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Tarus B, Tran TT, Nasica-Labouze J, Sterpone F, Nguyen PH, Derreumaux P. Structures of the Alzheimer's Wild-Type Aβ1-40 Dimer from Atomistic Simulations. J Phys Chem B 2015; 119:10478-87. [PMID: 26228450 DOI: 10.1021/acs.jpcb.5b05593] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the dimer of amyloid beta peptide Aβ of 40 residues by means of all-atom replica exchange molecular dynamics. The Aβ-dimers have been found to be the smallest toxic species in Alzheimer's disease, but their inherent flexibilities have precluded structural characterization by experimental methods. Though the 24-μs-scale simulation reveals a mean secondary structure of 18% β-strand and 10% α helix, we find transient configurations with an unstructured N-terminus and multiple β-hairpins spanning residues 17-21 and 30-36, but the antiparallel and perpendicular peptide orientations are preferred over the parallel organization. Short-lived conformational states also consist of all α topologies, and one compact peptide with β-sheet structure stabilized by a rather extended peptide with α-helical content. Overall, this first all-atom study provides insights into the equilibrium structure of the Aβ1-40 dimer in aqueous solution, opening a new avenue for a comprehensive understanding of the impact of pathogenic and protective mutations in early-stage Alzheimer's disease on a molecular level.
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Affiliation(s)
- Bogdan Tarus
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Thanh T Tran
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Jessica Nasica-Labouze
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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52
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Tran L, Ha-Duong T. Exploring the Alzheimer amyloid-β peptide conformational ensemble: A review of molecular dynamics approaches. Peptides 2015; 69:86-91. [PMID: 25908410 DOI: 10.1016/j.peptides.2015.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease is one of the most common dementia among elderly worldwide. There is no therapeutic drugs until now to treat effectively this disease. One main reason is due to the poorly understood mechanism of Aβ peptide aggregation, which plays a crucial role in the development of Alzheimer's disease. It remains challenging to experimentally or theoretically characterize the secondary and tertiary structures of the Aβ monomer because of its high flexibility and aggregation propensity, and its conformations that lead to the aggregation are not fully identified. In this review, we highlight various structural ensembles of Aβ peptide revealed and characterized by computational approaches in order to find converging structures of Aβ monomer. Understanding how Aβ peptide forms transiently stable structures prior to aggregation will contribute to the design of new therapeutic molecules against the Alzheimer's disease.
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Affiliation(s)
- Linh Tran
- BioCIS, UMR CNRS 8076, LabEx LERMIT, Faculty of Pharmacy, University Paris Sud, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France
| | - Tâp Ha-Duong
- BioCIS, UMR CNRS 8076, LabEx LERMIT, Faculty of Pharmacy, University Paris Sud, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France.
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53
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Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation. Int J Mol Sci 2015; 16:14291-304. [PMID: 26114384 PMCID: PMC4519842 DOI: 10.3390/ijms160714291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 01/22/2023] Open
Abstract
The dimeric structure of the N-terminal 12 residues drives the interaction of α-synuclein protein with membranes. Moreover, experimental studies indicated that the aggregation of α-synuclein is faster at low pH than neutral pH. Nevertheless, the effects of different pH on the structural characteristics of the α-syn12 dimer remain poorly understood. We performed 500 ns temperature replica exchange molecular dynamics (T-REMD) simulations of two α-syn12 peptides in explicit solvent. The free energy surfaces contain ten highly populated regions at physiological pH, while there are only three highly populated regions contained at acidic pH. The anti-parallel β-sheet conformations were found as the lowest free energy state. Additionally, these states are nearly flat with a very small barrier which indicates that these states can easily transit between themselves. The dimer undergoes a disorder to order transition from physiological pH to acidic pH and the α-syn12 dimer at acidic pH involves a faster dimerization process. Further, the Lys6–Asp2 contact may prevent the dimerization.
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54
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Xu L, Shan S, Chen Y, Wang X, Nussinov R, Ma B. Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization. J Chem Inf Model 2015; 55:1218-30. [PMID: 26017140 PMCID: PMC6407634 DOI: 10.1021/acs.jcim.5b00063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary structure on Aβ dimerization energies and kinetics. We found that random conformations do not contribute to dimerization either thermodynamically or kinetically. Zn(2+) couples with preformed secondary structures (α-helix and β-hairpin) to speed dimerization and stabilize the resulting dimer. Partial α-helices increase the dimerization speed, and dimers with α-helix rich conformations have the lowest energy. When Zn(2+) coordinates with residues D1, H6, H13, and H14, Aβ40 β-hairpin monomers have the fastest dimerization speed. Dimers with experimentally observed zinc coordination (E11, H6, H13, and H14) form with slower rate but have lower energy. Zn(2+) cannot stabilize fibril-like β-arch dimers. However, Zn(2+)-bound β-arch tetramers have the lowest energy. Collectively, zinc-stabilized β-hairpin oligomers could be important in the nucleation-polymerization of cross-β structures. Our results are consistent with experimental findings that α-helix to β-structural transition should accompany Aβ aggregation in the presence of zinc ions and that Zn(2+) stabilizes nonfibrillar Aβ oligomers and, thus, inhibits formation of less toxic Aβ fibrils.
