Table Of ContentTopics in Current Chemistry 337
Judith Klinman
Sharon Hammes-Schiffer Editors
Dynamics in
Enzyme Catalysis
337
Topics in Current Chemistry
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Judith Klinman Sharon Hammes-Schiffer
l
Editors
Dynamics in Enzyme
Catalysis
With contributions by
K.Arora(cid:1)C.L.Brooks(cid:1)C.M.Cheatum(cid:1)Q.Cui(cid:1)M.D.Daily(cid:1)K.W.Harpole(cid:1)
V.J.Hilser(cid:1)D.Hilvert(cid:1)A.Kohen(cid:1)B.Ma(cid:1)V.R.Moorman(cid:1)R.Nussinov(cid:1)
G.N.Phillips(cid:1)T.P.Schrank(cid:1)C.Schulenburg(cid:1)S.D.Schwartz(cid:1)A.J.Wand(cid:1)
J.O.Wrabl(cid:1)H.Yu
Editors
JudithKlinman SharonHammes-Schiffer
UniversityofCalifornia DepartmentofChemistry
DepartmentofChemistry UniversityofIllinoisat
DepartmentofMolecularand Urbana-Champaign
CellBiology,andtheCalifornia Urbana,IL
InstituteforQuantitativeBiosciences USA
Berkeley,CA
USA
ISSN0340-1022 ISSN1436-5049(electronic)
ISBN978-3-642-38961-0 ISBN978-3-642-38962-7(eBook)
DOI10.1007/978-3-642-38962-7
SpringerHeidelbergNewYorkDordrechtLondon
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Foreword
The enormous number of three-dimensional structures for proteins that emerged
duringthesecondhalfofthetwentiethcentury–asofNovember,2012,there are
ca.86,000entriesintheinternationalProteinDataBase–ledquitenaturallytoan
intensefocusontherelationshipbetweenproteinstructureandfunction.Therewas
recognitionthatallostericproteinscouldassumedifferentshapesinthepresenceof
allosteric regulators, and much work was dedicated to developing mathematical
modelsforthisbehavior[1,2].Theclassicalstudiesonhemoglobinshowedhowthe
remote binding of small molecules could tune the affinity of molecular oxygen at
theactivesiteheme-ironcenter[3].Theseproteinmotionswereconceptualizedas
rigidbodymovementsthatlinkedtheactiveandinactiveproteinstates.Thelatter
halfofthetwentiethcenturysawanincreasingfocusonthemoregeneralfeatureof
protein dynamics. Once again, the binding of small gaseous molecules to heme
proteins played an important role, with Frauenfelder and his co-workers demon-
strating aphoto-initiated,multi-exponentialrelease ofCOfrommyoglobinatlow
temperature[4].Theimplicationfromthesestudieswasthattheinherentflexibility
ofproteinsatroomtemperaturehadledtoafamilyoflow-temperatureconformers
with different inherent kinetic properties. Concomitant with experimental
approaches,Karplusandco-workersdevelopedmethodsforcomputersimulations
of rapid protein motions (picosecond timescale) using Newton’s equations of
motion[5]. Formanyyears,classical studiesofenzyme functionandthestudyof
protein dynamics moved on largely parallel trajectories, occasionally intersecting
butwithconsiderableskepticismandreservationonbothsides.
The lastdecade has seen a profound shift toward the recognition that the large
sizeandinherentfloppinessofproteinscanmanifestitselfateverylevelofprotein
function.Thistypeofmotiongoesbeyondtwostatemodelsforallostery,aswellas
the expected accommodationofaprotein’s shape to thebindingofsubstrates and
their conversion to products. The emerging models include a productive and
causativeroleforproteinmotionsateveryleveloffunction.Thisvolumehighlights
someoftheexcitingdirectionsthatthefieldofproteindynamicshasmadeinrecent
years. Here, the term “dynamics” refers to both equilibrium and non-equilibrium
motions on all timescales. We have aimed at a balanced presentation of four
v
vi Foreword
chaptersontheoryandanequalnumberonexperimentalapproaches.Thisisavery
active research area, and we apologize upfront to the many investigators who are
notincludedinthepresentvolume.Ourhopewasthattherangeofchapterschosen
wouldhighlighttopicsthatmaynotalwaysbeconsideredinthesamecontext.
From the experimental perspective, the role of protein dynamics in enzymatic
bond-making and bond-cleavage events is addressed by Kohen and Cheatum. As
has been discussed with increasing frequency in the literature, the enzymatic
activation of C–H bonds opens up a special window for analyzing the role of
heavy atom protein motions in catalysis [6]. Schulenberg and Hilvert address the
very active areaofintrinsically disordered proteins,andwhetherthe propertiesof
such enzymes can help us to understand the role of protein motions in native
enzymecatalysis.Thecorrelationofsidechainentropyamongproteinsidechains
withfunctionhasincreasinglyattractedwideattention,andWandandco-workers
describe careful and insightful studies of this feature of calmodulin function
according to an “entropy ruler.” Finally, Schrank, Wrabl, and Hilser talk about
the role of a lid closure on the function of adenylate kinase, building upon multi-
layeredexperimentaldatatogenerateamulti-statemodelfortheprogressionofthis
enzymefromanopentoaclosed,catalyticallyactivestate.
