Biological and Bio-inspired Nanomaterials: Properties and Assembly Mechanisms PDF
Preview Biological and Bio-inspired Nanomaterials: Properties and Assembly Mechanisms
Advances in Experimental Medicine and Biology 1174 Sarah Perrett Alexander K. Buell Tuomas P. J. Knowles Editors Biological and Bio-inspired Nanomaterials Properties and Assembly Mechanisms Advances in Experimental Medicine and Biology Volume 1174 EditorialBoard IRUNR.COHEN,TheWeizmannInstituteofScience,Rehovot,Israel ABELLAJTHA,N.S.KlineInstituteforPsychiatricResearch, Orangeburg,NY,USA JOHND.LAMBRIS,UniversityofPennsylvania,Philadelphia,PA,USA RODOLFOPAOLETTI,UniversityofMilan,Milan,Italy NIMAREZAEI,Children’sMedicalCenterHospital,TehranUniversityof MedicalSciences,Tehran,Iran Moreinformationaboutthisseriesathttp://www.springer.com/series/5584 Sarah Perrett • Alexander K. Buell Tuomas P. J. Knowles Editors Biological and Bio-inspired Nanomaterials Properties and Assembly Mechanisms 123 Editors SarahPerrett AlexanderK.Buell NationalLaboratoryofBiomacromolecules DepartmentofBiotechnology InstituteofBiophysics andBiomedicine ChineseAcademyofSciences TechnicalUniversityofDenmark Beijing,China DTU,Lyngby,Denmark TuomasP.J.Knowles DepartmentofChemistry UniversityofCambridge Cambridge,UK ISSN0065-2598 ISSN2214-8019 (electronic) AdvancesinExperimentalMedicineandBiology ISBN978-981-13-9790-5 ISBN978-981-13-9791-2 (eBook) https://doi.org/10.1007/978-981-13-9791-2 ©SpringerNatureSingaporePteLtd.2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor theeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictional claimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSingaporePteLtd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Contents 1 DynamicsandControlofPeptideSelf-AssemblyandAggregation... 1 Georg Meisl, Thomas C. T. Michaels, Paolo Arosio, Michele Vendruscolo,ChristopherM.Dobson,andTuomasP.J.Knowles 2 Peptide Self-Assembly and Its Modulation: Imaging ontheNanoscale............................................................ 35 LanlanYu,YanlianYang,andChenWang 3 TheKinetics,Thermodynamics andMechanisms ofShort AromaticPeptideSelf-Assembly.......................................... 61 ThomasO.MasonandAlexanderK.Buell 4 BacterialAmyloids:BiogenesisandBiomaterials ...................... 113 LineFriisBakmannChristensen,NicholasSchafer, AdrianaWolf-Perez,DanielJhafMadsen,andDanielE.Otzen 5 FungalHydrophobinsandTheirSelf-AssemblyintoFunctional Nanomaterials............................................................... 161 VictorLo,JenniferI-ChunLai,andMargaretSunde 6 Nanostructured, Self-AssembledSpiderSilkMaterialsfor BiomedicalApplications ................................................... 187 MartinHumenik,KiranPawar,andThomasScheibel 7 ProteinMicrogelsfromAmyloidFibrilNetworks...................... 223 LianneW.Y.Roode,UlyanaShimanovich,SiWu,SarahPerrett,and TuomasP.J.Knowles 8 Protein Nanofibrils as Storage Forms of Peptide Drugs andHormones .............................................................. 265 ReebaSusanJacob,A.Anoop,andSamirK.Maji 9 Nanozymes: BiomedicalApplicationsofEnzymaticFe O 3 4 NanoparticlesfromInVitrotoInVivo ................................... 291 LizengGaoandXiyunYan v vi Contents 10 Self-Assembly of Ferritin: Structure, Biological Function andPotentialApplicationsinNanotechnology.......................... 313 SoumyanandaChakrabortiandPinakChakrabarti 11 DNANanotechnologyforBuildingSensors,Nanoporesand Ion-Channels................................................................ 331 KerstinGöpfrichandUlrichF.Keyser 12 BioMimickingofExtracellularMatrix.................................. 371 MoumitaGhosh,MichalHalperin-Sternfeld, andLihiAdler-Abramovich 13 BioinspiredEngineeringofOrgan-on-ChipDevices.................... 401 LiWang,ZhongyuLi,CongXu,andJianhuaQin Chapter 1 Dynamics and Control of Peptide Self-Assembly and Aggregation GeorgMeisl,ThomasC.T.Michaels,PaoloArosio,MicheleVendruscolo, ChristopherM.Dobson,andTuomasP.J.Knowles Abstract The aggregation of proteins into fibrillar structures is a central process implicatedintheonsetanddevelopmentofseveraldevastatingneuro-degenerative diseases, but can, in contrast to these pathological roles, also fulfil important biological functions. In both scenarios, an understanding of the mechanisms by which soluble proteins convert to their fibrillar forms represents a fundamental objective for molecular sciences. This chapter details the different classes of microscopic processes responsible for this conversion and discusses how they can be described by a mathematical formulation of the aggregation kinetics. We presenteasilyaccessibleexperimentalquantitiesthatallowthedeterminationofthe dominant pathways ofaggregation, aswellasageneralstrategytoobtaindetailed solutions to the kinetic rate laws that yield the