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Affiliation(s)
- Liang Xu
- School of Chemistry, Dalian University of Technology, Dalian, China
| | - Shengsheng Shan
- School of Chemistry, Dalian University of Technology, Dalian, China
| | - Yonggang Chen
- Network and Information Center, Dalian University of Technology, Dalian, China
| | - Xiaojuan Wang
- School of Chemical Machinery, Dalian University of Technology, Dalian, China
| | - Ruth Nussinov
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702
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55
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Qiu T, Liu Q, Chen YX, Zhao YF, Li YM. Aβ42 and Aβ40: similarities and differences. J Pept Sci 2015; 21:522-9. [PMID: 26018760 DOI: 10.1002/psc.2789] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 01/03/2023]
Abstract
The abnormal accumulation of amyloid-β (Aβ) peptide in the brain is one of the most important hallmarks of Alzheimer's disease. Aβ is an aggregation-prone and toxic polypeptide with 39-43 residues, derived from the amyloid precursor protein proteolysis process. According to the amyloid hypothesis, abnormal accumulation of Aβ in the brain is the primary influence driving Alzheimer's disease pathologies. Among all kinds of Aβ isoforms, Aβ40 and Aβ42 are believed to be the most important ones. Although these two kinds of Aβ differ only in two amino acid residues, recent studies show that they differ significantly in their metabolism, physiological functions, toxicities, and aggregation mechanism. In this review, we mainly summarize the similarities and differences between Aβ42 and Aβ40, recent studies on selective inhibitors as well as probes will also be mentioned.
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Affiliation(s)
- Tian Qiu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Qian Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yu-Fen Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China.,Beijing Institute for Brain Disorders, Beijing, 100069, China
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56
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 474] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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57
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Pouplana R, Campanera JM. Energetic contributions of residues to the formation of early amyloid-β oligomers. Phys Chem Chem Phys 2014; 17:2823-37. [PMID: 25503571 DOI: 10.1039/c4cp04544k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-weight amyloid-β (Aβ) oligomers formed at early stages of oligomerization rather than fibril assemblies seem to be the toxic components that drive neurodegeneration in Alzheimer's disease. Unfortunately, detailed knowledge of the structure of these early oligomers at the residue level is not yet available. In this study, we performed all-atom explicit solvent molecular dynamics simulations to examine the oligomerization process of Aβ10-35 monomers when forming dimers, trimers, tetramers and octamers, with four independent simulations of a total simulated time of 3 μs for each oligomer system. The decomposition of the stability free energy by MM-GBSA methodology allowed us to unravel the network of energetic interactions that stabilize such oligomers. The contribution of the intermonomeric van der Waals term is the most significant energy feature of the oligomerization process, consistent with the so-called hydrophobic effect. Furthermore, the decomposition of the stability free energy into residues and residue-pairwise terms revealed that it is mainly apolar interactions between the three specific hydrophobic fragments 31-35 (C-terminal region), 17-20 (central hydrophobic core) and 12-14 (N-terminal region) that are responsible for such a favourable effect. The conformation in which the hydrophobic cthr-chc interaction is oriented perpendicularly is particularly important. We propose three other model substructures that favour the oligomerization process and can thus be considered as molecular targets for future inhibitors. Understanding Aβ oligomerization at the residue level could lead to more efficient design of inhibitors of this process.
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Affiliation(s)
- R Pouplana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII, s/n, Diagonal Sud, 08028, Barcelona, Catalonia, Spain.
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58
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59
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Eugene C, Laghaei R, Mousseau N. Early oligomerization stages for the non-amyloid component of α-synuclein amyloid. J Chem Phys 2014; 141:135103. [DOI: 10.1063/1.4896381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Cindie Eugene
- Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Rozita Laghaei
- Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
- Department of Chemistry, University of Pittsburgh, 319 Eberly Hall, Pittsburgh, Pennsylvania 15260, USA
| | - Normand Mousseau
- Department of Chemistry, University of Pittsburgh, 319 Eberly Hall, Pittsburgh, Pennsylvania 15260, USA
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60
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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61
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Tsigelny IF, Sharikov Y, Kouznetsova VL, Greenberg JP, Wrasidlo W, Gonzalez T, Desplats P, Michael SE, Trejo-Morales M, Overk CR, Masliah E. Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation. J Alzheimers Dis 2014; 39:583-600. [PMID: 24240640 DOI: 10.3233/jad-131589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteristics. Then we selected the dimers that would evolve to membranephilic annular oligomers. Nearly one third of the 28 evaluated annular oligomers had the dimer interfaces between the neighboring Aβ42 monomers with possible salt bridges between the residue K28 from one side and either residue E22 or D23 on the other. Based on these results, key amino acids were identified for point mutations that either enhanced or suppressed the formation and toxicity of oligomer rings. Our studies suggest a greater diversity of Aβ dimers. Understanding the structure of Aβ dimers might be important for the rationale design of small molecules that block formation of toxic oligomers.
