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Sun X, Lian Y, Tian T, Cui Z. Advancements in Functional Nanomaterials Inspired by Viral Particles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2402980. [PMID: 39058214 DOI: 10.1002/smll.202402980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Virus-like particles (VLPs) are nanostructures composed of one or more structural proteins, exhibiting stable and symmetrical structures. Their precise compositions and dimensions provide versatile opportunities for modifications, enhancing their functionality. Consequently, VLP-based nanomaterials have gained widespread adoption across diverse domains. This review focuses on three key aspects: the mechanisms of viral capsid protein self-assembly into VLPs, design methods for constructing multifunctional VLPs, and strategies for synthesizing multidimensional nanomaterials using VLPs. It provides a comprehensive overview of the advancements in virus-inspired functional nanomaterials, encompassing VLP assembly, functionalization, and the synthesis of multidimensional nanomaterials. Additionally, this review explores future directions, opportunities, and challenges in the field of VLP-based nanomaterials, aiming to shed light on potential advancements and prospects in this exciting area of research.
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Affiliation(s)
- Xianxun Sun
- College of Life Science, Jiang Han University, Wuhan, 430056, China
| | - Yindong Lian
- College of Life Science, Jiang Han University, Wuhan, 430056, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Tao Tian
- College of Life Science, Jiang Han University, Wuhan, 430056, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
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Rolf J, Handke J, Burzinski F, Lütz S, Rosenthal K. Amino acid balancing for the prediction and evaluation of protein concentrations in cell-free protein synthesis systems. Biotechnol Prog 2023; 39:e3373. [PMID: 37408088 DOI: 10.1002/btpr.3373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Cell-free protein synthesis (CFPS) systems are an attractive method to complement the usual cell-based synthesis of proteins, especially for screening approaches. The literature describes a wide variety of CFPS systems, but their performance is difficult to compare since the reaction components are often used at different concentrations. Therefore, we have developed a calculation tool based on amino acid balancing to evaluate the performance of CFPS by determining the fractional yield as the ratio between theoretically achievable and experimentally achieved protein molar concentration. This tool was applied to a series of experiments from our lab and to various systems described in the literature to identify systems that synthesize proteins very efficiently and those that still have potential for higher yields. The well-established Escherichia coli system showed a high efficiency in the utilization of amino acids, but interestingly, less considered systems, such as those based on Vibrio natriegens or Leishmania tarentolae, also showed exceptional fractional yields of over 70% and 90%, respectively, implying very efficient conversions of amino acids. The methods and tools described here can quickly identify when a system has reached its maximum or has limitations. We believe that this approach will facilitate the evaluation and optimization of existing CFPS systems and provides the basis for the systematic development of new CFPS systems.
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Affiliation(s)
- Jascha Rolf
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Julian Handke
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Frank Burzinski
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/24/2023] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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Kardynska M, Kogut D, Pacholczyk M, Smieja J. Mathematical modeling of regulatory networks of intracellular processes - Aims and selected methods. Comput Struct Biotechnol J 2023; 21:1523-1532. [PMID: 36851915 PMCID: PMC9958294 DOI: 10.1016/j.csbj.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Regulatory networks structure and signaling pathways dynamics are uncovered in time- and resource consuming experimental work. However, it is increasingly supported by modeling, analytical and computational techniques as well as discrete mathematics and artificial intelligence applied to to extract knowledge from existing databases. This review is focused on mathematical modeling used to analyze dynamics and robustness of these networks. This paper presents a review of selected modeling methods that facilitate advances in molecular biology.
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Affiliation(s)
- Malgorzata Kardynska
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland
| | - Daria Kogut
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Marcin Pacholczyk
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Jaroslaw Smieja
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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Rostami N, Choupani E, Hernandez Y, Arab SS, Jazayeri SM, Gomari MM. SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. J Cell Biochem 2021; 123:417-430. [PMID: 34783057 PMCID: PMC8657535 DOI: 10.1002/jcb.30181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/20/2022]
Abstract
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), a large number of mutations in its genome have been reported. Some of the mutations occur in noncoding regions without affecting the pathobiology of the virus, while mutations in coding regions are significant. One of the regions where a mutation can occur, affecting the function of the virus is at the receptor‐binding domain (RBD) of the spike protein. RBD interacts with angiotensin‐converting enzyme 2 (ACE2) and facilitates the entry of the virus into the host cells. There is a lot of focus on RBD mutations, especially the displacement of N501Y which is observed in the UK/Kent, South Africa, and Brazilian lineages of SARS‐CoV‐2. Our group utilizes computational biology approaches such as immunoinformatics, protein–protein interaction analysis, molecular dynamics, free energy computation, and tertiary structure analysis to disclose the consequences of N501Y mutation at the molecular level. Surprisingly, we discovered that this mutation reduces the immunogenicity of the spike protein; also, displacement of Asn with Tyr reduces protein compactness and significantly increases the stability of the spike protein and its affinity to ACE2. Moreover, following the N501Y mutation secondary structure and folding of the spike protein changed dramatically.
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Affiliation(s)
- Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Yaeren Hernandez
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Seyed S Arab
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed M Jazayeri
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad M Gomari
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
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