1
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Ha JH, Xu Y, Sekhon H, Wilkens S, Ren D, Loh SN. Mimicking Kidney Flow Shear Efficiently Induces Aggregation of LECT2, a Protein Involved in Renal Amyloidosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548788. [PMID: 37503176 PMCID: PMC10369975 DOI: 10.1101/2023.07.13.548788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Aggregation of leukocyte cell-derived chemotaxin 2 (LECT2) causes ALECT2, a systemic amyloidosis that affects the kidney and liver. Homozygosity of the I40V LECT2 mutation is believed to be necessary but not sufficient for the disease. Previous studies established that LECT2 fibrillogenesis is greatly accelerated by loss of its single bound zinc ion and stirring or shaking. These forms of agitation are often used to facilitate protein aggregation, but they create heterogeneous shear conditions, including air-liquid interfaces that denature proteins, that are not present in the body. Here, we determined the extent to which a more physiological form of mechanical stress-shear generated by fluid flow through a network of artery and capillary-sized channels-drives LECT2 fibrillogenesis. To mimic blood flow through the human kidney, where LECT2 and other proteins form amyloid deposits, we developed a microfluidic device consisting of progressively branched channels narrowing from 5 mm to 20 μm in width. Flow shear was particularly pronounced at the branch points and in the smallest capillaries, and this induced LECT2 aggregation much more efficiently than conventional shaking methods. EM images suggested the resulting fibril structures were different in the two conditions. Importantly, results from the microfluidic device showed the first evidence that the I40V mutation accelerated fibril formation and increased both size and density of the aggregates. These findings suggest that kidney-like flow shear, in combination with zinc loss, acts in combination with the I40V mutation to trigger LECT2 amyloidogenesis. These microfluidic devices may be of general use for uncovering the mechanisms by which blood flow induces misfolding and amyloidosis of circulating proteins.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Yikang Xu
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244
| | - Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244
- Department of Biology, Syracuse University, Syracuse, NY 13244
| | - Stewart N. Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
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2
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McCue C, Girard HL, Varanasi KK. Enhancing Protein Crystal Nucleation Using In Situ Templating on Bioconjugate-Functionalized Nanoparticles and Machine Learning. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12622-12630. [PMID: 36853011 PMCID: PMC10020963 DOI: 10.1021/acsami.2c17208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Although protein crystallization offers a promising alternative to chromatography for lower-cost protein purification, slow nucleation kinetics and high protein concentration requirements are major barriers for using crystallization as a viable strategy in downstream protein purification. Here, we demonstrate that nanoparticles functionalized with bioconjugates can result in an in situ template for inducing rapid crystallization of proteins at low protein concentration conditions. We use a microbatch crystallization setup to show that the range of successful crystallization conditions is expanded by the presence of functionalized nanoparticles. Furthermore, we use a custom machine learning-enabled emulsion crystallization setup to rigorously quantify nucleation parameters. We show that bioconjugate-functionalized nanoparticles can result in up to a 7-fold decrease in the induction time and a 3-fold increase in the nucleation rate of model proteins compared to those in control environments. We thus provide foundational insight that could enable crystallization to be used in protein manufacturing by reducing both the protein concentration and the time required to nucleate protein crystals.
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3
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Buell AK. Stability matters, too - the thermodynamics of amyloid fibril formation. Chem Sci 2022; 13:10177-10192. [PMID: 36277637 PMCID: PMC9473512 DOI: 10.1039/d1sc06782f] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.
