1
|
Pandey R, Urbanc B. Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid β-Protein. Biomolecules 2024; 14:774. [PMID: 39062488 PMCID: PMC11274879 DOI: 10.3390/biom14070774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Alzheimer's disease (AD) is a neurological disorder associated with amyloid β-protein (Aβ) assembly into toxic oligomers. In addition to the two predominant alloforms, Aβ1-40 and Aβ1-42, other C-terminally truncated Aβ peptides, including Aβ1-38 and Aβ1-43, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of Aβ1-38, Aβ1-40, Aβ1-42, and Aβ1-43. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, Aβ1-38 and Aβ1-40 adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas Aβ1-42 and Aβ1-43 oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for Aβ1-42) or octamers and pentadecamers (for Aβ1-43). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with Aβ1-42 alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure-function paradigm governing oligomers formed by various Aβ isoforms.
Collapse
Affiliation(s)
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA;
| |
Collapse
|
2
|
Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024; 5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.
Collapse
Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Anushka Biswas
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | | |
Collapse
|
3
|
Ruttenberg SM, Nowick JS. A turn for the worse: Aβ β-hairpins in Alzheimer's disease. Bioorg Med Chem 2024; 105:117715. [PMID: 38615460 DOI: 10.1016/j.bmc.2024.117715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
Amyloid-β (Aβ) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aβ peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aβ oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aβ oligomers, many of which consist of molecules of Aβ in β-hairpin conformations. β-Hairpins are intramolecular antiparallel β-sheets composed of two β-strands connected by a loop or turn. Three decades of research suggests that Aβ peptides form several different β-hairpin conformations, some of which are building blocks of toxic Aβ oligomers. The insights from these studies are currently being used to design anti-Aβ antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aβ may be more successful at treating AD than antibodies designed to target linear epitopes of Aβ or fibrillar Aβ. Aβ β-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aβ. This review summarizes the research on β-hairpins in Aβ peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.
Collapse
Affiliation(s)
- Sarah M Ruttenberg
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States.
| |
Collapse
|
4
|
Shi Y, Sun Y, Li C, Wang S, Wang J, Shi H. Edge Substitution Effects of Histidine Tautomerization Behaviors on the Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril. ACS Chem Neurosci 2024; 15:1055-1062. [PMID: 38379141 DOI: 10.1021/acschemneuro.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Histidine behaviors play critical roles in folding and misfolding processes due to the changes in net charge and the various N/N-H orientations on imidazole rings. However, the effect of histidine tautomerization (HIE (Nε-H, ε) and HID (Nδ-H, δ) states) behaviors on the edge chain of Aβ mature fibrils remains inadequately understood, which is critical for finding a strategy to disturb fibril elongation and growth. In the current study, eight independent molecular dynamics simulations were conducted to investigate such impacts on the structural and aggregation properties. Our results from three different binding models revealed that the binding contributions of edge substitution effects are primarily located between chains 1 and 2. Histidine states significantly influence the secondary structure of each domain. Further analysis confirmed that the C1_H6//C1_E11 intrachain interaction is essential in maintaining the internal stability of chain 1, while the C1_H13//C2_H13 and C1_H14//C2_H13 interchain interactions are critical in maintaining the interchain stability of the fibril structure. Our subsequent analysis revealed that the current edge substitution leads to the loss of the C1_H13//C1_E11 intrachain and C1_H13//C2_H14 interchain interactions. The N-terminal regularity was significantly directly influenced by histidine states, particularly by the residue of C1_H13. Our study provides valuable insights into the effect of histidine behaviors on the edge chain of Aβ mature fibril, advancing our understanding of the histidine behavior hypothesis in misfolding diseases.
Collapse
Affiliation(s)
- Yaru Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Yue Sun
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Changgui Li
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Shuo Wang
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Jinping Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan 250022, Shandong, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| |
Collapse
|
5
|
Maroli N. Aquaporin-4 Mediated Aggregation of Alzheimer's Amyloid β-Peptide. ACS Chem Neurosci 2023; 14:2683-2698. [PMID: 37486638 DOI: 10.1021/acschemneuro.3c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Clearance of Alzheimer's amyloid oligomers from the brain is crucial for preventing cell toxicity. Dementia complications arise as a result of apoptosis, which is caused by peptide plaques on the lipid surface of cells. Here, we employed all-atom and coarse-grained molecular dynamics simulations to investigate the aggregation of amyloid peptides at the lipid surface and the role of aquaporin-4 (AQP4) in facilitating peptide clearance from astrocytes. The network of protein-protein interactions through text mining revealed that the expression of AQP4 and amyloid aggregation were strongly correlated. It has also been revealed that the role of aquaporins in the etiology of Alzheimer's disease involves several interconnected proteins and pathways. The nature of aggregation at the surface of the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer was revealed by the interaction of amyloid oligomers. The membrane-bound pore region of AQP4 interacts with the peptide and slows its aggregation. This interaction maintains the helical content of the peptide while lowering its toxicity at the lipid surface. The hydrophobicity of the peptide also decreased because of these interactions, which may help in the removal of the peptide from astrocytes. Long-term coarse-grained MD simulations demonstrated different features of oligomer aggregation at the surface and strong oligomer attraction to AQP4, which inhibited aggregation. Additionally, the water dynamics of aquaporins demonstrate how the selectivity filter is broken to disrupt water flow. Our findings also provide insight into the physiological alterations in brain tissue associated with Alzheimer's disease, including water retention and increased water flow in the CSF. Furthermore, in vitro thioflavin fluorescence spectroscopy revealed a slower aggregation of the peptide in the presence of AQP4.
Collapse
Affiliation(s)
- Nikhil Maroli
- Computational Biology Division, DRDO Center for Life Science, Bharathiar University Campus, Coimbatore 641046, Tamil Nadu, India
| |
Collapse
|
6
|
Hnath B, Chen J, Reynolds J, Choi E, Wang J, Zhang D, Sha CM, Dokholyan NV. Big versus small: The impact of aggregate size in disease. Protein Sci 2023; 32:e4686. [PMID: 37243896 PMCID: PMC10273386 DOI: 10.1002/pro.4686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Protein aggregation results in an array of different size soluble oligomers and larger insoluble fibrils. Insoluble fibrils were originally thought to cause neuronal cell deaths in neurodegenerative diseases due to their prevalence in tissue samples and disease models. Despite recent studies demonstrating the toxicity associated with soluble oligomers, many therapeutic strategies still focus on fibrils or consider all types of aggregates as one group. Oligomers and fibrils require different modeling and therapeutic strategies, targeting the toxic species is crucial for successful study and therapeutic development. Here, we review the role of different-size aggregates in disease, and how factors contributing to aggregation (mutations, metals, post-translational modifications, and lipid interactions) may promote oligomers opposed to fibrils. We review two different computational modeling strategies (molecular dynamics and kinetic modeling) and how they are used to model both oligomers and fibrils. Finally, we outline the current therapeutic strategies targeting aggregating proteins and their strengths and weaknesses for targeting oligomers versus fibrils. Altogether, we aim to highlight the importance of distinguishing the difference between oligomers and fibrils and determining which species is toxic when modeling and creating therapeutics for protein aggregation in disease.
Collapse
Affiliation(s)
- Brianna Hnath
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jiaxing Chen
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Joshua Reynolds
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Esther Choi
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jian Wang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Dongyan Zhang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Congzhou M. Sha
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Nikolay V. Dokholyan
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of Biochemistry & Molecular BiologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of ChemistryPenn State UniversityUniversity ParkPennsylvaniaUSA
| |
Collapse
|
7
|
Fang M, Wang X, Su K, Jia X, Guan P, Hu X. Inhibition Effect and Molecular Mechanisms of Quercetin on the Aβ42 Dimer: A Molecular Dynamics Simulation Study. ACS OMEGA 2023; 8:18009-18018. [PMID: 37251196 PMCID: PMC10210038 DOI: 10.1021/acsomega.3c01208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023]
Abstract
Amyloid-β (Aβ) dimer as the smallest oligomer has recently been drawing attention due to its neurotoxicity, transient nature, and heterogeneity. The inhibition of Aβ dimer's aggregation is the key to primary intervention of Alzheimer's disease. Previous experimental studies have reported that quercetin, the widespread polyphenolic constituent of multiple fruits and vegetables, can hamper the formation of Aβ protofibrils and disaggregate Aβ fibrils. However, the molecular mechanisms of quercetin in the suppression of the Aβ(1-42) dimer's conformational changes still remain elusive. In this work, to investigate the inhibitory mechanisms of quercetin molecules on the Aβ(1-42) dimer, an Aβ(1-42) dimer based on monomeric the Aβ(1-42) peptide with enriched coil structures is constructed. The early molecular mechanisms of quercetin molecules on inhibiting the Aβ(1-42) dimer at two different Aβ42-to-quercetin molar ratios (1:5 and 1:10) are explored via all-atom molecular dynamics simulations. The results indicate that quercetin molecules can impede the configurational change of the Aβ(1-42) dimer. The interactions and the binding affinity between the Aβ(1-42) dimer and quercetin molecules in the Aβ42 dimer + 20 quercetin system are stronger in comparison with that in the Aβ42 dimer + 10 quercetin system. Our work may be helpful in developing new drug candidates for preventing the conformational transition and further aggregation of the Aβ dimer.