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Affiliation(s)
- Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Yuriy Sharikov
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jerry P Greenberg
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Wolfgang Wrasidlo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Tania Gonzalez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Paula Desplats
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Sarah E Michael
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Cassia R Overk
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA Department of Pathology, University of California, San Diego, La Jolla, CA, USA
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62
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Jose JC, Chatterjee P, Sengupta N. Cross dimerization of amyloid-β and αsynuclein proteins in aqueous environment: a molecular dynamics simulations study. PLoS One 2014; 9:e106883. [PMID: 25210774 PMCID: PMC4161357 DOI: 10.1371/journal.pone.0106883] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/07/2014] [Indexed: 11/18/2022] Open
Abstract
Self-assembly of the intrinsically unstructured proteins, amyloid beta (Aβ) and alpha synclein (αSyn), are associated with Alzheimer's Disease, and Parkinson's and Lewy Body Diseases, respectively. Importantly, pathological overlaps between these neurodegenerative diseases, and the possibilities of interactions between Aβ and αSyn in biological milieu emerge from several recent clinical reports and in vitro studies. Nevertheless, there are very few molecular level studies that have probed the nature of spontaneous interactions between these two sequentially dissimilar proteins and key characteristics of the resulting cross complexes. In this study, we have used atomistic molecular dynamics simulations to probe the possibility of cross dimerization between αSyn1-95 and Aβ1-42, and thereby gain insights into their plausible early assembly pathways in aqueous environment. Our analyses indicate a strong probability of association between the two sequences, with inter-protein attractive electrostatic interactions playing dominant roles. Principal component analysis revealed significant heterogeneity in the strength and nature of the associations in the key interaction modes. In most, the interactions of repeating Lys residues, mainly in the imperfect repeats 'KTKEGV' present in αSyn1-95 were found to be essential for cross interactions and formation of inter-protein salt bridges. Additionally, a hydrophobicity driven interaction mode devoid of salt bridges, where the non-amyloid component (NAC) region of αSyn1-95 came in contact with the hydrophobic core of Aβ1-42 was observed. The existence of such hetero complexes, and therefore hetero assembly pathways may lead to polymorphic aggregates with variations in pathological attributes. Our results provide a perspective on development of therapeutic strategies for preventing pathogenic interactions between these proteins.
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Affiliation(s)
- Jaya C. Jose
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Neelanjana Sengupta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- * E-mail:
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63
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Truong PM, Viet MH, Nguyen PH, Hu CK, Li MS. Effect of Taiwan Mutation (D7H) on Structures of Amyloid-β Peptides: Replica Exchange Molecular Dynamics Study. J Phys Chem B 2014; 118:8972-81. [DOI: 10.1021/jp503652s] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Phan Minh Truong
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Man Hoang Viet
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Chin-Kun Hu
- Institute
of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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64
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Szöllősi D, Horváth T, Han KH, Dokholyan NV, Tompa P, Kalmár L, Hegedűs T. Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins. PLoS One 2014; 9:e95795. [PMID: 24763499 PMCID: PMC3998973 DOI: 10.1371/journal.pone.0095795] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 03/30/2014] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available.
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Affiliation(s)
- Dániel Szöllősi
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics, University of Science and Technology, Yuseong-gu, Daejeon, Korea
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Péter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lajos Kalmár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás Hegedűs
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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65
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Hane FT, Attwood SJ, Leonenko Z. Comparison of three competing dynamic force spectroscopy models to study binding forces of amyloid-β (1-42). SOFT MATTER 2014; 10:1924-1930. [PMID: 24652035 DOI: 10.1039/c3sm52257a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We performed single molecule dynamic force spectroscopy experiments to study the dimerization of two amyloid-β (1-42) peptides and compared three different theoretical models used to fit experimental data: Bell-Evans, Dudko-Hummer-Szabo, and Friddle-De Yoreo. Using these models we extracted values of the dissociation rate at zero force, k0, and height and the width of the energy barrier, ΔG and xβ. We show the importance of including the effect of the linker molecule. All three models corrected for the linker effect give comparable results for xβ and show more discrepancy for k0 and ΔG values, ΔG parameter correlates well between Dudko-Hummer-Szabo and Friddle-De Yoreo models but differs for the Bell-Evans model.
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Affiliation(s)
- F T Hane
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
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66
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Redler RL, Shirvanyants D, Dagliyan O, Ding F, Kim DN, Kota P, Proctor EA, Ramachandran S, Tandon A, Dokholyan NV. Computational approaches to understanding protein aggregation in neurodegeneration. J Mol Cell Biol 2014; 6:104-15. [PMID: 24620031 DOI: 10.1093/jmcb/mju007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggregation, as well as the structural features of large-scale ordered aggregates and soluble non-native oligomers, would contribute significantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. However, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both all-atom and coarse-grained simulations to cover a wide range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here we review the current state of computational methodology for the study of protein self-assembly, with a focus on the application of these methods toward understanding of protein aggregates in human neurodegenerative disorders.
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Affiliation(s)
- Rachel L Redler
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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67
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Zhang T, Xu W, Mu Y, Derreumaux P. Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity. ACS Chem Neurosci 2014; 5:148-59. [PMID: 24246047 DOI: 10.1021/cn400197x] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12-28 and 17-42, none of these studies were conducted on the full-length Aβ1-42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1-42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1-42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1-42 dimer against AD.
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Affiliation(s)
- Tong Zhang
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- State Key Laboratory of Precision Spectroscopy, Department
of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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68
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Barz B, Wales DJ, Strodel B. A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly. J Phys Chem B 2014; 118:1003-11. [PMID: 24401100 PMCID: PMC3908877 DOI: 10.1021/jp412648u] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is generally accepted that oligomers of aggregating proteins play an important role in the onset of neurodegenerative diseases. While in silico aggregation studies of full length amyloidogenic proteins are computationally expensive, the assembly of short protein fragments derived from these proteins with similar aggregating properties has been extensively studied. In the present work, molecular dynamics simulations are performed to follow peptide aggregation on the microsecond time scale. By defining aggregation states, we identify transition networks, disconnectivity graphs, and first passage time distributions to describe the kinetics of the assembly process. This approach unravels differences in the aggregation into hexamers of two peptides with different primary structures. The first is GNNQQNY, a hydrophilic fragment from the prion protein Sup35, and the second is KLVFFAE, a fragment from amyloid-β protein, with a hydrophobic core delimited by two charged amino acids. The assembly of GNNQQNY suggests a mechanism of monomer addition, with a bias toward parallel peptide pairs and a gradual increase in the amount of β-strand content. For KLVFFAE, a mechanism involving dimers rather than monomers is revealed, involving a generally higher β-strand content and a transition toward a larger number of antiparallel peptide pairs during the rearrangement of the hexamer. The differences observed for the aggregation of the two peptides suggests the existence of a sequence-aggregation relationship.