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Affiliation(s)
- Alexander K Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine Søltofts Plads, Building 227 2800 Kgs. Lyngby Denmark
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4
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Xu Y, Zhu H, Denduluri A, Ou Y, Erkamp NA, Qi R, Shen Y, Knowles TPJ. Recent Advances in Microgels: From Biomolecules to Functionality. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200180. [PMID: 35790106 DOI: 10.1002/smll.202200180] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The emerging applications of hydrogel materials at different length scales, in areas ranging from sustainability to health, have driven the progress in the design and manufacturing of microgels. Microgels can provide miniaturized, monodisperse, and regulatable compartments, which can be spatially separated or interconnected. These microscopic materials provide novel opportunities for generating biomimetic cell culture environments and are thus key to the advances of modern biomedical research. The evolution of the physical and chemical properties has, furthermore, highlighted the potentials of microgels in the context of materials science and bioengineering. This review describes the recent research progress in the fabrication, characterization, and applications of microgels generated from biomolecular building blocks. A key enabling technology allowing the tailoring of the properties of microgels is their synthesis through microfluidic technologies, and this paper highlights recent advances in these areas and their impact on expanding the physicochemical parameter space accessible using microgels. This review finally discusses the emerging roles that microgels play in liquid-liquid phase separation, micromechanics, biosensors, and regenerative medicine.
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Affiliation(s)
- Yufan Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Hongjia Zhu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Akhila Denduluri
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Yangteng Ou
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Nadia A Erkamp
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Runzhang Qi
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Yi Shen
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
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5
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Landrieu I, Dupré E, Sinnaeve D, El Hajjar L, Smet-Nocca C. Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools. Front Chem 2022; 10:886382. [PMID: 35646824 PMCID: PMC9133342 DOI: 10.3389/fchem.2022.886382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.
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Affiliation(s)
- Isabelle Landrieu
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Elian Dupré
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Davy Sinnaeve
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Léa El Hajjar
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
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6
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Chen T, Wang Y, Xie J, Qu X, Liu C. Lysozyme Amyloid Fibril-Integrated PEG Injectable Hydrogel Adhesive with Improved Antiswelling and Antibacterial Capabilities. Biomacromolecules 2022; 23:1376-1391. [PMID: 35195006 DOI: 10.1021/acs.biomac.1c01597] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogels with inherent antibacterial activities have been attracting increasing attention, particularly for biomedical applications. Biology provides a range of materials and mechanisms to meet diverse requirements for bacterial combating. Lysozyme after fibrillation (LZMF) has a much superior antibacterial ability than globular native lysozyme due to its decreased positive charges and increased hydrophobic β-sheet component. Here, we propose to design a poly(ethylene glycol) (PEG) cross-linked LZMF composite antibacterial hydrogel by utilizing the nucleophilic substitution reaction between LZMF and N-hydroxysuccinimide end groups on four-arm PEG-NHS. The generated PEG-LZMF hydrogel is bacteria-resistant both in vitro and in vivo as expected and has good biocompatibility. Moreover, the volume expansion of PEG can be significantly inhibited due to the presence of hydrophobic lysozyme amyloid fibrils. In addition, the relatively fast cross-linking reaction can make PEG-LZMF both injectable and shape-compatible. The simultaneous reaction with tissue-exposed -NH2 or -SH also confers a tissue-adhesive ability. We envision that this hydrophobic lysozyme amyloid fibril-integrated PEG composite hydrogel can effectively adhere/protect open wounds and internal incisions and suppress pathogen infection through a biomimetic antibacterial mechanism. Considering the simple fabrication process, this multifunctional PEG-LZMF antibacterial hydrogel is promising for clinical transformation.
