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Zhao Z, Deng J, Fan D. Green biomanufacturing in recombinant collagen biosynthesis: trends and selection in various expression systems. Biomater Sci 2023; 11:5439-5461. [PMID: 37401335 DOI: 10.1039/d3bm00724c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Collagen, classically derived from animal tissue, is an all-important protein material widely used in biomedical materials, cosmetics, fodder, food, etc. The production of recombinant collagen through different biological expression systems using bioengineering techniques has attracted significant interest in consideration of increasing market demand and the process complexity of extraction. Green biomanufacturing of recombinant collagen has become one of the focus topics. While the bioproduction of recombinant collagens (type I, II, III, etc.) has been commercialized in recent years, the biosynthesis of recombinant collagen is extremely challenging due to protein immunogenicity, yield, degradation, and other issues. The rapid development of synthetic biology allows us to perform a heterologous expression of proteins in diverse expression systems, thus optimizing the production and bioactivities of recombinant collagen. This review describes the research progress in the bioproduction of recombinant collagen over the past two decades, focusing on different expression systems (prokaryotic organisms, yeasts, plants, insects, mammalian and human cells, etc.). We also discuss the challenges and future trends in developing market-competitive recombinant collagens.
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Affiliation(s)
- Zilong Zhao
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China.
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jianjun Deng
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China.
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, Shaanxi, China
| | - Daidi Fan
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China.
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, Shaanxi, China
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2
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Kong MS, Koh WG, Lee HJ. Controlled Release of Epidermal Growth Factor from Furfuryl-Gelatin Hydrogel Using in Situ Visible Light-Induced Crosslinking and Its Effects on Fibroblasts Proliferation and Migration. Gels 2022; 8:gels8040214. [PMID: 35448115 PMCID: PMC9032874 DOI: 10.3390/gels8040214] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/06/2023] Open
Abstract
Hydrogels are widely used in tissue engineering as materials that regulate cell proliferation, migration, and differentiation. They also act as promising biomaterials that can provide a variety of stimuli by influencing the surrounding microenvironment, which can be achieved by modulating their mechanical properties, thereby aiding soluble factor delivery. Here, we developed a gelatin-based injectable hydrogel that has controllable mechanical properties and demonstrates sustained drug release without the need for invasive surgery. Gelatin was modified with furfuryl groups, and riboflavin phosphate was used as a photoinitiator to crosslink the hydrogel using visible light. A hydrogel–with a storage modulus in the range of 0.2–15 kPa was formed by maintaining the concentration of furfuryl-gelatin within 10–30% w/v. Consequently, their mechanical properties can be tailored for their applications. The furfuryl-gelatin hydrogel was loaded with maleimide-modified epidermal growth factor (EGF) as a model drug to achieve a controlled-release system. The sustained release of maleimide-EGF due to gelatin hydrogel matrix degradation was observed. Cell proliferation and scratch assays were performed to verify its effect on fibroblasts. When EGF was physically entrapped in the hydrogel matrix, the released EGF considerably affected cell proliferation and scratch closure of fibroblasts at the beginning of the culture. By contrast, maleimide-EGF was released sustainably and steadily and affected cell proliferation and scratch closure after the initial stage. We demonstrated that the release of soluble factors could be controlled by modulating the mechanical properties. Thus, the injectable hydrogel formed by in situ visible light-induced crosslinking could be a promising biomaterial for tissue engineering and biomedical therapeutics.
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Affiliation(s)
- Min Sun Kong
- Department of Chemical and Biological Engineering, Gachon University, 1342 Seongnam-daero, Seongnam-si 13120, Korea;
| | - Won-Gun Koh
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
- Correspondence: (W.-G.K.); (H.J.L.)
| | - Hyun Jong Lee
- Department of Chemical and Biological Engineering, Gachon University, 1342 Seongnam-daero, Seongnam-si 13120, Korea;
- Correspondence: (W.-G.K.); (H.J.L.)
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3
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Zhou W, Liu L, Huang J, Cai Y, Cohen Stuart MA, de Vries R, Wang J. Supramolecular virus-like particles by co-assembly of triblock polypolypeptide and PAMAM dendrimers. SOFT MATTER 2021; 17:5044-5049. [PMID: 33928336 DOI: 10.1039/d1sm00290b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Virus-like particles are of special interest as functional delivery vehicles in a variety of fields ranging from nanomedicine to materials science. Controlled formation of virus-like particles relies on manipulating the assembly of the viral coat proteins. Herein, we report a new assembly system based on a triblock polypolypeptide C4-S10-BK12 and -COONa terminated PAMAM dendrimers. The polypolypeptide has a cationic BK12 block with 12 lysines; its binding with anionic PAMAM triggers the folding of the peptide's middle silk-like block and leads to formation of virus-like nanorods, stabilized against aggregation by the long hydrophilic "C" block of the polypeptide. Varying the dendrimer/polypeptide mixing ratio hardly influences the structure and size of the nanorod. However, increasing the dendrimer generation, that is, increasing the dendrimer size results in increased particle length and height, without affecting the width of the nanorod. The branched structure and well-defined size of the dendrimers allows delicate control of the particle size; it is impossible to achieve similar control over assembly of the polypeptide with linear polyelectrolyte as template. In conclusion, we report a novel protein assembling system with properties resembling a viral coat; the findings may therefore be helpful for designing functional virus-like particles like vaccines.
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Affiliation(s)
- Wenjuan Zhou
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Lei Liu
- Process Department, East China Engineering Science and Technology Co., Ltd, 70 East Wangjiang Road, 230024, Hefei, People's Republic of China
| | - Jianan Huang
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Ying Cai
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Martien A Cohen Stuart
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Junyou Wang
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
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4
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Calcines-Cruz C, Finkelstein IJ, Hernandez-Garcia A. CRISPR-Guided Programmable Self-Assembly of Artificial Virus-Like Nucleocapsids. NANO LETTERS 2021; 21:2752-2757. [PMID: 33729813 PMCID: PMC9724498 DOI: 10.1021/acs.nanolett.0c04640] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Designer virus-inspired proteins drive the manufacturing of more effective, safer gene-delivery systems and simpler models to study viral assembly. However, self-assembly of engineered viromimetic proteins on specific nucleic acid templates, a distinctive viral property, has proved difficult. Inspired by viral packaging signals, we harness the programmability of CRISPR-Cas12a to direct the nucleation and growth of a self-assembling synthetic polypeptide into virus-like particles (VLP) on specific DNA molecules. Positioning up to ten nuclease-dead Cas12a (dCas12a) proteins along a 48.5 kbp DNA template triggers particle growth and full DNA encapsidation at limiting polypeptide concentrations. Particle growth rate is further increased when dCas12a is dimerized with a polymerization silk-like domain. Such improved self-assembly efficiency allows for discrimination between cognate versus noncognate DNA templates by the synthetic polypeptide. CRISPR-guided VLPs will help to develop programmable bioinspired nanomaterials with applications in biotechnology as well as viromimetic scaffolds to improve our understanding of viral self-assembly.
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Affiliation(s)
- Carlos Calcines-Cruz
- Department of Chemistry of Biomacromolecules, Institute of Chemistry, National Autonomous University of Mexico, Mexico City C.P. 04510, Mexico
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5
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Gulevsky AK. COLLAGEN: STRUCTURE, METABOLISM, PRODUCTION AND INDUSTRIAL APPLICATION. BIOTECHNOLOGIA ACTA 2020. [DOI: 10.15407/biotech13.05.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
This review presents the current scientific literature data about structure, properties, and functions of collagen, which is known as one of the most abundant human and animal proteins. The building of collagen molecule from the primary structure to submolecular formations, the main stages of its synthesis and biodegradation are briefly described. The information about collagen diversity, its features and metabolic ways in various tissues, including skin, tendons, bones, etc. is presented. The problems of pathologies caused by collagen synthesis and breakdown disorders as well as age-related changes in collagen properties and their causes are discussed. A comparative analysis of the advantages and disadvantages of collagen and its derivatives obtaining from various sources (animals, marine, and recombinant) is given. The most productive methods for collagen extraction from various tissues are shown. The concept of collagen hydrolysis conditions influence on the physicochemical properties and biological activity of the obtained products is described. The applications of collagen and its products in various fields of industrial activity, such as pharmaceutical, cosmetic industry and medicine, are discussed. Further prospective directions of fundamental and applied investigations in this area of research are outlined.
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6
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Mizuguchi Y, Mashimo Y, Mie M, Kobatake E. Temperature-Responsive Multifunctional Protein Hydrogels with Elastin-like Polypeptides for 3-D Angiogenesis. Biomacromolecules 2020; 21:1126-1135. [PMID: 32003967 DOI: 10.1021/acs.biomac.9b01496] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Supramolecular protein hydrogels with tunable properties represent promising candidates for advanced designer extracellular matrices (ECMs). To control cellular functions, ECMs should be able to spatiotemporally regulate synergistic signaling between transmembrane receptors and growth factor (GF) receptors. In this study, we developed genetically engineered temperature-responsive multifunctional protein hydrogels. The designed hydrogel was fabricated by combining the following four peptide blocks: thermosensitive elastin-like polypeptides (ELPs), a polyaspartic acid (polyD) chain to control aggregation and delivery of GFs, a de novo-designed helix peptide that forms antiparallel homotetrameric coiled-coils, and a biofunctional peptide. The resultant coiled-coil unit bound ELPs (CUBEs) exhibit a controllable sol-gel transition with tunable mechanical properties. CUBEs were functionalized with bone sialoprotein-derived RGD (bRGD), and human umbilical vein endothelial cells (HUVECs) were three-dimensionally cultured in bRGD-modified CUBE (bRGD-CUBE) hydrogels. Proangiogenic activity of HUVECs was promoted by bRGD. Moreover, heparin-binding angiogenic GFs were immobilized to bRGD-CUBEs via electrostatic interactions. HUVECs cultured in GF-tethered bRGD-CUBE hydrogels formed three-dimensional (3-D) tubulelike structures. The designed CUBE hydrogels may demonstrate utility as advanced smart biomaterials for biomedical applications. Further, the protein hydrogel design strategy may provide a novel platform for constructing designer 3-D microenvironments for specific cell types.