Collapse
|
8
|
Hiew SH, Lu Y, Han H, Gonçalves RA, Alfarano SR, Mezzenga R, Parikh AN, Mu Y, Miserez A. Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations. J Am Chem Soc 2023; 145:3382-3393. [PMID: 36730942 DOI: 10.1021/jacs.2c09853] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.
Collapse
Affiliation(s)
- Shu Hui Hiew
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yang Lu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Hao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Rui A Gonçalves
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Serena Rosa Alfarano
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Atul N Parikh
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,Departments of Biomedical Engineering and Materials Science & Engineering, University of California, Davis, California 95616, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| |
Collapse
|
9
|
Sun Y, Yao Z, Shi H. Structural properties of Aβ (1-40) peptide in protonation stage of one, two, and three: New insights from the histidine protonation behaviors. Int J Biol Macromol 2022; 223:1556-1561. [PMID: 36370861 DOI: 10.1016/j.ijbiomac.2022.11.061] [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: 09/09/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022]
Abstract
Structural properties and aggregation tendency can be significantly influenced by histidine behaviors (histidine on Nδ-H state is defined as δ, likewise, Nε-H: ε and both Nδ-H and Nε-H: p). In current study, we investigated structural properties of Aβ(1-40) peptide during protonation evolution stage of one, two, and three by total 19 independent replica exchange molecular dynamics simulations using implicit solvent. Our results show that any kind of protonated state will promote β-sheet structure formation in comparison with deprotonated (εεε). With increase in number of protonation, the lowest β-sheet content increased. The highest averaged β-sheet structure content was detected in (δpδ) (46.0 %), (εpp) (36.8 %), and (ppp) (16.0 %) in each protonation stage. With three β-strand structures, (δpδ) shows more stable features and high hydrophobic properties. Further analysis confirmed that H13 and H14 are more important than H6. Specifically, H13 and H14 have a synergistic effect for structural formations by controlling H-bond networks in H13(p) with V39/V40 and H14(p/δ) with G37/G38. Finally, the Pearson correlation coefficient results confirmed that experimental result (ref. 44) is corresponding to our (εpp) system. Our current study will be conducive to understanding the effects of the histidine behaviors, it provides new insights for exploration protein folding and misfolding processes.
Collapse
Affiliation(s)
- Yue Sun
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Zeshuai Yao
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China; Institute of Molecular Science, Shanxi University, Taiyuan 030006, China.
| |
Collapse
|
10
|
Mishra P, Basak S, Mukherjee A, Basu A. Design and Study of In Silico Binding Dynamics of Certain Isoxazole Bearing Leads Against Aβ-42 and BACE-1 Loop in Protein Fibrillation. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210813120444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
Design isoxazole bearing leads as dual inhibitors against Amyloid β and BACE-1 loop
in protein fibrillation.
Background:
Protein fibrillation is one of the key reasons for several diseases, namely Alzheimer’s, Parkinson’s,
and many others. One of the key strategies of preventing protein fibrillation is destabilizing the
protein fibrils themselves or inhibiting the amyloid fibril-forming pathway in the initial stage.
Introduction:
Attempts have been taken to design newer leads to inhibit protein fibrillation by targeting
the β-amyloidogenesis pathway in the brain. To exploit interfenestration between Amyloid β -42 protein
and BACE-1 (β-site amyloid precursor protein cleaving enzyme) for amyloidogenesis, studies are undertaken
to design dual inhibitors against the same.
Method:
In vitro binding interactions were found using docking, de novo ligand design, and MD simulation
study.
Results:
Three compounds bearing an isoxazole heterocyclic nucleus were designed which could successfully
bind to the hydrophobic raft and salt bridge residues Asp 23-Lys-26 of Amyloid β, destabilizing the
growing fibril. Additionally, one of our candidate compounds exhibited force of interaction with Thr232
at the S3 pocket of BACE-1, interacted with key residue Asp228, Tyr71, and Thr72 of the β-hairpin flap
and hydrogen bonding with Gly11 at loop 10s.
Conclusion:
Protein flexibility dynamics of the Aβ-42 protein revealed that there is a considerable conformational
change of the same with or without ligand binding. The lower RMSF of the bound region and
reprogramming residual contacts within the Aβ-42 protein suggested successful binding of the ligand with
the protein, lowering the access for further β-β dimerization.
Collapse
Affiliation(s)
- Puja Mishra
- Dr. B.C. Roy College of Pharmacy & Allied Health Sciences, Durgapur, WB, India
| | - Souvik Basak
- Dr. B.C. Roy College of Pharmacy & Allied Health Sciences, Durgapur, WB, India
| | - Arup Mukherjee
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, WB, India
| | - Anindya Basu
- School of Pharmaceutical Sciences, Rajiv
Gandhi Proudyogiki Vishwavidyalaya, Bhopal, India
| |
Collapse
|
11
|
Fatafta H, Khaled M, Owen MC, Sayyed-Ahmad A, Strodel B. Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane. Proc Natl Acad Sci U S A 2021; 118:e2106210118. [PMID: 34544868 PMCID: PMC8488611 DOI: 10.1073/pnas.2106210118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Mounting evidence suggests that the neuronal cell membrane is the main site of oligomer-mediated neuronal toxicity of amyloid-β peptides in Alzheimer's disease. To gain a detailed understanding of the mutual interference of amyloid-β oligomers and the neuronal membrane, we carried out microseconds of all-atom molecular dynamics (MD) simulations on the dimerization of amyloid-β (Aβ)42 in the aqueous phase and in the presence of a lipid bilayer mimicking the in vivo composition of neuronal membranes. The dimerization in solution is characterized by a random coil to β-sheet transition that seems on pathway to amyloid aggregation, while the interactions with the neuronal membrane decrease the order of the Aβ42 dimer by attenuating its propensity to form a β-sheet structure. The main lipid interaction partners of Aβ42 are the surface-exposed sugar groups of the gangliosides GM1. As the neurotoxic activity of amyloid oligomers increases with oligomer order, these results suggest that GM1 is neuroprotective against Aβ-mediated toxicity.
Collapse
Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Mohammed Khaled
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael C Owen
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
| | | | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
12
|
Effects of Aβ-derived peptide fragments on fibrillogenesis of Aβ. Sci Rep 2021; 11:19262. [PMID: 34584131 PMCID: PMC8479085 DOI: 10.1038/s41598-021-98644-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022] Open
Abstract
Amyloid β (Aβ) peptide aggregation plays a central role in Alzheimer's disease (AD) etiology. AD drug candidates have included small molecules or peptides directed towards inhibition of Aβ fibrillogenesis. Although some Aβ-derived peptide fragments suppress Aβ fibril growth, comprehensive analysis of inhibitory potencies of peptide fragments along the whole Aβ sequence has not been reported. The aim of this work is (a) to identify the region(s) of Aβ with highest propensities for aggregation and (b) to use those fragments to inhibit Aβ fibrillogenesis. Structural and aggregation properties of the parent Aβ1-42 peptide and seven overlapping peptide fragments have been studied, i.e. Aβ1-10 (P1), Aβ6-15 (P2), Aβ11-20 (P3), Aβ16-25 (P4), Aβ21-30 (P5), Aβ26-36 (P6), and Aβ31-42 (P7). Structural transitions of the peptides in aqueous buffer have been monitored by circular dichroism and Fourier transform infrared spectroscopy. Aggregation and fibrillogenesis were analyzed by light scattering and thioflavin-T fluorescence. The mode of peptide-peptide interactions was characterized by fluorescence resonance energy transfer. Three peptide fragments, P3, P6, and P7, exhibited exceptionally high propensity for β-sheet formation and aggregation. Remarkably, only P3 and P6 exerted strong inhibitory effect on the aggregation of Aβ1-42, whereas P7 and P2 displayed moderate inhibitory potency. It is proposed that P3 and P6 intercalate between Aβ1-42 molecules and thereby inhibit Aβ1-42 aggregation. These findings may facilitate therapeutic strategies of inhibition of Aβ fibrillogenesis by Aβ-derived peptides.
Collapse
|
13
|
Sahoo A, Matysiak S. Effects of applied surface-tension on membrane-assisted Aβ aggregation. Phys Chem Chem Phys 2021; 23:20627-20633. [PMID: 34514475 DOI: 10.1039/d1cp02642a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accumulation of protein-based (Aβ) aggregates on cellular membranes with varying structural properties is commonly recognized as the key step in Alzheimer's pathogenesis. But experimental and computational challenges have made this biophysical characterization difficult. In particular, studies connecting biological membrane organization and Aβ aggregation are limited. While experiments have suggested that an increased membrane curvature results in faster Aβ peptide aggregation in the context of Alzheimer's disease, a mechanistic explanation for this relation is missing. In this work, we are leveraging molecular simulations with a physics-based coarse grained model to address and understand the relationships between curved cellular membranes and aggregation of a model template peptide Aβ 16-22. In agreement with experimental results, our simulations also suggest a positive correlation between increased peptide aggregation and membrane curvature. More curved membranes have higher lipid packing defects that engage peptide hydrophobic groups and promote faster diffusion leading to peptide fibrillar structures. In addition, we curated the effects of peptide aggregation on the membrane's structure and organization. Interfacial peptide aggregation results in heterogeneous headgroup-peptide interactions and an induced crowding effect at the lipid headgroup region, leading to a more ordered headgroup region and disordered lipid-tails at the membrane core. This work presents a mechanistic and morphological overview of the relationships between the biomembrane local structure and organization, and Aβ peptide aggregation.