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Affiliation(s)
- Bogdan Barz
- Forschungszentrum Jülich GmbH Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
| | - David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK
| | - Birgit Strodel
- Forschungszentrum Jülich GmbH Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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69
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Jónsson SÆ, Mitternacht S, Irbäck A. Mechanical resistance in unstructured proteins. Biophys J 2014; 104:2725-32. [PMID: 23790381 DOI: 10.1016/j.bpj.2013.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022] Open
Abstract
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force resistance, we perform pulling simulations of the amyloid β-peptide (Aβ) and α-synuclein (αS), starting from simulated conformational ensembles for the free monomers. For both proteins, the simulations yield a set of rupture events that agree well with the experimental data. By analyzing the conformations occurring shortly before rupture in each event, we find that the mechanically resistant structures share a common architecture, with similarities to the folds adopted by Aβ and αS in amyloid fibrils. The disease-linked Arctic mutation of Aβ is found to increase the occurrence of highly force-resistant structures. Our study suggests that the high rupture forces observed in Aβ and αS pulling experiments are caused by structures that might have a key role in amyloid formation.
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Affiliation(s)
- Sigurður Ægir Jónsson
- Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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70
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Effect of metals on kinetic pathways of amyloid-β aggregation. Biomolecules 2014; 4:101-16. [PMID: 24970207 PMCID: PMC4030978 DOI: 10.3390/biom4010101] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 01/04/2014] [Accepted: 01/07/2014] [Indexed: 12/22/2022] Open
Abstract
Metal ions, including copper and zinc, have been implicated in the pathogenesis of Alzheimer’s disease through a variety of mechanisms including increased amyloid-β affinity and redox effects. Recent reports have demonstrated that the amyloid-β monomer does not necessarily travel through a definitive intermediary en-route to a stable amyloid fibril structure. Rather, amyloid-β misfolding may follow a variety of pathways resulting in a fibrillar end-product or a variety of oligomeric end-products with a diversity of structures and sizes. The presence of metal ions has been demonstrated to alter the kinetic pathway of the amyloid-β peptide which may lead to more toxic oligomeric end-products. In this work, we review the contemporary literature supporting the hypothesis that metal ions alter the reaction pathway of amyloid-β misfolding leading to more neurotoxic species.
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71
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Barz B, Olubiyi OO, Strodel B. Early amyloid β-protein aggregation precedes conformational change. Chem Commun (Camb) 2014; 50:5373-5. [DOI: 10.1039/c3cc48704k] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aggregation of amyloid-β protein (1–42) is studied at experimental concentrations using all-atom molecular dynamics simulations.
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Affiliation(s)
- Bogdan Barz
- Forschungszentrum Jülich GmbH
- Institute of Complex Systems: Structural Biochemistry (ICS-6)
- 52425 Jülich, Germany
| | - Olujide O. Olubiyi
- Forschungszentrum Jülich GmbH
- Institute of Complex Systems: Structural Biochemistry (ICS-6)
- 52425 Jülich, Germany
| | - Birgit Strodel
- Forschungszentrum Jülich GmbH
- Institute of Complex Systems: Structural Biochemistry (ICS-6)
- 52425 Jülich, Germany
- Institute of Theoretical and Computational Chemistry
- Heinrich Heine University Düsseldorf
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72
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Smith MD, Srinivasa Rao J, Cruz L. Spontaneous dimer states of the Aβ21–30decapeptide. Phys Chem Chem Phys 2014; 16:13069-73. [DOI: 10.1039/c4cp01090f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Computational examination of the spontaneous dimerization of Aβ21–30and stability measures of the resulting parallel and anti-parallel aligned dimers.
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Affiliation(s)
| | - J. Srinivasa Rao
- Department of Physics
- New Jersey Institute of Technology
- University Heights
- Newark, USA
| | - Luis Cruz
- Department of Physics
- Drexel University
- Philadelphia, USA
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73
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Irbäck A, Mohanty S. All-Atom Monte Carlo Simulations of Protein Folding and Aggregation. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [DOI: 10.1007/978-3-642-28554-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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74
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Hayden EY, Teplow DB. Amyloid β-protein oligomers and Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2013; 5:60. [PMID: 24289820 PMCID: PMC3978746 DOI: 10.1186/alzrt226] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The oligomer cascade hypothesis, which states that oligomers are the initiating pathologic agents in Alzheimer’s disease, has all but supplanted the amyloid cascade hypothesis, which suggested that fibers were the key etiologic agents in Alzheimer’s disease. We review here the results of in vivo, in vitro and in silico studies of amyloid β-protein oligomers, and discuss important caveats that should be considered in the evaluation of these results. This article is divided into four sections that mirror the main approaches used in the field to better understand oligomers: (1) attempts to locate and examine oligomers in vivo in situ; that is, without removing these species from their environment; (2) studies involving oligomers extracted from human or animal tissues and the subsequent characterization of their properties ex vivo; (3) studies of oligomers that have been produced synthetically and studied using a reductionist approach in relatively simple in vitro biophysical systems; and (4) computational studies of oligomers in silico. These multiple orthogonal approaches have revealed much about the molecular and cell biology of amyloid β-protein. However, as informative as these approaches have been, the amyloid β-protein oligomer system remains enigmatic.
