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Title: Spontaneous self-assembly of amyloid β (1–40) into dimers

Journal Article · · Nanoscale Advances
DOI: https://doi.org/10.1039/c9na00380k · OSTI ID:1661023
ORCiD logo [1];  [2];  [3]; ORCiD logo [1]
  1. Univ. of Nebraska Medical Center, Omaha, NE (United States)
  2. Univ. of Nebraska Medical Center, Omaha, NE (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  3. Univ. of Nebraska Medical Center, Omaha, NE (United States); Bruker Nano Surfaces Division, Santa Barbara, CA (United States)

The self-assembly and fibrillation of amyloid β (Aβ) proteins is the neuropathological hallmark of Alzheimer's disease. However, the molecular mechanism of how disordered monomers assemble into aggregates remains largely unknown. In this work, we characterize the assembly of Aβ (1–40) monomers into dimers using long-time molecular dynamics simulations. Upon interaction, the monomers undergo conformational transitions, accompanied by change of the structure, leading to the formation of a stable dimer. The dimers are stabilized by interactions in the N-terminal region (residues 5–12), in the central hydrophobic region (residues 16–23), and in the C-terminal region (residues 30–40); with inter-peptide interactions focused around the N- and C-termini. The dimers do not contain long β-strands that are usually found in fibrils.

Research Organization:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA); National Institutes of Health (NIH); National Science Foundation (NSF)
Grant/Contract Number:
AC52-07NA27344; GM096039; GM100156; 1004094; ACI-1053575; R01GM116961
OSTI ID:
1661023
Report Number(s):
LLNL-JRNL-813715; 1021710
Journal Information:
Nanoscale Advances, Vol. 1, Issue 10; ISSN 2516-0230
Publisher:
Royal Society of ChemistryCopyright Statement
Country of Publication:
United States
Language:
English

References (89)