Collapse
Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Silvina Matysiak
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA.
| |
Collapse
|
14
|
Prabakaran R, Rawat P, Yasuo N, Sekijima M, Kumar S, Gromiha MM. Effect of charged mutation on aggregation of a pentapeptide: Insights from molecular dynamics simulations. Proteins 2021; 90:405-417. [PMID: 34460128 DOI: 10.1002/prot.26230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/30/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022]
Abstract
Aggregation of therapeutic monoclonal antibodies (mAbs) can negatively affect their chemistry, manufacturing, and control attributes and lead to undesirable immune responses in patients. Therefore, optimization of lead mAb drug candidates during discovery stages to mitigate aggregation is increasingly becoming an integral part of their developability assessments. The disruption of short sequence motifs called aggregation prone regions (APRs) found in amino acid sequences of mAb candidates can potentially mitigate their aggregation. In this work, we have performed molecular dynamics simulations to study the aggregation of an APR (VLVIY) found in λ light chains of human antibodies and its single point mutant KLVIY. Eighteen different multicopy peptide simulation systems of "VLVIY" and "KLVIY" were constructed by varying their concentrations, temperatures, termini capping, and flanking gate-keeper regions. Within 20 ns of the simulation, peptide "VLVIY" formed an aggregate of 100 peptides at ~0.1 M concentration with a 60% reduction in solvent accessible surface area (SASA). Furthermore, analysis of the SASA change, peptide cluster distribution, and water residence time demonstrated how Val ➔ Lys mutation resists aggregation and improves solubility. Presence of Lys slows down aggregation kinetics via charge-charge repulsions and by raising the kinetic barrier to formation of large oligomers. However, the effect of the Val ➔ Lys mutation is dependent on sequence and structural contexts around the APR. This mutation also alters the solvation shell around the peptide by favoring solute-solvent interactions, thereby increasing its solubility. This work has provided a detailed mechanistic explanation of how APR disruption can mitigate aggregation in biotherapeutics and improve their developability.
Collapse
Affiliation(s)
- R Prabakaran
- Protein Bioinformatics Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Puneet Rawat
- Protein Bioinformatics Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Nobuaki Yasuo
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Masakazu Sekijima
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, Connecticut, USA
| | - M Michael Gromiha
- Protein Bioinformatics Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India.,Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
15
|
Molecular insight into the early stage of amyloid-β(1-42) Homodimers aggregation influenced by histidine tautomerism. Int J Biol Macromol 2021; 184:887-897. [PMID: 34153362 DOI: 10.1016/j.ijbiomac.2021.06.078] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/23/2021] [Accepted: 06/10/2021] [Indexed: 11/20/2022]
Abstract
Aggregated amyloid β-peptide (Aβ) in small oligomeric forms inside the brain causes synaptic function disruption and the development of Alzheimer's disease (AD). Histidine is an important amino acid that may lead to structural changes. Aβ42 monomer chain includes 3 histidine residues that considering two ε and δ tautomers 8 isomers, including (εεε) and (εδδ) could be formed. Molecular dynamics simulation on homodimerization of (εεε) (the most common type of tautomers) and (εδδ) tautomers with different initial configurations using monomer chains from our previous work were performed to uncover the tautomeric behavior of histidine on Aβ42 aggregation in a physiological pH which is still largely unknown and impossible to observe experimentally. We found a higher propensity of forming β-sheet in (εδδ) homodimers and specifically in a greater amount from Aβ42 than from Aβ40. A smaller amount of β-sheet formation was observed for (εεε) homodimers compared with (εδδ). Additionally, interactions in (εδδ) homodimers may indicate the importance of the hydrophobic core and C-/N-terminals during oligomerization. Our findings indicate the important role of the tautomeric effect of histidine and (εδδ) homodimers at the early stage of Aβ aggregation.
Collapse
|
16
|
Gomes GN, Levine ZA. Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments. J Phys Chem B 2021; 125:1974-1996. [PMID: 33464098 PMCID: PMC8362740 DOI: 10.1021/acs.jpcb.0c09193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
Collapse
Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| |
Collapse
|
17
|
Abedin F, Tatulian SA. Mutual structural effects of unmodified and pyroglutamylated amyloid β peptides during aggregation. J Pept Sci 2021; 27:e3312. [PMID: 33631839 DOI: 10.1002/psc.3312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 11/09/2022]
Abstract
Amyloid β (Aβ) peptide aggregates are linked to Alzheimer's disease (AD). Posttranslationally pyroglutamylated Aβ (pEAβ) occurs in AD brains in significant quantities and is hypertoxic, but the underlying structural and aggregation properties remain poorly understood. Here, the structure and aggregation of Aβ1-40 and pEAβ3-40 are analyzed separately and in equimolar combination. Circular dichroism data show that Aβ1-40 , pEAβ3-40 , and their combination assume α-helical structure in dry state and transition to unordered structure in aqueous buffer. Aβ1-40 and the 1:1 combination gradually acquire β-sheet structure while pEAβ3-40 adopts an α-helix/β-sheet conformation. Thioflavin-T fluorescence studies suggest that the two peptides mutually inhibit fibrillogenesis. Fourier transform infrared (FTIR) spectroscopy identifies the presence of β-turn and α-helical structures in addition to β-sheet structure in peptides in aqueous buffer. The kinetics of transitions from the initial α-helical structure to β-sheet structure were resolved by slow hydration of dry peptides by D2 O vapor, coupled with isotope-edited FTIR. These data confirmed the mutual suppression of β-sheet formation by the two peptides. Remarkably, pEAβ3-40 maintained a significant fraction of α-helical structure in the combined sample, implying a reduced β-sheet propensity of pEAβ3-40 . Altogether, the data imply that the combination of unmodified and pyroglutamylated Aβ peptides resists fibrillogenesis and favors the prefibrillar state, which may underlie hypertoxicity of pEAβ.
Collapse
Affiliation(s)
- Faisal Abedin
- Physics Graduate Program, University of Central Florida, Orlando, Florida, USA
| | - Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, Florida, USA
| |
Collapse
|
18
|
Guyon A, Rousseau J, Lamothe G, Tremblay JP. The protective mutation A673T in amyloid precursor protein gene decreases Aβ peptides production for 14 forms of Familial Alzheimer's Disease in SH-SY5Y cells. PLoS One 2020; 15:e0237122. [PMID: 33370284 PMCID: PMC7769289 DOI: 10.1371/journal.pone.0237122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
The deposition of Aβ plaques in the brain leads to the onset and development of Alzheimer’s disease. The Amyloid precursor protein (APP) is cleaved by α-secretase (non-amyloidogenic processing of APP), however increased cleavage by β-secretase (BACE1) leads to the accumulation of Aβ peptides, which forms plaques. APP mutations mapping to exons 16 and 17 favor plaque accumulation and cause Familial Alzheimer Disease (FAD). However, a variant of the APP gene (A673T) originally found in an Icelandic population reduces BACE1 cleavage by 40%. A series of plasmids containing the APP gene, each with one of 29 different FAD mutations mapping to exon 16 and exon 17 was created. These plasmids were then replicated with the addition of the A673T mutation. Combined these formed the library of plasmids that was used in this study. The plasmids were transfected in neuroblastomas to assess the effect of this mutation on Aβ peptide production. The production of Aβ peptides was decreased for some FAD mutations due to the presence of the co-dominant A673T mutation. The reduction of Aβ peptide concentrations for the London mutation (V717I) even reached the same level as for A673T control in SH-SY5Y cells. These preliminary results suggest that the insertion of A673T in APP genes containing FAD mutations might confer a clinical benefit in preventing or delaying the onset of some FADs.