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Affiliation(s)
- Tianhao Chen
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yifei Wang
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiahui Xie
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xue Qu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, Shanghai 200237, China
| | - Changsheng Liu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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7
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Xu Y, Qi R, Zhu H, Li B, Shen Y, Krainer G, Klenerman D, Knowles TPJ. Liquid-Liquid Phase-Separated Systems from Reversible Gel-Sol Transition of Protein Microgels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2008670. [PMID: 34235786 DOI: 10.1002/adma.202008670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/12/2021] [Indexed: 06/13/2023]
Abstract
Liquid-liquid phase-separated biomolecular systems are increasingly recognized as key components in the intracellular milieu where they provide spatial organization to the cytoplasm and the nucleoplasm. The widespread use of phase-separated systems by nature has given rise to the inspiration of engineering such functional systems in the laboratory. In particular, reversible gelation of liquid-liquid phase-separated systems could confer functional advantages to the generation of new soft materials. Such gelation processes of biomolecular condensates have been extensively studied due to their links with disease. However, the inverse process, the gel-sol transition, has been less explored. Here, a thermoresponsive gel-sol transition of an extracellular protein in microgel form is explored, resulting in an all-aqueous liquid-liquid phase-separated system with high homogeneity. During this gel-sol transition, elongated gelatin microgels are demonstrated to be converted to a spherical geometry due to interfacial tension becoming the dominant energetic contribution as elasticity diminishes. The phase-separated system is further explored with respect to the diffusion of small particles for drug-release scenarios. Together, this all-aqueous system opens up a route toward size-tunable and monodisperse synthetic biomolecular condensates and controlled liquid-liquid interfaces, offering possibilities for applications in bioengineering and biomedicine.
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Affiliation(s)
- Yufan Xu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Hongjia Zhu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Bing Li
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Yi Shen
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Georg Krainer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
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8
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Shen Y, Levin A, Kamada A, Toprakcioglu Z, Rodriguez-Garcia M, Xu Y, Knowles TPJ. From Protein Building Blocks to Functional Materials. ACS NANO 2021; 15:5819-5837. [PMID: 33760579 PMCID: PMC8155333 DOI: 10.1021/acsnano.0c08510] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
Proteins are the fundamental building blocks for high-performance materials in nature. Such materials fulfill structural roles, as in the case of silk and collagen, and can generate active structures including the cytoskeleton. Attention is increasingly turning to this versatile class of molecules for the synthesis of next-generation green functional materials for a range of applications. Protein nanofibrils are a fundamental supramolecular unit from which many macroscopic protein materials are formed. In this Review, we focus on the multiscale assembly of such protein nanofibrils formed from naturally occurring proteins into new supramolecular architectures and discuss how they can form the basis of material systems ranging from bulk gels, films, fibers, micro/nanogels, condensates, and active materials. We review current and emerging approaches to process and assemble these building blocks in a manner which is different to their natural evolutionarily selected role but allows the generation of tailored functionality, with a focus on microfluidic approaches. We finally discuss opportunities and challenges for this class of materials, including applications that can be involved in this material system which consists of fully natural, biocompatible, and biodegradable feedstocks yet has the potential to generate materials with performance and versatility rivalling that of the best synthetic polymers.
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Affiliation(s)
- Yi Shen
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- School
of Chemical and Biomolecular Engineering, The University of Sydney, 2006 Sydney, New South Wales, Australia
| | - Aviad Levin
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Ayaka Kamada
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Zenon Toprakcioglu
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Marc Rodriguez-Garcia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Xampla, the BioInnovation Building, 25 Cambridge
Science Park Road, Cambridge CB4 0FW, U.K.
| | - Yufan Xu
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
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Tao K, Xue B, Han S, Aizen R, Shimon LJW, Xu Z, Cao Y, Mei D, Wang W, Gazit E. Bioinspired Suprahelical Frameworks as Scaffolds for Artificial Photosynthesis. ACS APPLIED MATERIALS & INTERFACES 2020; 12:45192-45201. [PMID: 32924412 PMCID: PMC7549093 DOI: 10.1021/acsami.0c13295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Framework materials have shown promising potential in various biological applications. However, the state-of-the-art components show low biocompatibility or mechanical instability, or cannot integrate both optics and electronics, thus severely limiting their extensive applications in biological systems. Herein, we demonstrate that amide-based bioorganic building blocks, including dipeptides and dipeptide nucleic acids, can self-assemble into hydrogen-bonded suprahelix architectures of controllable handedness, which then form suprahelical frameworks with diverse cavities. Especially, the cavities can be tuned to be hydrophilic or hydrophobic, and the shortest diagonal distance can be modulated from 0.5 to 1.8 nm, with the volume proportion in the unit cell changing from 5 to 60%. Furthermore, the hydrogen bonding networks result in high mechanical rigidity and semiconductively optoelectronic properties, which allow the utilization of the suprahelical frameworks as supramolecular scaffolds for artificial photosynthesis. Our findings reveal amide-based suprahelix architectures acting as bioinspired supramolecular frameworks, thus extending the constituents portfolio and increasing the feasibility of using framework materials for biological applications.