From the theoretical perspective, the effects of macromolecular crowding on
enzymeconformationaldynamicsandactivityarediscussedbyMaandNussinov.
Structured crowding, which refers to the highly organized cellular environment,
could potentially enhance enzyme efficiency and specificity. Cui and coworkers
discusshowatomisticandcoarse-grainedsimulationscanbeusedtoelucidatethe
mechanism of activation transitions, which often precede the chemical steps in
enzymes and are typically allosteric and multiscale in nature. In the simplest
enzymes, such as adenylate kinase, the activation transition corresponds to the
closure of the active site, but in biomolecular motors, such as myosin, it is more
complex.AroraandBrooksfocusontheenzymedihydrofolatereductase(DHFR),
which catalyzes the hydride transfer reaction required for the conversion of dihy-
drofolatetotetrahydrofolate.Thisenzymehasbeenstudiedextensivelywithawide
range of theoretical and experimental methods. The consensus is that equilibrium
conformational motions of the protein and ligands impact catalysis in DHFR by
generatingconfigurationsconducivetothehydridetransferreaction,butthereisno
evidencefordynamicalcouplingofproteinvibrationalmodestothebreakingand
formingofchemicalbonds[7].Schwartzproposesamorecontroversialperspective
about the role of protein dynamics in enzyme catalysis. While he agrees with the
above interpretation for DHFR, he also proposes that femtosecond to picosecond
“promoting vibrations” of the protein can be directly coupled to the passage over
thechemicalbarrier(i.e.,tobondbreaking/forming)andarecatalyticallyrelevant
forotherenzymes,suchaslactatedehydrogenaseandpurinenucleosidephosphor-
ylase.Thisaspectofcatalysiscontrastswiththemoregenerallyacceptedmodelof
equilibrium conformational sampling that has components of protein motions
rangingfromfemtosecondtomillisecondtimescales.
Asthereaderwillsee,theincludedchaptersare,attimes,eithercomplementary
ordivergentintheirconclusions.Webelievethatthisreflectsthecurrentvibrancy
Foreword vii
of the field of protein dynamics. One of the goals of this community – hopefully
achievableinthecomingdecades–willbetodevelopalevelofunderstandingthat
allows us to replicate in the test tube the exquisite specificity and enormous
catalyticrateaccelerationsofnativeproteins.
References
1. Monod J, Wyman J, Changeux JP (1965) On nature of allosteric transitions – a plausible
model.JMolBiol12:88–188
2. KoshlandDE,NemethyG,FilmerD(1966)Comparisonofexperimentalbindingdataand
theoreticalmodelsinproteinscontainingsubunits.Biochemistry5:365–368
3. EdelsteinSJ(1975)Cooperativeinteractionsofhemoglobin.AnnuRevBiochem44:209–232
4. HongMK,BraunsteinD,CowenBR,FrauenfelderH,IbenIET,MourantJR,OrmosP,Scholl
R,SchulteA,SteinbachPJ,XieAH,YoungRD(1990)Conformationalsubstatesandmotions
inmyoglobin–externalinfluencesonstructureanddynamics.BiophysJ58:429–436
5. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983)
Charmm–aprogramformacromolecularenergy,minimization,anddynamicscalculations.
JComputChem4:187–217
6. Klinman JP (2009) An integrated model for enzyme catalysis emerges from studies of
hydrogentunneling.ChemPhysLettFontiers471:179–193
7. Hammes-Schiffer S, Benkovic SJ (2006) Relating protein motion to catalysis. Annu Rev
Biochem75:519–541
ThiSisaFMBlankPage
Contents
RelationshipofFemtosecond–PicosecondDynamicsto
Enzyme-CatalyzedH-Transfer ................................................ 1
ChristopherM.CheatumandAmnonKohen
ProteinConformationalDisorderandEnzymeCatalysis .................. 41
CindySchulenburgandDonaldHilvert
ASurprisingRoleforConformationalEntropyinProteinFunction ..... 69
A.JoshuaWand,VeronicaR.Moorman,andKyleW.Harpole
ConformationalHeterogeneityWithintheLIDDomainMediates
SubstrateBindingtoEscherichiacoliAdenylateKinase:
FunctionFollowsFluctuations ............................................... 95
TravisP.Schrank,JamesO.Wrabl,andVincentJ.Hilser
StructuredCrowdingandItsEffectsonEnzymeCatalysis .............. 123
BuyongMaandRuthNussinov
AllostericActivationTransitionsinEnzymesandBiomolecularMotors:
InsightsfromAtomisticandCoarse-GrainedSimulations ............... 139
MichaelD.Daily,HaiboYu,GeorgeN.PhillipsJr,andQiangCui
MultipleIntermediates,DiverseConformations,andCooperative
ConformationalChangesUnderlietheCatalyticHydrideTransfer
ReactionofDihydrofolateReductase ....................................... 165
KaruneshAroraandCharlesL.BrooksIII
ProteinDynamicsandtheEnzymaticReactionCoordinate .............. 189
StevenD.Schwartz
Index .......................................................................... 209
ix
