Artificial Enzymes - The Nanobiotechnology - page 48

Enormous.numbers.of.possible.conformations.are.available.to.long.polypeptide.chains..
The. forces. that. govern. folding. are. subtle,. and. the. energetic. difference. between. two.
competing. folds. can. be. minuscule.. Predicting. the. three-dimensional. structure.that. will.
be. adopted. by. a. given. sequence. is. therefore. extremely. dificult. and. is. one. of. the. grand.
challenges.of.structural.biology..Increasing.computer.power.and.clever.algorithms.have.
allowed. researchers. to. make. great. progress. in. folding. prediction. in. recent. years,. and.
the. folds. of. most. proteins. of. fewer. than. ∼100. amino. acids. can. now. be. predicted. with.
reasonable.accuracy.(Zhang.2008)..In.considering.artiicial.enzymes,.we.are.perhaps.more.
interested. in. the. opposite. problem:. can. we. predict. what. sequences. will. adopt. a. given.
target. three-dimensional. structure?. This. is. known. as. the. protein. design. problem,. and.
great.progress.has.been.made.on.this.front.as.well..New.sequences.have.been.generated.
that.adopt.protein.structures.from.nature.(Dantas.et.al..2003).as.well.as.structures.not.yet.
found.in.nature.(Kuhlman.et.al..2003).
Enzymes.increase.by.many.orders.of.magnitude.the.rates.of.reactions.that.would.otherwise.
proceed.on.glacial.timescales..The.mechanisms.by.which.they.achieve.these.speedups.are.
often.so.delicate.as.to.be.nearly.impossible.to.understand,.much.less.replicate.by.design..
Enzymes. grab. speciic. substrates. and. hold. them. in. the. perfect. orientation. for. a. reaction.
to.occur..They.might.bring.two.reactants.into.just.the.right.geometric.proximity.to.allow.
a.new.bond.to.form.or.bend.a.molecule.to.strain.a.bond.enough.to.encourage.it.to.break..
Side.chains.are.preorganized.in.ideal.positions.to.abstract.protons.or.perform.nucleophilic.
attack..“Second.shell”.side.chains.modify.the.properties.of.these.“irst.shell”.groups,.tuning.
their.pK a s.and.enhancing.the.stability.of.the.catalytically.active.state..The.close.it.between.a.
binding.cleft.and.its.substrate,.and.the.geometrical.constraints.placed.on.a.bound.substrate,.
confer. incredible. speciicity. on. enzymes,. which. can. distinguish. between. nearly. identical.
potential. reactants. and. cut. unwanted. side. reactions. to. insigniicant. levels.. Hydrophobic.
amino.acids.within.a.binding.cleft.can.modify.the.local.environment.to.enable.chemistry.
usually. impossible. in. water. and. reserved. for. organic. solvents.. In. short,. enzymes. pick.
precise.target.molecules.out.of.the.complex.cellular.milieu.and.place.them.in.the.precise.
geometry. and. chemical. environment. that. minimizes. the. activation. energy. of. the. speciic.
desired.reaction..When.the.reaction.is.complete,.they.release.the.products,.ready.for.another.
cycle..Some.enzymes.do.their.work.with.such.remarkable.eficiency.that.the.reactions.they.
catalyze.are.limited.by.the.rate.at.which.reactant.molecules.can.reach.them.by.diffusion.
Nature. provides. us. with. countless. examples. of. beautiful,. complex. nanomachines.. The.
F o −F 1 .ATP.synthase.(Figure.3.1a).transforms.the.energy.contained.in.transmembrane.proton.
gradients.into.high-energy.chemical.bonds..It.harnesses.the.physical.energy.of.the.gradient.
via.a.mechanical.rotary.mechanism.(Boyer.1997)..Protons.passing.through.a.transmembrane.
channel.in.the.F o .region.of.ATP.synthase.ratchet.the.central.stalk.of.the.protein.in.120°.steps..
The.rotation.of.the.asymmetric.stalk.(green).causes.cyclic.conformational.changes.in.the.three.
beta.subunits.(red).that,.along.with.three.α.subunits.(blue),.make.up.the.F 1 .region.of.the.pro-
tein..In.the.“open”.state,.ATP.from.the.previous.cycle.is.released.and.new.ADP.and.phosphate.
are.bound..A.120°.rotation.of.the.stalk.changes.the.conformation.to.the.“loose”.state,.which.
binds.the.ADP.and.phosphate.more.tightly..A.inal.turn.induces.the.“tight”.state,.in.which.
the.ADP.and.phosphate.combine.to.form.ATP..The.cycle.continues.with.a.transition.back.to.
the.“open”.state..Under.certain.conditions,.the.enzyme.can.also.run.in.the.reverse.direction,.
consuming.ATP.to.generate.a.proton.gradient..Paul.D..Boyer.and.John.E..Walker.shared.half.
of.the.1997.Nobel.Prize.in.Chemistry.for.discovering.the.mechanism.of.ATP.synthase.
The. ribosome. (Figure. 3.1b),. a. molecular. machine. composed. of. protein. and. nucleic.
acid. subunits,. is. another. clear. inspiration. for. nanotechnology.. The. ribosome. reads. the.
information. encoded. in. mRNA. and. synthesizes. polypeptides. with. speciic. amino. acid.