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Affiliation(s)
- Yoshinori Mizuguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Yasumasa Mashimo
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Masayasu Mie
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Eiry Kobatake
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
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7
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Willems L, van Westerveld L, Roberts S, Weitzhandler I, Calcines Cruz C, Hernandez-Garcia A, Chilkoti A, Mastrobattista E, van der Oost J, de Vries R. Nature of Amorphous Hydrophilic Block Affects Self-Assembly of an Artificial Viral Coat Polypeptide. Biomacromolecules 2019; 20:3641-3647. [PMID: 31418550 PMCID: PMC6794640 DOI: 10.1021/acs.biomac.9b00512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/08/2019] [Indexed: 01/28/2023]
Abstract
Consensus motifs for sequences of both crystallizable and amorphous blocks in silks and natural structural analogues of silks vary widely. To design novel silklike polypeptides, an important question is therefore how the nature of either the crystallizable or the amorphous block affects the self-assembly and resulting physical properties of silklike polypeptides. We address herein the influence of the amorphous block on the self-assembly of a silklike polypeptide that was previously designed to encapsulate single DNA molecules into rod-shaped viruslike particles. The polypeptide has a triblock architecture, with a long N-terminal amorphous block, a crystallizable midblock, and a C-terminal DNA-binding block. We compare the self-assembly behavior of a triblock with a very hydrophilic collagen-like amorphous block (GXaaYaa)132 to that of a triblock with a less hydrophilic elastin-like amorphous block (GSGVP)80. The amorphous blocks have similar lengths and both adopt a random coil structure in solution. Nevertheless, atomic force microscopy revealed significant differences in the self-assembly behavior of the triblocks. If collagen-like amorphous blocks are used, there is a clear distinction between very short polypeptide-only fibrils and much longer fibrils with encapsulated DNA. If elastin-like amorphous blocks are used, DNA is still encapsulated, but the polypeptide-only fibrils are now much longer and their size distribution partially overlaps with that of the encapsulated DNA fibrils. We attribute the difference to the more hydrophilic nature of the collagen-like amorphous block, which more strongly opposes the growth of polypeptide-only fibrils than the elastin-like amorphous blocks. Our work illustrates that differences in the chemical nature of amorphous blocks can strongly influence the self-assembly and hence the functionality of engineered silklike polypeptides.
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Affiliation(s)
- Lione Willems
- Physical
Chemistry and Soft Matter and Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Larissa van Westerveld
- Physical
Chemistry and Soft Matter and Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Stefan Roberts
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Isaac Weitzhandler
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Carlos Calcines Cruz
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Armando Hernandez-Garcia
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Ashutosh Chilkoti
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Enrico Mastrobattista
- Department
of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences (UIPS),
Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - John van der Oost
- Physical
Chemistry and Soft Matter and Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical
Chemistry and Soft Matter and Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
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8
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Gellermann P, Schneider-Barthold C, Bolten SN, Overfelt E, Scheper T, Pepelanova I. Production of a Recombinant Non-Hydroxylated Gelatin Mimetic in Pichia pastoris for Biomedical Applications. J Funct Biomater 2019; 10:E39. [PMID: 31480684 PMCID: PMC6787575 DOI: 10.3390/jfb10030039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/23/2019] [Accepted: 08/29/2019] [Indexed: 01/10/2023] Open
Abstract
Proteins derived from the natural extracellular matrix like collagen or gelatin are common in clinical research, where they are prized for their biocompatibility and bioactivity. Cells are able to adhere, grow and remodel scaffolds based on these materials. Usually, collagen and gelatin are sourced from animal material, risking pathogenic transmission and inconsistent batch-to-batch product quality. A recombinant production in yeast circumvents these disadvantages by ensuring production with a reproducible quality in animal-component-free media. A gelatin mimetic protein, based on the alpha chain of human collagen I, was cloned in Pichia pastoris under the control of the methanol-inducible alcohol oxidase (AOX1) promoter. A producing clone was selected and cultivated at the 30 L scale. The protein was secreted into the cultivation medium and the final yield was 3.4 g·L-1. Purification of the target was performed directly from the cell-free medium by size exclusion chromatography. The gelatin mimetic protein was tested in cell culture for biocompatibility and for promoting cell adhesion. It supported cell growth and its performance was indistinguishable from animal-derived gelatin. The gelatin-mimetic protein represents a swift strategy to produce recombinant and human-based extracellular matrix proteins for various biomedical applications.
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Affiliation(s)
- Pia Gellermann
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | | | - Svenja Nicolin Bolten
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Ethan Overfelt
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Iliyana Pepelanova
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167 Hannover, Germany.
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9
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Werten MWT, Eggink G, Cohen Stuart MA, de Wolf FA. Production of protein-based polymers in Pichia pastoris. Biotechnol Adv 2019; 37:642-666. [PMID: 30902728 PMCID: PMC6624476 DOI: 10.1016/j.biotechadv.2019.03.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 02/03/2019] [Accepted: 03/17/2019] [Indexed: 01/09/2023]
Abstract
Materials science and genetic engineering have joined forces over the last three decades in the development of so-called protein-based polymers. These are proteins, typically with repetitive amino acid sequences, that have such physical properties that they can be used as functional materials. Well-known natural examples are collagen, silk, and elastin, but also artificial sequences have been devised. These proteins can be produced in a suitable host via recombinant DNA technology, and it is this inherent control over monomer sequence and molecular size that renders this class of polymers of particular interest to the fields of nanomaterials and biomedical research. Traditionally, Escherichia coli has been the main workhorse for the production of these polymers, but the methylotrophic yeast Pichia pastoris is finding increased use in view of the often high yields and potential bioprocessing benefits. We here provide an overview of protein-based polymers produced in P. pastoris. We summarize their physicochemical properties, briefly note possible applications, and detail their biosynthesis. Some challenges that may be faced when using P. pastoris for polymer production are identified: (i) low yields and poor process control in shake flask cultures; i.e., the need for bioreactors, (ii) proteolytic degradation, and (iii) self-assembly in vivo. Strategies to overcome these challenges are discussed, which we anticipate will be of interest also to readers involved in protein expression in P. pastoris in general.
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Affiliation(s)
- Marc W T Werten
- Wageningen Food & Biobased Research, NL-6708 WG Wageningen, The Netherlands.
| | - Gerrit Eggink
- Wageningen Food & Biobased Research, NL-6708 WG Wageningen, The Netherlands; Bioprocess Engineering, Wageningen University & Research, NL-6708 PB Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University & Research, NL-6708 WE Wageningen, The Netherlands
| | - Frits A de Wolf
- Wageningen Food & Biobased Research, NL-6708 WG Wageningen, The Netherlands
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10
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Marchetti M, Kamsma D, Cazares Vargas E, Hernandez García A, van der Schoot P, de Vries R, Wuite GJL, Roos WH. Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level. NANO LETTERS 2019; 19:5746-5753. [PMID: 31368710 PMCID: PMC6696885 DOI: 10.1021/acs.nanolett.9b02376] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/24/2019] [Indexed: 05/20/2023]
Abstract
While the structure of a multitude of viral particles has been resolved to atomistic detail, their assembly pathways remain largely elusive. Key unresolved issues are particle nucleation, particle growth, and the mode of genome compaction. These issues are difficult to address in bulk approaches and are effectively only accessible by the real-time tracking of assembly dynamics of individual particles. This we do here by studying the assembly into rod-shaped viruslike particles (VLPs) of artificial capsid polypeptides. Using fluorescence optical tweezers, we establish that small oligomers perform one-dimensional diffusion along the DNA. Larger oligomers are immobile and nucleate VLP growth. A multiplexed acoustic force spectroscopy approach reveals that DNA is compacted in regular steps, suggesting packaging via helical wrapping into a nucleocapsid. By reporting how real-time assembly tracking elucidates viral nucleation and growth principles, our work opens the door to a fundamental understanding of the complex assembly pathways of both VLPs and naturally evolved viruses.
