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 Editorial Board IRUN R. COHEN, The Weizmann Institute of Science, Rehovot, Israel ABEL LAJTHA, N.S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA JOHN D. LAMBRIS, University of Pennsylvania, Philadelphia, PA, USA RODOLFO PAOLETTI, University of Milan, Milan, Italy NIMA REZAEI, Children’s Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran More information about this series at http://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 Sarah Perrett Alexander K. Buell National Laboratory of Biomacromolecules Department of Biotechnology Institute of Biophysics and Biomedicine Chinese Academy of Sciences Technical University of Denmark Beijing, China DTU, Lyngby, Denmark Tuomas P. J. Knowles Department of Chemistry University of Cambridge Cambridge, UK ISSN 0065-2598 ISSN 2214-8019 (electronic) Advances in Experimental Medicine and Biology ISBN 978-981-13-9790-5 ISBN 978-981-13-9791-2 (eBook) https://doi.org/10.1007/978-981-13-9791-2 © Springer Nature Singapore Pte Ltd. 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. 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The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Contents 1 Dynamics and Control of Peptide Self-Assembly and Aggregation ... 1 Georg Meisl, Thomas C. T. Michaels, Paolo Arosio, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P. J. Knowles 2 Peptide Self-Assembly and Its Modulation: Imaging on the Nanoscale ............................................................ 35 Lanlan Yu, Yanlian Yang, and Chen Wang 3 The Kinetics, Thermodynamics and Mechanisms of Short Aromatic Peptide Self-Assembly .......................................... 61 Thomas O. Mason and Alexander K. Buell 4 Bacterial Amyloids: Biogenesis and Biomaterials ...................... 113 Line Friis Bakmann Christensen, Nicholas Schafer, Adriana Wolf-Perez, Daniel Jhaf Madsen, and Daniel E. Otzen 5 Fungal Hydrophobins and Their Self-Assembly into Functional Nanomaterials............................................................... 161 Victor Lo, Jennifer I-Chun Lai, and Margaret Sunde 6 Nanostructured, Self-Assembled Spider Silk Materials for Biomedical Applications ................................................... 187 Martin Humenik, Kiran Pawar, and Thomas Scheibel 7 Protein Microgels from Amyloid Fibril Networks ...................... 223 Lianne W. Y. Roode, Ulyana Shimanovich, Si Wu, Sarah Perrett, and Tuomas P. J. Knowles 8 Protein Nanofibrils as Storage Forms of Peptide Drugs and Hormones .............................................................. 265 Reeba Susan Jacob, A. Anoop, and Samir K. Maji 9 Nanozymes: Biomedical Applications of Enzymatic Fe3O4 Nanoparticles from In Vitro to In Vivo ................................... 291 Lizeng Gao and Xiyun Yan v vi Contents 10 Self-Assembly of Ferritin: Structure, Biological Function and Potential Applications in Nanotechnology .......................... 313 Soumyananda Chakraborti and Pinak Chakrabarti 11 DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels ................................................................ 331 Kerstin Göpfrich and Ulrich F. Keyser 12 Bio Mimicking of Extracellular Matrix .................................. 371 Moumita Ghosh, Michal Halperin-Sternfeld, and Lihi Adler-Abramovich 13 Bioinspired Engineering of Organ-on-Chip Devices.................... 401 Li Wang, Zhongyu Li, Cong Xu, and Jianhua Qin Chapter 1 Dynamics and Control of Peptide Self-Assembly and Aggregation Georg Meisl, Thomas C. T. Michaels, Paolo Arosio, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P. J. Knowles Abstract The aggregation of proteins into fibrillar structures is a central process implicated in the onset and development of several devastating neuro-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 present easily accessible experimental quantities that allow the determination of the dominant pathways of aggregation, as well as a general strategy to obtain detailed solutions to the kinetic rate laws that yield the microscopic rate constants of the individual processes of nucleation and growth. This chapter discusses a framework for a structured approach to address key questions regarding the dynamics of protein aggregation and shows how the use of chemical kinetics to tackle complex biophysical systems can lead to a deeper understanding of the underlying physical and chemical principles. Keywords Chemical kinetics · Aggregation mechanisms · Scaling exponent · Global analysis G. Meisl () · T. C. T. Michaels · M. Vendruscolo · C. M. Dobson Department of Chemistry, University of Cambridge, Cambridge, UK e-mail: [email protected] P. Arosio Department of Chemistry and Applied Bioscience, ETH Zurich, Zurich, Switzerland T. P. J. Knowles Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK Cavendish Laboratory, University of Cambridge, Cambridge, UK e-mail: [email protected] © Springer Nature Singapore Pte Ltd. 2019 1 S. Perrett et al. (eds.), Biological and Bio-inspired Nanomaterials, Advances in Experimental Medicine and Biology 1174, https://doi.org/10.1007/978-981-13-9791-2_1 2 G. Meisl et al. 1.1 Introduction The self-assembly of proteins into ordered linear structures is an important process 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 into elongated structures, amyloid fibrils, which may consist of thousands or more copies of the same protein [1, 2]. Surprisingly, a large variety of unrelated proteins have the ability to form amyloid structures, and once formed, these entities possess an inherent propensity towards promoting the conversion of further proteins into the 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]. Important examples of such functional protein assemblies include for instance biofilaments of actin and tubulin, that are key parts of the eukaryotic cytoskeleton [9–11], as well as functional amyloid structures [13] that possess roles as catalytic scaffolds [14], as depots for hormones [15], in the functioning of pathogens [16]or as components of bacterial biofilms [17, 18]. The existence of functional amyloids has also inspired the use of such structures as functional biomaterials in various nanotechnological applications [19, 20], a factor that has further contributed to the interest in understanding how filamentous self-assembly works. From a biophysical point of view, the formation of filamentous structures from dispersed proteins represents an elementary form of supra-molecular assembly since it is generally homo-molecular in nature [9, 21]. Yet, despite this apparent simplicity, many different molecular-level events contribute to the overall fibril formation process and the competition