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Affiliation(s)
- Eric Y Hayden
- Department of Neurology, 635 Charles E. Young Drive South, Room 455, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - David B Teplow
- Department of Neurology, 635 Charles E. Young Drive South, Room 455, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA ; Brain Research and Molecular Biology Institutes, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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75
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Xu L, Wang X, Wang X. Effects of Zn2+ binding on the structural and dynamic properties of amyloid β peptide associated with Alzheimer's disease: Asp1 or Glu11? ACS Chem Neurosci 2013; 4:1458-68. [PMID: 23947440 DOI: 10.1021/cn4001445] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Extensive experimental and computational studies have suggested that multiple Zn(2+) binding modes in amyloid β (Aβ) peptides could exist simultaneously. However, consistent results have not been obtained for the effects of Zn(2+) binding on Aβ structure, dynamics, and kinetics in particular. Some key questions such as why it is so difficult to distinguish the polymorphic states of metal ions binding to Aβ and what the underlying rationale is, necessitate elucidation. In this work, two 3N1O Zn(2+) binding modes were constructed with three histidines (His(6), His(13), and His(14)), and Asp(1)/Glu(11) of Aβ40 coordinated to Zn(2+). Results from molecular dynamics simulations reveal that the conformational ensembles of different Zn(2+)-Aβ40 complexes are nonoverlapping. The formation of turn structure and, especially, the salt bridge between Glu(22)/Asp(23) and Lys(28) is dependent on specific Zn(2+) binding mode. Agreement with available NMR observations of secondary and tertiary structures could be better achieved if the two simulation results are considered together. The free energy landscape constructed by combining both conformations of Aβ40 indicates that transitions between distinct Aβ40 conformations thar are ready for Zn(2+) binding could be possible in aqueous solution. Markov state model analyses reveal the complex network of conformational space of Aβ40 modeulated by Zn(2+) binding, suggesting various misfolding pathways. The binding free energies evaluated using a combination of quantum mechanics calculations and the MM/3D-RISM method suggest that Glu(11) is the preferred oxygen ligand of Zn(2+). However, such preference is dependent on the relative populations of different conformations with specific Zn(2+) binding modes, and therefore could be shifted when experimental or simulation conditions are altered.
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Affiliation(s)
- Liang Xu
- School of
Chemistry, ‡State Key Laboratory of Fine Chemicals, §School of
Chemical Machinery, ∥Department of Engineering Mechanics, ⊥State
Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
| | - Xiaojuan Wang
- School of
Chemistry, ‡State Key Laboratory of Fine Chemicals, §School of
Chemical Machinery, ∥Department of Engineering Mechanics, ⊥State
Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
| | - Xicheng Wang
- School of
Chemistry, ‡State Key Laboratory of Fine Chemicals, §School of
Chemical Machinery, ∥Department of Engineering Mechanics, ⊥State
Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
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76
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Viet MH, Nguyen PH, Ngo ST, Li MS, Derreumaux P. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci 2013; 4:1446-57. [PMID: 24041307 DOI: 10.1021/cn400110d] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent experiments have shown that the mutation Tottori (D7N) alters the toxicity, assembly and rate of fibril formation of the wild type (WT) amyloid beta (Aβ) Aβ40 and Aβ42 peptides. We used all-atom molecular dynamics simulations in explicit solvent of the monomer and dimer of both alloforms with their WT and D7N sequences. The monomer simulations starting from a random coil and totaling 3 μs show that the D7N mutation changes the fold and the network of salt bridges in both alloforms. The dimer simulations starting from the amyloid fibrillar states and totaling 4.4 μs also reveal noticeable changes in terms of secondary structure, salt bridge, and topology. Overall, this study provides physical insights into the enhanced rate of fibril formation upon D7N mutation and an atomic picture of the D7N-mediated conformational change on Aβ40 and Aβ42 peptides.
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Affiliation(s)
- Man Hoang Viet
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Son Tung Ngo
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc
District, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique, UPR
9080 CNRS, IBPC, Universite Denis Diderot, Paris Sorbonne Cité 13 rue Pierre et Marie Curie, 75005, Paris, France
- Institut Universitaire de France, Bvd
Saint Michel, 75005, Paris, France
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77
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Lv Z, Roychaudhuri R, Condron MM, Teplow DB, Lyubchenko YL. Mechanism of amyloid β-protein dimerization determined using single-molecule AFM force spectroscopy. Sci Rep 2013; 3:2880. [PMID: 24096987 PMCID: PMC3791449 DOI: 10.1038/srep02880] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/20/2013] [Indexed: 01/27/2023] Open
Abstract
Aβ42 and Aβ40 are the two primary alloforms of human amyloid β−protein (Aβ). The two additional C−terminal residues of Aβ42 result in elevated neurotoxicity compared with Aβ40, but the molecular mechanism underlying this effect remains unclear. Here, we used single−molecule force microscopy to characterize interpeptide interactions for Aβ42 and Aβ40 and corresponding mutants. We discovered a dramatic difference in the interaction patterns of Aβ42 and Aβ40 monomers within dimers. Although the sequence difference between the two peptides is at the C−termini, the N−terminal segment plays a key role in the peptide interaction in the dimers. This is an unexpected finding as N−terminal was considered as disordered segment with no effect on the Aβ peptide aggregation. These novel properties of Aβ proteins suggests that the stabilization of N−terminal interactions is a switch in redirecting of amyloids form the neurotoxic aggregation pathway, opening a novel avenue for the disease preventions and treatments.