Single-Molecule Atomic Force Microscopy Force Spectroscopy Study of Aβ-40 Interactions journal June 2011
Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations: Amyloid β Dimers journal March 2017
Function and toxicity of amyloid beta and recent therapeutic interventions targeting amyloid beta in Alzheimer's disease journal January 2015
On the nucleation of amyloid β-protein monomer folding journal June 2005
Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape journal June 2015
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
  • Pierce, Levi C. T.; Salomon-Ferrer, Romelia; Augusto F. de Oliveira, Cesar
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300284c
journal August 2012
Aβ42 assembles into specific β-barrel pore-forming oligomers in membrane-mimicking environments journal September 2016
Single-Molecule Studies of Intrinsically Disordered Proteins journal January 2014
Structural Characterization and Inhibition of Toxic Amyloid-β Oligomeric Intermediates journal July 2013
Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study journal March 2010
Common mechanisms of amyloid oligomer pathogenesis in degenerative disease journal April 2006
Intracellular amyloid-β in Alzheimer's disease journal July 2007
Nanoprobing of misfolding and interactions of amyloid β 42 protein journal May 2014
Atomic-Level Characterization of the Structural Dynamics of Proteins journal October 2010
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal February 2008
Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils journal April 2010
Mechanism of amyloid β−protein dimerization determined using single−molecule AFM force spectroscopy journal October 2013
The Alzheimer’s Peptides Aβ40 and 42 Adopt Distinct Conformations in Water: A Combined MD / NMR Study journal May 2007
Amyloid β-Protein Aggregation Produces Highly Reproducible Kinetic Data and Occurs by a Two-Phase Process journal September 2009
Comparison of simple potential functions for simulating liquid water journal July 1983
Atomic force microscopic imaging of seeded fibril formation and fibril branching by the Alzheimer's disease amyloid-β protein journal December 1997
3D structure of Alzheimer's amyloid- (1-42) fibrils journal November 2005
Atomic View of a Toxic Amyloid Small Oligomer journal March 2012
Alzheimer's Disease: Genes, Proteins, and Therapy journal April 2001
Solution structure of the Alzheimer amyloid β-peptide (1-42) in an apolar microenvironment: Similarity with a virus fusion domain journal October 2002
AMPAR Removal Underlies Aβ-Induced Synaptic Depression and Dendritic Spine Loss journal December 2006
The Amyloid Hypothesis of Alzheimer's Disease: Progress and Problems on the Road to Therapeutics journal July 2002
Amyloid β-Protein Monomer Folding: Free-Energy Surfaces Reveal Alloform-Specific Differences journal December 2008
Protein Misfolded Oligomers: Experimental Approaches, Mechanism of Formation, and Structure-Toxicity Relationships journal March 2012
Energy landscape of a small peptide revealed by dihedral angle principal component analysis journal November 2004
Structural Characterization of a Soluble Amyloid β-Peptide Oligomer journal March 2009
An Azobenzene Photoswitch Sheds Light on Turn Nucleation in Amyloid-β Self-Assembly journal February 2012
Direct characterization of amyloidogenic oligomers by single-molecule fluorescence journal September 2008
Design of small molecules that target metal-A  species and regulate metal-induced A  aggregation and neurotoxicity journal December 2010
Single Molecule Tracking Analysis Reveals That the Surface Mobility of Amyloid Oligomers Is Driven by Their Conformational Structure journal August 2011
Structural, morphological, and functional diversity of amyloid oligomers journal July 2015
Structure-neurotoxicity relationships of amyloid  -protein oligomers journal August 2009
Alzheimer's Disease and the Amyloid-β Peptide journal January 2010
Exploring the aggregation free energy landscape of the amyloid-β protein (1–40) journal October 2016
A comparative analysis of the aggregation behavior of amyloid-β peptide variants journal October 2012
Annular Protofibrils Are a Structurally and Functionally Distinct Type of Amyloid Oligomer journal December 2008
Quaternary Structure Defines a Large Class of Amyloid-β Oligomers Neutralized by Sequestration journal June 2015
Effect of acidic pH on the stability of α-synuclein dimers: Stability of α-Synuclein Dimers journal July 2016
Self-Propagating, Molecular-Level Polymorphism in Alzheimer's  -Amyloid Fibrils journal January 2005
A partially folded structure of amyloid-beta(1–40) in an aqueous environment journal July 2011
Structural Classification of Toxic Amyloid Oligomers journal August 2008
Regulation of NMDA receptor trafficking by amyloid-β journal July 2005
The Structure of Misfolded Amyloidogenic Dimers: Computational Analysis of Force Spectroscopy Data journal December 2014
Misfolding of the amyloid β-protein: A molecular dynamics study journal November 2005
Direct Detection of α-Synuclein Dimerization Dynamics: Single-Molecule Fluorescence Analysis journal April 2015
Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms journal January 2011
Molecular Mechanism of Misfolding and Aggregation of Aβ(13–23) journal May 2013
Cell-Membrane-Mimicking Lipid-Coated Nanoparticles Confer Raman Enhancement to Membrane Proteins and Reveal Membrane-Attached Amyloid-β Conformation journal August 2015
Thermodynamics of Aβ(1−40) Amyloid Fibril Elongation journal September 2005
Interactions of Zn(ii) and Cu(ii) ions with Alzheimer's amyloid-beta peptide. Metal ion binding, contribution to fibrillization and toxicity journal January 2011
Protein folding and misfolding journal December 2003
Structures of the Alzheimer’s Wild-Type Aβ1-40 Dimer from Atomistic Simulations journal August 2015
A series of PDB-related databanks for everyday needs journal October 2014
α-Synuclein Misfolding Assessed with Single Molecule AFM Force Spectroscopy: Effect of Pathogenic Mutations journal October 2013
The presenilin 2 mutation (N141I) linked to familial Alzheimer disease (Volga German families) increases the secretion of amyloid   protein ending at the 42nd (or 43rd) residue journal March 1997
Amyloid  -protein (A ) assembly: A 40 and A 42 oligomerize through distinct pathways journal December 2002
Self-assembly of the full-length amyloid Aβ42 protein in dimers journal January 2016
PROFASI: A Monte Carlo simulation package for protein folding and aggregation journal January 2006
Nanoscale Dynamics of Amyloid β-42 Oligomers As Revealed by High-Speed Atomic Force Microscopy journal October 2016
Significant Structural Differences between Transient Amyloid-β Oligomers and Less-Toxic Fibrils in Regions Known To Harbor Familial Alzheimer′s Mutations journal April 2014
Aβ(1–42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease journal May 2015
Dynamics of locking of peptides onto growing amyloid fibrils journal July 2009
Protein Misfolding, Functional Amyloid, and Human Disease journal June 2006
Selective cytotoxicity of intracellular amyloid β peptide1–42 through p53 and Bax in cultured primary human neurons journal January 2002
Computational Study on the Structural Diversity of Amyloid Beta Peptide (Aβ 10 - 35 ) Oligomers journal March 2008
Monomeric Aβ 1–40 and Aβ 1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil journal January 2016
Amyloid beta-protein monomer structure: A computational and experimental study journal February 2006
Amyloid pores from pathogenic mutations journal July 2002
High-Resolution Structures of the Amyloid-β 1–42 Dimers from the Comparison of Four Atomistic Force Fields journal June 2017
Comparative Studies of Disordered Proteins with Similar Sequences: Application to Aβ40 and Aβ42 journal April 2013
Natural Oligomers of the Alzheimer Amyloid-  Protein Induce Reversible Synapse Loss by Modulating an NMDA-Type Glutamate Receptor-Dependent Signaling Pathway journal March 2007
In silico study of amyloid  -protein folding and oligomerization journal December 2004
Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril journal July 2016
Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease journal June 2009
Characterization of cerebrospinal fluid aminoterminally truncated and oxidized amyloid-β peptides journal April 2012
Improved side-chain torsion potentials for the Amber ff99SB protein force field journal January 2010
Millisecond-scale molecular dynamics simulations on Anton conference January 2009
Significant Structural Differences between Transient Amyloid-β Oligomers and Less-Toxic Fibrils in Regions Known To Harbor Familial Alzheimer′s Mutations journal April 2014
Single-molecule studies of intrinsically disordered proteins text January 2014
Structural Characterization and Inhibition of Toxic Amyloid-β Oligomeric Intermediates journal July 2013
Common mechanisms of amyloid oligomer pathogenesis in degenerative disease journal April 2006
AMPAR Removal Underlies Aβ-Induced Synaptic Depression and Dendritic Spine Loss journal December 2006
Aβ(1–42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease journal May 2015
Self-Propagating, Molecular-Level Polymorphism in Alzheimer's  -Amyloid Fibrils journal January 2005