM, Arispe N, De Maio A. Modulation of Alzheimer's amyloid β peptide oligomerization and toxicity by extracellular Hsp70. Cell Stress Chaperones 2018; 23:269-279. [PMID: 28956268 PMCID: PMC5823807 DOI: 10.1007/s12192-017-0839-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder leading to dementia caused by advanced neuronal dysfunction and death. The most significant symptoms of AD are observed at late stages of the disease when interventions are most likely too late to ameliorate the condition. Currently, the predominant theory for AD is the "amyloid hypothesis," which states that abnormally increased levels of amyloid β (Aβ) peptides result in the production of a variety of aggregates that are neurotoxic. The specific mechanisms for Aβ peptide-induced cytotoxicity have not yet been completely elucidated. However, since the majority of Aβ is released into the extracellular milieu, it is reasonable to assume that toxicity begins outside the cells and makes its way inside where it disrupts the basic cellular process resulting in cell death. There is increasing evidence that hsp, particularly Hsp70, are exported into the extracellular milieu by an active export mechanism independent of cell death. Therefore, both Aβ peptides and Hsp70 may coexist in a common environment during pathological conditions. We observed that Hsp70 affected the Aβ assembling process in vitro preventing oligomer formation. Moreover, the presence of Hsp70 reduced the Aβ peptide-induced toxicity of cultured neurons (N2A cells). These results suggest a potential mechanism for the reduction of the detrimental effects of Aβ peptides in AD.
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Affiliation(s)
- Isabel Rivera
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA
- Initiative for Maximizing Student Development (IMSD) Program, University of California San Diego, La Jolla, CA, USA
| | - Ricardo Capone
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA
| | - David M Cauvi
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA
| | - Nelson Arispe
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
| | - Antonio De Maio
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA.
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18
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Polanco JC, Li C, Bodea LG, Martinez-Marmol R, Meunier FA, Götz J. Amyloid-β and tau complexity — towards improved biomarkers and targeted therapies. Nat Rev Neurol 2017; 14:22-39. [DOI: 10.1038/nrneurol.2017.162] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Membrane-Accelerated Amyloid-β Aggregation and Formation of Cross-β Sheets. MEMBRANES 2017; 7:membranes7030049. [PMID: 28858214 PMCID: PMC5618134 DOI: 10.3390/membranes7030049] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/26/2017] [Accepted: 08/23/2017] [Indexed: 11/17/2022]
Abstract
Amyloid- β aggregates play a causative role in Alzheimer's disease. These aggregates are a product of the physical environment provided by the basic neuronal membrane, composed of a lipid bilayer. The intrinsic properties of the lipid bilayer allow amyloid- β peptides to nucleate and form well-ordered cross- β sheets within the membrane. Here, we correlate the aggregation of the hydrophobic fragment of the amyloid- β protein, A β 25 - 35 , with the hydrophobicity, fluidity, and charge density of a lipid bilayer. We summarize recent biophysical studies of model membranes and relate these to the process of aggregation in physiological systems.
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