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Affiliation(s)
- Kai Tao
- State
Key Laboratory of Fluid Power and Mechatronic Systems & Key Laboratory
of Advanced Manufacturing Engineering of Zhejiang Province, School
of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Bin Xue
- National
Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, Jiangsu, China
| | - Shuyi Han
- China
Petroleum Engineering & Construction Corp. Southwest Company, No. 6th Shenghua Road, High-Tech
Zone, Chengdu 610094, Sichuan, China
| | - Ruth Aizen
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Linda J. W. Shimon
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Zhengyu Xu
- National
Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, Jiangsu, China
| | - Yi Cao
- National
Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, Jiangsu, China
| | - Deqing Mei
- State
Key Laboratory of Fluid Power and Mechatronic Systems & Key Laboratory
of Advanced Manufacturing Engineering of Zhejiang Province, School
of Mechanical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Wei Wang
- National
Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, Jiangsu, China
| | - Ehud Gazit
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
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10
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Robinson CV. Christopher Dobson, 1949-2019: Mentor, Friend, Scientist Extraordinaire. Annu Rev Biochem 2020; 89:1-19. [PMID: 32343910 DOI: 10.1146/annurev-biochem-011520-105226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is impossible to do justice in one review article to a researcher of the stature of Christopher Dobson. His career spanned almost five decades, resulting in more than 870 publications and a legacy that will continue to influence the lives of many for decades to come. In this review, I have attempted to capture Chris's major contributions: his early work, dedicated to understanding protein-folding mechanisms; his collaborative work with physicists to understand the process of protein aggregation; and finally, his later career in which he developed strategies to prevent misfolding. However, it is not only this body of work but also the man himself who inspired an entire generation of scientists through his patience, ability to mentor, and innate generosity. These qualities remain a hallmark of the way in which he conducted his research-research that will leave a lasting imprint on science.
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Affiliation(s)
- Carol V Robinson
- Department of Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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11
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Rho HS, Veltkamp HW, Hanke AT, Ottens M, Breukers C, Habibović P, Gardeniers H. Systematic Investigation of Insulin Fibrillation on a Chip. Molecules 2020; 25:molecules25061380. [PMID: 32197443 PMCID: PMC7144930 DOI: 10.3390/molecules25061380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/29/2022] Open
Abstract
A microfluidic protein aggregation device (microPAD) that allows the user to perform a series of protein incubations with various concentrations of two reagents is demonstrated. The microfluidic device consists of 64 incubation chambers to perform individual incubations of the protein at 64 specific conditions. Parallel processes of metering reagents, stepwise concentration gradient generation, and mixing are achieved simultaneously by pneumatic valves. Fibrillation of bovine insulin was selected to test the device. The effect of insulin and sodium chloride (NaCl) concentration on the formation of fibrillar structures was studied by observing the growth rate of partially folded protein, using the fluorescent marker Thioflavin-T. Moreover, dual gradients of different NaCl and hydrochloric acid (HCl) concentrations were formed, to investigate their interactive roles in the formation of insulin fibrils and spherulites. The chip-system provides a bird’s eye view on protein aggregation, including an overview of the factors that affect the process and their interactions. This microfluidic platform is potentially useful for rapid analysis of the fibrillation of proteins associated with many misfolding-based diseases, such as quantitative and qualitative studies on amyloid growth.