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Affiliation(s)
- Margherita Marchetti
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| | - Douwe Kamsma
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ernesto Cazares Vargas
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Armando Hernandez García
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Paul van der Schoot
- Institute
for Theoretical Physics, Utrecht University, 3512 JE Utrecht, The Netherlands
- Department
of Applied Physics, Eindhoven University
of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Renko de Vries
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Gijs J. L. Wuite
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- E-mail:
| | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
- E-mail:
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11
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Adivitiya, Babbal, Mohanty S, Dagar VK, Khasa YP. Development of a streptokinase expression platform using the native signal sequence of the protein with internal repeats 1 (PIR1) in P. pastoris: Gene dosage optimization and cell retention strategies. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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12
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Willems L, Roberts S, Weitzhandler I, Chilkoti A, Mastrobattista E, van der Oost J, de Vries R. Inducible Fibril Formation of Silk-Elastin Diblocks. ACS OMEGA 2019; 4:9135-9143. [PMID: 31172045 PMCID: PMC6545545 DOI: 10.1021/acsomega.9b01025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Silk-elastin block copolymers have such physical and biological properties that make them attractive biomaterials for applications ranging from tissue regeneration to drug delivery. Silk-elastin block copolymers that only assemble into fibrils at high concentrations can be used for a template-induced fibril assembly. This can be achieved by additionally including template-binding blocks that promote high local concentrations of polymers on the template, leading to a template-induced fibril assembly. We hypothesize that template-inducible silk-fibril formation, and hence high critical concentrations for fibril formation, requires careful tuning of the block lengths, to be close to a critical set of block lengths that separates fibril forming from nonfibril forming polymer architectures. Therefore, we explore herein the impact of tuning block lengths for silk-elastin diblock polypeptides on fibril formation. For silk-elastin diblocks ES m -SQ n , in which the elastin pentamer repeat is ES = GSGVP and the crystallizable silk octamer repeat is SQ = GAGAGAGQ, we find that no fibril formation occurs for n = 6 but that the n = 10 and 14 diblocks do show concentration-dependent fibril formation. For n = 14 diblocks, no effect is observed of the length m (with m = 40, 60, 80) of the amorphous block on the lengths of the fibrils. In contrast, for the n = 10 diblocks that are closest to the critical boundary for fibril formation, we find that long amorphous blocks (m = 80) oppose the growth of fibrils at low concentrations, making them suitable for engineering template-inducible fibril formation.
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Affiliation(s)
- Lione Willems
- Physical
Chemistry and Soft Matter and Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Stefan Roberts
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Isaac Weitzhandler
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Enrico Mastrobattista
- Department
of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences (UIPS),
Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - John van der Oost
- Physical
Chemistry and Soft Matter and Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical
Chemistry and Soft Matter and Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
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13
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Basak R, Liu F, Qureshi S, Gupta N, Zhang C, de Vries R, van Kan JA, Dheen ST, van der Maarel JRC. Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis. J Phys Chem Lett 2019; 10:316-321. [PMID: 30615463 DOI: 10.1021/acs.jpclett.8b03465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic profiling would benefit from linearization of ssDNA through the exposure of the unpaired bases to gene-targeting probes. This is compromised by ssDNA's high flexibility and tendency to form self-annealed structures. Here, we demonstrate that self-annealing can be avoided through controlled coating with a cationic-neutral diblock polypeptide copolymer. Coating does not preclude site-specific binding of fluorescence labeled oligonucleotides. Bottlebrush-coated ssDNA can be linearized by confinement inside a nanochannel or molecular combing. A stretch of 0.32 nm per nucleotide is achieved inside a channel with a cross-section of 100 nm and a 2-fold excess of polypeptide with respect to DNA charge. With combing, the complexes are stretched to a similar extent. Atomic force microscopy of dried complexes on silica revealed that the contour and persistence lengths are close to those of dsDNA in the B-form. Labeling is based on hybridization and not limited by restriction enzymes. Enzyme-free labeling offers new opportunities for the detection of specific sequences.
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Affiliation(s)
- Rajib Basak
- Department of Physics , National University of Singapore , Singapore 117542
| | - Fan Liu
- Department of Physics , National University of Singapore , Singapore 117542
| | - Sarfraz Qureshi
- Department of Physics , National University of Singapore , Singapore 117542
| | - Neelima Gupta
- Department of Anatomy , National University of Singapore , Singapore 117594
| | - Ce Zhang
- Institute of Photonics and Photon-Technology , Northwest University , Xi'an , China 710069
| | - Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science , Wageningen University , 6708 Wageningen , The Netherlands
| | - Jeroen A van Kan
- Department of Physics , National University of Singapore , Singapore 117542
| | - S Thameem Dheen
- Department of Anatomy , National University of Singapore , Singapore 117594
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14
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Li X, Rombouts W, van der Gucht J, de Vries R, Dijksman JA. Mechanics of composite hydrogels approaching phase separation. PLoS One 2019; 14:e0211059. [PMID: 30682112 PMCID: PMC6347237 DOI: 10.1371/journal.pone.0211059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
For polymer-particle composites, limited thermodynamic compatibility of polymers and particles often leads to poor dispersal and agglomeration of the particles in the matrix, which negatively impacts the mechanics of composites. To study the impact of particle compatibility in polymer matrices on the mechanical properties of composites, we here study composite silica- protein based hydrogels. The polymer used is a previously studied telechelic protein-based polymer with end groups that form triple helices, and the particles are silica nanoparticles that only weakly associate with the polymer matrix. At 1mM protein polymer, up to 7% of silica nanoparticles can be embedded in the hydrogel. At higher concentrations the system phase separates. Oscillatory rheology shows that at high frequencies the particles strengthen the gels by acting as short-lived multivalent cross-links, while at low frequencies, the particles reduce the gel strength, presumably by sequestering part of the protein polymers in such a way that they can no longer contribute to the network strength. As is generally observed for polymer/particle composites, shear-induced polymer desorption from the particles leads to a viscous dissipation that strongly increases with increasing particle concentration. While linear rheological properties as function of particle concentration provide no signals for an approaching phase separation, this is very different for the non-linear rheology, especially fracture. Strain-at-break decreases rapidly with increasing particle concentration and vanishes as the phase boundary is approached, suggesting that the interfaces between regions of high and low particle densities in composites close to phase separation provide easy fracture planes.
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Affiliation(s)
- Xiufeng Li
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Wolf Rombouts
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Joshua A. Dijksman
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, the Netherlands
- * E-mail:
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15
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Dagar VK, Khasa YP. Combined effect of gene dosage and process optimization strategies on high-level production of recombinant human interleukin-3 (hIL-3) in Pichia pastoris fed-batch culture. Int J Biol Macromol 2018; 108:999-1009. [DOI: 10.1016/j.ijbiomac.2017.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 02/01/2023]
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16
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Humenik M, Lang G, Scheibel T. Silk nanofibril self-assembly versus electrospinning. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1509. [PMID: 29393590 DOI: 10.1002/wnan.1509] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/18/2017] [Accepted: 12/19/2017] [Indexed: 01/16/2023]
Abstract
Natural silk fibers represent one of the most advanced blueprints for (bio)polymer scientists, displaying highly optimized mechanical properties due to their hierarchical structures. Biotechnological production of silk proteins and implementation of advanced processing methods enabled harnessing the potential of these biopolymer not just based on the mechanical properties. In addition to fibers, diverse morphologies can be produced, such as nonwoven meshes, films, hydrogels, foams, capsules and particles. Among them, nanoscale fibrils and fibers are particularly interesting concerning medical and technical applications due to their biocompatibility, environmental and mechanical robustness as well as high surface-to-volume ratio. Therefore, we introduce here self-assembly of silk proteins into hierarchically organized structures such as supramolecular nanofibrils and fabricated materials based thereon. As an alternative to self-assembly, we also present electrospinning a technique to produce nanofibers and nanofibrous mats. Accordingly, we introduce a broad range of silk-based dopes, used in self-assembly and electrospinning: natural silk proteins originating from natural spinning glands, natural silk protein solutions reconstituted from fibers, engineered recombinant silk proteins designed from natural blueprints, genetic fusions of recombinant silk proteins with other structural or functional peptides and moieties, as well as hybrids of recombinant silk proteins chemically conjugated with nonproteinaceous biotic or abiotic molecules. We highlight the advantages but also point out drawbacks of each particular production route. The scope includes studies of the natural self-assembly mechanism during natural silk spinning, production of silk fibrils as new nanostructured non-native scaffolds allowing dynamic morphological switches, as well as studying potential applications. This article is categorized under: Biology-Inspired Nanomaterials > Peptide-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Martin Humenik
- Biomaterials, Faculty of Engineering Science, University of Bayreuth, Bayreuth, Germany
| | - Gregor Lang
- Biomaterials, Faculty of Engineering Science, University of Bayreuth, Bayreuth, Germany
| | - Thomas Scheibel
- Biomaterials, Faculty of Engineering Science, University of Bayreuth, Bayreuth, Germany.,Bayreuth Center for Colloids and Interfaces (BZKG), Research Center Bio-Macromolecules (BIOmac), Bayreuth Center for Molecular Biosciences (BZMB), Bayreuth Center for Material Science (BayMAT), Bavarian Polymer Institute (BPI), Universität Bayreuth, Bayreuth, Germany
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17
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Rocha MS, Storm IM, Bazoni RF, Ramos ÉB, Hernandez-Garcia A, Cohen Stuart MA, Leermakers F, de Vries R. Force and Scale Dependence of the Elasticity of Self-Assembled DNA Bottle Brushes. Macromolecules 2018; 51:204-212. [PMID: 29339838 PMCID: PMC5763285 DOI: 10.1021/acs.macromol.7b01795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 12/13/2017] [Indexed: 11/30/2022]
Abstract
![]()
As a model system
to study the elasticity of bottle-brush polymers,
we here introduce self-assembled DNA bottle brushes, consisting of
a DNA main chain that can be very long and still of precisely defined
length, and precisely monodisperse polypeptide side chains that are
physically bound to the DNA main chains. Polypeptide side chains have
a diblock architecture, where one block is a small archaeal nucleoid
protein Sso7d that strongly binds to DNA. The other block is a net
neutral, hydrophilic random coil polypeptide with a length of exactly
798 amino acids. Light scattering shows that for saturated brushes
the grafting density is one side chain per 5.6 nm of DNA main chain.
