Nano: Armoring of Enzymes: Rational Design of Polymer-Wrapped Enzymes PDF
Preview Nano: Armoring of Enzymes: Rational Design of Polymer-Wrapped Enzymes
METHODS IN ENZYMOLOGY Editors-in-Chief ANNA MARIE PYLE Departments of Molecular, Cellular and Developmental Biology and Department of Chemistry Investigator, Howard Hughes Medical Institute Yale University DAVID W. CHRISTIANSON Roy and Diana Vagelos Laboratories Department of Chemistry University of Pennsylvania Philadelphia, PA Founding Editors SIDNEY P. COLOWICK and NATHAN O. KAPLAN AcademicPressisanimprintofElsevier 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates 525BStreet,Suite1800,SanDiego,CA92101–4495,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom 125LondonWall,London,EC2Y5AS,UnitedKingdom Firstedition2017 Copyright©2017ElsevierInc.Allrightsreserved. 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CarnegieMellonUniversity,Pittsburgh,PA,UnitedStates AninditaDas IndianInstituteofScience,Bangalore,India PuspenduK.Das IndianInstituteofScience,Bangalore,India MelissaL.Dougherty MiamiUniversity,Oxford,OH,UnitedStates RebeccaFalatach MiamiUniversity,Oxford,OH,UnitedStates HenryFischesser MiamiUniversity,Oxford,OH,UnitedStates JunGe KeyLabforIndustrialBiocatalysis,MinistryofEducation,TsinghuaUniversity,Beijing, China xi xii Contributors AntonellaGrigoletto UniversityofPadua,Padua,Italy KarstenHaupt SorbonneUniversit(cid:1)es,Universit(cid:1)edeTechnologiedeCompie`gne,CNRSEnzymeandCell EngineeringLaboratory,RueRogerCouttolenc,Compie`gneCedex,France MiaoHou KeyLabforIndustrialBiocatalysis,MinistryofEducation,TsinghuaUniversity,Beijing, China TusharJana SchoolofChemistry,UniversityofHyderabad,Hyderabad,India RajeswariM.Kasi UniversityofConnecticut;PolymerProgram,InstituteofMaterialsScience,Universityof Connecticut,Storrs,CT,UnitedStates PriyaKatyal UniversityofConnecticut,Storrs,CT,UnitedStates AndreasKu€chler ETHZu€rich,Zu€rich,Switzerland DominikKonkolewicz MiamiUniversity,Oxford,OH,UnitedStates SadagopanKrishnan OklahomaStateUniversity,Stillwater,OK,UnitedStates ChallaV.Kumar UniversityofConnecticut;PolymerProgram,InstituteofMaterialsScience,Universityof Connecticut,Storrs,CT,UnitedStates KondaR.Kunduru SchoolofChemistry,UniversityofHyderabad,Hyderabad,India S.N.RajuKutcherlapati SchoolofChemistry,UniversityofHyderabad,Hyderabad,India MelanieLeurs TUDortmund,Dortmund,Germany YaoLin PolymerProgram,InstituteofMaterialsScience,UniversityofConnecticut,Storrs,CT, UnitedStates YiLiu InstituteofNanochemistryandNanobiology,ShanghaiUniversity,Shanghai,China KatherineMakaroff MiamiUniversity,Oxford,OH,UnitedStates KatiaMaso UniversityofPadua,Padua,Italy Contributors xiii KrzysztofMatyjaszewski CenterforPolymer-BasedProteinEngineering,ICES,CarnegieMellonUniversity; CarnegieMellonUniversity,Pittsburgh,PA,UnitedStates MatthewMcCauley MiamiUniversity,Oxford,OH,UnitedStates PaulinaX.Medina-Rangel SorbonneUniversit(cid:1)es,Universit(cid:1)edeTechnologiedeCompie`gne,CNRSEnzymeandCell EngineeringLaboratory,RueRogerCouttolenc,Compie`gneCedex,France AnnaMero UniversityofPadua,Padua,Italy DanielMessmer ETHZu€rich,Zu€rich,Switzerland HironobuMurata CenterforPolymer-BasedProteinEngineering,ICES,CarnegieMellonUniversity; CarnegieMellonUniversity,Pittsburgh,PA,UnitedStates RamanathanNagarajan NatickSoldierResearch,DevelopmentandEngineeringCenter,Natick,MA,UnitedStates MatthewPaeth MiamiUniversity,Oxford,OH,UnitedStates RichardC.Page MiamiUniversity,Oxford,OH,UnitedStates JoseM.Palomo InstituteofCatalysis(CSIC),Madrid,Spain GianfrancoPasut UniversityofPadua,Padua,Italy GayanPremaratne OklahomaStateUniversity,Stillwater,OK,UnitedStates KishoreRaghupathi UniversityofMassachusetts,Amherst,MA,UnitedStates CaterinaM.Riccardi UniversityofConnecticut,Storrs,CT,UnitedStates AlanJ.Russell CenterforPolymer-BasedProteinEngineering,ICES,CarnegieMellonUniversity; CarnegieMellonUniversity,Pittsburgh,PA,UnitedStates A.DieterSchlu€ter ETHZu€rich,Zu€rich,Switzerland PatrickShahgaldian SchoolofLifeSciences,UniversityofAppliedSciencesandArtsNorthwesternSwitzerland, Muttenz,Switzerland