1
|
Miller LM, Draper BE, Wang JCY, Jarrold MF. Charge Detection Mass Spectrometry Reveals Favored Structures in the Assembly of Virus-Like Particles: Polymorphism in Norovirus GI.1. Anal Chem 2024. [PMID: 39074122 DOI: 10.1021/acs.analchem.4c01913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The main capsid protein (CP) of norovirus, the leading cause of gastroenteritis, is expected to self-assemble into virus-like particles with the same structure as the wild-type virus, a capsid with 180 CPs in a T = 3 icosahedron. Using charge detection mass spectrometry (CD-MS), we find that the norovirus GI.1 variant is structurally promiscuous, forming a wide variety of well-defined structures, some that are icosahedral capsids and others that are not. The structures that are present evolve with time and vary with solution conditions. The presence of icosahedral T = 3 and T = 4 capsids (240 CPs) under some conditions was confirmed by cryo-electron microscopy (cryo-EM). The cryo-EM studies also confirmed the presence of an unexpected prolate geometry based on an elongated T = 4 capsid with 300 CPs. In addition, CD-MS measurements indicate the presence of well-defined peaks with masses corresponding to 420, 480, 600, and 700 CPs. The peak corresponding to 420 CPs is probably due to an icosahedral T = 7 capsid, but this could not be confirmed by cryo-EM. It is possible that the T = 7 particles are too fragile to survive vitrification. There are no mass peaks associated with the T = 9 and T = 12 icosahedra with 540 and 720 CPs. The larger structures with 480, 600, and 700 CPs are not icosahedral; however, their measured charges suggest that they are hollow shells. The use of CD-MS to monitor virus-like particles assembly may have important applications in vaccine development and quality control.
Collapse
Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions Inc, 3750 E Bluebird Ln, Bloomington, Indiana 47401, United States
| | - Joseph C-Y Wang
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
2
|
Herpoldt KL, López CL, Sappington I, Pham MN, Srinivasan S, Netland J, Montgomery KS, Roy D, Prossnitz AN, Ellis D, Wargacki AJ, Pepper M, Convertine AJ, Stayton PS, King NP. Macromolecular Cargo Encapsulation via In Vitro Assembly of Two-Component Protein Nanoparticles. Adv Healthc Mater 2024; 13:e2303910. [PMID: 38180445 DOI: 10.1002/adhm.202303910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/19/2023] [Indexed: 01/06/2024]
Abstract
Self-assembling protein nanoparticles are a promising class of materials for targeted drug delivery. Here, the use of a computationally designed, two-component, icosahedral protein nanoparticle is reported to encapsulate multiple macromolecular cargoes via simple and controlled self-assembly in vitro. Single-stranded RNA molecules between 200 and 2500 nucleotides in length are encapsulated and protected from enzymatic degradation for up to a month with length-dependent decay rates. Immunogenicity studies of nanoparticles packaging synthetic polymers carrying a small-molecule TLR7/8 agonist show that co-delivery of antigen and adjuvant results in a more than 20-fold increase in humoral immune responses while minimizing systemic cytokine secretion associated with free adjuvant. Coupled with the precise control over nanoparticle structure offered by computational design, robust and versatile encapsulation via in vitro assembly opens the door to a new generation of cargo-loaded protein nanoparticles that can combine the therapeutic effects of multiple drug classes.
Collapse
Affiliation(s)
- Karla-Luise Herpoldt
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ciana L López
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Isaac Sappington
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Selvi Srinivasan
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Jason Netland
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
| | | | - Debashish Roy
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | | | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Adam J Wargacki
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
| | | | - Patrick S Stayton
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
3
|
Su Y, Liu B, Huang Z, Teng Z, Yang L, Zhu J, Huo S, Liu A. Virus-like particles nanoreactors: from catalysis towards bio-applications. J Mater Chem B 2023; 11:9084-9098. [PMID: 37697810 DOI: 10.1039/d3tb01112g] [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: 09/13/2023]
Abstract
Virus-like particles (VLPs) are self-assembled supramolecular structures found in nature, often used for compartmentalization. Exploiting their inherent properties, including precise nanoscale structures, monodispersity, and high stability, these architectures have been widely used as nanocarriers to protect or enrich catalysts, facilitating catalytic reactions and avoiding interference from the bulk solutions. In this review, we summarize the current progress of virus-like particles (VLPs)-based nanoreactors. First, we briefly introduce the physicochemical properties of the most commonly used virus particles to understand their roles in catalytic reactions beyond the confined space. Next, we summarize the self-assembly of nanoreactors forming higher-order hierarchical structures, highlighting the emerging field of nanoreactors as artificial organelles and their potential biomedical applications. Finally, we discuss the current findings and future perspectives of VLPs-based nanoreactors.
Collapse
Affiliation(s)
- Yuqing Su
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Beibei Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zhenkun Huang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zihao Teng
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jie Zhu
- National-Local Joint Engineering Research and High-Quality Utilization, Changzhou University, Changzhou 213164, China
| | - Shuaidong Huo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Aijie Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| |
Collapse
|
4
|
Beyrampour-Basmenj H, Pourhassan-Moghamddam M, Nakhjavani SA, Faraji N, Alivand M, Zarghami N, Talebi M, Rahmati M, Ebrahimi-Kalan A. Sensitive and convenient detection of miRNA-145 using a gold nanoparticle-HCR coupled system: computational and in vitro validations. IEEE Trans Nanobioscience 2022; PP:155-162. [PMID: 35533171 DOI: 10.1109/tnb.2022.3170530] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Multiple sclerosis (MS) remains a challenging disease that requires timely diagnosis. Therefore, an ultrasensitive optical biosensor based on hybridization chain reaction (HCR) was developed to detect microRNA-145 (miRNA-145) as an MS biomarker. To construct such a sensor, HCR occurred between specific hairpin probes, as MB1 contains a poly-cytosine nucleotide loop and MB2 has a poly-guanine nucleotide sticky end. By introducing miR-145 as a target sequence, long-range dsDNA polymers are formed. Then, positively charged gold nanoparticles (AuNPs) were incubated with the HCR product, which adsorbed onto the dsDNA polymers due to electrostatic adsorption. This resulted in the precipitation of the AuNPs. By incubating different concentrations of miR-145 with AuNPs, the changes in the UV-vis spectrum of the supernatant were analyzed. The proposed biosensor showed a great ability to detect miR-145 in a wide linear range from 1 pM-1 nM with an excellent detection limit (LOD) of 0.519 nM. Furthermore, the developed biosensor indicated considerable selectivity in discriminating between miR-145 and mismatched sequences. It shows high selectivity in differentiating targets. Interestingly, the proposed method was also able to detect miRNA-145 in the diluted serum samples. In conclusion, this sensing platform exhibits high selectivity and specificity for the detection of circulating microRNAs, which holds great promise for translation to routine clinical applications.
Collapse
|
5
|
Liu Q, Shaukat A, Kyllönen D, Kostiainen MA. Polyelectrolyte Encapsulation and Confinement within Protein Cage-Inspired Nanocompartments. Pharmaceutics 2021; 13:1551. [PMID: 34683843 PMCID: PMC8537137 DOI: 10.3390/pharmaceutics13101551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/17/2022] Open
Abstract
Protein cages are nanocompartments with a well-defined structure and monodisperse size. They are composed of several individual subunits and can be categorized as viral and non-viral protein cages. Native viral cages often exhibit a cationic interior, which binds the anionic nucleic acid genome through electrostatic interactions leading to efficient encapsulation. Non-viral cages can carry various cargo, ranging from small molecules to inorganic nanoparticles. Both cage types can be functionalized at targeted locations through genetic engineering or chemical modification to entrap materials through interactions that are inaccessible to wild-type cages. Moreover, the limited number of constitutional subunits ease the modification efforts, because a single modification on the subunit can lead to multiple functional sites on the cage surface. Increasing efforts have also been dedicated to the assembly of protein cage-mimicking structures or templated protein coatings. This review focuses on native and modified protein cages that have been used to encapsulate and package polyelectrolyte cargos and on the electrostatic interactions that are the driving force for the assembly of such structures. Selective encapsulation can protect the payload from the surroundings, shield the potential toxicity or even enhance the intended performance of the payload, which is appealing in drug or gene delivery and imaging.
