Structural and Thermodynamic Studies of Synuclein Proteins Related to Parkinson’s Disease: - Metallic Systems: A Quantum Chemist's Perspective - page 52

(a) A B C D E

(b) A B C D E

FIGURE 2.2 (a).Structures.of.the.A53T.α-synuclein.protein.obtained.from.classical.MD.
simulations.in.the.gas.phase.at.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.A53T.α-synuclein.protein.obtained.from.clas-
sical.MD.simulations.in.the.gas.phase.at.(A).0.ns,.(B).5.ns,.(C).10.ns,.(D).15.ns,.and.(E).20.ns..
The.α-helix.(purple),.bridge.β.(blue),.turn.(green),.and.coil.(red).are.depicted.

α-helix.to.a.combination.of.turns.and.coils.with.a.few.select.regions.of.a.3 10 -heli-
cal.structure.within.the.irst.nanosecond..Although.the.α-helical.structure.of.these.
initial.92.residues.is.no.longer.present,.the.general.U-shape.is.maintained.except.that.
the.position.and.the.length.of.the.connecting.coil.and.turn,.initially.residues.35-44,.
expands.to.residues.35-52..Additionally,.the.N-terminus.moves.such.that.it.appears.
to.be.positioned.close.to.residue.77.converting.the.U-shape.to.an.almost.tear.drop.
shape.. The. helical. region. of. the. protein. extends. through. residue. 99. before. ending.
in.a.long.C-terminal.tail.but.after.equilibration.and.without.the.presence.of.explicit.
solvent,.the.C-terminal.tail.region.begins.at.residue.77..The.C-terminal.tail.also.coils.
upon.itself.forming.a.small.clump,.leaving.only.the.last.20.residues.loose..The.last.
20.residues.then.link.the.U-portion.of.the.protein.and.the.clump.of.the.C-terminal.
tail,. resulting. in. the. inal. observed. structure.. These. structural. changes. equilibrate.