xiv Contributors JerryShepherd MiamiUniversity,Oxford,OH,UnitedStates JacobStapleton MiamiUniversity,Oxford,OH,UnitedStates NisarapornSuthiwangcharoen NatickSoldierResearch,DevelopmentandEngineeringCenter,Natick,MA,UnitedStates SabineSykora SchoolofLifeSciences,UniversityofAppliedSciencesandArtsNorthwesternSwitzerland, Muttenz,Switzerland SankaranThayumanavan UniversityofMassachusetts,Amherst,MA,UnitedStates JoergC.Tiller TUDortmund,Dortmund,Germany BernadetteTseSumBui SorbonneUniversit(cid:1)es,Universit(cid:1)edeTechnologiedeCompie`gne,CNRSEnzymeandCell EngineeringLaboratory,RueRogerCouttolenc,Compie`gneCedex,France OlgaVinogradova UniversityofConnecticut,Storrs,CT,UnitedStates PeterWalde ETHZu€rich,Zu€rich,Switzerland CameronWilliams MiamiUniversity,Oxford,OH,UnitedStates JingjingXu SorbonneUniversit(cid:1)es,Universit(cid:1)edeTechnologiedeCompie`gne,CNRSEnzymeandCell EngineeringLaboratory,RueRogerCouttolenc,Compie`gneCedex,France YongkunYang PolymerProgram,InstituteofMaterialsScience,UniversityofConnecticut,Storrs,CT, UnitedStates OmkarV.Zore UniversityofConnecticut;PolymerProgram,InstituteofMaterialsScience,Universityof Connecticut,Storrs,CT,UnitedStates PREFACE Enzymes are nature’s workhorses. These complex enzymes have a wide variety of essential roles in nature that include catalyzing reactions, transportingmolecules,andDNAreplication.Manystudiesinrecentyears havetakenadvantageofthespecificpropertiesofenzymesinordertodesign newmaterialsanddevices.Therearemanyadvantagesofusinganenzymeas the basis for a functional material: enzymes arehighly specificto their sub- strates, they are biodegradable, and they have many functional groups on theirsurface,whichcanbechemicallymodifiedtotunetheenzyme’sinter- actions with its environment. Compared to traditional organic synthesis reactions, enzymes are capable of catalyzing reactions in a more economic and green manner, and they also have very high activities and excellent selectivities. Enzymes, however, are often limited in their industrial and practical applications because of their poor stability—they are only stable in their physiological conditions (such as pH and temperature) and their poor recyclability and operational stability also limit their practical applica- tion. There arenumerous methods developed over thedecades to stabilize enzymes while maintaining their activity and selectivity. Stabilizationofenzymesisafundamentalthermodynamicissue.Thefree energy of denaturation (ΔG) of an enzyme decreases with increasing tem- perature.Abovethedenaturationtemperatureoftheenzyme,thedenatured state is thermodynamically more favored, and the enzyme unravels. Simi- larly,otherfactorssuchaspHandsolventalsoaffectthefreeenergychange andcontributetotheenzyme’sinstability.Inordertocontrolthefreeenergy of denaturation, one important thermodynamic component to consider is the entropy of denaturation (ΔS). When the enthalpy of denaturation is constant,△Gcanbeincreasedif△Sisdecreasedandstabilityoftheenzyme enhanced (Scheme 1). Many methods have been developed for the stabili- zationofenzymesviathisapproach.Onesuchmethodincludestheconju- gationofenzymetoasyntheticpolymer,wheretheconformationalentropy of theenzyme–polymerconjugate isreduced, andasaresulttheenzymeis armoredwithapolymershellanditsstabilityenhanced(Mudhivarthietal., 2012; Riccardi et al., 2014; Thilakarathne, Briand, Zhou, Kasi, & Kumar, 2011).Thenanoarmorprovidestheenzymewithprotectionfromtheharsh conditions encountered during various situations. Additionally, the armor alsoprotectstheenzymefromotherdegradingcomponentssuchasbacteria xv xvi Preface Scheme 1 Thermodynamic interconversion between the native (N) and denatured (D)statesofanenzyme(redlines)areinhibitedwhentheenzymeisconjugatedtoa nanoarmor suchasapolymer(green lines).Thisistypically achievedbyloweringthe conformationalentropyoftheenzyme(rightgraphic). and proteases as well as prevents the dissociation of the subunits of multi- meric