Collapse
Affiliation(s)
- Qing Liu
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
| | - Ahmed Shaukat
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
| | - Daniella Kyllönen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland; (Q.L.); (A.S.); (D.K.)
- HYBER Center, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| |
Collapse
|
6
|
Hou C, Xu H, Jiang X, Li Y, Deng S, Zang M, Xu J, Liu J. Virus-Based Supramolecular Structure and Materials: Concept and Prospects. ACS APPLIED BIO MATERIALS 2021; 4:5961-5974. [PMID: 35006905 DOI: 10.1021/acsabm.1c00633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rodlike and spherelike viruses are various monodisperse nanoparticles that can display small molecules or polymers with unique distribution following chemical modifications. Because of the monodisperse property, aggregates in synthetic protein-polymer nanoparticles could be eliminated, thus improving the probability for application in protein-polymer drug. In addition, the monodisperse virus could direct the growth of metal materials or inorganic materials, finding applications in hydrogel, drug delivery, and optoelectronic and catalysis materials. Benefiting from the advantages, the virus or viruslike particles have been widely explored in the field of supramolecular chemistry. In this review, we describe the modification and application of virus and viruslike particles in surpramolecular structures and biomedical research.
Collapse
Affiliation(s)
- Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Hanxin Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xiaojia Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yijia Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shengchao Deng
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Mingsong Zang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| |
Collapse
|
7
|
Kraj P, Selivanovitch E, Lee B, Douglas T. Polymer Coatings on Virus-like Particle Nanoreactors at Low Ionic Strength-Charge Reversal and Substrate Access. Biomacromolecules 2021; 22:2107-2118. [PMID: 33877799 PMCID: PMC8238134 DOI: 10.1021/acs.biomac.1c00208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Virus-like particles (VLPs) are a class of biomaterials which serve as platforms for achieving the desired functionality through interior and exterior modifications. Through ionic strength-mediated electrostatic interactions, VLPs have been assembled into hierarchically ordered materials. This work builds on predictive models to prepare polymer-coated VLP clusters at very low ionic strength. Zeta potential measurements showed that the clusters carried a strongly positive charge, a complete charge reversal from the VLP building block. SAXS analysis confirmed polymer adsorption onto the VLP exterior. We then studied the activity of an encapsulated enzyme toward small molecular and macromolecular substrates to determine the effect of each component of the hierarchically assembled material. We found that while encapsulation and polymer coating did not have a large effect on access to the enzyme by its native, small molecular substrate, substrate modification with a macromolecule caused the polymer coating and encapsulation to affect the access to the enzyme.
Collapse
Affiliation(s)
- Pawel Kraj
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne 60439, Illinois, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington 47405, Indiana, United States
| |
Collapse
|
8
|
Le DT, Müller KM. In Vitro Assembly of Virus-Like Particles and Their Applications. Life (Basel) 2021; 11:334. [PMID: 33920215 PMCID: PMC8069851 DOI: 10.3390/life11040334] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Virus-like particles (VLPs) are increasingly used for vaccine development and drug delivery. Assembly of VLPs from purified monomers in a chemically defined reaction is advantageous compared to in vivo assembly, because it avoids encapsidation of host-derived components and enables loading with added cargoes. This review provides an overview of ex cella VLP production methods focusing on capsid protein production, factors that impact the in vitro assembly, and approaches to characterize in vitro VLPs. The uses of in vitro produced VLPs as vaccines and for therapeutic delivery are also reported.
Collapse
Affiliation(s)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| |
Collapse
|
9
|
Välimäki S, Liu Q, Schoonen L, Vervoort DFM, Nonappa, Linko V, Nolte RJM, van Hest JCM, Kostiainen MA. Engineered protein cages for selective heparin encapsulation. J Mater Chem B 2021; 9:1272-1276. [PMID: 33427277 DOI: 10.1039/d0tb02541k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A heparin-specific binding peptide was conjugated to a cowpea chlorotic mottle virus (CCMV) capsid protein, which was subsequently allowed to encapsulate heparin and form capsid-like protein cages. The encapsulation is specific and the capsid-heparin assemblies display negligible hemolytic activity, indicating proper blood compatibility and promising possibilities for heparin antidote applications.
Collapse
Affiliation(s)
- Salla Välimäki
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland.
| | - Qing Liu
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland.
| | - Lise Schoonen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Daan F M Vervoort
- Department of Bio-Organic Chemistry, Eindhoven University of Technology, Institute of Complex Molecular Systems (ICMS), Het Kranenveld 14, Eindhoven 5600 MB, The Netherlands
| | - Nonappa
- HYBER Centre, Department of Applied Physics, Aalto University, Aalto FI-00076, Finland
| | - Veikko Linko
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland. and HYBER Centre, Department of Applied Physics, Aalto University, Aalto FI-00076, Finland
| | - Roeland J M Nolte
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jan C M van Hest
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands and Department of Bio-Organic Chemistry, Eindhoven University of Technology, Institute of Complex Molecular Systems (ICMS), Het Kranenveld 14, Eindhoven 5600 MB, The Netherlands
| | - Mauri A Kostiainen
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto FI-00076, Espoo, Finland. and HYBER Centre, Department of Applied Physics, Aalto University, Aalto FI-00076, Finland
| |
Collapse
|
10
|
Fu J, Woycechowsky KJ. Guest Sequence Can Influence RNA Encapsulation by an Engineered Cationic Protein Capsid. Biochemistry 2020; 59:1517-1526. [DOI: 10.1021/acs.biochem.0c00077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiannan Fu
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
| | | |
Collapse
|
11
|
Lou UK, Wong CH, Chen Y. A simple and rapid colorimetric detection of serum lncRNA biomarkers for diagnosis of pancreatic cancer. RSC Adv 2020; 10:8087-8092. [PMID: 35497850 PMCID: PMC9049936 DOI: 10.1039/c9ra07858d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/17/2020] [Indexed: 11/21/2022] Open
Abstract
A colorimetric assay is developed for detection of lncRNA HOTTIP by one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) coupled with positively-charged gold nanoparticles ((+)AuNP) for diagnosis of pancreatic cancer. This assay allows simple, rapid, and sensitive quantification of lncRNA down to 50 copies.
