SELF-ASSEMBLING PEPTIDE SYSTEMS IN BIOLOGY, MEDICINE AND ENGINEERING SELF-ASSEMBLING PEPTIDE SYSTEMS IN BIOLOGY, MEDICINE AND ENGINEERING editedby AMALIA AGGELI NEVILLE BODEN University ofLeeds,United Kingdom and SHUGUANGZHANG Massachusetts Institute of Technology, Cambridge,MA,U.S.A. KLUWER ACADEMIC PUBLISHERS NEW YORK / BOSTON / DORDRECHT / LONDON / MOSCOW eBook ISBN: 0-306-46890-5 Print ISBN: 0-792-37090-2 ©2002 Kluwer Academic Publishers New York, Boston, Dordrecht, London, Moscow Print ©2000 Kluwer Academic Publishers Dordrecht All rights reserved No part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher Created in the United States of America Visit Kluwer Online at: http://kluweronline.com and Kluwer's eBookstore at: http://ebooks.kluweronline.com TABLEOFCONTENTS Self-assemblingpeptidesystemsinbiologymedicineandengineering Foreword xi Chapter 1 ExploitingPeptideSelf-assemblytoEngineerNovelBiopolymers:Tapes,Ribbons, FibrilsandFibres 1 A.Aggeli,I.A.Nyrkova,M.Bell,L.Carrick,T.C.B.McLeish,A.N.Semenovand N.Boden 1.1. Abstract 1 1.2. Introduction 1 1.3. MaterialsandMethods 2 1.4. ResultsandDiscussion 4 Acknowledgements 16 References 16 Chapter 2 Ribbon-likeLamellarStructuresfromChain-foldedPolypeptides 19 E.D.T. Atkins 2.1. IntroductionandBackground 19 2.2. Choice of Poly(Ag)EG Sequence 20 x 2.3 Antiparallelβ -sheetStructuresfoundinSilks 20 2.4. X-rayDiffractionResults 22 2.5. Structure of Poly(AG)EG Crystals 24 3 2.6. PhaseRelationshipbetweenSequenceandFolding 26 2.7. Effect of Animo Acid Side-chain Volume on Sheet Stacking 28 2.8. Whyγ -foldsintheseChain-foldedStructures? 30 2.9. Conclusions 32 Acknowledgements 32 References 33 Chapter 3 Designof Self-assembling PeptidesasCatalystMimetics Using Synthetic Combinatorial Libraries 35 S.E. Blondelle, E. Crooks,N. ReixachandE. P.Pérez-Payá 3.1. Introduction 35 3.2. Secondary Structure Optimization 36 3.3. Hydrophobic Core Optimization 39 3.4. Identification ofCatalytic Mimetics 41 3.5. Conclusion 43 References 44 vi Chapter 4 Thermodynamics ofProtein-Protein and Peptide Interactions 47 A. Cooper 4.1. Summary 47 4.2. Introduction 48 4.3. Thermodynamics and Microcalorimetry 48 4.4. Enthalpy-Entropy Compensation 57 4.5. Acknowledgements 64 4.6. References 64 Chapter 5 The Mechanism of Amyloid Formation and its Links to Human Disease and Biological Evolution 65 C.M. Dobson Protein misfolding is linked to disease 65 Soluble proteins convert into aggregates under denaturing conditions 66 Amyloid is ageneric structural form ofproteins 67 Living systems avoid forming amyloid 69 New insights into evolutionarybiology? 70 OpportunitiesfortheFuture 71 Acknowledgements 72 References 73 Chapter6 Transgenic Plants forLarge Scale Production ofPeptidesandProteins 75 K. Düring Introduction 76 Advantages 76 Perspectives 80 Applications 81 Antibodies: avaluable example forproteinproduction in transgenicplants 81 Small peptides: a challenging type of proteins to be produced in transgenic plants 82 Application ofpeptides for plant resistance engineering 82 Summary 83 References 84 Chapter 7 Assembly Modulation of Channel-forming Peptides 87 S. Futaki 7.1. Introduction 87 7.2. Assemblycontroloftransmembranepeptidesthroughextramembranepeptide segments 91 7.3. Conclusions 102 Acknowledgement 102 References 102 vii Chapter 8 Molecular Casting of Infectious Amyloids, Inorganic and Organic Replication: Nucleation, Conformational Change and Self-assembly 105 D.C. Gajdusek 8.1. Abstract 105 8.2. Introduction 105 8.3. Fantasy of a ‘‘Virus’’ without Carbon Atoms 106 8.4. Material Science andEngineering ofSelf-assembling Inorganic - Organic ComplexSolids 107 8.5. AmyloidEnhancingFactorsare Scrapie-LikeAgents 107 References 110 Chapter 9 Structure and Stabilisation ofSelf-assembling Peptide Filaments 113 N.J. Gay, M. Symmons, M. Martin-FernandezandG.Jones Abstract 113 9.1. Introduction 113 9.2. AsingleunitLRRfromtheTollreceptorformsspontaneouslyintofilaments 115 9.3. The conservedamide residue ofLRRN plays acriticalrole in filament polymerisation 116 9.4. Predispositionstoamyloiddiseaseofteninvolvemutationtoamideresidues 118 9.5. Howcanwe studyearlyevents infilamentformation? 