Collapse
Affiliation(s)
- Antoine Guyon
- Centre de Recherche du CHU, Québec-Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire, l’Université Laval Québec, Québec, Québec, Canada
- * E-mail:
| | - Joël Rousseau
- Centre de Recherche du CHU, Québec-Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire, l’Université Laval Québec, Québec, Québec, Canada
| | - Gabriel Lamothe
- Centre de Recherche du CHU, Québec-Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire, l’Université Laval Québec, Québec, Québec, Canada
| | - Jacques P. Tremblay
- Centre de Recherche du CHU, Québec-Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire, l’Université Laval Québec, Québec, Québec, Canada
| |
Collapse
|
19
|
Kakeshpour T, Ramanujam V, Barnes CA, Shen Y, Ying J, Bax A. A lowly populated, transient β-sheet structure in monomeric Aβ 1-42 identified by multinuclear NMR of chemical denaturation. Biophys Chem 2020; 270:106531. [PMID: 33453683 DOI: 10.1016/j.bpc.2020.106531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023]
Abstract
Chemical denaturation is a well-established approach for probing the equilibrium between folded and unfolded states of proteins. We demonstrate applicability of this method to the detection of a small population of a transiently folded structural element in a system that is often considered to be intrinsically fully disordered. The 1HN, 15N, 13Cα, and 13C' chemical shifts of Aβ1-40 and Aβ1-42 peptides and their M35-oxidized variants were monitored as a function of urea concentration and compared to analogous urea titrations of synthetic pentapeptides of homologous sequence. Fitting of the chemical shift titrations yields a 10 ± 1% population for a structured element at the C-terminus of Aβ1-42 that folds with a cooperativity of m = 0.06 kcal/mol·M. The fit also yields the chemical shifts of the folded state and, using a database search, for Aβ1-42 these shifts identified an antiparallel intramolecular β-sheet for residues I32-A42, linked by a type I' β-turn at G37 and G38. The structure is destabilized by oxidation of M35. Paramagnetic relaxation rates and two previously reported weak, medium-range NOE interactions are consistent with this transient β-sheet. Introduction of the requisite A42C mutation and tagging with MTSL resulted in a small stabilization of this β-sheet. Chemical shift analysis suggests a C-terminal β-sheet may be present in Aβ1-40 too, but the turn type at G37 is not type I'. The approach to derive Transient Structure from chemical Denaturation by NMR (TSD-NMR), demonstrated here for Aβ peptides, provides a sensitive tool for identifying the presence of lowly populated, transiently ordered elements in proteins that are considered to be intrinsically disordered, and permits extraction of structural data for such elements.
Collapse
Affiliation(s)
- Tayeb Kakeshpour
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Venkat Ramanujam
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - C Ashley Barnes
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
| |
Collapse
|
20
|
Effect of Amyloid-β Monomers on Lipid Membrane Mechanical Parameters-Potential Implications for Mechanically Driven Neurodegeneration in Alzheimer's Disease. Int J Mol Sci 2020; 22:ijms22010018. [PMID: 33375009 PMCID: PMC7792773 DOI: 10.3390/ijms22010018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 01/21/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease that results in memory loss and the impairment of cognitive skills. Several mechanisms of AD’s pathogenesis were proposed, such as the progressive accumulation of amyloid-β (Aβ) and τ pathology. Nevertheless, the exact neurodegenerative mechanism of the Aβ remains complex and not fully understood. This paper proposes an alternative hypothesis of the mechanism based on maintaining the neuron membrane’s mechanical balance. The incorporation of Aβ decreases the lipid membrane’s elastic properties, which eventually leads to the impairment of membrane clustering, disruption of mechanical wave propagation, and change in gamma oscillations. The first two disrupt the neuron’s ability to function correctly while the last one decreases sensory encoding and perception enabling. To begin discussing this mechanical-balance hypothesis, we measured the effect of two selected peptides, Aβ-40 and Aβ-42, as well as their fluorescently labeled modification, on membrane mechanical properties. The decrease of bending rigidity, consistent for all investigated peptides, was observed using molecular dynamic studies and experimental flicker-noise techniques. Additionally, wave propagation was investigated with molecular dynamic studies in membranes with and without incorporated neurodegenerative peptides. A change in membrane behavior was observed in the membrane system with incorporated Aβ.
Collapse
|
21
|
Childers MC, Daggett V. Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions. Biophys J 2020; 119:1995-2009. [PMID: 33091379 DOI: 10.1016/j.bpj.2020.08.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/09/2020] [Accepted: 08/31/2020] [Indexed: 01/18/2023] Open
Abstract
During amyloidogenesis, proteins undergo conformational changes that allow them to aggregate and assemble into insoluble, fibrillar structures. Soluble oligomers that form during this process typically contain 2-24 monomeric subunits and are cytotoxic. Before the formation of these soluble oligomers, monomeric species first adopt aggregation-competent conformations. Knowledge of the structures of these intermediate states is invaluable to the development of molecular strategies to arrest pathological amyloid aggregation. However, the highly dynamic and interconverting nature of amyloidogenic species limits biophysical characterization of their structures during amyloidogenesis. Here, we use molecular dynamics simulations to probe conformations sampled by monomeric transthyretin under amyloidogenic conditions. We show that certain β-strands in transthyretin tend to unfold and sample nonnative conformations and that the edge strands in one β-sheet (the DAGH sheet) are particularly susceptible to conformational changes in the monomeric state. We also find that changes in the tertiary structure of transthyretin can be associated with disruptions to the secondary structure. We evaluated the conformations produced by molecular dynamics by calculating how well molecular-dynamics-derived structures reproduced NMR-derived interatomic distances. Finally, we leverage our computational results to produce experimentally testable hypotheses that may aid experimental explorations of pathological conformations of transthyretin.
Collapse
Affiliation(s)
- Matthew C Childers
- Department of Bioengineering, University of Washington, Seattle, Washington.
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, Washington
| |
Collapse
|
22
|
Differences in the free energies between the excited states of A β40 and A β42 monomers encode their aggregation propensities. Proc Natl Acad Sci U S A 2020; 117:19926-19937. [PMID: 32732434 DOI: 10.1073/pnas.2002570117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The early events in the aggregation of the intrinsically disordered peptide, amyloid-β (Aβ), involve transitions from the disordered free energy ground state to assembly-competent states. Are the fingerprints of order found in the amyloid fibrils encoded in the conformations that the monomers access at equilibrium? If so, could the enhanced aggregation rate of Aβ42 compared to Aβ40 be rationalized from the sparsely populated high free energy states of the monomers? Here, we answer these questions in the affirmative using coarse-grained simulations of the self-organized polymer-intrinsically disordered protein (SOP-IDP) model of Aβ40 and Aβ42. Although both the peptides have practically identical ensemble-averaged properties, characteristic of random coils (RCs), the conformational ensembles of the two monomers exhibit sequence-specific heterogeneity. Hierarchical clustering of conformations reveals that both the peptides populate high free energy aggregation-prone ([Formula: see text]) states, which resemble the monomers in the fibril structure. The free energy gap between the ground (RC) and the [Formula: see text] states of Aβ42 peptide is smaller than that for Aβ40. By relating the populations of excited states of the two peptides to the fibril formation time scales using an empirical formula, we explain nearly quantitatively the faster aggregation rate of Aβ42 relative to Aβ40. The [Formula: see text] concept accounts for fibril polymorphs, leading to the prediction that the less stable [Formula: see text] state of Aβ42, encoding for the U-bend fibril, should form earlier than the structure with the S-bend topology, which is in accord with Ostwald's rule rationalizing crystal polymorph formation.
Collapse
|
23
|
Del Carmen SLM, Laura GV, Leonardo OL, Bernabé RRG, Antonio MRM. Aβ40 Oligomers Promote Survival and Early Neuronal Differentiation of Dentate Gyrus-Isolated Precursor Cells Through Activation of the Akt Signaling Pathway. Neurotox Res 2020; 38:611-625. [PMID: 32623694 DOI: 10.1007/s12640-020-00253-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 06/13/2020] [Accepted: 06/29/2020] [Indexed: 11/26/2022]
Abstract
The amyloid beta-peptide (Aβ) is the low-abundance product of amyloid precursor protein (APP), which is produced lifelong in the healthy brain. The functional properties of Aβ40 and Aβ42 peptides have not been completely elucidated to date. Although, several studies suggest that these peptides have a number of neurotrophic and neurotoxic properties, respectively. Interestingly, low concentrations of Aβ40 and Aβ42 regulate synaptic plasticity and improve cognitive functions, whereas the accumulation of Aβ42, coupled with the effects of age, can cause dysregulation of synaptic function, as is shown in Alzheimer's disease. Additionally, several studies suggest that both peptides, Aβ40 and Aβ42, are involved in neurogenic processes; however, these results are still controversial. Moreover, existing data indicate a direct relationship between the physicochemical characteristics of the peptides and their effects. Herein, we evaluated the effect of Aβ40 oligomers on hippocampal precursor cells isolated from the dentate gyrus of adult female C57Bl6 mice (mADGPCs). To this end, mADGPCs were treated with nanomolar and micromolar range concentrations of oligomeric forms of Aβ40 for 24, 48, and 72 h to evaluate their effects on several events in the neurogenic process in vitro, including viability, proliferation, and early differentiation. The results indicate that Aβ40 favors mADGPC proliferation, survival, and neuronal differentiation following a mechanism that involves activation of the Akt signaling pathway. Thus, this study provides evidence about the positive effects of Aβ40 oligomers on the neurogenic process in adult mouse hippocampal precursor cells in vitro.
