Chemistry Reference
In-Depth Information
TABLE 2.9
Molecular Mechanics Potential Energy, Gibbs Free Energy of 
Solvation and Entropic Contributions to Calculation of the 
Gibbs Free Energy of the Monomers in Solution for Each ns 
of Our Simulations
E MM
(kcal/mol)
G PBSA
(kcal/mol)
−TS 
(kcal/mol)
Protein
Time
G  (kcal/mol)
Wild-type
1 ns
1511.911.
(±211.867)
−4466.61.
(±64.47)
−372
−3326.698.
(±221.459)
2 ns
1312.136.
(±199.188)
−4161.64.
(±124.65)
−372.93
−3222.434.
(±234.975)
3 ns
1325.735.
(±83.658)
−4152.66.
(±81.81)
−372.62
−3199.545.
(±117.011)
4 ns
1374.319.
(±116.706)
−4249.12.
(±121.6)
−375.41
−3250.211.
(±168.543)
A53T
1 ns
1494.363.
(±214.044)
−4442.37.
(±69.51)
−376.03
−3324.037.
(±225.048)
2 ns
1306.162.
(±107.126)
−4201.75.
(±85.31)
−367.04
−3262.628.
(±136.944)
3 ns
1300.654.
(±62.364)
−4239.32.
(±58.73)
−366.73
−3305.396.
(±85.665)
4 ns
1322.308.
(±129.356)
−4230.01.
(±86.97)
−371.07
−3278.772.
(±155.874)
Fe 3+ .in.water.using.CPMD.simulations.coupled.with.TPS.calculations. 71 .The.geom-
etry.of.the.resulting.Fe(OH) 3 (H 2 O) 6 .ion.with.the.surrounding.water..molecules.and.
aqua.ions.(H 3 O + .and.OH .complexes).was.obtained.from.the.trajectories.computed.
in.those.studies..This.geometry.has.been.used.in.the.present.studies.as.the.basis.
for.the.QM.part.of.the.simulation.to.investigate.the.coordination.chemistry.of.the.
hydrated.Fe 3+ .ion.with.α-synuclein.proteins.and.the.impact.of.dissociated.states.of.
water.on.this.coordination.chemistry..For.details.of.the.Fe 3+ .work.see.the.Chapter.
entitled. Metal Ions in Aqueous Solution ..Dangling.bonds.in.our.QM/MM.studies.
were.terminated.with.hydrogen.bonds..For.the.portion.of.the.system.treated.with.
molecular.mechanics,.the.same.procedure.presented.in.the.Methods.section.was.
used.except.that.a.velocity.Verlet.propagation.algorithm.was.applied.with.a.time.
step.of.0.12.fs.
The. results. of. several. experiments. suggest. that. the. C-terminal. region. of.
α-synucleins. has. a. low. afinity. for. binding. metal. ions. whereas. the. N-terminal.
region. has. a. high. afinity. for. binding. metal. ions.. The. molecular. mechanism. of.
metal.binding.in.PD.and.the.binding.afinities.of.various.metal.ions.to.α-synuclein.
are.unknown..Various.spectroscopic.measurements.have.proposed.His50.and.the.
residues. between. 110. and. 140. to. be. active. toward. Fe(III). binding.. The. reason.
for.the.chemical.reactivity.of.the.region.between.residues.110.and.140.might.be.
 
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