A Computational Study of Amyloid β-Protein Assembly in Crowded Environments
Matthew Voelker, Mark Betnel, and Brigita Urbanc, Department of Physics, Drexel University
Abstract
Results and Analysis
Alzheimer's disease is strongly associated with aberrant amyloid β-protein
(Aβ) assembly into heterogeneous, metastable oligomeric assemblies with
structures that have not been experimentally characterized yet. The 40 and
42 amino acids long Aβ40 and Aβ42 are the two predominant Aβ alloforms in
the brain. Whereas Aβ40 and Aβ42 oligomer formation from monomeric
state is still inaccessible to fully atomistic explicit-solvent molecular
dynamics, and A β42 oligomers were structurally characterized using discrete
molecular dynamics (DMD) and an intermediate-resolution protein model
within the DMD4B-HYDRA implicit solvent force feld and the corresponding
oligomer size distributions well matched to available in vitro data. In vivo,
however, Aβ coexists with other biomolecules in a rather crowded
environment. To understand the effect of crowding on Aβ oligomer
formation, we used the DMD4B-HYDRA force feld and added to an ensemble
of 32 monomeric Aβ40 or Aβ42 peptides inert spherical "crowders" with a
diameter of 0.5 nm at a concentration of 1:100 peptides:crowders to examine
their effect on Aβ40 and Aβ42 oligomerization pathways. Our results show
that crowding shifts oligomer size distributions towards smaller oligomer sizes
and increases solubility of both peptides. The effect is stronger for Aβ40,
where crowding abolishes the multimodal character of the oligomer size
distribution. Our structural analysis revealed that the stability of larger
oligomers is compromised by effective osmotic pressure exerted by the
crowders, resulting in an increased rate of assembly breakage. While in vivo
crowding agents are not inert as the crowders in out study, we here reveal that
crowding—induced osmotic pressure strongly affects protein assembly
dynamics, which is of signifcance to the disease.
Conclusions
In contrast to simulations of Aβ40 and Aβ42 with no
crowders present, a 1:100 peptide:crowder
concentration results in the following:
•
The solubility of both species is increased
•
The oligomer distribution is shifted towards smaller
oligomer sizes
•
Aβ42 tetramers, which are observed to be unstable
in simulations with no crowders present, become
more stable in crowded environments
•
All other Aβ40 and Aβ42 oligomer s are
destabilized via an effective osmotic pressure which
acts to disband oligomeric assemblies, resulting in
an increased rate of assembly breakage
•
The kinetics of Aβ40 and Aβ42 assembly is altered
via a substantial decrease in the oligomer lifetimes
Both species attain a meta-stable distribution within
80M time units
Crowders increase the solubility of both species and
shifts the oligomers distribution towards lower-ordered
oligomers
Characteristic multi-modal distribution of Aβ42 does
not arise when crowders are present
Class A
Distribution of oligomer sizes sampled from the fnal 10M time units
of the simulations
Crowders result in a larger free energy minima for
Aβ42 tetramers, which have a much high propensity to occur
in simulations with crowders
β-strand content of Aβ42 monomers and dimers altered
Free energy landscapes and β-strand content of other
Aβ40 and Aβ42 oligomers are largely unaffected!
Alzheimer's Disease
Chronic neurodegenerative disease with cognitive and memory
symptoms, eventually resulting in neuron death
Class B
Future Work
Characterized in part by amyloid plaques, protein aggregates in
the brain which contain Aβ40 and Aβ42
Amyloid β-protein oligomers
are hypothesized to be the
proximate neurotoxic species
causing an onset of the AD
pathology
The mechanisms which drive
the formation of these
structures may give insight
into this disease
Class
Photo courtesy of www.neurology.org
Simulations
Discrete Molecular Dynamics
(DMD) simulations
Eight 80 million steps long
trajectories of peptide assembly
of 32 initially spatially separated
and unstructured peptides
Simulations undergo an initial high-temperature run to create a diverse set of initial
conformations before being simulated at a physiological temperature
●
Currently running simulations with 1:1, 1:10 and
1:100 peptide:crowder concentrations
●
Explore the impact of varying crowder concentration
with added parameters of crowder size and shape
●
Develop analysis to further analyze kinetic effect of
crowders
Beta-strand propensity averaged over all amino acids in each peptide
Oligomer lifetimes are
measured as a given
oligomer's occurrence in
consecutive simulation frames
taken 100,000 time units apart
The presence of crowders
reduces the average lifetime of
nearly all oligomer sizes for
both Aβ40 and Aβ42
Aβ42 tetramers have a longer
average lifetime and are thus
stabilized by crowders relative
to Aβ42 tetramers with no
crowders present
References
1. B. Urbanc, M. Betnel, L. Cruz, G. Bitan, and D.B. Teplow. Elucidation of Amyloid β-Protein
Oligomerization Mechanisms: Discrete Molecular Dynamics Study, J. Am. Chem. Soc. 132, 42664280 (2010)
2. M. Betnel, N.V. Dokholyan, and B. Urbanc. From disordered amyloid β-proteins to soluble
oligomers and protofbrils using Discrete Molecular Dynamics, in Alzheimer'sdisease: Molecular
basis of amyloid β-protein aggregation and cytotoxic aggregatesfrom computer simulations,
Molecular Medicine and Medicinal Chemistry 7, Part B, Ch. 12, 333-358, Ed. P. Derreumaux,
Imperial College Press (2013)
Acknowledgements
Four-Bead Protein Model with
Backbone Hydrogen Bonding and
Amino Acid-Specifc Hydropathy
and Charge
Crowders interact via hardsphere interaction only
Potential of mean force (PMF) plots with parameters of N-C terminal distance and total solvent
accessible surface area of all hydrophobic amino acids. All conformations from the fnal 40M time
Class C
units of each run are sampled
B
This research was supported in part by the National Science Foundation
through XSEDE resources provided by Purdue University under the
grant number PHYS100030.
Four-Bead Model
Contact info: Matthew Voelker (mjvoelke@gmail.com/mjv45@drexel.edu)
Brigita Urbanc (bu25@drexel.edu)