According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle
brushes using AFM, we find that the effective persistence of the saturated
DNA bottle brushes is Peff = 95 nm, but
from force–extension curves of single DNA bottle brushes measured
using optical tweezers we find Peff =
15 nm. The latter is equal to the value expected for DNA coated by
the Sso7d binding block alone. The apparent discrepancy between the
two measurements is rationalized in terms of the scale dependence
of the bottle-brush elasticity using theory previously developed to
analyze the scale-dependent electrostatic stiffening of DNA at low
ionic strengths.
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Affiliation(s)
- Márcio Santos Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Ingeborg M Storm
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Raniella Falchetto Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Ésio Bessa Ramos
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Armando Hernandez-Garcia
- Departamento de Química de Biomacromoleculas, Instituto de Química, Universidad Nacional Autónoma de México, México City, México
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Frans Leermakers
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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18
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Zheng T, Perona Martínez F, Storm IM, Rombouts W, Sprakel J, Schirhagl R, de Vries R. Recombinant Protein Polymers for Colloidal Stabilization and Improvement of Cellular Uptake of Diamond Nanosensors. Anal Chem 2017; 89:12812-12820. [PMID: 29111679 DOI: 10.1021/acs.analchem.7b03236] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fluorescent nanodiamonds are gaining increasing attention as fluorescent labels in biology in view of the fact that they are essentially nontoxic, do not bleach, and can be used as nanoscale sensors for various physical and chemical properties. To fully realize the nanosensing potential of nanodiamonds in biological applications, two problems need to be addressed: their limited colloidal stability, especially in the presence of salts, and their limited ability to be taken up by cells. We show that the physical adsorption of a suitably designed recombinant polypeptide can address both the colloidal stability problem and the problem of the limited uptake of nanodiamonds by cells in a very straightforward way, while preserving both their spectroscopic properties and their excellent biocompatibility.
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Affiliation(s)
- Tingting Zheng
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Shenzhen Key Laboratory for Drug Addiction and Medication Safety, Department of Ultrasound, Peking University Shenzhen Hospital & Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center , 518036 Shenzhen, China
| | - Felipe Perona Martínez
- Department of Biomedical Engineering, University Medical Center Groningen, Groningen University , Antonius Deusinglaan 1, 9713 AW Groningen, The Netherlands
| | - Ingeborg Maria Storm
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Wolf Rombouts
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Romana Schirhagl
- Department of Biomedical Engineering, University Medical Center Groningen, Groningen University , Antonius Deusinglaan 1, 9713 AW Groningen, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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19
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Garming MWH, Weppelman IGC, de Boer P, Martínez FP, Schirhagl R, Hoogenboom JP, Moerland RJ. Nanoparticle discrimination based on wavelength and lifetime-multiplexed cathodoluminescence microscopy. NANOSCALE 2017; 9:12727-12734. [PMID: 28829093 DOI: 10.1039/c7nr00927e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nanomaterials can be identified in high-resolution electron microscopy images using spectrally-selective cathodoluminescence. Capabilities for multiplex detection can however be limited, e.g., due to spectral overlap or availability of filters. Also, the available photon flux may be limited due to degradation under electron irradiation. Here, we demonstrate single-pass cathodoluminescence-lifetime based discrimination of different nanoparticles, using a pulsed electron beam. We also show that cathodoluminescence lifetime is a robust parameter even when the nanoparticle cathodoluminescence intensity decays over an order of magnitude. We create lifetime maps, where the lifetime of the cathodoluminescence emission is correlated with the emission intensity and secondary-electron images. The consistency of lifetime-based discrimination is verified by also correlating the emission wavelength and the lifetime of nanoparticles. Our results show how cathodoluminescence lifetime provides an additional channel of information in electron microscopy.
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Affiliation(s)
- Mathijs W H Garming
- Delft University of Technology, Lorentzweg 1, NL-2628CJ Delft, The Netherlands.
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20
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Lima LA, de Vries R, Biswaro LS, Vasconcelos IM, Franco OL, Dias SC. Fusion of plectasin derivative NZ2114 with hydrophilic random coil polypeptide: Recombinant production in Pichia pastoris and antimicrobial activity against clinical strain MRSA. Biopolymers 2017; 110. [PMID: 28608428 DOI: 10.1002/bip.23034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/27/2017] [Accepted: 05/30/2017] [Indexed: 11/06/2022]
Abstract
One of the roadblocks towards the practical use of antimicrobial peptides for medical use is their relatively high cost when synthesized chemically. Effective recombinant production has only been successful in some cases, such as the previously reported production in Pichia pastoris of the antimicrobial plectasin derivative peptide NZ2114. The same production host has also been used extensively to produce so-called protein-polymers: sequences that consist of repetitions of simple amino acid motifs found in structural proteins such as collagen and elastin, and that can be designed to self-assemble in micelles, fibers and hydrogels. With the eventual goal of producing recombinant biomaterials such as antimicrobial protein polymer, we here explore the secreted production in Pichia pastoris of a fusion of NZ2114 with a hydrophilic random coil protein polymer CP4 . The intact NZ2114-CP4 fusion copolymer was produced with a yield of purified protein on the order of 1 g.L-1 supernatant. We find that purified NZ2114-CP4 has an activity against clinical strain MRSA, but very much lower than activity of chemically synthesized NZ2114. We conclude that possibly, the activity of NZ2114 is impaired by the C-terminal attachment to the protein polymer chain, but other reasons for the low activity cannot yet be excluded either. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- L A Lima
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - R de Vries
- Physical Chemistry and Soft Matter, Wageningen University Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - L S Biswaro
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - I M Vasconcelos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - O L Franco
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-Inova, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - S C Dias
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
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21
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Jekhmane S, de Haas R, Paulino da Silva Filho O, van Asbeck AH, Favretto ME, Hernandez Garcia A, Brock R, de Vries R. Virus-Like Particles of mRNA with Artificial Minimal Coat Proteins: Particle Formation, Stability, and Transfection Efficiency. Nucleic Acid Ther 2017; 27:159-167. [DOI: 10.1089/nat.2016.0660] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Shehrazade Jekhmane
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, the Netherlands
| | - Rob de Haas
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, the Netherlands
| | - Omar Paulino da Silva Filho
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Alexander H. van Asbeck
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marco Emanuele Favretto
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, the Netherlands
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22
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Sigar M, Maity N, Mishra S. Enhancing granulocyte colony-stimulating factor expression in Pichia pastoris through fusion with human serum albumin. Prep Biochem Biotechnol 2017; 47:364-370. [DOI: 10.1080/10826068.2016.1252922] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Moolchand Sigar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Nitu Maity
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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23
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Cingil HE, Boz EB, Biondaro G, de Vries R, Cohen Stuart MA, Kraft DJ, van der Schoot P, Sprakel J. Illuminating the Reaction Pathways of Viromimetic Assembly. J Am Chem Soc 2017; 139:4962-4968. [PMID: 28326772 PMCID: PMC5388896 DOI: 10.1021/jacs.7b01401] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
The coassembly of well-defined biological
nanostructures relies
on a delicate balance between attractive and repulsive interactions
between biomolecular building blocks. Viral capsids are a prototypical
example, where coat proteins exhibit not only self-interactions but
also interact with the cargo they encapsulate. In nature, the balance
between antagonistic and synergistic interactions has evolved to avoid
kinetic trapping and polymorphism. To date, it has remained a major challenge to experimentally disentangle
the complex kinetic reaction pathways that underlie successful coassembly
of biomolecular building blocks in a noninvasive approach with high
temporal resolution. Here we show how macromolecular force sensors,
acting as a genome proxy, allow us to probe the pathways through which
a viromimetic protein forms capsids. We uncover the complex multistage
process of capsid assembly, which involves recruitment and complexation,
followed by allosteric growth of the proteinaceous coat. Under certain
conditions, the single-genome particles condense into capsids containing
multiple copies of the template. Finally, we derive a theoretical
model that quantitatively describes the kinetics of recruitment and
growth. These results shed new light on the origins of the pathway
complexity in biomolecular coassembly.
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Affiliation(s)
- Hande E Cingil
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Emre B Boz
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giovanni Biondaro
- Soft Matter Physics, Huygens-Kamerling Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Daniela J Kraft
- Soft Matter Physics, Huygens-Kamerling Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Paul van der Schoot
- Theory of Polymers and Soft Matter, Eindhoven University of Technology , PO Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Theoretical Physics, Utrecht University , Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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24
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Rombouts WH, Domeradzka NE, Werten MWT, Leermakers FAM, de Vries RJ, de Wolf FA, van der Gucht J. Enhanced stiffness of silk-like fibers by loop formation in the corona leads to stronger gels. Biopolymers 2017; 105:795-801. [PMID: 27400673 DOI: 10.1002/bip.22909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/03/2016] [Accepted: 07/06/2016] [Indexed: 11/07/2022]
Abstract
We study the self-assembly of protein polymers consisting of a silk-like block flanked by two hydrophilic blocks, with a cysteine residue attached to the C-terminal end. The silk blocks self-assemble to form fibers while the hydrophilic blocks form a stabilizing corona. Entanglement of the fibers leads to the formation of hydrogels. Under oxidizing conditions the cysteine residues form disulfide bridges, effectively connecting two corona chains at their ends to form a loop. We find that this leads to a significant increase in the elastic modulus of the gels. Using atomic force microscopy, we show that this stiffening is due to an increase of the persistence length of the fibers. Self-consistent-field calculations indicate a slight decrease of the lateral pressure in the corona upon loop formation. We argue that this small decrease in the repulsive interactions affects the stacking of the silk-like blocks in the core, resulting in a more rigid fiber.