Collapse
Affiliation(s)
- Silva-Lucero María Del Carmen
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, 07360, Mexico City, Mexico
| | - Gómez-Virgilio Laura
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, 07360, Mexico City, Mexico
| | - Ortíz-López Leonardo
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico
| | - Ramírez-Rodríguez Gerardo Bernabé
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico.
| | - Meraz-Ríos Marco Antonio
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, 07360, Mexico City, Mexico.
| |
Collapse
|
24
|
Liang J, Pitsillou E, Man AYL, Madzima S, Bresnehan SM, Nakai ME, Hung A, Karagiannis TC. Utilisation of the OliveNet™ Library to investigate phenolic compounds using molecular modelling studies in the context of Alzheimer's disease. Comput Biol Chem 2020; 87:107271. [PMID: 32521495 DOI: 10.1016/j.compbiolchem.2020.107271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 01/05/2023]
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative disease that affects over 47 million people worldwide, and is the most common form of dementia. There is a vast body of literature demonstrating that the disease is caused by an accumulation of toxic extracellular amyloid-β (Aβ) peptides and intracellular neurofibrillary tangles that consist of hyperphosphorylated tau. Adherence to the Mediterranean diet has been shown to reduce the incidence of AD and the phenolic compounds in extra virgin olive oil, including oleocanthal, have gained a significant amount of attention. A large number of these ligands have been described in the pre-existing literature and 222 of these compounds have been characterised in the OliveNet™ database. In this study, molecular docking was used to screen the 222 phenolic compounds from the OliveNet™ database and assess their ability to bind to various forms of the Aβ and tau proteins. The phenolic ligands were found to be binding strongly to the hairpin-turn of the Aβ1-40 and Aβ1-42 monomers, and binding sites were also identified in the tau fibril protein structures. Luteolin-4'-O-rutinoside, oleuricine A, isorhoifolin, luteolin-7-O-rutinoside, cyanidin-3-O-rutinoside and luteolin-7,4-O-diglucoside were predicted to be novel lead compounds. Molecular dynamics (MD) simulations performed using well-known olive ligands bound to Aβ1-42 oligomers highlighted that future work may examine potential anti-aggregating properties of novel compounds in the OliveNet™ database. This may lead to the development and evaluation of new compounds that may have efficacy against Alzheimer's disease.
Collapse
Affiliation(s)
- Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; School of Science, RMIT University, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Abella Y L Man
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Sibonginkosi Madzima
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah M Bresnehan
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Michael E Nakai
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
| |
Collapse
|
25
|
Sahoo BR, Cox SJ, Ramamoorthy A. High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease. Chem Commun (Camb) 2020; 56:4627-4639. [PMID: 32300761 PMCID: PMC7254607 DOI: 10.1039/d0cc01551b] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna in establishing the structure to function relationship for Aβ oligomers prevents the development of an effective treatment for AD. While the transient and heterogeneous properties of Aβ oligomers impose many challenges for structural investigation, an effective use of a combination of NMR techniques has successfully identified and characterized them at atomic-resolution. Here, we review the successful utilization of solution and solid-state NMR techniques to probe the aggregation and structures of small and large oligomers of Aβ. Biophysical studies utilizing the commonly used solution and 19F based NMR experiments to identify the formation of small size early intermediates and to obtain their structures, and dock-lock mechanism of fiber growth at atomic-resolution are discussed. In addition, the use of proton-detected magic angle spinning (MAS) solid-state NMR experiments to obtain high-resolution insights into the aggregation pathways and structures of large oligomers and other aggregates is also presented. We expect these NMR based studies to be valuable for real-time monitoring of the depletion of monomers and the formation of toxic oligomers and high-order aggregates under a variety of conditions, and to solve the high-resolution structures of small and large size oligomers for most amyloid proteins, and therefore to develop inhibitors and drugs.
Collapse
Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | | | | |
Collapse
|
26
|
Adhikari R, Yang M, Saikia N, Dutta C, Alharbi WFA, Shan Z, Pandey R, Tiwari A. Acetylation of Aβ42 at Lysine 16 Disrupts Amyloid Formation. ACS Chem Neurosci 2020; 11:1178-1191. [PMID: 32207962 PMCID: PMC7605495 DOI: 10.1021/acschemneuro.0c00069] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The residue lysine 28 (K28) is known to form an important salt bridge that stabilizes the Aβ amyloid structure, and acetylation of lysine 28 (K28Ac) slows the Aβ42 fibrillization rate but does not affect fibril morphology. On the other hand, acetylation of lysine 16 (K16Ac) residue greatly diminishes the fibrillization property of Aβ42 peptide and also affects its toxicity. This is due to the fact that lysine 16 acetylated amyloid beta peptide forms amorphous aggregates instead of amyloid fibrils. This is likely a result of increased hydrophobicity of the K16-A21 region due to K16 acetylation, as confirmed by molecular dynamic simulation studies. The calculated results show that the hydrophobic patches of aggregates from acetylated peptides were different when compared to wild-type (WT) peptide. K16Ac and double acetylated (KKAc) peptide aggregates show significantly higher cytotoxicity compared to the WT or K28Ac peptide aggregates alone. However, the heterogeneous mixture of WT and acetylated Aβ42 peptide aggregates exhibited higher free radical formation as well as cytotoxicity, suggesting dynamic interactions between different species could be a critical contributor to Aβ pathology.
Collapse
Affiliation(s)
- Rashmi Adhikari
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Mu Yang
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nabanita Saikia
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Colina Dutta
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Wafa F A Alharbi
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Zhiying Shan
- Department of Kinesiology and Integrative Physiology, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ravindra Pandey
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ashutosh Tiwari
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| |
Collapse
|
27
|
Penke B, Szűcs M, Bogár F. Oligomerization and Conformational Change Turn Monomeric β-Amyloid and Tau Proteins Toxic: Their Role in Alzheimer's Pathogenesis. Molecules 2020; 25:molecules25071659. [PMID: 32260279 PMCID: PMC7180792 DOI: 10.3390/molecules25071659] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
The structural polymorphism and the physiological and pathophysiological roles of two important proteins, β-amyloid (Aβ) and tau, that play a key role in Alzheimer's disease (AD) are reviewed. Recent results demonstrate that monomeric Aβ has important physiological functions. Toxic oligomeric Aβ assemblies (AβOs) may play a decisive role in AD pathogenesis. The polymorph fibrillar Aβ (fAβ) form has a very ordered cross-β structure and is assumed to be non-toxic. Tau monomers also have several important physiological actions; however, their oligomerization leads to toxic oligomers (TauOs). Further polymerization results in probably non-toxic fibrillar structures, among others neurofibrillary tangles (NFTs). Their structure was determined by cryo-electron microscopy at atomic level. Both AβOs and TauOs may initiate neurodegenerative processes, and their interactions and crosstalk determine the pathophysiological changes in AD. TauOs (perhaps also AβO) have prionoid character, and they may be responsible for cell-to-cell spreading of the disease. Both extra- and intracellular AβOs and TauOs (and not the previously hypothesized amyloid plaques and NFTs) may represent the novel targets of AD drug research.
Collapse
Affiliation(s)
- Botond Penke
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (M.S.); (F.B.)
- Correspondence:
| | - Mária Szűcs
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (M.S.); (F.B.)
| | - Ferenc Bogár
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (M.S.); (F.B.)
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Hungary
| |
Collapse
|
28
|
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]
|
29
|
Masutani K, Yamamori Y, Kim K, Matubayasi N. Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation. J Chem Phys 2019; 150:145101. [DOI: 10.1063/1.5088395] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Keiichi Masutani
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center and Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Kang Kim
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
30
|
Huang Q, Wang H, Gao H, Cheng P, Zhu L, Wang C, Yang Y. In Situ Observation of Amyloid Nucleation and Fibrillation by FastScan Atomic Force Microscopy. J Phys Chem Lett 2019; 10:214-222. [PMID: 30543438 DOI: 10.1021/acs.jpclett.8b03143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amyloidogenic proteins are key components in various amyloid diseases. The aggregation process and the local structural changes of the toxic species from toxic oligomers to protofibrils and subsequently to mature fibrils are crucial for understanding the molecular mechanism of the amyloidgenic process and also for developing a treatment strategy. Exploration on amyloid aggregation dynamics in situ under real liquid condition is feasible for reflection of the whole process with biological correlations. Herein we report the in situ dynamic study and structure exploration of Amylin1-37 aggregation by FastScan atomic force microscopy. Amylin1-37 nucleation process was observed in which smaller oligomers or monomers were assimilated by the surrounding big oligomers. Amylin1-37 protofibril aggregation was positively correlated with monomer concentration, whereas no direct relationship was observed between fibril elongation and monomer concentration. Growing end and passivated end were found during Amylin1-37 fibrillation. In the assembly process, the growing end kept its structure, and its stiffness was lower than the aggregate body, whereas the passivated end might experience rearrangements of β-structures, which eventually enabled fibril growth from this end. This work is beneficial to the insights of amyloid fibrillation and may shed light on the development of drugs targeting the specific phase of amyloid aggregation.