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Affiliation(s)
- Hoon Suk Rho
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands; (H.S.R.); (P.H.)
- Mesoscale Chemical Systems Group, MESA+ Institute for Nanotechnology, University of Twente, 7522 NB Enschede, The Netherlands
| | - Henk-Willem Veltkamp
- Integrated Devices and Systems Group, MESA+ Institute for Nanotechnology, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Alexander Thomas Hanke
- BioProcess Engineering Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, 2628 CD Delft, The Netherlands; (A.T.H.); (M.O.)
| | - Marcel Ottens
- BioProcess Engineering Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, 2628 CD Delft, The Netherlands; (A.T.H.); (M.O.)
| | - Christian Breukers
- Medical Cell BioPhysics Group, Technical Medical Centre, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Pamela Habibović
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands; (H.S.R.); (P.H.)
| | - Han Gardeniers
- Mesoscale Chemical Systems Group, MESA+ Institute for Nanotechnology, University of Twente, 7522 NB Enschede, The Netherlands
- Correspondence: ; Tel.: +31-(0)53-489-4356
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12
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Miyasaka Y, Murakami K, Ito K, Kumaki J, Makabe K, Hatori K. Condensed desmin and actin cytoskeletal communication in lipid droplets. Cytoskeleton (Hoboken) 2019; 76:477-490. [DOI: 10.1002/cm.21573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Yoshiya Miyasaka
- Department of Bio‐Systems Engineering, Graduate School of Science and EngineeringYamagata University Yamagata Japan
| | - Keigo Murakami
- Department of Bio‐Systems Engineering, Graduate School of Science and EngineeringYamagata University Yamagata Japan
| | - Koji Ito
- Department of Bio‐Systems Engineering, Graduate School of Science and EngineeringYamagata University Yamagata Japan
| | - Jiro Kumaki
- Department of Organic Materials Science, Graduate School of Organic Materials ScienceYamagata University Yamagata Japan
| | - Koki Makabe
- Department of Biochemical Engineering, Graduate School of Science and EngineeringYamagata University Yamagata Japan
| | - Kuniyuki Hatori
- Department of Bio‐Systems Engineering, Graduate School of Science and EngineeringYamagata University Yamagata Japan
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13
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Arnon ZA, Gilead S, Gazit E. Microfluidics for real-time direct monitoring of self- and co-assembly biomolecular processes. NANOTECHNOLOGY 2019; 30:102001. [PMID: 30537683 DOI: 10.1088/1361-6528/aaf7b1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Molecular self-assembly is a major approach for the fabrication of functional supramolecular nanomaterials. This dynamic, straightforward, bottom-up procedure may result in the formation of various architectures at the nano-scale, with remarkable physical and chemical characteristics. Biological and bio-inspired building blocks are especially attractive due to their intrinsic tendency to assemble into well-organized structures, as well as their inherent biocompatibility. To further expand the morphological diversity, co-assembly methods have been developed, allowing to produce alternative unique architectures, enhanced properties, and improved structural control. However, in many cases, mechanistic understanding of the self- and co-assembly processes is still lacking. Microfluidic techniques offer a set of exclusive tools for real-time monitoring of biomolecular self-organization, which is crucial for the study of such dynamic processes. Assembled nuclei, confined by micron-scale pillars, could be subjected to controlled environments aiming to assess the effect of different conditions on the assembly process. Other microfluidics setups can produce droplets at a rate of over 100 s-1, with volumes as small as several picoliters. Under these conditions, each droplet can serve as an individual pico/nano-reactor allowing nucleation and assembly. These processes can be monitored, analyzed and imaged, by various techniques including simple bright-field microscopy. Elucidating the mechanism of such molecular events may serve as a conceptual stepping-stone for the rational control of the resulting physicochemical properties.