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Affiliation(s)
- Wolf H Rombouts
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen, NL-6708 WE, The Netherlands
| | - Natalia E Domeradzka
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen, NL-6708 WE, The Netherlands.,Wageningen UR Food & Biobased Research, Bornse Weilanden 9, Wageningen, NL-6708 WG, The Netherlands
| | - Marc W T Werten
- Wageningen UR Food & Biobased Research, Bornse Weilanden 9, Wageningen, NL-6708 WG, The Netherlands
| | - Frans A M Leermakers
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen, NL-6708 WE, The Netherlands
| | - Renko J de Vries
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen, NL-6708 WE, The Netherlands
| | - Frits A de Wolf
- Wageningen UR Food & Biobased Research, Bornse Weilanden 9, Wageningen, NL-6708 WG, The Netherlands
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen, NL-6708 WE, The Netherlands
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25
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Estrich NA, Hernandez-Garcia A, de Vries R, LaBean TH. Engineered Diblock Polypeptides Improve DNA and Gold Solubility during Molecular Assembly. ACS NANO 2017; 11:831-842. [PMID: 28048935 DOI: 10.1021/acsnano.6b07291] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc.) and significant concentrations of various ions (Mg2+, Na+, Cl-, etc.). Given a desire to assemble diverse inorganic components (metallic nanoparticles, quantum dots, carbon nanostructures, etc.), it will be increasingly difficult to find solution conditions simultaneously compatible with all components. Frequently, the use of chemical surfactants is undesirable, leaving a need for the development of alternative strategies. Herein, we discuss the use of artificial, diblock polypeptides in the role of solution compatibilizing agents for molecular assembly. We describe the use of two distinct diblock polypeptides with affinity for DNA in the stabilization of DNA origami and DNA-functionalized gold nanoparticles (spheres and rods) in solution, protection of DNA from enzymatic degradation, as well as two 3D tetrahedral DNA origamis. We present initial data showing that the diblock polypeptides promote the formation in the solution of desired organic/inorganic assemblies.
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Affiliation(s)
- Nicole A Estrich
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
| | - Armando Hernandez-Garcia
- Simpson Querrey Institute for Bionanotechnology, Northwestern University , Evanston, Illinois 60208, United States
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
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26
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Hernandez-Garcia A, Estrich NA, Werten MWT, Van Der Maarel JRC, LaBean TH, de Wolf FA, Cohen Stuart MA, de Vries R. Precise Coating of a Wide Range of DNA Templates by a Protein Polymer with a DNA Binding Domain. ACS NANO 2017; 11:144-152. [PMID: 27936577 DOI: 10.1021/acsnano.6b05938] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Emerging DNA-based nanotechnologies would benefit from the ability to modulate the properties (e.g., solubility, melting temperature, chemical stability) of diverse DNA templates (single molecules or origami nanostructures) through controlled, self-assembling coatings. We here introduce a DNA coating agent, called C8-BSso7d, which binds to and coats with high specificity and affinity, individual DNA molecules as well as folded origami nanostructures. C8-BSso7d coats and protects without condensing, collapsing or destroying the spatial structure of the underlying DNA template. C8-BSso7d combines the specific nonelectrostatic DNA binding affinity of an archeal-derived DNA binding domain (Sso7d, 7 kDa) with a long hydrophilic random coil polypeptide (C8, 73 kDa), which provides colloidal stability (solubility) through formation of polymer brushes around the DNA templates. C8-BSso7d is produced recombinantly in yeast and has a precise (but engineerable) amino acid sequence of precise length. Using electrophoresis, AFM, and fluorescence microscopy we demonstrate protein coat formation with stiffening of one-dimensional templates (linear dsDNA, supercoiled dsDNA and circular ssDNA), as well as coat formation without any structural distortion or disruption of two-dimensional DNA origami template. Combining the programmability of DNA with the nonperturbing precise coating capability of the engineered protein C8-BSso7d holds promise for future applications such as the creation of DNA-protein hybrid networks, or the efficient transfection of individual DNA nanostructures into cells.
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Affiliation(s)
- Armando Hernandez-Garcia
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nicole A Estrich
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Marc W T Werten
- Wageningen UR Food and Biobased Research, Wageningen University and Research , Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | | | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Frits A de Wolf
- Wageningen UR Food and Biobased Research, Wageningen University and Research , Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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27
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Hernandez-Garcia A, Velders AH, Stuart MAC, de Vries R, van Lent JWM, Wang J. Supramolecular Virus-Like Nanorods by Coassembly of a Triblock Polypeptide and Reversible Coordination Polymers. Chemistry 2016; 23:239-243. [DOI: 10.1002/chem.201603968] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Armando Hernandez-Garcia
- Laboratory of Physical Chemistry and Soft Matter; Wageningen University and Research Centre; Wageningen 6703HB The Netherlands
- Simpson Querrey Institute for BioNanotechnology; Northwestern University; Chicago Illinois 60611-2875 USA
| | - Aldrik H. Velders
- Laboratory of Bionanotechnology; Wageningen University and Research Centre; Wageningen 6703HB The Netherlands
| | - Martien A. Cohen Stuart
- Laboratory of Physical Chemistry and Soft Matter; Wageningen University and Research Centre; Wageningen 6703HB The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter; Wageningen University and Research Centre; Wageningen 6703HB The Netherlands
| | - Jan W. M. van Lent
- Wageningen Electron Microscopy Centre; Wageningen University and Research Centre; Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands
| | - Junyou Wang
- Laboratory of Bionanotechnology; Wageningen University and Research Centre; Wageningen 6703HB The Netherlands
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28
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Domeradzka NE, Werten MWT, de Wolf FA, de Vries R. Cross-Linking and Bundling of Self-Assembled Protein-Based Polymer Fibrils via Heterodimeric Coiled Coils. Biomacromolecules 2016; 17:3893-3901. [DOI: 10.1021/acs.biomac.6b01242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natalia E. Domeradzka
- Wageningen UR
Food and Biobased Research, 6708 WG Wageningen, The Netherlands
- Physical
Chemistry and Soft Matter, Wageningen University Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marc W. T. Werten
- Wageningen UR
Food and Biobased Research, 6708 WG Wageningen, The Netherlands
| | - Frits A. de Wolf
- Wageningen UR
Food and Biobased Research, 6708 WG Wageningen, The Netherlands
| | - Renko de Vries
- Physical
Chemistry and Soft Matter, Wageningen University Stippeneng 4, 6708 WE Wageningen, The Netherlands
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29
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Storm IM, Kornreich M, Voets IK, Beck R, de Vries R, Cohen Stuart MA, Leermakers FAM. Loss of bottlebrush stiffness due to free polymers. SOFT MATTER 2016; 12:8004-8014. [PMID: 27604959 DOI: 10.1039/c6sm01227b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A recently introduced DNA-bottlebrush system, which is formed by the co-assembly of DNA with a genetically engineered cationic polymer-like protein, is subjected to osmotic stress conditions. We measured the inter-DNA distances by X-ray scattering. Our co-assembled DNA-bottlebrush system is one of the few bottlebrushes known to date that shows liquid crystalline behaviour. The alignment of the DNA bottlebrushes was expected to increase with imposed pressure, but interestingly this did not always happen. Molecularly detailed self-consistent field calculations targeted to complement the experiments, focused on the role of molecular crowding on the induced persistence length lp due to the side chains and the cross-sectional width D of the molecular bottlebrushes. Both the thickness as well as the backbone persistence length drop with increasing protein-polymer bulk concentrations and dramatic effects are found above the overlap threshold. The flexibilisation is more significant and therefore the bottlebrush aspect ratio, lp/D, decreases with protein-polymer concentration. This loss in aspect ratio is yet another argument why molecular bottlebrushes rarely order in anisotropic phases and may explain why bottlebrushes are excellent lubricants.
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Affiliation(s)
- Ingeborg M Storm
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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30
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Domeradzka NE, Werten MWT, de Vries R, de Wolf FA. Production in Pichia pastoris of complementary protein-based polymers with heterodimer-forming WW and PPxY domains. Microb Cell Fact 2016; 15:105. [PMID: 27286861 PMCID: PMC4902918 DOI: 10.1186/s12934-016-0498-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/31/2016] [Indexed: 01/30/2023] Open
Abstract
Background Specific coupling of de novo designed recombinant protein polymers for the construction of precisely structured nanomaterials is of interest for applications in biomedicine, pharmaceutics and diagnostics. An attractive coupling strategy is to incorporate specifically interacting peptides into the genetic design of the protein polymers. An example of such interaction is the binding of particular proline-rich ligands by so-called WW-domains. In this study, we investigated whether these domains can be produced in the yeast Pichia pastoris as part of otherwise non-interacting protein polymers, and whether they bring about polymer coupling upon mixing. Results We constructed two variants of a highly hydrophilic protein-based polymer that differ only in their C-terminal extensions. One carries a C-terminal WW domain, and the other a C-terminal proline-rich ligand (PPxY). Both polymers were produced in P.pastoris with a purified protein yield of more than 2 g L−1 of cell-free broth. The proline-rich module was found to be O-glycosylated, and uncommonly a large portion of the attached oligosaccharides was phosphorylated. Glycosylation was overcome by introducing a Ser → Ala mutation in the PPxY peptide. Tryptophan fluorescence monitored during titration of the polymer containing the WW domain with either the glycosylated or nonglycosylated PPxY-containing polymer revealed binding. The complementary polymers associated with a Kd of ~3 µM, regardless of glycosylation state of the PPxY domain. Binding was confirmed by isothermal titration calorimetry, with a Kd of ~9 µM. Conclusions This article presents a blueprint for the production in P. pastoris of protein polymers that can be coupled using the noncovalent interaction between WW domains and proline-rich ligands. The availability of this highly specific coupling tool will hereafter allow us to construct various supramolecular structures and biomaterials. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0498-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia E Domeradzka
- Wageningen UR Food and Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands.,Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Marc W T Werten
- Wageningen UR Food and Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands.
