Dimerization of the full-length alzheimer amyloid β-peptide (Aβ42) in explicit aqueous solution: A molecular dynamics study

Xiaoxia Zhu, Ram Prasad Bora, Arghya Barman, Rajiv Singh, Rajeev Prabhakar

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Abstract

In this study, the mechanism of dimerization of the full-length Alzheimer amyloid beta (Aβ42) peptide and structural properties of the three most stable dimers have been elucidated through 0.8 μs classical molecular dynamics (MD) simulations. The Aβ42 dimer has been reported to be the smallest neurotoxic species that adversely affects both memory and synaptic plasticity. On the basis of interactions between the distinct regions of the Aβ42 monomer, 10 different starting configurations were developed from their native folded structures. However, only six of them were found to form dimers and among them the three most stable (XP, C-CAP, and N-NP) were chosen for the detailed analysis. The structural properties of these dimers were compared with the available experimental and theoretical data. The MD simulations show that hydrophobic regions of both monomers play critical roles in the dimerization process. The high content of the α-helical structure in all the dimers is in line with its experimentally proposed role in the oligomerization. The formation of a zipper-like structure in XP is also in accordance with its existence in the aggregates of several short amyloidogenic peptides. The computed values of translational (DT) and rotational (DR) diffusion constants of 0.63×10-6 cm2/s and 0.035 ns -1, respectively, for this dimer are supported by the corresponding values of the Aβ42 monomer. These simulations have also elucidated several other key structural properties of these peptides. This information will be very useful to design small molecules for the inhibition and disruption of the critical Aβ42 dimers.

Original languageEnglish
Pages (from-to)4405-4416
Number of pages12
JournalJournal of Physical Chemistry B
Volume116
Issue number15
DOIs
StatePublished - Apr 19 2012

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Dimerization
dimerization
Amyloid
Dimers
Peptides
peptides
Molecular dynamics
dimers
molecular dynamics
aqueous solutions
Structural properties
monomers
Monomers
zippers
Oligomerization
simulation
Fasteners
Computer simulation
peptide A42
plastic properties

ASJC Scopus subject areas

  • Materials Chemistry
  • Surfaces, Coatings and Films
  • Physical and Theoretical Chemistry

Cite this

Dimerization of the full-length alzheimer amyloid β-peptide (Aβ42) in explicit aqueous solution : A molecular dynamics study. / Zhu, Xiaoxia; Bora, Ram Prasad; Barman, Arghya; Singh, Rajiv; Prabhakar, Rajeev.

In: Journal of Physical Chemistry B, Vol. 116, No. 15, 19.04.2012, p. 4405-4416.

Research output: Contribution to journalArticle

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