1
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Mishra R, Gerlach GJ, Sahoo B, Camacho CJ, Wetzel R. A Targetable Self-association Surface of the Huntingtin exon1 Helical Tetramer Required for Assembly of Amyloid Pre-nucleation Oligomers. J Mol Biol 2024; 436:168607. [PMID: 38734203 DOI: 10.1016/j.jmb.2024.168607] [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: 12/13/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Polyglutamine (polyQ) sequences undergo repeat-length dependent formation of disease-associated, amyloid-like cross-β core structures with kinetics and aggregate morphologies often influenced by the flanking sequences. In Huntington's disease (HD), the httNT segment on the polyQ's N-terminal flank enhances aggregation rates by changing amyloid nucleation from a classical homogeneous mechanism to a two-step process requiring an ɑ-helix-rich oligomeric intermediate. A folded, helix-rich httNT tetrameric structure suggested to be this critical intermediate was recently reported. Here we employ single alanine replacements along the httNT sequence to assess this proposed structure and refine the mechanistic model. We find that Ala replacement of hydrophobic residues within simple httNT peptides greatly suppresses helicity, supporting the tetramer model. These same helix-disruptive replacements in the httNT segment of an exon-1 analog greatly reduce aggregation kinetics, suggesting that an ɑ-helix rich multimer - either the tetramer or a larger multimer - plays an on-pathway role in nucleation. Surprisingly, several other Ala replacements actually enhance helicity and/or amyloid aggregation. The spatial localization of these residues on the tetramer surface suggests a self-association interface responsible for formation of the octomers and higher-order multimers most likely required for polyQ amyloid nucleation. Multimer docking of the tetramer, using the protein-protein docking algorithm ClusPro, predicts this symmetric surface to be a viable tetramer dimerization interface. Intriguingly, octomer formation brings the emerging polyQ chains into closer proximity at this tetramer-tetramer interface. Further supporting the potential importance of tetramer super-assembly, computational docking with a known exon-1 aggregation inhibitor predicts ligand contacts with residues at this interface.
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Affiliation(s)
- Rakesh Mishra
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Gabriella J Gerlach
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA
| | - Bankanidhi Sahoo
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Ronald Wetzel
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
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2
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Nilsson BL, Celebi Torabfam G, Dias CL. Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations. J Phys Chem B 2024; 128:3320-3328. [PMID: 38447080 DOI: 10.1021/acs.jpcb.3c07861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional fibrillar morphology as in amyloid fibrils. Deposits of the latter in tissues of individuals with degenerative diseases like Alzheimer's and Parkinson's has motivated extensive efforts to understand the sequence of molecular events accounting for their formation. These studies aim to identify on-pathway intermediates that may be the targets for therapeutic intervention. This detailed knowledge of fibril formation remains obscure, in part due to challenges with experimental analyses of these processes. However, important progress is being achieved for short amyloid peptides due to advances in our ability to perform completely unbiased all-atom simulations of the self-assembly process. This perspective discusses recent developments, their implications, and the hurdles that still need to be overcome to further advance the field.
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Affiliation(s)
- Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- Materials Science Program, University of Rochester, Rochester, New York 14627-0216, United States
| | - Gizem Celebi Torabfam
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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3
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Krokidis MG, Dimitrakopoulos GN, Vrahatis AG, Exarchos TP, Vlamos P. Challenges and limitations in computational prediction of protein misfolding in neurodegenerative diseases. Front Comput Neurosci 2024; 17:1323182. [PMID: 38250244 PMCID: PMC10796696 DOI: 10.3389/fncom.2023.1323182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Affiliation(s)
| | | | | | | | - Panagiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
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4
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Nguyen PH, Derreumaux P. Recent Computational Advances Regarding Amyloid-β and Tau Membrane Interactions in Alzheimer's Disease. Molecules 2023; 28:7080. [PMID: 37894559 PMCID: PMC10609340 DOI: 10.3390/molecules28207080] [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: 09/05/2023] [Revised: 09/26/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The interactions of amyloid proteins with membranes have been subject to many experimental and computational studies, as these interactions contribute in part to neurodegenerative diseases. In this review, we report on recent simulations that have focused on the adsorption and insertion modes of amyloid-β and tau proteins in membranes. The atomistic-resolution characterization of the conformational changes of these amyloid proteins upon lipid cell membrane and free lipid interactions is of interest to rationally design drugs targeting transient oligomers in Alzheimer's disease.