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Affiliation(s)
- Zhengjian Lv
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198, United States
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78
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Binding, conformational transition and dimerization of amyloid-β peptide on GM1-containing ternary membrane: insights from molecular dynamics simulation. PLoS One 2013; 8:e71308. [PMID: 23951128 PMCID: PMC3739818 DOI: 10.1371/journal.pone.0071308] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/27/2013] [Indexed: 12/16/2022] Open
Abstract
Interactions of amyloid-β (Aβ) with neuronal membrane are associated with the progression of Alzheimer's disease (AD). Ganglioside GM1 has been shown to promote the structural conversion of Aβ and increase the rate of peptide aggregation; but the exact nature of interaction driving theses processes remains to be explored. In this work, we have carried out atomistic-scale computer simulations (totaling 2.65 µs) to investigate the behavior of Aβ monomer and dimers in GM1-containing raft-like membrane. The oligosaccharide head-group of GM1 was observed to act as scaffold for Aβ-binding through sugar-specific interactions. Starting from the initial helical peptide conformation, a β-hairpin motif was formed at the C-terminus of the GM1-bound Aβ-monomer; that didn't appear in absence of GM1 (both in fluid POPC and liquid-ordered cholesterol/POPC bilayers and also in aqueous medium) within the simulation time span. For Aβ-dimers, the β-structure was further enhanced by peptide-peptide interactions, which might influence the propensity of Aβ to aggregate into higher-ordered structures. The salt-bridges and inter-peptide hydrogen bonds were found to account for dimer stability. We observed spontaneous formation of intra-peptide D(23)-K(28) salt-bridge and a turn at V(24)GSN(27) region - long been accepted as characteristic structural-motifs for amyloid self-assembly. Altogether, our results provide atomistic details of Aβ-GM1 and Aβ-Aβ interactions and demonstrate their importance in the early-stages of GM1-mediated Aβ-oligomerisation on membrane surface.
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79
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Meral D, Urbanc B. Discrete molecular dynamics study of oligomer formation by N-terminally truncated amyloid β-protein. J Mol Biol 2013; 425:2260-75. [PMID: 23500806 PMCID: PMC3665754 DOI: 10.1016/j.jmb.2013.03.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 03/05/2013] [Indexed: 01/09/2023]
Abstract
In Alzheimer's disease (AD), amyloid β-protein (Aβ) self-assembles into toxic oligomers. Of the two predominant Aβ alloforms, Aβ1-40 and Aβ1-42, the latter is particularly strongly linked to AD. N-terminally truncated and pyroglutamated Aβ peptides were recently shown to seed Aβ aggregation and contribute significantly to Aβ-mediated toxicity, yet their folding and assembly were not explored computationally. Discrete molecular dynamics approach previously captured in vitro-derived distinct Aβ1-40 and Aβ1-42 oligomer size distributions and predicted that the more toxic Aβ1-42 oligomers had more flexible and solvent-exposed N-termini than Aβ1-40 oligomers. Here, we examined oligomer formation of Aβ3-40, Aβ3-42, Aβ11-40, and Aβ11-42 by the discrete molecular dynamics approach. The four N-terminally truncated peptides showed increased oligomerization propensity relative to the full-length peptides, consistent with in vitro findings. Conformations formed by Aβ3-40/42 had significantly more flexible and solvent-exposed N-termini than Aβ1-40/42 conformations. In contrast, in Aβ11-40/42 conformations, the N-termini formed more contacts and were less accessible to the solvent. The compactness of the Aβ11-40/42 conformations was in part facilitated by Val12. Two single amino acid substitutions that reduced and abolished hydrophobicity at position 12, respectively, resulted in a proportionally increased structural variability. Our results suggest that Aβ11-40 and Aβ11-42 oligomers might be less toxic than Aβ1-40 and Aβ1-42 oligomers and offer a plausible explanation for the experimentally observed increased toxicity of Aβ3-40 and Aβ3-42 and their pyroglutamated forms.