microscopic rate constants of the individualprocessesofnucleationandgrowth.Thischapterdiscussesaframework for a structured approach to address key questions regarding the dynamics of proteinaggregationandshowshowtheuseofchemicalkineticstotacklecomplex biophysicalsystemscanleadtoadeeperunderstandingoftheunderlyingphysical andchemicalprinciples. Keywords Chemicalkinetics · Aggregationmechanisms · Scalingexponent · Globalanalysis G.Meisl((cid:2))·T.C.T.Michaels·M.Vendruscolo·C.M.Dobson DepartmentofChemistry,UniversityofCambridge,Cambridge,UK e-mail:[email protected] P.Arosio DepartmentofChemistryandAppliedBioscience,ETHZurich,Zurich,Switzerland T.P.J.Knowles CentreforMisfoldingDiseases,DepartmentofChemistry,UniversityofCambridge,Cambridge, UK CavendishLaboratory,UniversityofCambridge,Cambridge,UK e-mail:[email protected] ©SpringerNatureSingaporePteLtd.2019 1 S.Perrettetal.(eds.),BiologicalandBio-inspiredNanomaterials, AdvancesinExperimentalMedicineandBiology1174, https://doi.org/10.1007/978-981-13-9791-2_1 2 G.Meisletal. 1.1 Introduction Theself-assemblyofproteinsintoorderedlinearstructuresisanimportantprocess for many living systems, for example in the context of the formation of the cytoskeletal filaments. When it occurs in a controlled manner, this process can therefore be central to the functionality of an organism, but conversely, unwanted filamentous aggregation of proteins can have devastating effects on an organism’s health. One such process of particular significance is the aggregation of proteins intoelongatedstructures,amyloidfibrils,whichmayconsistofthousandsormore copiesofthesameprotein[1,2].Surprisingly,alargevarietyofunrelatedproteins havetheabilitytoformamyloidstructures,andonceformed,theseentitiespossess aninherentpropensitytowardspromotingtheconversionoffurtherproteinsintothe amyloid form [3, 4]. The study of protein aggregation has become an important area of research largely because the proliferation of amyloid fibrils is closely associated with several devastating and increasingly prevalent diseases, including type II diabetes, Parkinson’s and Alzheimer’s diseases [5–7]. However, there is also a number of proteins that self-assemble into fibrillar structures that are not associated with disease but are functional and essential for living organisms [8– 12].Importantexamplesofsuchfunctionalproteinassembliesincludeforinstance biofilaments of actin and tubulin, that are key parts of the eukaryotic cytoskeleton [9–11],aswellasfunctionalamyloidstructures[13]thatpossessrolesascatalytic scaffolds[14],asdepotsforhormones[15],inthefunctioningofpathogens[16]or ascomponentsofbacterialbiofilms[17,18].Theexistenceoffunctionalamyloids has also inspired the use of such structures as functional biomaterials in various nanotechnologicalapplications[19,20],afactorthathasfurthercontributedtothe interestinunderstandinghowfilamentousself-assemblyworks. From a biophysical point of view, the formation of filamentous structures from dispersedproteinsrepresentsanelementaryformofsupra-molecularassemblysince itisgenerallyhomo-molecularinnature[9,21].Yet,despitethisapparentsimplicity, many different molecular-level events contribute to the overall fibril formation process and the competition and interplay between these microscopic steps often resultsinrichdynamicalbehaviour.Obtainingamolecular-levelkineticdescription of self-assembling systems is thus a particularly challenging task which involves considering a complex interconnected network of several distinct microscopic steps, such as nucleation, growth or fragmentation processes [22, 23]. In this chapter we describe in detail how the use of chemical kinetics in the context of protein aggregation allows one to overcome this challenge. We demonstrate that this approach provides a general strategy for quantifying the rates of the individualmicroscopicstepsoffilamentousgrowth.Thisadvanceilluminateswhich parts of the full reaction network determine the aggregation behaviour in a given system and which ones can instead be neglected, thus providing a very useful mechanisticframeworkfordesigningstrategiesforcontrollingproteinaggregation intechnologicalapplicationsorsuppressingitfortherapeuticpurposes. 1 DynamicsandControlofSelf-Assembly 3 The chapter is organized as follows. In the first section, we discuss the microscopic-level processes that contribute to the overall protein aggregation reactionandoutlineageneralapproachformathematicallymodellingtheresulting reaction network. We then consider the interaction and competition between these individual processes and describe in detail how such complex scenarios can be understood within the framework of kinetic theory. The following section briefly looks at the application of these kinetic models of protein aggregation in the context of data analysis for discovering the dominant microscopic processes in action. Finally, we conclude with a discussion on how the resulting mechanistic understandingofproteinaggregationformsthebasisofdevisingrationalstrategies toemployinhibitorycompoundsormodulationsoftheenvironmentalconditionsto controlthepathwaysbywhichtheaggregationreactionproceeds. 