Collapse
Affiliation(s)
- Qunxing Huang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Huayi Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Houqian Gao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Peng Cheng
- State Key Laboratory of Tribology, Department of Mechanical Engineering , Tsinghua University , Beijing 100084 , China
| | - Ling Zhu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , 19 A Yuquan Rd , Shijingshan District, Beijing 100049 , China
| |
Collapse
|
31
|
Sahoo A, Xu H, Matysiak S. Pathways of amyloid-beta absorption and aggregation in a membranous environment. Phys Chem Chem Phys 2019; 21:8559-8568. [PMID: 30964132 DOI: 10.1039/c9cp00040b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aggregation of misfolded oligomeric amyloid-beta (Aβ) peptides on lipid membranes has been identified as a primary event in Alzheimer's pathogenesis. However, the structural and dynamical features of this membrane assisted Aβ aggregation have not been well characterized. The microscopic characterization of dynamic molecular-level interactions in peptide aggregation pathways has been challenging both computationally and experimentally. In this work, we explore differential patterns of membrane-induced Aβ 16-22 (K-L-V-F-F-A-E) aggregation from the microscopic perspective of molecular interactions. Physics-based coarse-grained molecular dynamics (CG-MD) simulations were employed to investigate the effect of lipid headgroup charge - zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPC) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine: POPS) - on Aβ 16-22 peptide aggregation. Our analyses present an extensive overview of multiple pathways for peptide absorption and biomechanical forces governing peptide folding and aggregation. In agreement with experimental observations, anionic POPS molecules promote extended configurations in Aβ peptides that contribute towards faster emergence of ordered β-sheet-rich peptide assemblies compared to POPC, suggesting faster fibrillation. In addition, lower cumulative rates of peptide aggregation in POPS due to higher peptide-lipid interactions and slower lipid diffusion result in multiple distinct ordered peptide aggregates that can serve as nucleation seeds for subsequent Aβ aggregation. This study provides an in-silico assessment of experimentally observed aggregation patterns, presents new morphological insights and highlights the importance of lipid headgroup chemistry in modulating the peptide absorption and aggregation process.
Collapse
Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
| | | | | |
Collapse
|
32
|
Sneha P, Panda PK, Gharemirshamlu FR, Bamdad K, Balaji S. Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior- a computational perspective. J Theor Biol 2018; 451:35-45. [PMID: 29705491 DOI: 10.1016/j.jtbi.2018.04.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 02/14/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022]
Abstract
HIV-1 being the most widespread type worldwide, its accounts for almost 95% of all infections including HIV associated dementia (HAD) that triggers neurological dysfunction and neurodegeneration in patients. The common features associated with HAD and other neurodegenerative diseases are accumulation of amyloid plaques, neuronal loss and deterioration of cognitive abilities, amongst which amyloid fibrillation is considered to be a hallmark. The success of effective therapeutics lies in the understanding of mechanisms leading to neurotoxicity. Few viral proteins like gp-120 are known to be involved in aggregation and enhancement of viral infectivity while comprehending the neurotoxic role of some other proteins is still underway. In the current study, amyloidogenic potential of HIV-1 Vpu protein from brain isolate is investigated through computational approaches. The aggregation propensity of brain derived HIV-1 Vpu was assessed by several amyloid prediction servers that projected the region 4-35 to be amyloidogenic. The protein structure was modeled and subjected to 70 ns molecular dynamics (MD) simulation to investigate the transformation of α-helical conformation of the predicted aggregate region into β-sheet, proposing the protein's ability to initiate fibril formation that is central to amyloidogenic proteins. The structural features of brain derived HIV-1 Vpu were consistent with the in silico amyloid prediction results that depicts the conformational change in the region 8-28 of which residues Ala8, Ile9, Val10, Ala19, Ile20 and Val21 constitutes β-sheet formation. The α-helix/β-sheet discordance of the predicted region was reflected in the simulation study highlighting the possible structural transition associated with HIV-1 Vpu protein of brain isolate.
Collapse
Affiliation(s)
- Patil Sneha
- School of Biotechnology and Bioinformatics, D.Y. Patil deemed to be University, CBD Belapur, Sector 15, Navi Mumbai, Maharashtra 400614, India; Research and Development Centre, Bharathiar University, Coimbatore 641046 India
| | - Pritam Kumar Panda
- School of Biotechnology and Bioinformatics, D.Y. Patil deemed to be University, CBD Belapur, Sector 15, Navi Mumbai, Maharashtra 400614, India
| | | | - Kourosh Bamdad
- Faculty of Science(,) Payame Noor University, 19395-4697 Iran
| | - Seetharaman Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104 Karnataka, India.
| |
Collapse
|
33
|
Das P, Matysiak S, Mittal J. Looking at the Disordered Proteins through the Computational Microscope. ACS CENTRAL SCIENCE 2018; 4:534-542. [PMID: 29805999 PMCID: PMC5968442 DOI: 10.1021/acscentsci.7b00626] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 05/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.
Collapse
Affiliation(s)
- Payel Das
- IBM Thomas J.
Watson Research Center, Yorktown Heights, New York 10598, United States
- E-mail:
| | - Silvina Matysiak
- Fischell
Department of Bioengineering, University
of Maryland, College Park, Maryland 20742, United States
| | - Jeetain Mittal
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
34
|
Abstract
β- N-Methylamino-l-alanine (BMAA) is a neurotoxic agent implicated in ALS as well as Parkinson's and Alzheimer's diseases. It is produced by blue-green algae and could find its way via fish and seafood into the human food supply. Isolation from biological samples yields the compound in monomeric and protein-bound form. It has been suggested that the protein-bound fraction may result from genetic misincorporation into proteins in place of serine. Concomitant misfolding of the mutated proteins may be responsible for the neurological diseases. Recent reports that contradict the misincorporation theory leave unresolved the nature of the protein-bound form of BMAA. We have found from quantum mechanical calculations on model systems that it is possible to bind BMAA with high affinity in a noncovalent fashion to proteins. Because of our interest in Alzheimer's disease, molecular dynamics simulations were applied to search for such binding between BMAA and the β-amyloid peptide and to discover whether replacement of either of its two serine residues could affect its aggregation into neurotoxic oligomers. No stable noncovalently bound complex was found, and it was concluded that incorporation of BMAA in place of serine would not alter the conformational dynamics of the β-amyloid peptide.
Collapse
Affiliation(s)
- Arvi Rauk
- Department of Chemistry , University of Calgary , 2500 University Dr. NW , Calgary , Alberta , Canada T2N 1N4
| |
Collapse
|
35
|
Zhang Y, Wang A, DeBenedictis EP, Keten S. Bending energy penalty enhances the adhesive strength of functional amyloid curli to surfaces. NANOTECHNOLOGY 2017; 28:464002. [PMID: 28952462 DOI: 10.1088/1361-6528/aa8f72] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The functional amyloid curli fiber, a major proteinaceous component of biofilm extracellular matrices, plays an important role in biofilm formation and enterobacteriaceae adhesion. Curli nanofibers exhibit exceptional underwater adhesion to various surfaces, have high rigidity and strong tensile mechanical properties, and thus hold great promise in biomaterials. The mechanisms of how curli fibers strongly attach to surfaces and detach under force remain elusive. To investigate curli fiber adhesion to surfaces, we developed a coarse-grained curli fiber model, in which the protein subunit CsgA (curli specific gene A) self-assembles into the fiber. The coarse-grained model yields physiologically relevant and tunable bending rigidity and persistence length. The force-induced desorption of a single curli fiber is examined using coarse-grained modeling and theoretical analysis. We find that the bending energy penalty arising from high persistence length enhances the resistance of the curli fiber against desorption and thus strengthens the adhesion of the curli fiber to surfaces. The CsgA-surface adhesion energy and the curli fiber bending rigidity both play crucial roles in the resistance of curli fiber against desorption from surfaces. To enable the desorption process, the applied peeling force must overcome both the interfacial adhesion energy and the energy barrier for bending the curli fiber at the peeling front. We show that the energy barrier to desorption increases with the interfacial adhesion energy, however, the bending induced failure of a single curli fiber limits the work of adhesion if the proportion of the CsgA-surface adhesion energy to the CsgA-CsgA cohesive energy becomes large. These results illustrate that the optimal adhesion performance of nanofibers is dictated by the interplay between bending, surface energy and cohesive energy. Our model provides timely insight into enterobacteriaceae adhesion mechanisms as well as future designs of engineered curli fiber based adhesives.
Collapse
Affiliation(s)
- Yao Zhang
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, United States of America
| | | | | | | |
Collapse
|
36
|
Weber OC, Uversky VN. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β 42 in water. INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1377813. [PMID: 30250773 DOI: 10.1080/21690707.2017.1377813] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022]
Abstract
Amyloid-β42 (Aβ42) is an intrinsically disordered peptide intimately related to the pathogenesis of several neurodegenerative diseases. Molecular dynamics (MD) simulations are extensively utilized in the characterization of the structures and conformational dynamics of intrinsically disordered proteins (IDPs) including Aβ42, with AMBER and CHARMM parameters being commonly used in these studies. Recently, comparison of the effects of force field parameters on the Aβ42 structures has started to gain significant attention. In this study, the structures of Aβ42 are simulated using AMBER FF99SB and CHARMM22/CMAP parameters via replica exchange MD simulations utilizing a widely used clustering algorithm. These analyses show that the structural properties (extent and positioning of the elements of secondary and tertiary structure), radius of gyration values, number and position of salt bridges are extremely dependent on the chosen force field parameters notably with the usage of clustering algorithms. For example, predicted secondary structure elements, which are of the great importance for better understanding of the molecular mechanisms of neurodegenerative diseases, deviate enormously in models generated using currently available force field parameters for proteins. Based on the derived models, chemical shift values are calculated and compared to the experimentally determined data. This comparison revealed that although both force field parameters yield results in agreement with experiments, the obtained structural properties were rather different using a clustering algorithm. In other words, these results show that the predicted structures depend heavily on the force field parameters. Importantly, since none of the force field parameters currently utilized in MD studies were developed specifically taking into account the disordered nature of IDPs, these findings clearly indicate that new force field parameters have to be developed for IDPs considering their rapid flexibility and dynamics with high amplitude. Furthermore, molecular simulations of IDPs are typically conducted using one water volume. We show that the confined aqueous volume impacts the predicted structural properties of Aβ42 in water. Although up to date, confined aqueous volume effects have been ignored in the MD simulations of IDPs in water, our data indicate that these effects have to be taken into account in predicting the structural and thermodynamic properties of disordered proteins in solution.