enzymes. Thereareseveralexperimentalprotocols,whichhavebeenreportedfor nanoarmoringofenzymes,suchasencapsulationinnanoparticles,incorpo- ration in metal-organic frameworks, modification with polymers, and immobilization in organosilica (Scheme 2). One example is to encapsulate enzymesinsidenanoparticles,wheretheporesizeofthenanoparticlecanbe tunedwhilealsobeingabletotunethesizeoftheoverallparticleforspecific applicationssuchascellularimaging(Scheme2,1)(Caoetal.,2010).Immo- bilizationofenzymesontothesurfaceofmagneticnanoparticles(Scheme2,10) is also used to impart stability and easy recovery of the enzyme and thus enhanceitsindustrialvalue(Premaratneetal.,2016).Entrapmentandimmo- bilization are sometimes even used together, where the enzyme is first immobilizedonthesurfaceofonenanoparticle,andthenothernanoparticles arethenattachedaroundittocreateanenzymearmor(Correroetal.,2016). Theenzyme–nanoparticleinteractionsareimportantinthisdesignandseveral factorsthatmaycontributearethebindingfreeenergy,bindingstoichiometry, and structure distortion upon binding (Scheme 2, 2) (Das, Chakrabarti, & Das, 2016). Similar to the encapsulation method in nanoparticles, metal-organic frameworksarealsoreportedforarmoringenzymes—astheyarestructurally diverseandcanbetunedtothedesiredfunctionality(Scheme2,3–4)with retention of activity (Ge, Lei, & Zare, 2012). Scheme2 Nanoarmoringofenzymesbythevariousmethodsillustratedinthisbook.Eachnumbercorrespondstothechapternumber andtitle. xviii Preface Polymer-based armoring (Scheme 2, 5–9) is another widely studied method. Specific functional groups on the polymers are used to covalently conjugate to the enzyme, e.g., polyethylene glycol, poly(acrylic acid), poly(acrylamide), cellulose, and polyamide. The conjugation of enzyme tothepolymercantunethepreferredpropertiesofenzymes.Forexample, the operational temperature of urease was controlled so that it can be used effectively at room temperature (Kutcherlapati, Yeole, & Jana, 2016). In addition to using the polymer alone, hybrid methods of using poly(acrylic acid) and graphene oxide sheets further stabilized enzymes (Scheme 2, 8) so that they were active in organic solvents, a condition in which an non- armored enzyme would otherwise denature (Zore, Lenehan, Kumar, & Kasi, 2014). Interlocking of the enzyme–polymer conjugate, as a further step, has been done in the fibers of ordinary paper, without any need for activation of the cellulose support (Riccardi et al., 2016). Another advantage of using polymer as a support for enzyme armoring is that the polymer hierarchical structure can also be modified, such as in dendronized polymer–enzyme conjugates (Scheme 2, 18). The more branching points a dendronized polymer has, the stiffer the polymer becomes, thus potentially decreasing the free energy of the immobilized enzyme (Gustafsson, Ku€chler, Holmberg, & Walde, 2015). The composi- tion and sequencing of block copolymers can also be modified so that the polymer itself can assemble into specific shapes such as micelles (Suthiwangcharoen & Nagarajan, 2014). Highly dense polymer shells around an enzyme can also serve like armor, as achieved by the “grafting-to” and “grafting-from” methods, where the nature of the poly- mer can be designed to impart stimuli responsiveness to the conjugate (Cummings, Murata, Koepsel, & Russell, 2014). From nanoparticles, to metal-organic-based frameworks, to polymer- based materials, etc., these nanoarmors have all shown to enhance the sta- bilities of enzymes. There is still much to explore and understand this approach, but it is clear that these methods are crucial for developing and influencing the development of new biocatalysts, biomaterials, and devices on a global scale. REFERENCES Cao,A.,Ye,Z.,Cai,Z.,Dong,E.,Yang,X.,Liu,G.,…Liu,Y.(2010).Afacilemethodto encapsulateproteinsinsilicananoparticles:Encapsulatedgreenfluorescentproteinasa robust fluorescence probe. Angewandte Chemie, International Edition, 49(17), 3022–3025.https://doi.org/10.1002/anie.200906883.
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