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Affiliation(s)
- Zohar A Arnon
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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14
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Shin Y, Chang YC, Lee DSW, Berry J, Sanders DW, Ronceray P, Wingreen NS, Haataja M, Brangwynne CP. Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome. Cell 2018; 175:1481-1491.e13. [PMID: 30500535 PMCID: PMC6724728 DOI: 10.1016/j.cell.2018.10.057] [Citation(s) in RCA: 404] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/28/2018] [Accepted: 10/26/2018] [Indexed: 01/19/2023]
Abstract
Phase transitions involving biomolecular liquids are a fundamental mechanism underlying intracellular organization. In the cell nucleus, liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is implicated in assembly of the nucleolus, as well as transcriptional clusters, and other nuclear bodies. However, it remains unclear whether and how physical forces associated with nucleation, growth, and wetting of liquid condensates can directly restructure chromatin. Here, we use CasDrop, a novel CRISPR-Cas9-based optogenetic technology, to show that various IDPs phase separate into liquid condensates that mechanically exclude chromatin as they grow and preferentially form in low-density, largely euchromatic regions. A minimal physical model explains how this stiffness sensitivity arises from lower mechanical energy associated with deforming softer genomic regions. Targeted genomic loci can nonetheless be mechanically pulled together through surface tension-driven coalescence. Nuclear condensates may thus function as mechano-active chromatin filters, physically pulling in targeted genomic loci while pushing out non-targeted regions of the neighboring genome. VIDEO ABSTRACT.
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Affiliation(s)
- Yongdae Shin
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Department of Mechanical and Aerospace Engineering, Seoul National University, Seoul 08826, South Korea
| | - Yi-Che Chang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Daniel S W Lee
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Joel Berry
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David W Sanders
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Pierre Ronceray
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ 08544, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mikko Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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15
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Charmet J, Arosio P, Knowles TP. Microfluidics for Protein Biophysics. J Mol Biol 2018; 430:565-580. [DOI: 10.1016/j.jmb.2017.12.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 01/09/2023]
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16
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Li G, Sasaki T, Asahina S, Roy MC, Mochizuki T, Koizumi K, Zhang Y. Patching of Lipid Rafts by Molecular Self-Assembled Nanofibrils Suppresses Cancer Cell Migration. Chem 2017. [DOI: 10.1016/j.chempr.2017.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Ekiz MS, Cinar G, Khalily MA, Guler MO. Self-assembled peptide nanostructures for functional materials. NANOTECHNOLOGY 2016; 27:402002. [PMID: 27578525 DOI: 10.1088/0957-4484/27/40/402002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.
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Affiliation(s)
- Melis Sardan Ekiz
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800 Turkey
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18
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Liu L, Kheifets S, Ginis V, Capasso F. Subfemtonewton Force Spectroscopy at the Thermal Limit in Liquids. PHYSICAL REVIEW LETTERS 2016; 116:228001. [PMID: 27314738 DOI: 10.1103/physrevlett.116.228001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Indexed: 06/06/2023]
Abstract
We demonstrate thermally limited force spectroscopy using a probe formed by a dielectric microsphere optically trapped in water near a dielectric surface. We achieve force resolution below 1 fN in 100 s, corresponding to a 2 Å rms displacement of the probe. Our measurement combines a calibrated evanescent wave particle tracking technique and a lock-in detection method. We demonstrate the accuracy of our method by measurement of the height-dependent force exerted on the probe by an evanescent wave, the results of which are in agreement with Mie theory calculations.