Collapse
Affiliation(s)
- Ut Kei Lou
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong Shatin NT Hong Kong +852 26035123 +852 39431100
| | - Chi Hin Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong Shatin NT Hong Kong +852 26035123 +852 39431100
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong Shatin NT Hong Kong +852 26035123 +852 39431100
- Shenzhen Research Institute, The Chinese University of Hong Kong Shenzhen 518087 China
| |
Collapse
|
12
|
Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
Abstract
Viruses are highly ordered supramolecular complexes that have evolved to propagate by hijacking the host cell's machinery. Although viruses are very diverse, spreading through cells of all kingdoms of life, they share common functions and properties. Next to the general interest in virology, fundamental viral mechanisms are of growing importance in other disciplines such as biomedicine and (bio)nanotechnology. However, in order to optimally make use of viruses and virus-like particles, for instance as vehicle for targeted drug delivery or as building blocks in electronics, it is essential to understand their basic chemical and physical properties and characteristics. In this context, the number of studies addressing the mechanisms governing viral properties and processes has recently grown drastically. This review summarizes a specific part of these scientific achievements, particularly addressing physical virology approaches aimed to understand the self-assembly of viruses and the mechanical properties of viral particles. Using a physicochemical perspective, we have focused on fundamental studies providing an overview of the molecular basis governing these key aspects of viral systems. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
Collapse
Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| |
Collapse
|
13
|
Korpi A, Anaya-Plaza E, Välimäki S, Kostiainen M. Highly ordered protein cage assemblies: A toolkit for new materials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1578. [PMID: 31414574 DOI: 10.1002/wnan.1578] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/19/2019] [Accepted: 06/28/2019] [Indexed: 12/16/2022]
Abstract
Protein capsids are specialized and versatile natural macromolecules with exceptional properties. Their homogenous, spherical, rod-like or toroidal geometry, and spatially directed functionalities make them intriguing building blocks for self-assembled nanostructures. High degrees of functionality and modifiability allow for their assembly via non-covalent interactions, such as electrostatic and coordination bonding, enabling controlled self-assembly into higher-order structures. These assembly processes are sensitive to the molecules used and the surrounding conditions, making it possible to tune the chemical and physical properties of the resultant material and generate multifunctional and environmentally sensitive systems. These materials have numerous potential applications, including catalysis and drug delivery. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
Collapse
Affiliation(s)
- Antti Korpi
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Eduardo Anaya-Plaza
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Salla Välimäki
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Mauri Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| |
Collapse
|
14
|
McAdam CJ, Hanton LR, Moratti SC, Simpson J, Wickramasinhage RN. Structure and Hirshfeld surface analysis of the salt N, N, N-trimethyl-1-(4-vinyl-phen-yl)methanaminium 4-vinyl-benzene-sulfonate. Acta Crystallogr E Crystallogr Commun 2019; 75:946-950. [PMID: 31392001 PMCID: PMC6659345 DOI: 10.1107/s2056989019007758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/28/2019] [Indexed: 11/17/2022]
Abstract
In the title compound, the asymmetric unit comprises an N,N,N-trimethyl-1-(4-vinyl-phen-yl)methanaminium cation and a 4-vinyl-benzene-sulfonate anion, C12H18N+·C8H7O3S-. The salt has a polymerizable vinyl group attached to both the cation and the anion. The methanaminium and vinyl substituents on the benzene ring of the cation subtend angles of 86.6 (3) and 10.5 (9)° to the ring plane, while the anion is planar excluding the sulfonate O atoms. The vinyl substituent on the benzene ring of the cation is disordered over two sites with a refined occupancy ratio of 0.542 (11):0.458 (11). In the crystal, C-H⋯O hydrogen bonds dominate the packing and combine with a C-H⋯π(ring) contact to stack the cations and anions along the a-axis direction. Hirshfeld surface analysis of the salt and of the individual cation and anion components is also reported.
Collapse
Affiliation(s)
- C. John McAdam
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Lyall R. Hanton
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Stephen C. Moratti
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Jim Simpson
- Department of Chemistry, University of Otago, PO Box 56, Dunedin, New Zealand
| | | |
Collapse
|
15
|
Abstract
While small single-stranded viral shells encapsidate their genome spontaneously, many large viruses, such as the herpes simplex virus or infectious bursal disease virus (IBDV), typically require a template, consisting of either scaffolding proteins or an inner core. Despite the proliferation of large viruses in nature, the mechanisms by which hundreds or thousands of proteins assemble to form structures with icosahedral order (IO) is completely unknown. Using continuum elasticity theory, we study the growth of large viral shells (capsids) and show that a nonspecific template not only selects the radius of the capsid, but also leads to the error-free assembly of protein subunits into capsids with universal IO. We prove that as a spherical cap grows, there is a deep potential well at the locations of disclinations that later in the assembly process will become the vertices of an icosahedron. Furthermore, we introduce a minimal model and simulate the assembly of a viral shell around a template under nonequilibrium conditions and find a perfect match between the results of continuum elasticity theory and the numerical simulations. Besides explaining available experimental results, we provide a number of predictions. Implications for other problems in spherical crystals are also discussed.
Collapse
|
16
|
Maassen SJ, van der Schoot P, Cornelissen JJLM. Experimental and Theoretical Determination of the pH inside the Confinement of a Virus-Like Particle. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802081. [PMID: 30102454 DOI: 10.1002/smll.201802081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/17/2018] [Indexed: 06/08/2023]
Abstract
In biology, a variety of highly ordered nanometer-size protein cages is found. Such structures find increasing application in, for example, vaccination, drug delivery, and catalysis. Understanding the physiochemical properties, particularly inside the confinement of a protein cage, helps to predict the behavior and properties of new materials based on such particles. Here, the relation between the bulk solution pH and the local pH inside a model protein cage, based on virus-like particles (VLPs) built from the coat proteins of the cowpea chlorotic mottle virus, is investigated. The pH is a crucial parameter in a variety of processes and is potentially significantly influenced by the high concentration of charges residing on the interior of the VLPs. The data show a systematic more acidic pH of 0.5 unit inside the VLP compared to that of the bulk solution for pH values above pH 6, which is explained using a theoretical model based on a Donnan equilibrium. The model agrees with the experimental data over almost two orders of magnitude, while below pH 6 the experimental data point to a buffering capacity of the VLP. These results are a first step in a better understanding of the physiochemical conditions inside a protein cage.
Collapse
Affiliation(s)
- Stan J Maassen
- Laboratory of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, Enschede, 7500, AE, The Netherlands
| | - Paul van der Schoot
- Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, PO Box 513, 5600, MB, Eindhoven, The Netherlands
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584, CC, Utrecht, The Netherlands
| | - Jeroen J L M Cornelissen
- Laboratory of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, Enschede, 7500, AE, The Netherlands
| |
Collapse
|
17
|
Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte. Nat Commun 2018; 9:3071. [PMID: 30082710 PMCID: PMC6078970 DOI: 10.1038/s41467-018-05426-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/05/2018] [Indexed: 11/20/2022] Open
Abstract
The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape. The mechanism by which virus capsules assemble around RNA to package their genetic material is not clear. Here, the authors observed the assembly of the cowpea chlorotic mottle virus capsid around viral RNA or poly(styrene sulfonic acid) using time-resolved small-angle X-ray scattering measurements.
Collapse
|
18
|
de Ruiter MV, Overeem NJ, Singhai G, Cornelissen JJLM. Induced Förster resonance energy transfer by encapsulation of DNA-scaffold based probes inside a plant virus based protein cage. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:184002. [PMID: 29512513 PMCID: PMC7104908 DOI: 10.1088/1361-648x/aab4a9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/16/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Insight into the assembly and disassembly of viruses can play a crucial role in developing cures for viral diseases. Specialized fluorescent probes can benefit the study of interactions within viruses, especially during cell studies. In this work, we developed a strategy based on Förster resonance energy transfer (FRET) to study the assembly of viruses without labeling the exterior of viruses. Instead, we exploit their encapsulation of nucleic cargo, using three different fluorescent ATTO dyes linked to single-stranded DNA oligomers, which are hybridised to a longer DNA strand. FRET is induced upon assembly of the cowpea chlorotic mottle virus, which forms monodisperse icosahedral particles of about 22 nm, thereby increasing the FRET efficiency by a factor of 8. Additionally, encapsulation of the dyes in virus-like particles induces a two-step FRET. When the formed constructs are disassembled, this FRET signal is fully reduced to the value before encapsulation. This reversible behavior makes the system a good probe for studying viral assembly and disassembly. It, furthermore, shows that multi-component supramolecular materials are stabilized in the confinement of a protein cage.