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Affiliation(s)
- Phuong H. Nguyen
- CNRS, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Université Paris Cité, UPR 9080, 13 rue Pierre et Marie Curie, 75005 Paris, France;
| | - Philippe Derreumaux
- CNRS, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Université Paris Cité, UPR 9080, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut Universitaire de France (IUF), 75005 Paris, France
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5
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Nguyen PH, Derreumaux P. Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations. J Chem Phys 2023; 158:235101. [PMID: 37318171 DOI: 10.1063/5.0149419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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6
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Lin R, Tang G, Gao Z, Lei J, Ma B, Mo Y. Molecular Insights into the Self-Assembly of a Full-Length hIAPP Trimer: β-Protofibril Formed by β-Hairpin Lateral or Longitudinal Association. J Phys Chem B 2023. [PMID: 37262327 DOI: 10.1021/acs.jpcb.3c02633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The fibrillar protein deposits of the human islet amyloid polypeptide (hIAPP) in the pancreatic islet of Langerhans are pathological hallmark of type II diabetes. Extensive experimental studies have revealed that the oligomeric formations of the hIAPP are more toxic than the mature fibrils. Exploring the oligomeric conformations in the early aggregation state is valuable for effective therapeutics. In this work, using the all-atom explicit-solvent replica exchange molecular dynamic (REMD) simulations, we investigated the structural features and the assembly mechanisms of the full-length hIAPP trimer in solution. The hIAPP trimer adopted more β-sheets than a-helix conformations, and three types of ordered conformations including open β-barrel, single-layer, and double-layer U-shaped β-sheet structures with five β-strands were captured in our simulations. A representative single-layer β-sheet conformation with a CCS value of 1400 Å2 in our simulations matches exactly the experimentally ESI-IMS-MS-derived hIAPP trimer sample. These five β-strand conformations formed via the β-hairpin lateral and longitudinal association, respectively, showing two β-protofibril formation models. To the best of our knowledge, it is the first time to reveal two routes to β-sheet formation in the hIAPP trimers on the atomic level. The contact probabilities between pairs of the β-stranded residue show that the hydrophobic interactions between the residues F15 ∼ V17 and A25 ∼ L27 are responsible for the inter- and intra-peptide β-hairpin formations. All of these results indicate that the β-sheet formation is the first step in the conformational changes toward pathological aggregation and provides evidence of the β-sheet assembly mechanism into hIAPP aggregation.
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Affiliation(s)
- Rongmei Lin
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
| | - Guoning Tang
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
| | - Zhonggui Gao
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
| | - Jiangtao Lei
- Institute of Space Science and Technology, Nanchang University, Nanchang, Jiangxi 330031, People's Republic of China
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody, School of Pharmacy, Shanghai Jiaotong University, Shanghai 200240, People's Republic of China
| | - Yuxiang Mo
- College of Physical Science and Technology, Guangxi Normal University, Guilin, Guangxi 541004, People's Republic of China
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7
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Yuan N, Ye L, Sun Y, Wu H, Xiao Z, Fu W, Chen Z, Pei Y, Min Y, Wang D. Molecular Integrative Analysis of the Inhibitory Effects of Dipeptides on Amyloid β Peptide 1-42 Polymerization. Int J Mol Sci 2023; 24:ijms24087673. [PMID: 37108834 PMCID: PMC10141046 DOI: 10.3390/ijms24087673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The major pathological feature of Alzheimer's disease (AD) is the aggregation of amyloid β peptide (Aβ) in the brain. Inhibition of Aβ42 aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of aggregated Aβ with ThT, cell viability, and flow cytometry for the detection of reactive oxygen species (ROS) and apoptosis. Aβ42 polymerizes into fibrils due to hydrophobic interactions to minimize free energy, adopting a β-strand structure and forming three hydrophobic areas. Eight dipeptides were screened by molecular docking from a structural database of 20 L-α-amino acids, and the docking was validated by molecular dynamics (MD) analysis of binding stability and interaction potential energy. Among the dipeptides, arginine dipeptide (RR) inhibited Aβ42 aggregation the most. The ThT assay and EM revealed that RR reduced Aβ42 aggregation, whereas the circular dichroism spectroscopy analysis showed a 62.8% decrease in β-sheet conformation and a 39.3% increase in random coiling of Aβ42 in the presence of RR. RR also significantly reduced the toxicity of Aβ42 secreted by SH-SY5Y cells, including cell death, ROS production, and apoptosis. The formation of three hydrophobic regions and polymerization of Aβ42 reduced the Gibbs free energy, and RR was the most effective dipeptide at interfering with polymerization.
