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that.can.only.be.observed.on.an.atomic.level.and.yield.insight.to.possible.aggregation.
mechanisms.
Pictorial.descriptions.of.the.wild-type.α-synuclein.and.the.A53T.mutant.confor-
mations.taken.from.our.MD.simulations.in.the.gas.phase.are.depicted.in.Figures.2.1a.
and. 2.2a,. respectively.. The. corresponding. secondary. structures. are. illustrated. in.
Figures.2.1b.and.2.2b..Even.before.an.in-depth.analysis.of.structural.changes.during.
the.course.of.our.simulations,.drastic.differences.between.the.equilibrated.structures.
of.the.wild-type.and.A53T.mutant,.as.well.as.between.the.initial.and.equilibrated.
structures.of.each.respective.mutant,.are.obvious.
Considering. only. the. wild-type. α-synuclein. structure. in. the. gas. phase.
(Figure.2.1a),.the.equilibrated.structure.forms.an.ovoid.donut.shape.that.looks.noth-
ing.like.the.original.experimental.structure..However,.this.depiction.does.not.provide.
an.accurate.illustration.of.the.changes.in.the.secondary.structure.of.the.protein.dur-
ing.the.course.of.the.simulation..The.structure.of.the.protein.is.completely.different.
from.the.initial.experimental.structure.within.a.matter.of.nanoseconds..As.shown.
in. Figure. 2.1b,. the. α-helical. structure. from. residue. 1. to. 92. has. changed. from. an.
(a)
A
B
C
D
E
(b)
A
B
C
D
E
FIGURE 2.1
(a).Structures.of.wild-type.α-synuclein.obtained.from.our.classical.MD.simu-
lations.in.the.gas.phase.at.various.times:.(A).0.ns,.(B).5.ns,.(C).10.ns,.(D).15.ns,.and.(E).20.ns..
(b). (
See color insert.
). Secondary. structures. of.the.wild-type.α-synuclein. protein. obtained.
from.classical.MD.simulations.in.the.gas.phase.at.various.times:.(A).0.ns,.(B).5.ns,.(C).10.ns,.
(D).15.ns,.and.(E).20.ns..The.different.secondary.structures.are.presented.utilizing.various.
colors:.α-helix.(purple),.3
10
.helix.(orange),.bridge.β.(blue),.turn.(green),.coil.(red).
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