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Frits A de Wolf
- Wageningen UR Food and Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
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31
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Beun LH, Albertazzi L, van der Zwaag D, de Vries R, Cohen Stuart MA. Unidirectional Living Growth of Self-Assembled Protein Nanofibrils Revealed by Super-resolution Microscopy. ACS NANO 2016; 10:4973-4980. [PMID: 27124596 DOI: 10.1021/acsnano.6b01017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein-based nanofibrils are emerging as a promising class of materials that provide unique properties for applications such as biomedical and food engineering. Here, we use atomic force microscopy and stochastic optical reconstruction microscopy imaging to elucidate the growth dynamics, exchange kinetics, and polymerization mechanism for fibrils composed of a de novo designed recombinant triblock protein polymer. This macromolecule features a silk-inspired self-assembling central block composed of GAGAGAGH repeats, which are known to fold into a β roll with turns at each histidine and, once folded, to stack, forming a long, ribbon-like structure. We find several properties that allow the growth of patterned protein nanofibrils: the self-assembly takes place on only one side of the growing fibrils by the essentially irreversible addition of protein polymer subunits, and these fibril ends remain reactive indefinitely in the absence of monomer ("living ends"). Exploiting these characteristics, we can grow stable diblock protein nanofibrils by the sequential addition of differently labeled proteins. We establish control over the block length ratio by simply varying monomer feed conditions. Our results demonstrate the use of engineered protein polymers in creating precisely patterned protein nanofibrils and open perspectives for the hierarchical self-assembly of functional biomaterials.
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Affiliation(s)
- Lennart H Beun
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University , Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Lorenzo Albertazzi
- Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Bioengineering of Catalonia Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Daan van der Zwaag
- Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University , Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University , Dreijenplein 6, 6703 HB Wageningen, The Netherlands
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32
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Soleimani M, Mirmohammad-Sadeghi H, Sadeghi-Aliabadi H, Jahanian-Najafabadi A. Expression and purification of toxic anti-breast cancer p28-NRC chimeric protein. Adv Biomed Res 2016; 5:70. [PMID: 27169101 PMCID: PMC4854029 DOI: 10.4103/2277-9175.180639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/25/2015] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Chimeric proteins consisting of a targeting moiety and a cytotoxic moiety are now under intense research focus for targeted therapy of cancer. Here, we report cloning, expression, and purification of such a targeted chimeric protein made up of p28 peptide as both targeting and anticancer moiety fused to NRC peptide as a cytotoxic moiety. However, since the antimicrobial activity of the NRC peptide would intervene expression of the chimeric protein in Escherichia coli, we evaluated the effects of two fusion tags, that is, thioredoxin (Trx) and 6x-His tags, and various expression conditions, on the expression of p28-NRC chimeric protein. MATERIALS AND METHODS In order to express the chimeric protein with only 6x-His tag, pET28 expression plasmid was used. Cloning in pET32 expression plasmid was performed to add both Trx and 6x-His tags to the chimeric protein. Expression of the chimeric protein with both plasmids was evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis following optimization of expression conditions and host strains. RESULTS Expression of the chimeric protein in pET28a was performed. However, expression yield of the chimeric protein was low. Optimization of culture conditions and host strains led to reasonable expression yield of the toxic chimeric protein in pET32a vector. In cases of both plasmids, approximately 10 kDa deviation of the apparent molecular weight from the theoretical one was seen in SDS-PAGE of purified chimeric proteins. CONCLUSIONS The study leads to proper expression and purification yield of p28-NRC chimeric protein with Trx tag following optimizing culture conditions and host strains.
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Affiliation(s)
- Meysam Soleimani
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Hojjat Sadeghi-Aliabadi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
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33
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Patra S, Basak P, Tibarewala D. Synthesis of gelatin nano/submicron particles by binary nonsolvent aided coacervation (BNAC) method. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 59:310-318. [DOI: 10.1016/j.msec.2015.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/18/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
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34
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Pham TTH, Snijkers F, Storm IM, de Wolf FA, Cohen Stuart MA, van der Gucht J. Physical and mechanical properties of thermosensitive xanthan/collagen-inspired protein composite hydrogels. INT J POLYM MATER PO 2015. [DOI: 10.1080/00914037.2015.1074904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Setina CM, Haase JP, Glatz CE. Process integration for recovery of recombinant collagen type I α1 from corn seed. Biotechnol Prog 2015; 32:98-107. [DOI: 10.1002/btpr.2191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/07/2015] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Charles E. Glatz
- Dept. of Chemical and Biological Engineering; Iowa State University; 2114 Sweeney Hall Ames IA 50011
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36
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Domeradzka NE, Werten MWT, de Vries R, de Wolf FA. Production in Pichia pastoris of protein-based polymers with small heterodimer-forming blocks. Biotechnol Bioeng 2015; 113:953-60. [PMID: 26479855 DOI: 10.1002/bit.25861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/27/2015] [Accepted: 10/12/2015] [Indexed: 11/11/2022]
Abstract
Some combinations of leucine zipper peptides are capable of forming α-helical heterodimeric coiled coils with very high affinity. These can be used as physical cross-linkers in the design of protein-based polymers that form supramolecular structures, for example hydrogels, upon mixing solutions containing the complementary blocks. Such two-component physical networks are of interest for many applications in biomedicine, pharmaceutics, and diagnostics. This article describes the efficient secretory production of A and B type leucine zipper peptides fused to protein-based polymers in Pichia pastoris. By adjusting the fermentation conditions, we were able to significantly reduce undesirable proteolytic degradation. The formation of A-B heterodimers in mixtures of the purified products was confirmed by size exclusion chromatography. Our results demonstrate that protein-based polymers incorporating functional heterodimer-forming blocks can be produced with P. pastoris in sufficient quantities for use in future supramolecular self-assembly studies and in various applications.
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Affiliation(s)
- Natalia E Domeradzka
- Wageningen UR Food & Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands.,Physical Chemistry and Soft Matter, Wageningen University and Research Centre, Dreijenplein 6, 6703 HB, Wageningen, The Netherlands
| | - Marc W T Werten
- Wageningen UR Food & Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands.
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University and Research Centre, Dreijenplein 6, 6703 HB, Wageningen, The Netherlands
| | - Frits A de Wolf
- Wageningen UR Food & Biobased Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
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37
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Parvizi M, Plantinga JA, van Speuwel-Goossens CA, van Dongen EM, Kluijtmans SG, Harmsen MC. Development of recombinant collagen-peptide-based vehicles for delivery of adipose-derived stromal cells. J Biomed Mater Res A 2015; 104:503-16. [DOI: 10.1002/jbm.a.35588] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/05/2015] [Accepted: 10/12/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Mojtaba Parvizi
- Department of Pathology and Medical Biology; University of Groningen, University Medical Center Groningen; Groningen The Netherlands
| | - Josée A. Plantinga
- Department of Pathology and Medical Biology; University of Groningen, University Medical Center Groningen; Groningen The Netherlands
| | | | | | | | - Martin C. Harmsen
- Department of Pathology and Medical Biology; University of Groningen, University Medical Center Groningen; Groningen The Netherlands
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38
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Maity N, Thawani A, Sharma A, Gautam A, Mishra S, Sahai V. Expression and Control of Codon-Optimized Granulocyte Colony-Stimulating Factor in Pichia pastoris. Appl Biochem Biotechnol 2015; 178:159-72. [PMID: 26410223 DOI: 10.1007/s12010-015-1865-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/15/2015] [Indexed: 11/25/2022]
Abstract
Granulocyte colony-stimulating factor (GCSF) has therapeutic applications due to its proven efficacy in different forms of neutropenia and chemotherapy-induced leucopenia. The original 564-bp nucleotide sequence from NCBI was codon optimized and assembled by overlapping PCR method comprising of 16 oligos of 50-nt length with 15 base overhang. The synthetic gene (CO-GCSF) was cloned under glucose utilizing glyceraldehyde 3-phosphate dehydrogenase (GAP) and methanol-utilizing alcohol oxidase (AOX1) promoters and expressed in Pichia pastoris SMD1168 strain. Constitutive expression under GAP resulted in cellular toxicity while AOX1 promoter controlled expression was stable. Variation in the levels of expression was observed among the transformant colonies with transformant #2 secreting up to ∼4 mg/L of GCSF. The molecular mass of the expressed GCSF in P. pastoris was ∼19.0 kDa. Quatitation of the expressed protein was carried out by a highly reproducible gel densitometric method. Effect of several operational and nutritional conditions was studied on GCSF production and the results suggest a general approach for increasing the yield of GCSF several folds (2- to 5-fold) over the standard conditions employed currently. Cultivation of the single-copy integrant in the chemically defined medium in a 5-L fermenter resulted in a volumetric productivity of ∼0.7 mg/L/h at the end of the induction phase, which was about 4-fold higher than attained in the shake flask.