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Affiliation(s)
- Nan Yuan
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Lianmeng Ye
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yan Sun
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Hao Wu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zhengpan Xiao
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Wanmeng Fu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zuqian Chen
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yechun Pei
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yi Min
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Dayong Wang
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Key Laboratory of Tropical Biological Resources of the Ministry of China, Hainan University, Haikou 570228, China
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8
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Nguyen PH, Sterpone F, Derreumaux P. Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers. Proteins 2023. [PMID: 37038252 DOI: 10.1002/prot.26495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023]
Abstract
Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and simulations on Aβ42 monomer point to random coil conformations with either transient helical or β-strand content. Our current conformational description of small Aβ42 oligomers is funneled toward amorphous aggregates with some β-sheet content and rare high energy states with well-ordered assemblies of β-sheets. In this study, we emphasize another view based on metastable α-helix bundle oligomers spanning the C-terminal residues, which are predicted by the machine-learning AlphaFold2 method and supported indirectly by low-resolution experimental data on many amyloid polypeptides. This finding has consequences in developing novel chemical tools and to design potential therapies to reduce aggregation and toxicity.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris, 75005, France
- Institut Universitaire de France (IUF), Paris, 75005, France
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9
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Bordin N, Dallago C, Heinzinger M, Kim S, Littmann M, Rauer C, Steinegger M, Rost B, Orengo C. Novel machine learning approaches revolutionize protein knowledge. Trends Biochem Sci 2023; 48:345-359. [PMID: 36504138 PMCID: PMC10570143 DOI: 10.1016/j.tibs.2022.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/24/2022] [Accepted: 11/17/2022] [Indexed: 12/10/2022]
Abstract
Breakthrough methods in machine learning (ML), protein structure prediction, and novel ultrafast structural aligners are revolutionizing structural biology. Obtaining accurate models of proteins and annotating their functions on a large scale is no longer limited by time and resources. The most recent method to be top ranked by the Critical Assessment of Structure Prediction (CASP) assessment, AlphaFold 2 (AF2), is capable of building structural models with an accuracy comparable to that of experimental structures. Annotations of 3D models are keeping pace with the deposition of the structures due to advancements in protein language models (pLMs) and structural aligners that help validate these transferred annotations. In this review we describe how recent developments in ML for protein science are making large-scale structural bioinformatics available to the general scientific community.
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Affiliation(s)
- Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, Gower St, WC1E 6BT London, UK
| | - Christian Dallago
- Technical University of Munich (TUM) Department of Informatics, Bioinformatics and Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany; VantAI, 151 W 42nd Street, New York, NY 10036, USA
| | - Michael Heinzinger
- Technical University of Munich (TUM) Department of Informatics, Bioinformatics and Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany; TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748 Garching, Germany
| | - Stephanie Kim
- School of Biological Sciences, Seoul National University, Seoul, South Korea; Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
| | - Maria Littmann
- Technical University of Munich (TUM) Department of Informatics, Bioinformatics and Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany
| | - Clemens Rauer
- Institute of Structural and Molecular Biology, University College London, Gower St, WC1E 6BT London, UK
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea; Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
| | - Burkhard Rost
- Technical University of Munich (TUM) Department of Informatics, Bioinformatics and Computational Biology - i12, Boltzmannstr. 3, 85748 Garching/Munich, Germany; Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748 Garching/Munich, Germany; TUM School of Life Sciences Weihenstephan (TUM-WZW), Alte Akademie 8, Freising, Germany
| | - Christine Orengo
- Institute of Structural and Molecular Biology, University College London, Gower St, WC1E 6BT London, UK.