Collapse
Affiliation(s)
- Mark V de Ruiter
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
| | - Nico J Overeem
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
| | - Gaurav Singhai
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
- Flinders Centre for Nanoscale Science and Technology, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Jeroen J L M Cornelissen
- Laboratory of Biomolecular Nanotechnology, MESA + Institute of Nanotechnology, University of Twente, P O Box 217, 7500 AE, Enschede, Netherlands
| |
Collapse
|
19
|
van Dongen SFM, Clerx J, van den Boomen OI, Pervaiz M, Trakselis MA, Ritschel T, Schoonen L, Schoenmakers DC, Nolte RJM. Synthetic polymers as substrates for a DNA-sliding clamp protein. Biopolymers 2018; 109:e23119. [PMID: 29700825 PMCID: PMC6001473 DOI: 10.1002/bip.23119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 11/08/2022]
Abstract
The clamp protein (gp45) of the DNA polymerase III of the bacteriophage T4 is known to bind to DNA and stay attached to it in order to facilitate the process of DNA copying by the polymerase. As part of a project aimed at developing new biomimetic data-encoding systems we have investigated the binding of gp45 to synthetic polymers, that is, rigid, helical polyisocyanopeptides. Molecular modelling studies suggest that the clamp protein may interact with the latter polymers. Experiments aimed at verifying these interactions are presented and discussed.
Collapse
Affiliation(s)
- S. F. M. van Dongen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135Nijmegen6525AJThe Netherlands
| | - J. Clerx
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135Nijmegen6525AJThe Netherlands
| | - O. I. van den Boomen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135Nijmegen6525AJThe Netherlands
| | - M. Pervaiz
- Center for Molecular and Biomolecular Informatics (CMBI). Radboud University Medical Center, Geert Grooteplein Zuid 26‐28NijmegenHB6500The Netherlands
| | - M. A. Trakselis
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place #97348WacoTexas76798‐7348
| | - T. Ritschel
- Center for Molecular and Biomolecular Informatics (CMBI). Radboud University Medical Center, Geert Grooteplein Zuid 26‐28NijmegenHB6500The Netherlands
| | - L. Schoonen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135Nijmegen6525AJThe Netherlands
| | - D. C. Schoenmakers
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135Nijmegen6525AJThe Netherlands
| | - R. J. M. Nolte
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135Nijmegen6525AJThe Netherlands
| |
Collapse
|
20
|
Maassen SJ, de Ruiter MV, Lindhoud S, Cornelissen JJLM. Oligonucleotide Length-Dependent Formation of Virus-Like Particles. Chemistry 2018. [PMID: 29518273 DOI: 10.1002/chem.201800285] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Understanding the assembly pathway of viruses can contribute to creating monodisperse virus-based materials. In this study, the cowpea chlorotic mottle virus (CCMV) is used to determine the interactions between the capsid proteins of viruses and their cargo. The assembly of the capsid proteins in the presence of different lengths of short, single-stranded (ss) DNA is studied at neutral pH, at which the protein-protein interactions are weak. Chromatography, electrophoresis, microscopy, and light scattering data show that the assembly efficiency and speed of the particles increase with increasing length of oligonucleotides. The minimal length required for assembly under the conditions used herein is 14 nucleotides. Assembly of particles containing such short strands of ssDNA can take almost a month. This slow assembly process enabled the study of intermediate states, which confirmed a low cooperative assembly for CCMV and allowed for further expansion of current assembly theories.
Collapse
Affiliation(s)
- Stan J Maassen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Saskia Lindhoud
- Department of Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
| | - Jeroen J L M Cornelissen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, Enschede, The Netherlands
| |
Collapse
|
21
|
Li S, Orland H, Zandi R. Self consistent field theory of virus assembly. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:144002. [PMID: 29460850 PMCID: PMC7104907 DOI: 10.1088/1361-648x/aab0c6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/12/2018] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The ground state dominance approximation (GSDA) has been extensively used to study the assembly of viral shells. In this work we employ the self-consistent field theory (SCFT) to investigate the adsorption of RNA onto positively charged spherical viral shells and examine the conditions when GSDA does not apply and SCFT has to be used to obtain a reliable solution. We find that there are two regimes in which GSDA does work. First, when the genomic RNA length is long enough compared to the capsid radius, and second, when the interaction between the genome and capsid is so strong that the genome is basically localized next to the wall. We find that for the case in which RNA is more or less distributed uniformly in the shell, regardless of the length of RNA, GSDA is not a good approximation. We observe that as the polymer-shell interaction becomes stronger, the energy gap between the ground state and first excited state increases and thus GSDA becomes a better approximation. We also present our results corresponding to the genome persistence length obtained through the tangent-tangent correlation length and show that it is zero in case of GSDA but is equal to the inverse of the energy gap when using SCFT.
Collapse
Affiliation(s)
- Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No.10 East Xibeiwang Road, Haidan District, Beijing 100193, People’s Republic of China
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No.10 East Xibeiwang Road, Haidan District, Beijing 100193, People’s Republic of China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
| |
Collapse
|
22
|
van der Holst B, Kegel WK, Zandi R, van der Schoot P. The different faces of mass action in virus assembly. J Biol Phys 2018; 44:163-179. [PMID: 29616429 PMCID: PMC5928020 DOI: 10.1007/s10867-018-9487-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
The spontaneous encapsulation of genomic and non-genomic polyanions by coat proteins of simple icosahedral viruses is driven, in the first instance, by electrostatic interactions with polycationic RNA binding domains on these proteins. The efficiency with which the polyanions can be encapsulated in vitro, and presumably also in vivo, must in addition be governed by the loss of translational and mixing entropy associated with co-assembly, at least if this co-assembly constitutes a reversible process. These forms of entropy counteract the impact of attractive interactions between the constituents and hence they counteract complexation. By invoking mass action-type arguments and a simple model describing electrostatic interactions, we show how these forms of entropy might settle the competition between negatively charged polymers of different molecular weights for co-assembly with the coat proteins. In direct competition, mass action turns out to strongly work against the encapsulation of RNAs that are significantly shorter, which is typically the case for non-viral (host) RNAs. We also find that coat proteins favor forming virus particles over nonspecific binding to other proteins in the cytosol even if these are present in vast excess. Our results rationalize a number of recent in vitro co-assembly experiments showing that short polyanions are less effective at attracting virus coat proteins to form virus-like particles than long ones do, even if both are present at equal weight concentrations in the assembly mixture.
Collapse
Affiliation(s)
- Bart van der Holst
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Willem K Kegel
- Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California Riverside, Riverside, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands. .,Institute for Theoretical Physics, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
23
|
Sinn S, Yang L, Biedermann F, Wang D, Kübel C, Cornelissen JJLM, De Cola L. Templated Formation of Luminescent Virus-like Particles by Tailor-Made Pt(II) Amphiphiles. J Am Chem Soc 2018; 140:2355-2362. [PMID: 29357236 PMCID: PMC5817621 DOI: 10.1021/jacs.7b12447] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Virus-like particles
(VLPs) have been created from luminescent
Pt(II) complex amphiphiles, able to form supramolecular structures
in water solutions, that can be encapsulated or act as templates of
cowpea chlorotic mottle virus capsid proteins. By virtue of a bottom-up
molecular design, icosahedral and nonicosahedral (rod-like) VLPs have
been constructed through diverse pathways, and a relationship between
the molecular structure of the complexes and the shape and size of
the VLPs has been observed. A deep insight into the mechanism for
the templated formation of the differently shaped VLPs was achieved,
by electron microscopy measurements (TEM and STEM) and bulk analysis
(FPLC, DLS, photophysical investigations). Interestingly, the obtained
VLPs can be visualized by their intense emission at room temperature,
generated by the self-assembly of the Pt(II) complexes. The encapsulation
of the luminescent species is further verified by their higher emission
quantum yields inside the VLPs, which is due to the confinement effect
of the protein cage. These hybrid materials demonstrate the potential
of tailor-made supramolecular systems able to control the assembly
of biological building blocks.