Collapse
Affiliation(s)
- Orkid Coskuner Weber
- Department of Chemistry and Neurosciences Institute, The University of Texas at San Antonio, San Antonio, TX, USA.,Institut für Physikalische Chemie, Universität zu Köln, Köln, Germany.,Molecular Biotechnology Division, Turkisch-Deutsche Universität, Istanbul Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| |
Collapse
|
37
|
Dorosh L, Stepanova M. Probing oligomerization of amyloid beta peptide in silico. MOLECULAR BIOSYSTEMS 2017; 13:165-182. [PMID: 27844078 DOI: 10.1039/c6mb00441e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aggregation of amyloid β (Aβ) peptide is implicated in fatal Alzheimer's disease, for which no cure is available. Understanding the mechanisms responsible for this aggregation is required in order for therapies to be developed. In an effort to better understand the molecular mechanisms involved in spontaneous aggregation of Aβ peptide, extensive molecular dynamics simulations are reported, and the results are analyzed through a combination of structural biology tools and a novel essential collective dynamics method. Several model systems composed of ten or twelve Aβ17-42 chains in water are investigated, and the influence of metal ions is probed. The results suggest that Aβ monomers tend to aggregate into stable globular-like oligomers with 13-23% of β-sheet content. Two stages of oligomer formation have been identified: quick collapse within the first 40 ns of the simulation, characterized by a decrease in inter-chain separation and build-up of β-sheets, and the subsequent slow relaxation of the oligomer structure. The resulting oligomers comprise a stable, coherently moving sub-aggregate of 6-9 strongly inter-correlated chains. Cu2+ and Fe2+ ions have been found to develop coordination bonds with carboxylate groups of E22, D23 and A42, which remain stable during 200 ns simulations. The presence of Fe2+, and particularly Cu2+ ions, in negatively charged cavities has been found to cause significant changes in the structure and dynamics of the oligomers. The results indicate, in particular, that formation of non-fibrillar oligomers might be involved in early template-free aggregation of Aβ17-42 monomers, with charged species such as Cu2+ or Fe2+ ions playing an important role.
Collapse
Affiliation(s)
- L Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada
| | - M Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada. and National Research Council of Canada, Edmonton, Alberta, Canada and Department of Physics, Astronomy, and Materials Science, Missouri State University, Springfield, MO, USA
| |
Collapse
|
38
|
Trusova VM, Gorbenko GP. Molecular dynamics simulations of lysozyme-lipid systems: probing the early steps of protein aggregation. J Biomol Struct Dyn 2017; 36:2249-2260. [PMID: 28665188 DOI: 10.1080/07391102.2017.1349691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Using the molecular dynamics simulation, the role of lipids in the lysozyme transition into the aggregation-competent conformation has been clarified. Analysis of the changes of lysozyme secondary structure upon its interactions with the model bilayer membranes composed of phosphatidylcholine and its mixtures with phosphatidylglycerol (10, 40, and 80 mol%) within the time interval of 100 ns showed that lipid-bound protein is characterized by the increased content of β-structures. Along with this, the formation of protein-lipid complexes was accompanied by the increase in the gyration radius and the decrease in RMSD of polypeptide chain. The results obtained were interpreted in terms of the partial unfolding of lysozyme molecule on the lipid matrix, with the magnitude of this effect being increased with increasing the fraction of anionic lipids. Based on the results of molecular dynamics simulation, a hypothetical model of the nucleation of lysozyme amyloid fibrils in a membrane environment was suggested.
Collapse
Affiliation(s)
- Valeriya M Trusova
- a Department of Nuclear and Medical Physics , V.N. Karazin Kharkov National University , 4 Svobody Sq., Kharkov 61022 , Ukraine
| | - Galyna P Gorbenko
- a Department of Nuclear and Medical Physics , V.N. Karazin Kharkov National University , 4 Svobody Sq., Kharkov 61022 , Ukraine
| |
Collapse
|
39
|
Brown AM, Bevan DR. Molecular Dynamics Simulations of Amyloid β-Peptide (1-42): Tetramer Formation and Membrane Interactions. Biophys J 2017; 111:937-49. [PMID: 27602722 DOI: 10.1016/j.bpj.2016.08.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 01/10/2023] Open
Abstract
The aggregation cascade and peptide-membrane interactions of the amyloid β-peptide (Aβ) have been implicated as toxic events in the development and progression of Alzheimer's disease. Aβ42 forms oligomers and ultimately plaques, and it has been hypothesized that these oligomeric species are the main toxic species contributing to neuronal cell death. To better understand oligomerization events and subsequent oligomer-membrane interactions of Aβ42, we performed atomistic molecular-dynamics (MD) simulations to characterize both interpeptide interactions and perturbation of model membranes by the peptides. MD simulations were utilized to first show the formation of a tetramer unit by four separate Aβ42 peptides. Aβ42 tetramers adopted an oblate ellipsoid shape and showed a significant increase in β-strand formation in the final tetramer unit relative to the monomers, indicative of on-pathway events for fibril formation. The Aβ42 tetramer unit that formed in the initial simulations was used in subsequent MD simulations in the presence of a pure POPC or cholesterol-rich raft model membrane. Tetramer-membrane simulations resulted in elongation of the tetramer in the presence of both model membranes, with tetramer-raft interactions giving rise to the rearrangement of key hydrophobic regions in the tetramer and the formation of a more rod-like structure indicative of a fibril-seeding aggregate. Membrane perturbation by the tetramer was manifested in the form of more ordered, rigid membranes, with the pure POPC being affected to a greater extent than the raft membrane. These results provide critical atomistic insight into the aggregation pathway of Aβ42 and a putative toxic mechanism in the pathogenesis of Alzheimer's disease.
Collapse
Affiliation(s)
- Anne M Brown
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - David R Bevan
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia.
| |
Collapse
|
40
|
Jong K, Grisanti L, Hassanali A. Hydrogen Bond Networks and Hydrophobic Effects in the Amyloid β30–35 Chain in Water: A Molecular Dynamics Study. J Chem Inf Model 2017; 57:1548-1562. [DOI: 10.1021/acs.jcim.7b00085] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- KwangHyok Jong
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
- Department
of Physics, Kim II Sung University, RyongNam Dong, TaeSong District, Pyongyang, D.P.R., Korea
| | - Luca Grisanti
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
| | - Ali Hassanali
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| |
Collapse
|
41
|
|
42
|
Meric G, Robinson AS, Roberts CJ. Driving Forces for Nonnative Protein Aggregation and Approaches to Predict Aggregation-Prone Regions. Annu Rev Chem Biomol Eng 2017; 8:139-159. [DOI: 10.1146/annurev-chembioeng-060816-101404] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gulsum Meric
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Anne S. Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118
| | - Christopher J. Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| |
Collapse
|
43
|
Menon S, Sengupta N. Influence of Hyperglycemic Conditions on Self-Association of the Alzheimer's Amyloid β (Aβ 1-42) Peptide. ACS OMEGA 2017; 2:2134-2147. [PMID: 30023655 PMCID: PMC6044820 DOI: 10.1021/acsomega.7b00018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/08/2017] [Indexed: 06/08/2023]
Abstract
Clinical studies have identified a correlation between type-2 diabetes mellitus and cognitive decrements en route to the onset of Alzheimer's disease (AD). Recent studies have established that post-translational modifications of the amyloid β (Aβ) peptide occur under hyperglycemic conditions; particularly, the process of glycation exacerbates its neurotoxicity and accelerates AD progression. In view of the assertion that macromolecular crowding has an altering effect on protein self-assembly, it is crucial to characterize the effects of hyperglycemic conditions via crowding on Aβ self-assembly. Toward this purpose, fully atomistic molecular dynamics simulations were performed to study the effects of glucose crowding on Aβ dimerization, which is the smallest known neurotoxic species. The dimers formed in the glucose-crowded environment were found to have weaker associations as compared to that of those formed in water. Binding free energy calculations show that the reduced binding strength of the dimers can be mainly attributed to the overall weakening of the dispersion interactions correlated with substantial loss of interpeptide contacts in the hydrophobic patches of the Aβ units. Analysis to discern the differential solvation pattern in the glucose-crowded and pure water systems revealed that glucose molecules cluster around the protein, at a distance of 5-7 Å, which traps the water molecules in close association with the protein surface. This preferential exclusion of glucose molecules and resulting hydration of the Aβ peptides has a screening effect on the hydrophobic interactions, which in turn diminishes the binding strength of the resulting dimers. Our results imply that physical effects attributed to crowded hyperglycemic environments are incapable of solely promoting Aβ self-assembly, indicating that further mechanistic studies are required to provide insights into the self-assembly of post-translationally modified Aβ peptides, known to possess aggravated toxicity, under these conditions.