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10
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Nguyen PH, Sterpone F, Derreumaux P. Self-Assembly of Amyloid-Beta (Aβ) Peptides from Solution to Near In Vivo Conditions. J Phys Chem B 2022; 126:10317-10326. [PMID: 36469912 DOI: 10.1021/acs.jpcb.2c06375] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding the atomistic resolution changes during the self-assembly of amyloid peptides or proteins is important to develop compounds or conditions to alter the aggregation pathways and suppress the toxicity and potentially aid in the development of drugs. However, the complexity of protein aggregation and the transient order/disorder of oligomers along the pathways to fibril are very challenging. In this Perspective, we discuss computational studies of amyloid polypeptides carried out under various conditions, including conditions closely mimicking in vivo and point out the challenges in obtaining physiologically relevant results, focusing mainly on the amyloid-beta Aβ peptides.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, 75005 Paris, France.,Institut Universitaire de France (IUF), 75005, Paris, France
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11
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Pham T, Cheng KH. Exploring the binding kinetics and behaviors of self-aggregated beta-amyloid oligomers to phase-separated lipid rafts with or without ganglioside-clusters. Biophys Chem 2022; 290:106874. [PMID: 36067650 DOI: 10.1016/j.bpc.2022.106874] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022]
Abstract
Lipid binding kinetics and energetics of self-aggregated and disordered beta-amyloid oligomers of various sizes, from solution to lipid raft surfaces, were investigated using MD simulations. Our systems include small (monomers to tetramers) and larger (octamers and dodecamers) oligomers. Our lipid rafts contain saturated and unsaturated phosphatidylcholine (PC), cholesterol, and with or without asymmetrically distributed monosialotetrahexosylganglioside (GM1). All rafts exhibited dynamic and structurally diversified domains including liquid-ordered (Lo), liquid-disordered (Ld), and interfacial Lod domains. For rafts without GM1, all oligomers bound to the Lod domain. For GM1-containing rafts, all small oligomers and most larger oligomers bound specifically to the GM1-clusters embedded in the Lo domain. Lipid-protein binding energies followed an order of GM1 >> unsaturated PC > saturated PC > cholesterol for all rafts. In addition, protein-induced membrane structural disruption increased progressively with the size of the oligomer for the annular lipids surrounding the membrane-bound protein in non-GM1-containing rafts. We propose that the tight binding of beta-amyloid oligomers to the GM1-clusters and the structural perturbation of lipids surrounding the membrane-bound proteins at the Lod domain are early molecular events of the beta-amyloid aggregation process on neuronal membrane surfaces that trigger the onset of Alzheimer's.
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Affiliation(s)
- Thuong Pham
- Department of Physics, Trinity University, United States of America
| | - Kwan H Cheng
- Department of Physics, Trinity University, United States of America; Department of Neuroscience, Trinity University, United States of America.
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12
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Gallego-Villarejo L, Wallin C, Król S, Enrich-Bengoa J, Suades A, Aguilella-Arzo M, Gomara MJ, Haro I, Wärmlander S, Muñoz FJ, Gräslund A, Perálvarez-Marín A. Big dynorphin is a neuroprotector scaffold against amyloid β-peptide aggregation and cell toxicity. Comput Struct Biotechnol J 2022; 20:5672-5679. [PMID: 36284704 PMCID: PMC9582793 DOI: 10.1016/j.csbj.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/09/2022] [Accepted: 10/09/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloid β-peptide (Aβ) misfolding into β-sheet structures triggers neurotoxicity inducing Alzheimer’s disease (AD). Molecules able to reduce or to impair Aβ aggregation are highly relevant as possible AD treatments since they should protect against Aβ neurotoxicity. We have studied the effects of the interaction of dynorphins, a family of opioid neuropeptides, with Aβ40 the most abundant species of Aβ. Biophysical measurements indicate that Aβ40 interacts with Big Dynorphin (BigDyn), lowering the amount of hydrophobic aggregates, and slowing down the aggregation kinetics. As expected, we found that BigDyn protects against Aβ40 aggregates when studied in human neuroblastoma cells by cell survival assays. The cross-interaction between BigDyn and Aβ40 provides insight into the mechanism of amyloid pathophysiology and may open up new therapy possibilities.
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Affiliation(s)
- Lucía Gallego-Villarejo
- Unit of Biophysics Dept of Biochemistry and Molecular Biology, Institute of Neurosciences, Universitat Autònoma de Barcelona, Facultat de Medicina, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Cecilia Wallin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sylwia Król
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jennifer Enrich-Bengoa
- Unit of Biophysics Dept of Biochemistry and Molecular Biology, Institute of Neurosciences, Universitat Autònoma de Barcelona, Facultat de Medicina, 08193 Cerdanyola del Vallés, Catalonia, Spain
| | - Albert Suades
- Unit of Biophysics Dept of Biochemistry and Molecular Biology, Institute of Neurosciences, Universitat Autònoma de Barcelona, Facultat de Medicina, 08193 Cerdanyola del Vallés, Catalonia, Spain,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Marcel Aguilella-Arzo
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - María José Gomara
- Unitat de Síntesis i Aplicacions Biomèdiques de Pèptids, Institut de Química Avançada de Catalunya, IQAC-CSIC, Jordi Girona, 18-26, 08034 Barcelona, Catalonia, Spain
| | - Isabel Haro
- Unitat de Síntesis i Aplicacions Biomèdiques de Pèptids, Institut de Química Avançada de Catalunya, IQAC-CSIC, Jordi Girona, 18-26, 08034 Barcelona, Catalonia, Spain
| | - Sebastian Wärmlander
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Francisco J. Muñoz
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Alex Perálvarez-Marín
- Unit of Biophysics Dept of Biochemistry and Molecular Biology, Institute of Neurosciences, Universitat Autònoma de Barcelona, Facultat de Medicina, 08193 Cerdanyola del Vallés, Catalonia, Spain,Corresponding author.