Collapse
Affiliation(s)
- Stephan Sinn
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS , 8 Rue Gaspard Monge, 67000 Strasbourg, France
| | - Liulin Yang
- Laboratory for Biomolecular Nanotechnology, MESA+ Institute, University of Twente , P.O. Box 207, 7500 AE Enschede, The Netherlands
| | | | | | | | - Jeroen J L M Cornelissen
- Laboratory for Biomolecular Nanotechnology, MESA+ Institute, University of Twente , P.O. Box 207, 7500 AE Enschede, The Netherlands
| | - Luisa De Cola
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg & CNRS , 8 Rue Gaspard Monge, 67000 Strasbourg, France
| |
Collapse
|
24
|
Li S, Erdemci-Tandogan G, van der Schoot P, Zandi R. The effect of RNA stiffness on the self-assembly of virus particles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:044002. [PMID: 29235442 PMCID: PMC7104906 DOI: 10.1088/1361-648x/aaa159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 05/21/2023]
Abstract
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.
Collapse
Affiliation(s)
- Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
| | - Gonca Erdemci-Tandogan
- Department of Physics, Syracuse University, Syracuse, NY 13244, United States of America
| | - Paul van der Schoot
- Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, Netherlands
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America
| |
Collapse
|
25
|
Miao X, Cheng Z, Ma H, Li Z, Xue N, Wang P. Label-Free Platform for MicroRNA Detection Based on the Fluorescence Quenching of Positively Charged Gold Nanoparticles to Silver Nanoclusters. Anal Chem 2017; 90:1098-1103. [DOI: 10.1021/acs.analchem.7b01991] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiangmin Miao
- School
of Life Science, and ‡School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Zhiyuan Cheng
- School
of Life Science, and ‡School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Haiyan Ma
- School
of Life Science, and ‡School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Zongbing Li
- School
of Life Science, and ‡School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Ning Xue
- School
of Life Science, and ‡School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Po Wang
- School
of Life Science, and ‡School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| |
Collapse
|
26
|
Angelescu DG. Role of polyion length in the co-assembly of stoichiometric viral-like nanoparticles. JOURNAL OF POLYMER RESEARCH 2017. [DOI: 10.1007/s10965-017-1416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
27
|
Narayanan KB, Han SS. Icosahedral plant viral nanoparticles - bioinspired synthesis of nanomaterials/nanostructures. Adv Colloid Interface Sci 2017; 248:1-19. [PMID: 28916111 DOI: 10.1016/j.cis.2017.08.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
Abstract
Viral nanotechnology utilizes virus nanoparticles (VNPs) and virus-like nanoparticles (VLPs) of plant viruses as highly versatile platforms for materials synthesis and molecular entrapment that can be used in the nanotechnological fields, such as in next-generation nanoelectronics, nanocatalysis, biosensing and optics, and biomedical applications, such as for targeting, therapeutic delivery, and non-invasive in vivo imaging with high specificity and selectivity. In particular, plant virus capsids provide biotemplates for the production of novel nanostructured materials with organic/inorganic moieties incorporated in a very precise and controlled manner. Interestingly, capsid proteins of spherical plant viruses can self-assemble into well-organized icosahedral three-dimensional (3D) nanoscale multivalent architectures with high monodispersity and structural symmetry. Using viral genetic and protein engineering of icosahedral viruses with a variety of sizes, the interior, exterior and the interfaces between coat protein (CP) subunits can be manipulated to fabricate materials with a wide range of desirable properties allowing for biomineralization, encapsulation, infusion, controlled self-assembly, and multivalent ligand display of nanoparticles or molecules for varied applications. In this review, we discuss the various functional nanomaterials/nanostructures developed using the VNPs and VLPs of different icosahedral plant viruses and their nano(bio)technological and nanomedical applications.
Collapse
|
28
|
Li S, Erdemci-Tandogan G, Wagner J, van der Schoot P, Zandi R. Impact of a nonuniform charge distribution on virus assembly. Phys Rev E 2017; 96:022401. [PMID: 28950450 DOI: 10.1103/physreve.96.022401] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Indexed: 01/04/2023]
Abstract
Many spherical viruses encapsulate their genomes in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genomes. We model the effect of the nonuniform icosahedral charge distribution from the protein shell instead using a mean-field theory. We find that this nonuniform charge distribution strongly affects the optimal genome length and that it can explain the experimentally observed phenomenon of overcharging of virus and viruslike particles.
Collapse
Affiliation(s)
- Siyu Li
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Gonca Erdemci-Tandogan
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Jef Wagner
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Paul van der Schoot
- Group Theory of Polymers and Soft Matter, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Theoretical Physics, Utrecht University, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| |
Collapse
|
29
|
Schoonen L, Maassen S, Nolte RJM, van Hest JCM. Stabilization of a Virus-Like Particle and Its Application as a Nanoreactor at Physiological Conditions. Biomacromolecules 2017. [PMID: 28631927 PMCID: PMC5686562 DOI: 10.1021/acs.biomac.7b00640] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Virus-like particles are very interesting
tools for application
in bionanotechnology, due to their monodisperse features and biocompatibility.
In particular, the cowpea chlorotic mottle virus (CCMV) capsid has
been studied extensively as it can be assembled and disassembled reversibly,
facilitating cargo encapsulation. CCMV is, however, only stable at
physiological conditions when its endogenous nucleic acid cargo is
present. To gain more flexibility in the type of cargo encapsulated
and to broaden the window of operation, it is interesting to improve
the stability of the empty virus-like particles. Here, a method is
described to utilize the CCMV capsid at close to physiological conditions
as a stable, enzyme-filled nanoreactor. As a proof-of-principle, the
encapsulation of T4 lysozyme (T4L) was chosen; this enzyme is a promising
antibiotic, but its clinical application is hampered by, for example,
its cationic character. It was shown that four T4L molecules can successfully
be encapsulated inside CCMV capsids, while remaining catalytically
active, which could thus improve the enzyme’s application potential.
Collapse
Affiliation(s)
- Lise Schoonen
- Radboud University, Institute for Molecules and Materials , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Sjors Maassen
- Radboud University, Institute for Molecules and Materials , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roeland J M Nolte
- Radboud University, Institute for Molecules and Materials , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jan C M van Hest
- Eindhoven University of Technology , P.O. Box 513 (STO 3.31), 5600 MB Eindhoven, The Netherlands.,Radboud University, Institute for Molecules and Materials , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
30
|
Angelescu DG. Assembled viral-like nanoparticles from elastic capsomers and polyion. J Chem Phys 2017; 146:134902. [DOI: 10.1063/1.4979496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
|
31
|
Brasch M, Putri RM, de Ruiter MV, Luque D, Koay MST, Castón JR, Cornelissen JJLM. Assembling Enzymatic Cascade Pathways inside Virus-Based Nanocages Using Dual-Tasking Nucleic Acid Tags. J Am Chem Soc 2017; 139:1512-1519. [PMID: 28055188 PMCID: PMC5330652 DOI: 10.1021/jacs.6b10948] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 12/21/2022]
Abstract
The packaging of proteins into discrete compartments is an essential feature for cellular efficiency. Inspired by Nature, we harness virus-like assemblies as artificial nanocompartments for enzyme-catalyzed cascade reactions. Using the negative charges of nucleic acid tags, we develop a versatile strategy to promote an efficient noncovalent co-encapsulation of enzymes within a single protein cage of cowpea chlorotic mottle virus (CCMV) at neutral pH. The encapsulation results in stable 21-22 nm sized CCMV-like particles, which is characteristic of an icosahedral T = 1 symmetry. Cryo-EM reconstruction was used to demonstrate the structure of T = 1 assemblies templated by biological soft materials as well as the extra-swelling capacity of these T = 1 capsids. Furthermore, the specific sequence of the DNA tag is capable of operating as a secondary biocatalyst as well as bridging two enzymes for co-encapsulation in a single capsid while maintaining their enzymatic activity. Using CCMV-like particles to mimic nanocompartments can provide valuable insight on the role of biological compartments in enhancing metabolic efficiency.