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Affiliation(s)
- Derya Meral
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
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80
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Hoshino T, Mahmood MI, Mori K, Matsuzaki K. Binding and Aggregation Mechanism of Amyloid β-Peptides onto the GM1 Ganglioside-Containing Lipid Membrane. J Phys Chem B 2013; 117:8085-94. [DOI: 10.1021/jp4029062] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tyuji Hoshino
- Graduate School of Pharmaceutical
Sciences, Chiba University, Inohana 1-8-1,
Chuo-ku, Chiba 260-8675, Japan
| | - Md. Iqbal Mahmood
- Graduate School of Pharmaceutical
Sciences, Chiba University, Inohana 1-8-1,
Chuo-ku, Chiba 260-8675, Japan
| | - Kenichi Mori
- Graduate School of Pharmaceutical
Sciences, Chiba University, Inohana 1-8-1,
Chuo-ku, Chiba 260-8675, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
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81
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Schweitzer-Stenner R. Different Degrees of Disorder in Long Disordered Peptides Can Be Discriminated by Vibrational Spectroscopy. J Phys Chem B 2013; 117:6927-36. [DOI: 10.1021/jp402869k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department
of Chemistry, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
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82
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Zhang T, Zhang J, Derreumaux P, Mu Y. Molecular mechanism of the inhibition of EGCG on the Alzheimer Aβ(1-42) dimer. J Phys Chem B 2013; 117:3993-4002. [PMID: 23537203 DOI: 10.1021/jp312573y] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Growing evidence supports that amyloid β (Aβ) oligomers are the major causative agents leading to neural cell death in Alzheimer's disease. The polyphenol (-)-epigallocatechin gallate (EGCG) was recently reported to inhibit Aβ fibrillization and redirect Aβ aggregation into unstructured, off-pathway oligomers. Given the experimental challenge to characterize the structures of Aβ/EGCG complexes, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer in the present and absence of EGCG in explicit solvent. Our equilibrium Aβ dimeric structures free of EGCG are consistent with the collision cross section from ion-mobility mass spectrometry and the secondary structure composition from circular dichroism experiment. In the presence of EGCG, the Aβ structures are characterized by increased inter-center-of-mass distances, reduced interchain and intrachain contacts, reduced β-sheet content, and increased coil and α-helix contents. Analysis of the free energy surfaces reveals that the Aβ dimer with EGCG adopts new conformations, affecting therefore its propensity to adopt fibril-prone states. Overall, this study provides, for the first time, insights on the equilibrium structures of Aβ1-42 dimer in explicit aqueous solution and an atomic picture of the EGCG-mediated conformational change on Aβ dimer.
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Affiliation(s)
- Tong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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83
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Hane F, Tran G, Attwood SJ, Leonenko Z. Cu(2+) affects amyloid-β (1-42) aggregation by increasing peptide-peptide binding forces. PLoS One 2013; 8:e59005. [PMID: 23536847 PMCID: PMC3594192 DOI: 10.1371/journal.pone.0059005] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/04/2013] [Indexed: 11/19/2022] Open
Abstract
The link between metals, Alzheimer's disease (AD) and its implicated protein, amyloid-β (Aβ), is complex and highly studied. AD is believed to occur as a result of the misfolding and aggregation of Aβ. The dyshomeostasis of metal ions and their propensity to interact with Aβ has also been implicated in AD. In this work, we use single molecule atomic force spectroscopy to measure the rupture force required to dissociate two Aβ (1–42) peptides in the presence of copper ions, Cu2+. In addition, we use atomic force microscopy to resolve the aggregation of Aβ formed. Previous research has shown that metal ions decrease the lag time associated with Aβ aggregation. We show that with the addition of copper ions the unbinding force increases notably. This suggests that the reduction of lag time associated with Aβ aggregation occurs on a single molecule level as a result of an increase in binding forces during the very initial interactions between two Aβ peptides. We attribute these results to copper ions acting as a bridge between the two peptide molecules, increasing the stability of the peptide-peptide complex.
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Affiliation(s)
- Francis Hane
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Gary Tran
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Simon J. Attwood
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
| | - Zoya Leonenko
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
- * E-mail:
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84
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Liang G, Zhao J, Yu X, Zheng J. Comparative molecular dynamics study of human islet amyloid polypeptide (IAPP) and rat IAPP oligomers. Biochemistry 2013; 52:1089-100. [PMID: 23331123 DOI: 10.1021/bi301525e] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human islet amyloid polypeptide (hIAPP or amylin) is a causative agent in pancreatic amyloid deposits found in patients with type 2 diabetes. The aggregation of full-length hIAPP(1-37) into small oligomeric species is increasingly believed to be responsible for cell dysfunction and death. However, rat IAPP (rIAPP(1-37)), which differs from hIAPP in only six of 37 residues, loses its aggregation ability to form toxic amyloid species. Atomic details of the effect of sequence on the structure and toxicity between the amyloidogenic, toxic hIAPP peptide and the nonamyloidogenic, nontoxic rIAPP peptide remain unclear. Here, we probe sequence-induced differences in structural stability, conformational dynamics, and driving forces between different hIAPP and rIAPP polymorphic forms from monomer to pentamer using molecular dynamics simulations. Simulations show that hIAPP forms from trimer to pentamer exhibit high structural stability with well-preserved in-register parallel β-sheet and the U-bend conformation. The hIAPP trimer appears to be a smallest minimal seed in solution. The stabilities of parallel hIAPP oligomers increase with the number of peptides. Conversely, replacement of hIAPP sequence by rIAPP sequence causes a significant loss of favorable interpeptide interactions in all rIAPP oligomers, destabilizing the C-terminal β-sheet, turn conformation, and overall stability. A less β-sheet-rich structure and a disturbed U-shaped topology exert a large energy penalty on the self-assemble of the rIAPP peptides into highly ordered, in-register β-sheet-rich protofibrils and fibrils, which explains the nonamyloidogenic activity of rIAPP. Moreover, the absence of interior water within the U-turn region in the well-packed higher-order hIAPP oligomers, not in the poorly packed rIAPP oligomers, also stabilizes peptide association. This work provides atomic details of the sequence-structure relationship between the amyloidogenic hIAPP and its analogues such as the nonamyloidogenic rIAPP and some mutants, which could help in the development of novel therapeutic agents to block the formation of toxic hIAPP oligomeric species for type 2 diabetes.
