Chemistry Reference
In-Depth Information
1
1
A
B
0.9
0.9
0.8
0.8
0.7
0.7
0.6
0.6
0.5
0.4
0.3
0.2
0.5
0.4
0.3
0.2
0.1
0.1
0
0
0
2
4
6
8
10
0
2
4
6
8
10
(d)
r (Å)
r (Å)
2
1.8
1.6
1.4
1.2
1
0.8
0.6
0.4
0.2
2
1.8
1.6
1.4
1.2
1
0.8
0.6
0.4
0.2
0
A
B
0
0
2
4
6
8
10
0
2
4
6
8
10
(e)
r (Å)
r (Å)
1.2
1
0.8
0.6
0.4
0.2
0
1.2
1
0.8
0.6
0.4
0.2
A
B
0
0
2
4
6
8
10
0
2
4
6
8
10
(f)
r (Å)
r (Å)
FIGURE  2.5  (continued)  (d). the. backbone. nitrogen. of. residue. 53,. (e). the. backbone. car-
boxyl.carbone.of.residue.140,.and.(f).the.backbone.nitrogen.of.residue.140.for.the.wild-type.
(A).and.mutant.(B).synucleins.at.1.ns.(.),.2.ns.(-.-),.3.ns.(-·-).and.4.ns.(····).
.contribution.(−TS)..Also,.the.overall.enthalpic.contribution.decreases.throughout.the.
course.of.the.simulations.(Table.2.9).
We. now. turn. from. purely. classical. studies. to. mixed. QM/MM. studies.. In. the.
following,. we. present. coordination. chemistry. studies. of. Fe 3+ . with. the. tyrosine.
residue. of. the. wild-. and. mutant-type. α-synuclein. proteins. in. aqueous. solution,.
using. the. trajectories. that. we. obtained. from. our. classical. MD. studies. presented.
earlier..For.studying.the.coordination.of.the.transition.metal.ion.to.the.protein,.we.
.performed.QM/MM.simulations.(25.ps)..Recently,.we.predicted.the.water.disso-
ciation.mechanism.in.aqueous.solution.that.is.induced.by.the.presence.of.the.Fe 3+ .
ion.and.the.impact.of.the.dissociated.states.of.water.on.the.hydration.structure.of.
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