Collapse
Affiliation(s)
- Melanie Brasch
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Rindia M. Putri
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Mark V. de Ruiter
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - Daniel Luque
- Department
of Structure of Macromolecules, Centro Nacional
de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
- Centro
Nacional de Microbiología/Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Melissa. S. T. Koay
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| | - José R. Castón
- Department
of Structure of Macromolecules, Centro Nacional
de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Jeroen J. L. M. Cornelissen
- Department
of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
| |
Collapse
|
32
|
Tagit O, de Ruiter M, Brasch M, Ma Y, Cornelissen JJLM. Quantum dot encapsulation in virus-like particles with tuneable structural properties and low toxicity. RSC Adv 2017. [DOI: 10.1039/c7ra06684h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Quantum dot encapsulation within cowpea chlorotic mottle virus-based capsid proteins to obtain size-tuneable, non-toxic, luminescent imaging probes is presented.
Collapse
Affiliation(s)
- O. Tagit
- Laboratory of Biomolecular Nanotechnology
- MESA + Institute of Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| | - M. V. de Ruiter
- Laboratory of Biomolecular Nanotechnology
- MESA + Institute of Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| | - M. Brasch
- Laboratory of Biomolecular Nanotechnology
- MESA + Institute of Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| | - Y. Ma
- Laboratory of Biomolecular Nanotechnology
- MESA + Institute of Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| | - J. J. L. M. Cornelissen
- Laboratory of Biomolecular Nanotechnology
- MESA + Institute of Nanotechnology
- University of Twente
- Enschede
- The Netherlands
| |
Collapse
|
33
|
Miao X, Ning X, Li Z, Cheng Z. Sensitive detection of miRNA by using hybridization chain reaction coupled with positively charged gold nanoparticles. Sci Rep 2016; 6:32358. [PMID: 27576601 PMCID: PMC5006024 DOI: 10.1038/srep32358] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/04/2016] [Indexed: 01/21/2023] Open
Abstract
Positively charged gold nanoparticles (+)AuNPs can adsorb onto the negatively charged surface of single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). Herein, long-range dsDNA polymers could form based on the hybridization chain reaction (HCR) of two hairpin probes (H1 and H2) by using miRNA-21 as an initiator. (+)AuNPs could adsorb onto the negatively charged surface of such long-range dsDNA polymers based on the electrostatic adsorption, which directly resulted in the precipitation of (+)AuNPs and the decrease of (+)AuNPs absorption spectra. Under optimal conditions, miRNA-21 detection could be realized in the range of 20 pM-10 nM with a detection limit of 6.8 pM. In addition, (+)AuNPs used here are much more stable than commonly used negatively charged gold nanoparticles ((−)AuNPs) in mixed solution that contained salt, protein or other metal ions. Importantly, the assay could realize the detection of miRNA in human serum samples.
Collapse
Affiliation(s)
- Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Xue Ning
- KeWen College, JiangSu Normal University, Xuzhou 221116, PR China
| | - Zongbing Li
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Zhiyuan Cheng
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| |
Collapse
|
34
|
Maassen SJ, van der Ham AM, Cornelissen JJLM. Combining Protein Cages and Polymers: from Understanding Self-Assembly to Functional Materials. ACS Macro Lett 2016; 5:987-994. [PMID: 35607217 DOI: 10.1021/acsmacrolett.6b00509] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein cages, such as viruses, are well-defined biological nanostructures which are highly symmetrical and monodisperse. They are found in various shapes and sizes and can encapsulate or template non-native materials. Furthermore, the proteins can be chemically or genetically modified giving them new properties. For these reasons, these protein structures have received increasing attention in the field of polymer-protein hybrid materials over the past years, however, advances are still to be made. This Viewpoint highlights the different ways polymers and protein cages or their subunits have been combined to understand self-assembly and create functional materials.
Collapse
Affiliation(s)
- Stan J. Maassen
- Laboratory for Biomolecular
Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 207, 7500 AE Enschede, The Netherlands
| | - Anne M. van der Ham
- Laboratory for Biomolecular
Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 207, 7500 AE Enschede, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Laboratory for Biomolecular
Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 207, 7500 AE Enschede, The Netherlands
| |
Collapse
|
35
|
van Rijn P, Schirhagl R. Viruses, Artificial Viruses and Virus-Based Structures for Biomedical Applications. Adv Healthc Mater 2016; 5:1386-400. [PMID: 27119823 DOI: 10.1002/adhm.201501000] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/14/2016] [Indexed: 12/17/2022]
Abstract
Nanobiomaterials such as virus particles and artificial virus particles offer tremendous opportunities to develop new biomedical applications such as drug- or gene-delivery, imaging and sensing but also improve understanding of biological mechanisms. Recent advances within the field of virus-based systems give insights in how to mimic viral structures and virus assembly processes as well as understanding biodistribution, cell/tissue targeting, controlled and triggered disassembly or release and circulation times. All these factors are of high importance for virus-based functional systems. This review illustrates advances in mimicking and enhancing or controlling these aspects to a high degree toward delivery and imaging applications.
Collapse
Affiliation(s)
- Patrick van Rijn
- University of Groningen University Medical Center Groningen Biomedical Engineering‐FB40 W.J. Kolff Institute for Biomedical Engineering and Materials Science‐FB41 Antonius Deusinglaan 1 9713 AW Groningen Netherlands
- Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Romana Schirhagl
- University of Groningen University Medical Center Groningen Biomedical Engineering‐FB40 W.J. Kolff Institute for Biomedical Engineering and Materials Science‐FB41 Antonius Deusinglaan 1 9713 AW Groningen Netherlands
| |
Collapse
|
36
|
Wagner J, Zandi R. The Robust Assembly of Small Symmetric Nanoshells. Biophys J 2016; 109:956-65. [PMID: 26331253 DOI: 10.1016/j.bpj.2015.07.041] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 06/18/2015] [Accepted: 07/28/2015] [Indexed: 12/20/2022] Open
Abstract
Highly symmetric nanoshells are found in many biological systems, such as clathrin cages and viral shells. Many studies have shown that symmetric shells appear in nature as a result of the free-energy minimization of a generic interaction between their constituent subunits. We examine the physical basis for the formation of symmetric shells, and by using a minimal model, demonstrate that these structures can readily grow from the irreversible addition of identical subunits. Our model of nanoshell assembly shows that the spontaneous curvature regulates the size of the shell while the mechanical properties of the subunit determine the symmetry of the assembled structure. Understanding the minimum requirements for the formation of closed nanoshells is a necessary step toward engineering of nanocontainers, which will have far-reaching impact in both material science and medicine.