Collapse
Affiliation(s)
- Sneha Menon
- Physical
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Training and Development Complex, CSIR Campus,
CSIR Road, Chennai 600113, India
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur 741246, West Bengal, India
| |
Collapse
|
44
|
Goldblatt G, Cilenti L, Matos JO, Lee B, Ciaffone N, Wang QX, Tetard L, Teter K, Tatulian SA. Unmodified and pyroglutamylated amyloid β peptides form hypertoxic hetero-oligomers of unique secondary structure. FEBS J 2017; 284:1355-1369. [PMID: 28294556 DOI: 10.1111/febs.14058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 11/29/2022]
Abstract
Amyloid β (Aβ) peptide plays a major role in Alzheimer's disease (AD) and occurs in multiple forms, including pyroglutamylated Aβ (AβpE). Identification and characterization of the most cytotoxic Aβ species is necessary for advancement in AD diagnostics and therapeutics. While in brain tissue multiple Aβ species act in combination, structure/toxicity studies and immunotherapy trials have been focused on individual forms of Aβ. As a result, the molecular composition and the structural features of "toxic Aβ oligomers" have remained unresolved. Here, we have used a novel approach, hydration from gas phase coupled with isotope-edited Fourier transform infrared (FTIR) spectroscopy, to identify the prefibrillar assemblies formed by Aβ and AβpE and to resolve the structures of both peptides in combination. The peptides form unusual β-sheet oligomers stabilized by intramolecular H-bonding as opposed to intermolecular H-bonding in the fibrils. Time-dependent morphological changes in peptide assemblies have been visualized by atomic force microscopy. Aβ/AβpE hetero-oligomers exert unsurpassed cytotoxic effect on PC12 cells as compared to oligomers of individual peptides or fibrils. These findings lead to a novel concept that Aβ/AβpE hetero-oligomers, not just Aβ or AβpE oligomers, constitute the main neurotoxic conformation. The hetero-oligomers thus present a new biomarker that may be targeted for development of more efficient diagnostic and immunotherapeutic strategies to combat AD.
Collapse
Affiliation(s)
- Greg Goldblatt
- Biomedical Sciences Graduate Program, University of Central Florida, Orlando, FL, USA
| | - Lucia Cilenti
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Jason O Matos
- Biotechnology Graduate Program, University of Central Florida, Orlando, FL, USA
| | - Briana Lee
- Nanotechnology Graduate Program, NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Nicholas Ciaffone
- Nanotechnology Graduate Program, NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Qing X Wang
- Physics Graduate Program, College of Sciences, University of Central Florida, Orlando, FL, USA
| | - Laurene Tetard
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Physics, College of Sciences, University of Central Florida, Orlando, FL, USA
| | - Ken Teter
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Suren A Tatulian
- Department of Physics, College of Sciences, University of Central Florida, Orlando, FL, USA
| |
Collapse
|
45
|
Das P, Chacko AR, Belfort G. Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aβ 42 Dimer Structure. ACS Chem Neurosci 2017; 8:606-618. [PMID: 28292185 DOI: 10.1021/acschemneuro.6b00357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aβ dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aβ1-42 dimers have been performed, resulting into a total of 51 μs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aβ42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aβ42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.
Collapse
Affiliation(s)
- Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Anita R. Chacko
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Georges Belfort
- Howard
P. Isermann Department of Chemical and Biological Engineering, and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180-3590, United States
| |
Collapse
|
46
|
Pagadala NS, Syed K, Bhat R. In silico strategies on prion pathogenic conversion and inhibition from PrPC–PrPSc. Expert Opin Drug Discov 2017; 12:241-248. [DOI: 10.1080/17460441.2017.1287171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Nataraj S. Pagadala
- Department of Medical Microbiology and Immunology, 6-020 Katz Group Centre, University of Alberta, Edmonton, Canada
| | - Khajamohiddin Syed
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, South Africa
| | - Rakesh Bhat
- Department of Medical Microbiology and Immunology, 6-020 Katz Group Centre, University of Alberta, Edmonton, Canada
| |
Collapse
|
47
|
Zhang Y, Hashemi M, Lv Z, Lyubchenko YL. Self-assembly of the full-length amyloid Aβ42 protein in dimers. NANOSCALE 2016; 8:18928-18937. [PMID: 27714140 PMCID: PMC5114164 DOI: 10.1039/c6nr06850b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The self-assembly of amyloid (Aβ) proteins into nano-aggregates is a hallmark of Alzheimer's disease (AD) development, yet the mechanism of how disordered monomers assemble into aggregates remains elusive. Here, we applied long-time molecular dynamics simulations to fully characterize the assembly of Aβ42 monomers into dimers. Monomers undergo conformational changes during their interaction, but the resulting dimer structures do not resemble those found in fibril structures. To identify natural conformations of dimers among a set of simulated ones, validation approaches were developed and applied, and a subset of dimer conformations were characterized. These dimers do not contain long β-strands that are usually found in fibrils. The dimers are stabilized primarily by interactions within the central hydrophobic regions and the C-terminal regions, with a contribution from local hydrogen bonding. The dimers are dynamic, as evidenced by the existence of a set of conformations and by the quantitative analyses of the dimer dissociation process.
Collapse
Affiliation(s)
- Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 69198, USA.
| | | | | | | |
Collapse
|
48
|
Cheon M, Kang M, Chang I. Polymorphism of fibrillar structures depending on the size of assembled Aβ 17-42 peptides. Sci Rep 2016; 6:38196. [PMID: 27901087 PMCID: PMC5128875 DOI: 10.1038/srep38196] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/04/2016] [Indexed: 01/16/2023] Open
Abstract
The size of assembled Aβ17-42 peptides can determine polymorphism during oligomerization and fibrillization, but the mechanism of this effect is unknown. Starting from separate random monomers, various fibrillar oligomers with distinct structural characteristics were identified using discontinuous molecular dynamics simulations based on a coarse-grained protein model. From the structures observed in the simulations, two characteristic oligomer sizes emerged, trimer and paranuclei, which generated distinct structural patterns during fibrillization. A majority of the simulations for trimers and tetramers formed non-fibrillar oligomers, which primarily progress to off-pathway oligomers. Pentamers and hexamers were significantly converted into U-shape fibrillar structures, meaning that these oligomers, called paranuclei, might be potent on-pathway intermediates in fibril formation. Fibrillar oligomers larger than hexamers generated substantial polymorphism in which hybrid structures were readily formed and homogeneous fibrillar structures appeared infrequently.
Collapse
Affiliation(s)
- Mookyung Cheon
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea.,Department of Neural Development and Disease, Korea Brain Research Institute, Daegu 41068, Korea
| | - Mooseok Kang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| |
Collapse
|
49
|
Goldblatt G, Matos JO, Gornto J, Tatulian SA. Isotope-edited FTIR reveals distinct aggregation and structural behaviors of unmodified and pyroglutamylated amyloid β peptides. Phys Chem Chem Phys 2016. [PMID: 26214017 DOI: 10.1039/c5cp03343h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amyloid β peptide (Aβ) is causatively associated with Alzheimer's disease (AD), and N-terminally truncated and pyroglutamylated Aβ peptides (AβpE) exert hypertoxic effect by an unknown mechanism. Recent evidence has identified the prefibrillar oligomers of Aβ, not the fibrils, as the prevalent cytotoxic species. Structural characterization of Aβ and AβpE oligomers is therefore important for better understanding of their toxic effect. Here we have used isotope-edited Fourier transform infrared (FTIR) spectroscopy to identify the conformational changes in Aβ(1-42) and AβpE(3-42) upon aggregation, individually and in 1 : 1 molar combination. During the first two hours of exposure to aqueous buffer, the peptides undergo transition from mostly α-helical to mostly β-sheet structure. Data on peptides (13)C,(15)N-labeled at K(16)L(17)V(18) or V(36)G(37)G(38)V(39) allowed construction of structural models for the monomer and early oligomers. The peptide monomer comprises a β-hairpin that involves residues upstream of the K(16)L(17)V(18) sequence and an N-terminal α-helix. The oligomers form by non-H-bonding interactions between the β-strands of neighboring β-hairpins, in lateral or staggered manner, with the strands running parallel or antiparallel. Relative α-helical and β-sheet propensities of Aβ(1-42) and AβpE(3-42) depend on the ionic strength of the buffer, emphasizing the importance of ionic interactions in Aβ peptide structure and aggregation. It is inferred that N-terminal modification of AβpE(3-42) affects the helix stability and thereby modulates β-sheet oligomer formation. The data thus provide new insight into the molecular mechanism of Aβ oligomerization by emphasizing the role of the N-terminal transient α-helical structure and by identifying structural constraints for molecular organization of the oligomers.
Collapse
Affiliation(s)
- Greg Goldblatt
- Biomedical Sciences Graduate Program, University of Central Florida, Orlando, FL, USA
| | - Jason O Matos
- Biotechnology Graduate Program, University of Central Florida, Orlando, FL, USA
| | - Jeremy Gornto
- Undergraduate student, University of Central Florida, Orlando, FL, USA
| | - Suren A Tatulian
- Department of Physics, Physical Sciences Room 456, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816-2385, USA.
| |
Collapse
|
50
|
Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| |
Collapse
|