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Affiliation(s)
- Guizhao Liang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA
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85
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Nag S, Sarkar B, Chandrakesan M, Abhyanakar R, Bhowmik D, Kombrabail M, Dandekar S, Lerner E, Haas E, Maiti S. A folding transition underlies the emergence of membrane affinity in amyloid-β. Phys Chem Chem Phys 2013; 15:19129-33. [DOI: 10.1039/c3cp52732h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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86
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Gallion SL. Modeling amyloid-beta as homogeneous dodecamers and in complex with cellular prion protein. PLoS One 2012; 7:e49375. [PMID: 23145167 PMCID: PMC3493521 DOI: 10.1371/journal.pone.0049375] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/11/2012] [Indexed: 12/16/2022] Open
Abstract
Soluble amyloid beta (Aβ) peptide has been linked to the pathology of Alzheimer's disease. A variety of soluble oligomers have been observed to be toxic, ranging from dimers to protofibrils. No tertiary structure has been identified as a single biologically relevant form, though many models are comprised of highly ordered β-sheets. Evidence exists for much less ordered toxic oligomers. The mechanism of toxicity remains highly debated and probably involves multiple pathways. Interaction of Aβ oligomers with the N-terminus of the cellular form of the prion protein (PrP(c)) has recently been proposed. The intrinsically disordered nature of this protein and the highly polymorphic nature of Aβ oligomers make structural resolution of the complex exceptionally challenging. In this study, molecular dynamics simulations are performed for dodecameric assemblies of Aβ comprised of monomers having a single, short antiparallel β-hairpin at the C-terminus. The resulting models, devoid of any intermolecular hydrogen bonds, are shown to correlate well with experimental data and are found to be quite stable within the hydrophobic core, whereas the α-helical N-termini transform to a random coil state. This indicates that highly ordered assemblies are not required for stability and less ordered oligomers are a viable component in the population of soluble oligomers. In addition, a tentative model is proposed for the association of Aβ dimers with a double deletion mutant of the intrinsically disordered N-terminus of PrP(c). This may be useful as a conceptual working model for the binding of higher order oligomers and in the design of further experiments.
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87
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Barz B, Turner BS, Bansil R, Urbanc B. Folding of pig gastric mucin non-glycosylated domains: a discrete molecular dynamics study. J Biol Phys 2012; 38:681-703. [PMID: 24615227 DOI: 10.1007/s10867-012-9280-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/27/2012] [Indexed: 11/26/2022] Open
Abstract
Mucin glycoproteins consist of tandem-repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in polymerization of mucin and play an important role in the pH-dependent gelation of gastric mucin, which is essential for protecting the stomach from autodigestion. We examine folding of the non-repetitive sequence of PGM-2X (242 amino acids) and the von Willebrand factor vWF-C1 domain (67 amino acids) at neutral and low pH using discrete molecular dynamics (DMD) in an implicit solvent combined with a four-bead peptide model. Using the same implicit solvent parameters, folding of both domains is simulated at neutral and low pH. In contrast to vWF-C1, PGM-2X folding is strongly affected by pH as indicated by changes in the contact order, radius of gyration, free-energy landscape, and the secondary structure. Whereas the free-energy landscape of vWF-C1 shows a single minimum at both neutral and low pH, the free-energy landscape of PGM-2X is characterized by multiple minima that are more numerous and shallower at low pH. Detailed structural analysis shows that PGM-2X partially unfolds at low pH. This partial unfolding is facilitated by the C-terminal region GLU236-PRO242, which loses contact with the rest of the domain due to effective "mean-field" repulsion among highly positively charged N- and C-terminal regions. Consequently, at low pH, hydrophobic amino acids are more exposed to the solvent. In vWF-C1, low pH induces some structural changes, including an increased exposure of CYS at position 67, but these changes are small compared to those found in PGM-2X. For PGM-2X, the DMD-derived average β-strand propensity increases from 0.26 ± 0.01 at neutral pH to 0.38 ± 0.01 at low pH. For vWF-C1, the DMD-derived average β-strand propensity is 0.32 ± 0.02 at neutral pH and 0.35 ± 0.02 at low pH. The DMD-derived structural information provides insight into pH-induced changes in the folding of two distinct mucin domains and suggests plausible mechanisms of the aggregation/gelation of mucin.
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Affiliation(s)
- Bogdan Barz
- Physics Dept., Drexel University, Philadelphia, PA, 19104, USA
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88
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Zhao LN, Long H, Mu Y, Chew LY. The toxicity of amyloid β oligomers. Int J Mol Sci 2012; 13:7303-7327. [PMID: 22837695 PMCID: PMC3397527 DOI: 10.3390/ijms13067303] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 12/13/2022] Open
Abstract
In this review, we elucidate the mechanisms of Aβ oligomer toxicity which may contribute to Alzheimer's disease (AD). In particular, we discuss on the interaction of Aβ oligomers with the membrane through the process of adsorption and insertion. Such interaction gives rises to phase transitions in the sub-structures of the Aβ peptide from α-helical to β-sheet structure. By means of a coarse-grained model, we exhibit the tendency of β-sheet structures to aggregate, thus providing further insights to the process of membrane induced aggregation. We show that the aggregated oligomer causes membrane invagination, which is a precursor to the formation of pore structures and ion channels. Other pathological progressions to AD due to Aβ oligomers are also covered, such as their interaction with the membrane receptors, and their direct versus indirect effects on oxidative stress and intraneuronal accumulation. We further illustrate that the molecule curcumin is a potential Aβ toxicity inhibitor as a β-sheet breaker by having a high propensity to interact with certain Aβ residues without binding to them. The comprehensive understanding gained from these current researches on the various toxicity mechanisms show promises in the provision of better therapeutics and treatment strategies in the near future.
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Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
| | - HonWai Long
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
- High Performance Computing Centre, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Lock Yue Chew
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
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