Collapse
Affiliation(s)
- Jef Wagner
- Department of Physics and Astronomy, University of California at Riverside, Riverside, California.
| | - Roya Zandi
- Department of Physics and Astronomy, University of California at Riverside, Riverside, California
| |
Collapse
|
37
|
Liu A, Verwegen M, de Ruiter MV, Maassen SJ, Traulsen CHH, Cornelissen JJLM. Protein Cages as Containers for Gold Nanoparticles. J Phys Chem B 2016; 120:6352-7. [PMID: 27135176 DOI: 10.1021/acs.jpcb.6b03066] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abundant and highly diverse, viruses offer new scaffolds in nanotechnology for the encapsulation, organization, or even synthesis of novel materials. In this work the coat protein of the cowpea chlorotic mottle virus (CCMV) is used to encapsulate gold nanoparticles with different sizes and stabilizing ligands yielding stable particles in buffered solutions at neutral pH. The sizes of the virus-like particles correspond to T = 1, 2, and 3 Caspar-Klug icosahedral triangulation numbers. We developed a simple one-step process enabling the encapsulation of commercially available gold nanoparticles without prior modification with up to 97% efficiency. The encapsulation efficiency is further increased using bis-p-(sufonatophenyl)phenyl phosphine surfactants up to 99%. Our work provides a simplified procedure for the preparation of metallic particles stabilized in CCMV protein cages. The presented results are expected to enable the preparation of a variety of similar virus-based colloids for current focus areas.
Collapse
Affiliation(s)
- Aijie Liu
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Martijn Verwegen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Stan J Maassen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Christoph H-H Traulsen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| | - Jeroen J L M Cornelissen
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7500 AE, The Netherlands
| |
Collapse
|
38
|
Liu A, Traulsen CHH, Cornelissen JJLM. Nitroarene Reduction by a Virus Protein Cage Based Nanoreactor. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00106] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Aijie Liu
- Laboratory for Biomolecular
Nanotechnology MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Christoph H.-H. Traulsen
- Laboratory for Biomolecular
Nanotechnology MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Laboratory for Biomolecular
Nanotechnology MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| |
Collapse
|
39
|
Rother M, Nussbaumer MG, Renggli K, Bruns N. Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science. Chem Soc Rev 2016; 45:6213-6249. [DOI: 10.1039/c6cs00177g] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein cages have become essential tools in bionanotechnology due to their well-defined, monodisperse, capsule-like structure. Combining them with synthetic polymers greatly expands their application, giving rise to novel nanomaterials fore.g.drug-delivery, sensing, electronic devices and for uses as nanoreactors.
Collapse
Affiliation(s)
- Martin Rother
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Martin G. Nussbaumer
- Wyss Institute for Biologically Inspired Engineering
- Harvard University
- Cambridge
- USA
| | - Kasper Renggli
- Department of Biosystems Science and Engineering
- ETH Zürich
- 4058 Basel
- Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute
- University of Fribourg
- CH-1700 Fribourg
- Switzerland
| |
Collapse
|
40
|
Tu Y, Peng F, Adawy A, Men Y, Abdelmohsen LKEA, Wilson DA. Mimicking the Cell: Bio-Inspired Functions of Supramolecular Assemblies. Chem Rev 2015; 116:2023-78. [DOI: 10.1021/acs.chemrev.5b00344] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yingfeng Tu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Fei Peng
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alaa Adawy
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yongjun Men
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Loai K. E. A. Abdelmohsen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Daniela A. Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| |
Collapse
|
41
|
Angelescu DG, Caragheorgheopol D. Influence of the shell thickness and charge distribution on the effective interaction between two like-charged hollow spheres. J Chem Phys 2015; 143:144902. [DOI: 10.1063/1.4932372] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Daniel G. Angelescu
- Romanian Academy, “Ilie Murgulescu” Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania
| | - Dan Caragheorgheopol
- Romanian Academy, “Ilie Murgulescu” Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania
- Technical University of Civil Engineering Bucharest, Lacul Tei Blvd., 122-124, 020396 Bucharest, Romania
| |
Collapse
|
42
|
The Role of Packaging Sites in Efficient and Specific Virus Assembly. J Mol Biol 2015; 427:2451-2467. [PMID: 25986309 DOI: 10.1016/j.jmb.2015.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/21/2015] [Accepted: 05/10/2015] [Indexed: 12/25/2022]
Abstract
During the life cycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively assemble around the viral RNA amidst diverse host RNAs is a key question in virology. In one proposed mechanism, short sequences (packaging sites) within the genomic RNA promote rapid and efficient assembly through specific interactions with the capsid proteins. In this work, we develop a coarse-grained particle-based computational model for capsid proteins and RNA that represents protein-RNA interactions arising both from nonspecific electrostatics and from specific packaging site interactions. Using Brownian dynamics simulations, we explore how the efficiency and specificity of assembly depend on solution conditions (which control protein-protein and nonspecific protein-RNA interactions) and the strength and number of packaging sites. We identify distinct regions in parameter space in which packaging sites lead to highly specific assembly via different mechanisms and others in which packaging sites lead to kinetic traps. We relate these computational predictions to in vitro assays for specificity in which cognate viral RNAs compete against non-cognate RNAs for assembly by capsid proteins.
Collapse
|
43
|
Abstract
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid and in some cases are surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assemble within their host cells and in vitro. We describe the thermodynamics and kinetics for the assembly of protein subunits into icosahedral capsid shells and how these are modified in cases in which the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques used to characterize capsid assembly, and we highlight aspects of virus assembly that are likely to receive significant attention in the near future.
Collapse
Affiliation(s)
- Jason D Perlmutter
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454;
| | | |
Collapse
|
44
|
Abstract
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.
Collapse
|
45
|
Kolomanska J, Johnston P, Gregori A, Fraga Domínguez I, Egelhaaf HJ, Perrier S, Rivaton A, Dagron-Lartigau C, Topham PD. Design, synthesis and thermal behaviour of a series of well-defined clickable and triggerable sulfonate polymers. RSC Adv 2015. [DOI: 10.1039/c5ra13867a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the printing industry, the exploitation of triggerable materials that can have their surface properties altered on application of a post-deposition external stimulus has been crucial for the production of robust layers and patterns.
Collapse
Affiliation(s)
- Joanna Kolomanska
- Chemical Engineering and Applied Chemistry
- Aston University
- Birmingham
- UK
| | | | - Alberto Gregori
- Chemical Engineering and Applied Chemistry
- Aston University
- Birmingham
- UK
- Université de Pau et des Pays de l'Adour
| | - Isabel Fraga Domínguez
- Chemical Engineering and Applied Chemistry
- Aston University
- Birmingham
- UK
- Institut de Chimie de Clermont-Ferrand
| | | | - Sébastien Perrier
- Department of Chemistry
- University of Warwick
- UK
- Faculty of Pharmacy and Pharmaceutical Sciences
- Monash University
| | - Agnès Rivaton
- Institut de Chimie de Clermont-Ferrand
- Equipe Photochimie
- UMR 6296
- Université Blaise Pascal
- 63171 Aubière Cedex
| | - Christine Dagron-Lartigau
- Université de Pau et des Pays de l'Adour
- Institut Plurisdisciplinaire de Recherche sur l'Environnement et les Matériaux
- UMR 5254
- 64 053 Pau Cedex 09
- France
| | - Paul D. Topham
- Chemical Engineering and Applied Chemistry
- Aston University
- Birmingham
- UK
| |
Collapse
|
46
|
Kumar K, Kumar Doddi S, Kalle Arunasree M, Paik P. CPMV-induced synthesis of hollow mesoporous SiO2 nanocapsules with excellent performance in drug delivery. Dalton Trans 2015; 44:4308-17. [DOI: 10.1039/c4dt02549k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Synthesis of CPMV- hollow silica nanocapsules and their use in nanomedicine.