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Affiliation(s)
- Lulu Liu
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Simon Kheifets
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Vincent Ginis
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, USA
- Applied Physics, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Federico Capasso
- School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, USA
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19
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Ranganathan S, Ghosh D, Maji SK, Padinhateeri R. A minimal conformational switching-dependent model for amyloid self-assembly. Sci Rep 2016; 6:21103. [PMID: 26883720 PMCID: PMC4756677 DOI: 10.1038/srep21103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/19/2016] [Indexed: 11/14/2022] Open
Abstract
Amyloid formation is associated with various pathophysiological conditions like Alzheimer’s and Parkinson’s diseases as well as many useful functions. The hallmark of amyloid assemblies is a conformational transition of the constituent proteins into a β - sheet rich filament. Accounting for this conformational transition in amyloidogenic proteins, we develop an analytically solvable model that can probe the dynamics of an ensemble of single filaments. Using the theory and Monte Carlo simulations, we show the presence of two kinetic regimes for the growth of a self-assembling filament – switching-dependent and –independent growth regimes. We observe a saturation in fibril elongation velocities at higher concentrations in the first regime, providing a novel explanation to the concentration-independence of growth velocities observed experimentally. We also compute the length fluctuation of the filaments to characterize aggregate heterogeneity. From the early velocities and length fluctuation, we propose a novel way of estimating the conformational switching rate. Our theory predicts a kinetic phase diagram that has three distinct phases – short oligomers/monomers, disordered aggregates and β -rich filaments. The model also predicts the force generation potential and the intermittent growth of amyloid fibrils evident from single molecular experiments. Our model could contribute significantly to the physical understanding of amyloid aggregation.
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Affiliation(s)
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
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20
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Mazza G, Simons JP, Al-Shawi R, Ellmerich S, Urbani L, Giorgetti S, Taylor GW, Gilbertson JA, Hall AR, Al-Akkad W, Dhar D, Hawkins PN, De Coppi P, Pinzani M, Bellotti V, Mangione PP. Amyloid persistence in decellularized liver: biochemical and histopathological characterization. Amyloid 2016; 23:1-7. [PMID: 26646718 PMCID: PMC4819572 DOI: 10.3109/13506129.2015.1110518] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Systemic amyloidoses are a group of debilitating and often fatal diseases in which fibrillar protein aggregates are deposited in the extracellular spaces of a range of tissues. The molecular basis of amyloid formation and tissue localization is still unclear. Although it is likely that the extracellular matrix (ECM) plays an important role in amyloid deposition, this interaction is largely unexplored, mostly because current analytical approaches may alter the delicate and complicated three-dimensional architecture of both ECM and amyloid. We describe here a decellularization procedure for the amyloidotic mouse liver which allows high-resolution visualization of the interactions between amyloid and the constitutive fibers of the extracellular matrix. The primary structure of the fibrillar proteins remains intact and the amyloid fibrils retain their amyloid enhancing factor activity.
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Affiliation(s)
| | - J Paul Simons
- b Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins , and
| | - Raya Al-Shawi
- c Centre for Biomedical Science, Division of Medicine, University College London , London , UK
| | - Stephan Ellmerich
- b Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins , and
| | - Luca Urbani
- d Stem Cells and Regenerative Medicine Section, Developmental Biology and Cancer Programme, UCL Institute for Child Health, Great Ormond Street Hospital, University College London , London UK
| | - Sofia Giorgetti
- e Department of Molecular Medicine , Institute of Biochemistry, University of Pavia , Pavia , Italy , and
| | - Graham W Taylor
- b Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins , and
| | - Janet A Gilbertson
- b Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins , and
| | | | | | - Dipok Dhar
- a Institute for Liver and Digestive Health .,f Organ Transplantation Centre and Comparative Medicine Department, King Faisal Specialist Hospital , Riyadh , Saudi Arabia
| | - Philip N Hawkins
- b Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins , and
| | - Paolo De Coppi
- d Stem Cells and Regenerative Medicine Section, Developmental Biology and Cancer Programme, UCL Institute for Child Health, Great Ormond Street Hospital, University College London , London UK
| | | | - Vittorio Bellotti
- b Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins , and.,e Department of Molecular Medicine , Institute of Biochemistry, University of Pavia , Pavia , Italy , and
| | - P Patrizia Mangione
- b Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins , and.,e Department of Molecular Medicine , Institute of Biochemistry, University of Pavia , Pavia , Italy , and
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