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Affiliation(s)
- Nitu Maity
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Ankita Thawani
- Lilly Hall of Biological Sciences, Purdue University - West Lafayette, Indiana, USA
| | - Anshul Sharma
- Biochemical Engineering Department, University College London, London, UK
| | - Ashwani Gautam
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Vikram Sahai
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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39
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Rombouts WH, de Kort DW, Pham TTH, van Mierlo CPM, Werten MWT, de Wolf FA, van der Gucht J. Reversible Temperature-Switching of Hydrogel Stiffness of Coassembled, Silk-Collagen-Like Hydrogels. Biomacromolecules 2015; 16:2506-13. [DOI: 10.1021/acs.biomac.5b00766] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wolf H. Rombouts
- Physical
Chemistry and Soft Matter, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
| | - Daan W. de Kort
- TI-COAST, Science Park 904, NL-1098 XH Amsterdam, The Netherlands
| | - Thao T. H. Pham
- Physical
Chemistry and Soft Matter, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
| | | | - Marc W. T. Werten
- Wageningen
UR Food
and Biobased Research, Bornse Weilanden
9, NL-6708 WG Wageningen, The Netherlands
| | - Frits A. de Wolf
- Wageningen
UR Food
and Biobased Research, Bornse Weilanden
9, NL-6708 WG Wageningen, The Netherlands
| | - Jasper van der Gucht
- Physical
Chemistry and Soft Matter, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
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40
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Hernandez-Garcia A, Kraft DJ, Janssen AFJ, Bomans PHH, Sommerdijk NAJM, Thies-Weesie DME, Favretto ME, Brock R, de Wolf FA, Werten MWT, van der Schoot P, Stuart MC, de Vries R. Design and self-assembly of simple coat proteins for artificial viruses. NATURE NANOTECHNOLOGY 2014; 9:698-702. [PMID: 25150720 DOI: 10.1038/nnano.2014.169] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 07/17/2014] [Indexed: 06/03/2023]
Abstract
Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing artificial life. Moreover, they are used in biomedical and biotechnological applications, such as targeted delivery of nucleic acids for gene therapy and as scaffolds in material science. In a natural setting, survival of viruses requires that a significant fraction of the replicated genomes be completely protected by coat proteins. Complete protection of the genome is ensured by a highly cooperative supramolecular process between the coat proteins and the nucleic acids, which is based on reversible, weak and allosteric interactions only. However, incorporating this type of supramolecular cooperativity into artificial viruses remains challenging. Here, we report a rational design for a self-assembling minimal viral coat protein based on simple polypeptide domains. Our coat protein features precise control over the cooperativity of its self-assembly with single DNA molecules to finally form rod-shaped virus-like particles. We confirm the validity of our design principles by showing that the kinetics of self-assembly of our virus-like particles follows a previous model developed for tobacco mosaic virus. We show that our virus-like particles protect DNA against enzymatic degradation and transfect cells with considerable efficiency, making them promising delivery vehicles.
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Affiliation(s)
- Armando Hernandez-Garcia
- 1] Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands [2] Dutch Polymer Institute, John F. Kennedylaan 2, 5612 AB Eindhoven, The Netherlands [3]
| | - Daniela J Kraft
- 1] Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands [2] Center for Soft Matter Research, Department of Physics, New York University, 4 Washington Place, New York, New York 10003, USA
| | - Anne F J Janssen
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Paul H H Bomans
- Laboratory of Materials and Interface Chemistry &Soft Matter CryoTEM Research Unit, Department of Chemical Engineering and Chemistry, and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Nico A J M Sommerdijk
- Laboratory of Materials and Interface Chemistry &Soft Matter CryoTEM Research Unit, Department of Chemical Engineering and Chemistry, and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Dominique M E Thies-Weesie
- Utrecht University, Van't Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute of Nanomaterials Science, PO Box 80.051, 3508 TB Utrecht, The Netherlands
| | - Marco E Favretto
- 1] Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands [2] Dutch Polymer Institute, John F. Kennedylaan 2, 5612 AB Eindhoven, The Netherlands
| | - Roland Brock
- Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Frits A de Wolf
- Wageningen UR Food &Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Marc W T Werten
- Wageningen UR Food &Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Paul van der Schoot
- 1] Theory of Polymers and Soft Matter, Department of Applied Physics, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands [2] Institute for Theoretical Physics, Utrecht University, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Martien Cohen Stuart
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Renko de Vries
- 1] Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands [2] Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, PO Box 196, 9700 AD Groningen, The Netherlands
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41
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Beun LH, Storm IM, Werten MWT, de Wolf FA, Cohen Stuart MA, de Vries R. From micelles to fibers: balancing self-assembling and random coiling domains in pH-responsive silk-collagen-like protein-based polymers. Biomacromolecules 2014; 15:3349-57. [PMID: 25133990 PMCID: PMC4260859 DOI: 10.1021/bm500826y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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We
study the self-assembly of genetically engineered protein-based
triblock copolymers consisting of a central pH-responsive silk-like
middle block (SHn, where SH is a silk-like octapeptide, (GA)3GH and n is the number of repeats) flanked by hydrophilic random
coil outer blocks (C2). Our previous work has already shown
that triblocks with very long midblocks (n = 48)
self-assemble into long, stiff protein filaments at pH values where
the middle blocks are uncharged. Here we investigate the self-assembly
behavior of the triblock copolymers for a range of midblock lengths,
n = 8, 16, 24, 48. Upon charge neutralization of SHn by adjusting the pH, we find that C2SH8C2 and C2SH16C2 form spherical micelles, whereas both C2SH24C2 and C2SH48C2 form protein filaments with a characteristic
beta-roll secondary structure of the silk midblocks. Hydrogels formed
by C2SH48C2 are much stronger
and form much faster than those formed by C2SH24C2. Enzymatic digestion of much of the hydrophilic
outer blocks is used to show that with much of the hydrophilic outer
blocks removed, all silk-midblocks are capable of self-assembling
into stiff protein filaments. In that case, reduction of the steric
repulsion by the hydrophilic outer blocks also leads to extensive
fiber bundling. Our results highlight the opposing roles of the hydrophilic
outer blocks and central silk-like midblocks in driving protein filament
formation. They provide crucial information for future designs of
triblock protein-based polymers that form stiff filaments with controlled
bundling, that could mimick properties of collagen in the extracellular
matrix.
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Affiliation(s)
- Lennart H Beun
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University , Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
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42
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Włodarczyk-Biegun MK, Werten MW, de Wolf FA, van den Beucken JJ, Leeuwenburgh SC, Kamperman M, Cohen Stuart MA. Genetically engineered silk-collagen-like copolymer for biomedical applications: production, characterization and evaluation of cellular response. Acta Biomater 2014; 10:3620-9. [PMID: 24814883 DOI: 10.1016/j.actbio.2014.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/24/2014] [Accepted: 05/02/2014] [Indexed: 12/25/2022]
Abstract
Genetically engineered protein polymers (GEPP) are a class of multifunctional materials with precisely controlled molecular structure and property profile. Representing a promising alternative for currently used materials in biomedical applications, GEPP offer multiple benefits over natural and chemically synthesized polymers. However, producing them in sufficient quantities for preclinical research remains challenging. Here, we present results from an in vitro cellular response study of a recombinant protein polymer that is soluble at low pH but self-organizes into supramolecular fibers and physical hydrogels at neutral pH. It has a triblock structure denoted as C2S(H)48C2, which consists of hydrophilic collagen-inspired and histidine-rich silk-inspired blocks. The protein was successfully produced by the yeast Pichia pastoris in laboratory-scale bioreactors, and it was purified by selective precipitation. This efficient and inexpensive production method provided material of sufficient quantities, purity and sterility for cell culture study. Rheology and erosion studies showed that it forms hydrogels exhibiting long-term stability, self-healing behavior and tunable mechanical properties. Primary rat bone marrow cells cultured in direct contact with these hydrogels remained fully viable; however, proliferation and mineralization were relatively low compared to collagen hydrogel controls, probably because of the absence of cell-adhesive motifs. As biofunctional factors can be readily incorporated to improve material performance, our approach provides a promising route towards biomedical applications.