Collapse
Affiliation(s)
- Koushi Kumar
- School of Engineering Sciences and Technology
- University of Hyderabad
- India
| | | | | | - Pradip Paik
- School of Engineering Sciences and Technology
- University of Hyderabad
- India
- Advanced Research Centre for High Energy Materials
- University of Hyderabad
| |
Collapse
|
47
|
Verwegen M, Cornelissen JJLM. Clustered nanocarriers: the effect of size on the clustering of CCMV virus-like particles with soft macromolecules. Macromol Biosci 2014; 15:98-110. [PMID: 25388619 DOI: 10.1002/mabi.201400326] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/18/2014] [Indexed: 12/22/2022]
Abstract
Virus-like particles (VLP) could enable a wide variety of biomedical applications in therapy, drug delivery, and imaging. They are biocompatible and can be self-assembled into larger structured materials for additional functionality and potentially better biodistribution, which is still a challenging aspect. Here we investigate the role of the VLPs size and resulting Caspar Klug symmetry in forming clusters out of these building blocks, showing that the onset point for clustering is determined by steric considerations of the binding site and binding agent. The clustering is independent of cargo and the data suggests that rotational symmetry in the T = 3 capsid allows for hexagonal close packed structures, whereas the T = 1 capsid that lacks a six-fold and twofold rotational axis does not show such organization.
Collapse
Affiliation(s)
- Martijn Verwegen
- Laboratory for Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands
| | | |
Collapse
|
48
|
Obayemi JD, Dozie-Nwachukwu S, Danyuo Y, Odusanya OS, Anuku N, Malatesta K, Soboyejo WO. Biosynthesis and the conjugation of magnetite nanoparticles with luteinizing hormone releasing hormone (LHRH). MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 46:482-96. [PMID: 25492013 DOI: 10.1016/j.msec.2014.10.081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 10/03/2014] [Accepted: 10/29/2014] [Indexed: 01/02/2023]
Abstract
This paper presents the results of an experimental study of the biosynthesis of magnetite nanoparticles (BMNPs) with particle sizes between 10 nm and 60 nm. The biocompatible magnetic nanoparticles are produced from Magnetospirillum magneticum (M.M.) bacteria that respond to magnetic fields. M.M. bacteria were cultured and used to synthesize magnetite nanoparticles. This was done in an enriched magnetic spirillum growth medium (EMSGM) at different pH levels. The nanoparticle concentrations were characterized with UV-Visible (UV-Vis) spectroscopy, while the particle shapes were elucidated via transmission electron microscopy (TEM). The structure of the particles was studied using X-ray diffraction (XRD), while the hydrodynamic radii, particle size distributions and polydispersity of the nanoparticles were characterized using dynamic light scattering (DLS). Carbodiimide reduction was also used to functionalize the BMNPs with a molecular recognition unit (luteinizing hormone releasing hormone, LHRH) that attaches specifically to receptors that are over-expressed on the surfaces of most breast cancer cell types. The resulting nanoparticles were examined using Fourier Transform Infrared (FTIR) spectroscopy and quantitative image analysis. The implications of the results are then discussed for the potential development of magnetic nanoparticles for the specific targeting and treatment of breast cancer.
Collapse
Affiliation(s)
- J D Obayemi
- Department of Materials Science and Engineering, African University of Science and Technology (AUST) Abuja, Federal Capital Territory, Nigeria; Department of Materials Science and Engineering, Kwara State University, Malete, Kwara State, Nigeria
| | - S Dozie-Nwachukwu
- Department of Materials Science and Engineering, African University of Science and Technology (AUST) Abuja, Federal Capital Territory, Nigeria; Sheda Science and Technology Complex (SHESTCO) Abuja, Federal Capital Territory, Nigeria
| | - Y Danyuo
- Department of Materials Science and Engineering, African University of Science and Technology (AUST) Abuja, Federal Capital Territory, Nigeria; Department of Electronics and Electricals Engineering, Nigerian Turkish Nile University, Abuja, Nigeria
| | - O S Odusanya
- Department of Materials Science and Engineering, African University of Science and Technology (AUST) Abuja, Federal Capital Territory, Nigeria; Sheda Science and Technology Complex (SHESTCO) Abuja, Federal Capital Territory, Nigeria
| | - N Anuku
- Department of Chemistry, Bronx Community College, New York, NY 10453, USA; Princeton Institute of Science and Technology of Materials (PRISM), Princeton, NJ 08544, USA
| | - K Malatesta
- Princeton Institute of Science and Technology of Materials (PRISM), Princeton, NJ 08544, USA; Department of Mechanical and Aerospace Engineering, Princeton University, NJ 08544, USA
| | - W O Soboyejo
- Department of Materials Science and Engineering, African University of Science and Technology (AUST) Abuja, Federal Capital Territory, Nigeria; Princeton Institute of Science and Technology of Materials (PRISM), Princeton, NJ 08544, USA; Department of Mechanical and Aerospace Engineering, Princeton University, NJ 08544, USA.
| |
Collapse
|
49
|
Tresset G, Tatou M, Le Cœur C, Zeghal M, Bailleux V, Lecchi A, Brach K, Klekotko M, Porcar L. Weighing polyelectrolytes packaged in viruslike particles. PHYSICAL REVIEW LETTERS 2014; 113:128305. [PMID: 25279650 DOI: 10.1103/physrevlett.113.128305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 06/03/2023]
Abstract
This Letter reports on the remarkable selectivity of capsid proteins for packaging synthetic polyelectrolytes in viruslike particles. By applying the contrast variation method in small-angle neutron scattering, we accurately estimated the mean mass of packaged polyelectrolytes ⟨Mp⟩ and that of the surrounding capsid ⟨Mcap⟩. Remarkably, the mass ratio ⟨Mp⟩/⟨Mcap⟩ was invariant for polyelectrolyte molecular weights spanning more than 2 orders of magnitude. To do so, capsids either packaged several chains simultaneously or selectively retained the shortest chains that could fit the capsid interior. Our data are in qualitative agreement with theoretical predictions based on free energy minimization and emphasize the importance of protein self-energy. These findings may give new insights into the nonspecific origin of genome selectivity for a number of viral systems.
Collapse
Affiliation(s)
- Guillaume Tresset
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Mouna Tatou
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Clémence Le Cœur
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Mehdi Zeghal
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Virginie Bailleux
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Amélie Lecchi
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS, 91400 Orsay, France
| | - Katarzyna Brach
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, 27 Wybrzeże Wyspiańskiego, 50-370 Wrocław, Poland
| | - Magdalena Klekotko
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, 27 Wybrzeże Wyspiańskiego, 50-370 Wrocław, Poland
| | - Lionel Porcar
- Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| |
Collapse
|
50
|
Perlmutter JD, Perkett MR, Hagan MF. Pathways for virus assembly around nucleic acids. J Mol Biol 2014; 426:3148-3165. [PMID: 25036288 DOI: 10.1016/j.jmb.2014.07.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/17/2014] [Accepted: 07/07/2014] [Indexed: 12/25/2022]
Abstract
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work, we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find that assembly pathways can be categorized into two classes, in which intermediates are either predominantly ordered or disordered. Our results suggest that estimating the protein-protein and the protein-genome binding affinities may be sufficient to predict which pathway occurs. Furthermore, the calculated phase diagrams suggest that knowledge of the dominant assembly pathway and its relationship to control parameters could identify optimal strategies to thwart or redirect assembly to block infection. Finally, analysis of simulation trajectories suggests that the two classes of assembly pathways can be distinguished in single-molecule fluorescence correlation spectroscopy or bulk time-resolved small-angle X-ray scattering experiments.
Collapse
Affiliation(s)
- Jason D Perlmutter
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Matthew R Perkett
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA.
| |
Collapse
|