1.2 KineticTheoryofProteinAggregation Chemical kinetics provide the mathematical framework for predicting the time courseofachemicalreaction.Ingeneral,akineticdescriptionofachemicalreaction is derived by breaking the overall process down into a sequence of one or more relevant steps. The law of mass action then yields differential equations (so called rate laws) that describe the rates of each one of these individual steps in terms of the concentrations of the species involved. The rate constants are the constants of proportionality entering such relationships and the reaction orders describe the power a particular concentration is raised to. Although for simple elementary reactions the reaction orders correspond to the actual number of species involved in the reaction, such a simple physical interpretation of reaction orders may not apply to reactions with many steps, such as encountered in the complex models discussedhere.Ratelawsemergedirectlyfromaconsiderationofthevarioussteps thatconstitutetheoverall reaction and thusrepresentthebesttoolforestablishing unknown mechanisms. As we will discuss later, if the reaction mechanism is unknown, we can carry out experiments to determine the reaction orders with respect to each reactant and then try out various trial reaction mechanisms to see which one fits best with the experimental data. An important point to recognize here is that the rate constants and reaction orders need to be constrained by the experiments. In the following, we apply these concepts from chemical kinetics to thestudyofproteinaggregationphenomena. 1.2.1 FundamentalProcessesin ProteinAggregation Inordertodevelopakineticmodelofaggregation,itisfirstnecessarytoestablish the species and the microscopic-level processes that are likely to be involved in the overall assembly reaction. In this context, it is important to keep the kinetic 4 G.Meisletal. 1onucleation Elongation Fragmentation 2o nucleation kn k+ k k k off - 2 Fig.1.1 Microscopic processes of aggregation. A schematic depiction of the fundamental microscopicprocessesofaggregation,alsoconsideredinthebasicmodeldiscussedinSects.1.2.2 and1.2.3.Spheresrepresentmonomer,cylindersfibrillarspecies.Extensionstotheseprocesses to account for their multi-step nature, which may become evident under certain conditions, are discussedinSect.1.3 modelasminimalisticaspossibleandonlyincludethosemicroscopicstepsthatare requiredtoexplainexperimentalobservationsorthataresuggestedbyourphysical intuitionofthesystem.Forthisreason,wediscussherethesimplestkineticmodelof filamentousassembly[23],inwhichfilamentousaggregatesaredescribedaslinear chainsofmonomersthatareformed,growandmultiplyaccordingtothefollowing three basic categories of processes that form the core parts of the aggregation reaction(seeFig.1.1foraschematicvisualizationoftheindividualprocesses): (cid:129) Denovoformationofaggregates–Primarynucleation–Primarynucleation is the spontaneous formation of a growth-competent aggregate (nucleus) from monomersalone,withouttheinvolvementoffibrillarspecies.Assuch,primary nucleation represents always the first event in an aggregation process starting with monomers only. The primary nucleation step reflects the fact that the formation of small filaments is unfavourable so that aggregates smaller than a certain critical size are unstable; the nucleus represents the smallest aggregate species that is more likely to grow than to dissociate back into monomers. Although it involves only monomers, it can, and in many cases does, happen heterogeneously, on surfaces such as for example the air-solution interface or lipid membranes [24, 25]. Removal of specific interfaces or experiments at differentsurfacetovolumeratioscangiveinsightsintotheextenttowhichsuch interfaceeffectsalterthekinetics[26]. (cid:129) Growth of existing aggregates – Elongation and dissociation – Existing aggregatesarecapableoffurthergrowththroughelongation,butmayalsoshrink through dissociation processes. During the elongation reaction, soluble protein addsontotheendsofanexistingfibrilthusleadingtoanincreaseoftheoverall aggregate mass. This process typically involves the attachment of monomeric protein to either end of an existing fibril followed by a conformational rear- rangementoftheaddedmonomerintoastructurewithhighβ-sheetcontent.The additionstepistypicallyrate-determining,butundercertainconditionsthemulti- step nature of the elongation reaction can become apparent (see Sect.1.3.2).
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