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13
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Sonar K, Mancera RL. Characterization of the Conformations of Amyloid Beta 42 in Solution That May Mediate Its Initial Hydrophobic Aggregation. J Phys Chem B 2022; 126:7916-7933. [PMID: 36179370 DOI: 10.1021/acs.jpcb.2c04743] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intrinsically disordered peptides, such as amyloid β42 (Aβ42), lack a well-defined structure in solution. Aβ42 can undergo abnormal aggregation and amyloidogenesis in the brain, forming fibrillar plaques, a hallmark of Alzheimer's disease. The insoluble fibrillar forms of Aβ42 exhibit well-defined, cross β-sheet structures at the molecular level and are less toxic than the soluble, intermediate disordered oligomeric forms. However, the mechanism of initial interaction of monomers and subsequent oligomerization is not well understood. The structural disorder of Aβ42 adds to the challenges of determining the structural properties of its monomers, making it difficult to understand the underlying molecular mechanism of pathogenic aggregation. Certain regions of Aβ42 are known to exhibit helical propensity in different physiological conditions. NMR spectroscopy has shown that the Aβ42 monomer at lower pH can adopt an α-helical conformation and as the pH is increased, the peptide switches to β-sheet conformation and aggregation occurs. CD spectroscopy studies of aggregation have shown the presence of an initial spike in the amount of α-helical content at the start of aggregation. Such an increase in α-helical content suggests a mechanism wherein the peptide can expose critical non-polar residues for interaction, leading to hydrophobic aggregation with other interacting peptides. We have used molecular dynamics simulations to characterize in detail the conformational landscape of monomeric Aβ42 in solution to identify molecular properties that may mediate the early stages of oligomerization. We hypothesized that conformations with α-helical structure have a higher probability of initiating aggregation because they increase the hydrophobicity of the peptide. Although random coil conformations were found to be the most dominant, as expected, α-helical conformations are thermodynamically accessible, more so than β-sheet conformations. Importantly, for the first time α-helical conformations are observed to increase the exposure of aromatic and hydrophobic residues to the aqueous solvent, favoring their hydrophobically driven interaction with other monomers to initiate aggregation. These findings constitute a first step toward characterizing the mechanism of formation of disordered, low-order oligomers of Aβ42.
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Affiliation(s)
- Krushna Sonar
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Computation, Curtin University, P. O. Box U1987, Perth, Western Australia6845, Australia
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Computation, Curtin University, P. O. Box U1987, Perth, Western Australia6845, Australia
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Nie RZ, Cai S, Yu B, Fan WY, Li HH, Tang SW, Huo YQ. Molecular insights into the very early steps of Aβ1-42 pentameric protofibril disassembly by PGG: A molecular dynamics simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Fang M, Zhang Q, Wang X, Su K, Guan P, Hu X. Inhibition Mechanisms of (-)-Epigallocatechin-3-gallate and Genistein on Amyloid-beta 42 Peptide of Alzheimer's Disease via Molecular Simulations. ACS OMEGA 2022; 7:19665-19675. [PMID: 35721940 PMCID: PMC9202277 DOI: 10.1021/acsomega.2c01412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 05/06/2023]
Abstract
The misfolding and self-assembly of amyloid-beta (Aβ) peptides are one of the most important factors contributing to Alzheimer's disease (AD). This study aims to reveal the inhibition mechanisms of (-)-epigallocatechin-3-gallate (EGCG) and genistein on the conformational changes of Aβ42 peptides by using molecular docking and molecular dynamics (MD) simulation. The results indicate that both EGCG and genistein have inhibitory effects on the conformational transition of Aβ42 peptide. EGCG and genistein reduce the ratio of β-sheet secondary structures of Aβ42 peptide while inducing random coil structures. In terms of hydrophobic interactions in the central hydrophobic core of Aβ42 peptide, the binding affinities of EGCG are significantly larger in comparison with that of genistein. Our findings illustrate the inhibition mechanisms of EGCG and genistein on the Aβ42 peptides and prove that EGCG is a very promising inhibitor in impeding the conformational change of Aβ42 peptide.
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Affiliation(s)
- Mei Fang
- Department
of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Quan Zhang
- Department
of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Xin Wang
- Department
of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Kehe Su
- Department
of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Ping Guan
- Department
of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Xiaoling Hu
- Department
of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
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