120 9.6. References 122 Chapter10 Designed Combinatorial Libraries of Novel Amyloid-like Proteins 127 M.H. Hecht, M.W.West,J.Patterson,J.D. Mancias,J.R. Beasley, B.M. Broome andW.Wang 10.1. Abstract 127 10.2. Introduction 127 10.3. Results 128 10.4. Discussion 136 References 137 Chapter 11 DesignofSyntheticBranchedChainPolymericPolypeptidesforTargeting/Delivering BioactiveMolecules 139 F. Hudecz 11.1. Introduction 139 11.2. Synthesis and Chemical Structure 142 11.3. Chemical Characterisation of Branched Polypeptides 147 11.4. Interaction of Polymers with Phospholipid Mono- and Bilayers 150 11.5. Biological Properties ofBranchedPolypeptides 151 11.6. Conjugates with Branched Polypeptides 155 11.7. Acknowledgement 156 11.8. References 156 viii Chapter12 Amyloid-like Fibrils from a Peptide-analogueofthe Central Domain ofSilkmoth ChorionProteins 161 V.A. Iconomidou and S.J. Hamodrakas Results 163 Discussion 167 Acknowledgements 168 References 168 Chapter 13 Amyloidogenesis ofIsletAmyloid Polypeptide (IAPP) 171 A. Kapurniotu Introduction 171 ResultsandDiscussion 172 Conclusions 184 Acknowledgements 184 References 184 Chapter 14 Engineering Self-assembly ofPeptides byAmphiphilic 2DMotifs: α -to β TransitionsofPeptides 187 H.Mihara,Y.Takahashi,I.ObatayaandS.Sakamoto 14.1. Introduction 187 14.2. PeptidesThatUndergoAutocatalyticα→ β TransitionsandAmyloidFormation 188 14.3. Regulation of α/β -Folding of a Designed Peptide by a Heme Cofactor 198 14.4. ConclusionandFutureDirections 202 14.5. Acknowledgements 202 14.6. References 203 Chapter 15 Model Signal Peptides: Probes ofMolecularInteractions During Protein Secretion 207 A.Miller,L. WangandD.A.Kendall Abstract 207 15.1. Introduction 207 15.2. ResultsandDiscussion 209 15.3. Conclusions 218 15.4. References 219 Chapter 16 Structure, Folding andAssembly ofAdenovirusFibers 221 A. Mitraki, M. van Raaij, R. Ruigrok, S. Cusack, J.-F. Hernandez and M. Luckey Abstract 22 1 Morphology of the fiber 22 1 The fiber as a model system for folding and assembly 223 Thefiberunfoldsviaastableintermediatecomprisingtheheadandpartoftheshaft 225 Crystal structure of the stable domain 228 Assembly versus misassembly of the fibers 23 1 The adenovirus fiber as a model for synthetic fiber design 23 1 ix Perspectives 232 Acknowledgements 233 References 233 Chapter17 Solving the Structure ofCollagen A.Rich Followthatfiber 235 Chasing Collagen 236 Structure ofcollagen 238 References 240 Chapter18 Disulfide Bond Based Self-assemblyofPeptides Leadingto Spheroidal Cyclic Trimers 243 , M.Royo,M.A. Contreras,J.Cebrián,E. Giralt,F.AlbericioandM.Pons Abstract 243 18.1. Covalentpeptideself-assembly 243 18.2. Spontaneous cyclic trimerformationbybis-cysteinepeptides 246 18.3. Sequencevariability 248 18.4. Serine residues inthecentralpositions are essential fortrimerformation 251 18.5. Trimerformation arises fromfrustratedparalleldimers 252 18.6. Applicationsprospects 254 18.7. Acknowledgements 255 18.8. References 256 Chapter19 ANew Circular Helicoid-Type Sequential Oligopeptide CarrierforAssembling MultipleAntigenic Peptides 257 M. Sakarellos-Daitsiotis, V.TsikarisandC. Sakarellos Abstract 257 19.1. Introduction 258 19.2. Concept and design of the Sequential Oligopeptide Carriers (SOCs) 258 19.3. Selectedapplications ofSOC-I and SOC-II 259 n n 19.4. Synthetic aspectsofSOCs andconjugates 263 19.5. Conformational studyofSOCs andconjugates 264 19.6. Biologicalstudies 266 19.7. Conclusions 268 References 269 Chapter 20 Molecular Recognition in the Membrane: Role in the Folding of Membrane Proteins 273 Y. Shai 20.1. Introduction 273 References 288 x Chapter 21 Novel PeptideNucleicAcidswith Improved Solubility andDNA-bindingAbility 295 M. SisidoandM. Kuwahara 21.1. Introduction 295 21.2. Peptides that Contain α -AminoAcids withNucleobases onthe Side Chain 295 21.3. Peptides that Contain δ-AminoAcidswithNucleobases onthe SideChain 300 