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43
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Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing. PLoS Comput Biol 2014; 10:e1003532. [PMID: 24722239 PMCID: PMC3983058 DOI: 10.1371/journal.pcbi.1003532] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/05/2014] [Indexed: 02/06/2023] Open
Abstract
Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain (CasSD) of p130Cas (or BCAR1) has eluded an experimentally validated structural understanding. Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility, sensing force at the leading edge of cell migration. Circular dichroism shows CasSD is intrinsically disordered with dominant polyproline type II conformations. Strongly conserved in placental mammals, the proline-rich sequence exhibits a pseudo-repeat unit with variation hotspots 2–9 residues before substrate tyrosine residues. Atomic-force microscopy pulling experiments show CasSD requires minimal extension force and exhibits infrequent, random regions of weak stability. Proteolysis, light scattering and ultracentrifugation results show that a monomeric intrinsically disordered form persists for CasSD in solution with an expanded hydrodynamic radius. All-atom 3D conformer sampling with the TraDES package yields ensembles in agreement with experiment when coil-biased sampling is used, matching the experimental radius of gyration. Increasing β-sampling propensities increases the number of prolate conformers. Combining the results, we conclude that CasSD has no stable compact structure and is unlikely to efficiently autoinhibit phosphorylation. Taking into consideration the structural propensity of CasSD and the fact that it is known to bind to LIM domains, we propose a model of how CasSD and LIM domain family of transcription factor proteins may function together to regulate phosphorylation of CasSD and effect machanosensing. Mechanical stretching of cells causes the substrate domain of p130Cas (CasSD) to be phosphorylated on 15 tyrosine residues embedded along its length. CasSD is rich in proline and surprisingly well conserved in placental mammals. Stretching of CasSD by atomic force microscopy has identified that it requires far less force than normal folded proteins. Classical biophysical analyses have determined that CasSD is a typical intrinsically disordered protein, a difficult-to-study group of molecules covering about 30% of human proteins. The average size of CasSD is larger and elongated than folded globular proteins but smaller than chemically denatured proteins. We have simulated a large number of all-atom protein structures using a fast all-atom sampling method. The result is in good agreement with the experimental observation. As it is already known that stretching somehow exposes the tyrosine residues to phosphorylation, a mechanism is proposed where straightening of the p130Cas substrate domain backbone conformation through mechanical stretching can lead to dissociation of p130Cas-binding LIM domain proteins and exposure of CasSD tyrosine residues for phosphorylation. This study has led to a new model of a protein-based mechanism of force sensing at the leading edge of cells that allows the cells to feel their way as they move.
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44
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Charbonneau C, Kleijn JM, Cohen Stuart MA. Subtle charge balance controls surface-nucleated self-assembly of designed biopolymers. ACS NANO 2014; 8:2328-2335. [PMID: 24571369 DOI: 10.1021/nn405799t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report the surface-nucleated self-assembly into fibrils of a biosynthetic amino acid polymer synthesized by the yeast Pichia pastoris. This polymer has a block-like architecture, with a central silk-like block labeled SH, responsible for the self-assembly into fibrils, and two collagen-like random coil end blocks (C) that colloidally stabilize the fibers in aqueous solution. The silk-like block contains histidine residues (pKa≈6) that are positively charged in the low pH region, which hinders self-assembly. In aqueous solution, CSHC self-assembles into fibers above a pH-dependent critical nucleation concentration Ccb. Below Ccb, where no self-assembly occurs in solution, fibril formation can be induced by a negatively charged surface (silica) in the pH range of 3.5-7. The density of the fibers at the surface and their length are controlled by a subtle balance in charge between the protein polymer and the silica surface, which is evidenced from the dependence on pH. With increasing number density of the fibers at the surface, their average length decreases. The results can be explained on the basis of a nucleation-and-growth mechanism: the surface density of fibers depends on the rate of nucleation, while their growth rate is limited by transport of proteins from solution. Screening of the charges on the surface and histidine units by adding NaCl influences the nucleation-and-growth process in a complicated fashion: at low pH, the growth is improved, while at high pH, the nucleation is limited. Under conditions where nucleation in the bulk solution is not possible, growth of the surface-nucleated fibers into the solution--away from the surface--can still occur.
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Affiliation(s)
- Céline Charbonneau
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University , Dreijenplein 6, 6703 HB Wageningen, The Netherlands
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45
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Rombouts WH, Giesbers M, van Lent J, de Wolf FA, van der Gucht J. Synergistic Stiffening in Double-Fiber Networks. Biomacromolecules 2014; 15:1233-9. [DOI: 10.1021/bm401810w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Wolf H. Rombouts
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
| | - Marcel Giesbers
- Wageningen
Electron Microscopy Centre, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Jan van Lent
- Wageningen
Electron Microscopy Centre, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Frits A. de Wolf
- Wageningen UR Food & Biobased Research, Bornse Weilanden 9, NL-6708 WG Wageningen, The Netherlands
| | - Jasper van der Gucht
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
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46
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Golinska MD, Włodarczyk-Biegun MK, Werten MWT, Stuart MAC, de Wolf FA, de Vries R. Dilute Self-Healing Hydrogels of Silk-Collagen-Like Block Copolypeptides at Neutral pH. Biomacromolecules 2014; 15:699-706. [DOI: 10.1021/bm401682n] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monika D. Golinska
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
| | - Małgorzata K. Włodarczyk-Biegun
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
| | - Marc W. T. Werten
- Wageningen
UR
Food and Biobased Research, Bornse
Weilanden 9, NL-6708 WG Wageningen, The Netherlands
| | - Martien A. Cohen Stuart
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
| | - Frits A. de Wolf
- Wageningen
UR
Food and Biobased Research, Bornse
Weilanden 9, NL-6708 WG Wageningen, The Netherlands
| | - Renko de Vries
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The Netherlands
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47
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Cherdkiatikul T, Suwanwong Y. Production of the α and β Subunits of Spirulina Allophycocyanin and C-Phycocyanin in Escherichia coli : A Comparative Study of Their Antioxidant Activities. ACTA ACUST UNITED AC 2014; 19:959-65. [PMID: 24464435 DOI: 10.1177/1087057113520565] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/28/2013] [Indexed: 12/31/2022]
Abstract
Allophycocyanin and c-phycocyanin have been reported to be potent antioxidants. In this work, the genes encoding the apo-proteins of allophycocyanin α (ApcA), allophycocyanin β (ApcB), c-phycocyanin α (CpcA), and c-phycocyanin β (CpcB) from Spirulina platensis were cloned, and the recombinant proteins were produced in Escherichia coli to study their antioxidant effects. All four recombinant phycocyanins could be produced in the soluble form and purified to more than 97% purity. The results of radical scavenging assays showed that the Trolox equivalent values for peroxyl radical scavenging by the ApcA, ApcB, CpcA, and CpcB proteins were 1.81 ± 0.2 µM, 1.98 ± 0.22 µM, 0.95 ± 0.15 µM, and 1.49 ± 0.15 µM, respectively. The IC50 values for hydroxyl radical scavenging of ApcA, ApcB, CpcA, CpcB, and Trolox were 269 ± 9 µg/mL, 190 ± 5 µg/mL, 129 ± 8 µg/mL, 108 ± 4 µg/mL, and 195 ± 12 µg/mL, respectively. These results indicated that allophycocyanin exhibited higher activity than c-phycocyanin in scavenging peroxyl radicals, whereas c-phycocyanin exhibited higher activity than allophycocyanin in scavenging hydroxyl radicals. All of the apo-phycocyanin subunits possessed strong antioxidant activities and can be further developed and applied to the food and drug industries. However, the selection of the most useful antioxidant should depend on the type of targeted free radical to obtain the highest efficiency.
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Affiliation(s)
- Thiti Cherdkiatikul
- Graduate Program of Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Yaneenart Suwanwong
- Center for Research and Development in Molecular Hematology Sciences, Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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48
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Xiong GM, Yuan S, Tan CK, Wang JK, Liu Y, Yang Tan TT, Tan NS, Choong C. Endothelial cell thrombogenicity is reduced by ATRP-mediated grafting of gelatin onto PCL surfaces. J Mater Chem B 2014; 2:485-493. [DOI: 10.1039/c3tb20760a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Zhang C, Hernandez-Garcia A, Jiang K, Gong Z, Guttula D, Ng SY, Malar PP, van Kan JA, Dai L, Doyle PS, de Vries R, van der Maarel JRC. Amplified stretch of bottlebrush-coated DNA in nanofluidic channels. Nucleic Acids Res 2013; 41:e189. [PMID: 24003032 PMCID: PMC3814371 DOI: 10.1093/nar/gkt783] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/05/2013] [Accepted: 08/09/2013] [Indexed: 01/22/2023] Open
Abstract
The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.
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Affiliation(s)
- Ce Zhang
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Armando Hernandez-Garcia
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kai Jiang
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zongying Gong
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Durgarao Guttula
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Siow Yee Ng
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Piravi P. Malar
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jeroen A. van Kan
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liang Dai
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Patrick S. Doyle
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Renko de Vries
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Johan R. C. van der Maarel
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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50
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Golinska MD, Pham TTH, Werten MWT, de Wolf FA, Cohen Stuart MA, van der Gucht J. Fibril Formation by pH and Temperature Responsive Silk-Elastin Block Copolymers. Biomacromolecules 2012; 14:48-55. [DOI: 10.1021/bm3011775] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monika D. Golinska
- Laboratory
of Physical
Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The
Netherlands
| | - Thao T. H. Pham
- Laboratory
of Physical
Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The
Netherlands
- Foundation FOM, Van Vollenhovenlaan 659,
NL-3527 JP Utrecht, The Netherlands
| | - Marc W. T. Werten
- Wageningen UR Food and Biobased Research, Bornse Weilanden 9, NL-6708 WG
Wageningen, The Netherlands
| | - Frits A. de Wolf
- Wageningen UR Food and Biobased Research, Bornse Weilanden 9, NL-6708 WG
Wageningen, The Netherlands
| | - Martien A. Cohen Stuart
- Laboratory
of Physical
Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The
Netherlands
| | - Jasper van der Gucht
- Laboratory
of Physical
Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, NL-6703 HB Wageningen, The
Netherlands
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