Chemistry Reference
In-Depth Information
this.residue.occurs.at.the.carboxyl.on.the.C-terminus..The.presence.of.two.oxygens,.
versus.one.in.comparison.to.the..nonterminal.residues,.explains.the.increased.water.
.coordination.of.this.residue.
In. addition. to. the. effect. of. hydration. on. the. proteins,. the. average. Gibbs. free.
energy.changes.of.both.the.wild-type.and.A53T.mutant.α-synuclein.have.been.cal-
culated.as.described.in.the.methods.section..For.the.calculations.of.the.overall.Gibbs.
free. energy. (
G
). of. each. protein. for. each. nanosecond. of. the. simulation,. the. stan-
dard.deviation.is.too.high.to.make.a.direct.comparison.of.these.values..However,.a.
trend.can.be.observed.from.these.values..The.enthalpic.contribution.(
E
MM
.+.
G
PBSA
).
to. the. overall. Gibbs. free. energy. of. the. proteins. is. much. greater. than. the. entropic.
1.4
1.4
A
B
1.2
1.2
1
0.8
0.6
0.4
0.2
0
1
0.8
0.6
0.4
0.2
0
0
2
4
6
8
10
0
2
4
6
8
10
(a)
r
(Å)
r
(Å)
4
4
A
B
3.5
3.5
3
3
2.5
2
1.5
1
0.5
0
2.5
2
1.5
1
0.5
0
0
2
4
6
8
10
0
2
4
6
8
10
(b)
r
(Å)
r
(Å)
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
(c)
r
(Å)
r
(Å)
FIGURE 2.5
Radial.distribution.functions.of.water.molecules.around.(a).the.backbone.car-
boxyl.carbon.of.residue.1,.(b).the.backbone.nitrogen.of.residue.1,.(c).the.backbone.carboxyl.
carbon.of.residue.53,.
(
continued
)
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