21.4. Sequence-SpecificHybridizationbetweenTwoArtificialNucleicAcidAnalogs 306 21.5. Conclusions 308 21.6. References 309 Chapter 22 ChiralLipidTubules 311 M.S. Spector, R.R. Price and J.M. Schnur References 320 Chapter 23 ∆ -T -Mechanismin the Design of Self-assembling Structures 323 t D.W.Urry,L.Hayes, C. Luan,D. C. Gowda,D.McPherson,J.XuandT.Parker Abstract 323 23.1. Introduction 324 23.2. Materials andMethods 329 23.3. Results 333 23.4. Discussion 339 23.5. Acknowledgments 340 23.6. References 340 Chapter 24 Self-assembling Peptide Systems in Biology and Biomedical Engineering 343 S. Zhang and M. Altman 24.1. Abstract 343 24.2. Introduction 343 24.3. Type I Self-assembling peptides 344 24.4. Type II Self-assembling peptides 352 24.5. Type III Self-assembling peptides 355 Acknowledgement 358 References 358 Index 36 1 FOREWORD One of the major drivers in biological research is the establishment of structures and functions of the 50,000 or so proteins in our bodies. Each has a characteristic 3- dimensional structure, highly "ordered" yet "disordered"! This structure is essential for a protein's function and, significantly, it must be sustained in the competitive and complex environment of the living cell. It is now being recognised that when a cell loses control, proteins can self- assemble into more complex supermolecular structures such as the amyloid fibres and plaques associated with the pathogenesis of prion (CJD) or age-related (Alzheimer's) diseases. This is a pointer to the wider significance of the self-assembling properties of polypeptides. It has been long known that, in silk, polypeptides are assembled into ß- sheet structures which impart on the material its highly exploitable properties of flexibility combined with high tensile strength. But only now emerging is the recognition that peptides can Self-assemble into a wide variety of non-protein-like structures, including fibrils, fibres, tubules, sheets and monolayers. These are exciting observations and, more so, the potential for materials and medical exploitations is so wide ranging that over 80 scientists from Europe, USA, Japan and Israel. met 1-6 July 1999 in Crete, to discuss the wide-ranging implications of these novel developments. Therewas a spiritof excitementaboutthe workshop indicative ofan important new endeavor. The emerging perception is that of a new class of materials set to become commercially viable early in the 21st century. This stems from the opportunities for processing by the self-assembly route combined with the fact, just as in the case of proteins, that functionality can be designed into the self-assembled structures. They can be made responsive to pH change, mechanical forces, temperature, pressure, electro-chemical potential, electrical and magnetic fields, and light. They can function as sensors and actuators and can act as molecular motors capable of interconverting energies ( vis-à-vis metabolism). They can even be programmed for biodegradation! Extraordinary and widely exploitable properties. Particularly in view of the exceptional thermal stability of peptides (up to 350°C). Nor are production costs insurmountable. Large scale production by the fermentation or transgenic plant or animal routes, at the ton level if needed, are already being developed. Projected costs are as low as a few pounds per kilogram. Applications in tissue engineering, biomedical devices, industrial fluids and personal care products are all under development. Could thesenewmaterialsbecomethewonderpolymersof the21stcentury! The workshop was charged with a vibrant atmosphere as may be expected of this newly developing interdisciplinary area. As Francis Crick best put it "In Nature hybrid species are usually sterile, but in science the reverse is often true. Hybrid subjects are often astonishingly fertile, whereas if a scientific discipline remains too pure it usually wilts". In view of the exciting prospects for this new area of endeavor, it was felt that it would be useful to record the proceedings of the workshop for those unable to attend. xi