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Luo H, Ma Y, Bi J, Li Z, Wang Y, Su Z, Gerstweiler L, Ren Y, Zhang S. Experimental and molecular dynamics simulation studies on the physical properties of three HBc-VLP derivatives as nanoparticle protein vaccine candidates. Vaccine 2024:S0264-410X(24)00599-1. [PMID: 38811268 DOI: 10.1016/j.vaccine.2024.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Self-assembling virus-like particles (VLPs) are promising platforms for vaccine development. However, the unpredictability of the physical properties, such as self-assembly capability, hydrophobicity, and overall stability in engineered protein particles fused with antigens, presents substantial challenges in their downstream processing. We envision that these challenges can be addressed by combining more precise computer-aided molecular dynamics (MD) simulations with experimental studies on the modified products, with more to-date forcefield descriptions and larger models closely resembling real assemblies, realized by rapid advancement in computing technology. In this study, three chimeric designs based on the hepatitis B core (HBc) protein as model vaccine candidates were constructed to study and compare the influence of inserted epitopes as well as insertion strategy on HBc modifications. Large partial VLP models containing 17 chains for the HBc chimeric model vaccines were constructed based on the wild-type (wt) HBc assembly template. The findings from our simulation analysis have demonstrated good consistency with experimental results, pertaining to the surface hydrophobicity and overall stability of the chimeric vaccine candidates. Furthermore, the different impact of foreign antigen insertions on the HBc scaffold was investigated through simulations. It was found that separately inserting two epitopes into the HBc platform at the N-terminal and the major immunogenic regions (MIR) yields better results compared to a serial insertion at MIR in terms of protein structural stability. This study substantiates that an MD-guided design approach can facilitate vaccine development and improve its manufacturing efficiency by predicting products with extreme surface hydrophobicity or structural instability.
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Affiliation(s)
- Hong Luo
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia; State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Yanyan Ma
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jingxiu Bi
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yingli Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Lukas Gerstweiler
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia.
| | - Ying Ren
- State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
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Mao R, Zhang H, Bie L, Liu LN, Gao J. Million-atom molecular dynamics simulations reveal the interfacial interactions and assembly of plant PSII-LHCII supercomplex. RSC Adv 2023; 13:6699-6712. [PMID: 36860540 PMCID: PMC9969236 DOI: 10.1039/d2ra08240c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Protein-protein interface interactions dictate efficient excitation energy transfer from light-harvesting antennas to the photosystem II (PSII) core. In this work, we construct a 1.2 million atom-scale model of plant C2S2-type PSII-LHCII supercomplex and perform microsecond-scale molecular dynamics (MD) simulations to explore the interactions and assembly mechanisms of the sizeable PSII-LHCII supercomplex. We optimize the nonbonding interactions of the PSII-LHCII cryo-EM structure using microsecond-scale MD simulations. Binding free energy calculations with component decompositions reveal that hydrophobic interactions predominantly drive antenna-core association and the antenna-antenna interactions are relatively weak. Despite the positive electrostatic interaction energies, hydrogen bonds and salt bridges mainly provide directional or anchoring forces for interface binding. Analysis of the roles of small intrinsic subunits of PSII suggests that LHCII and CP26 first interact with small intrinsic subunits and then bind to the core proteins, whereas CP29 adopts a one-step binding process to the PSII core without the assistance of other factors. Our study provides insights into the molecular underpinnings of the self-organization and regulation of plant PSII-LHCII. It lays the framework for deciphering the general assembly principles of photosynthetic supercomplexes and possibly other macromolecular structures. The finding also has implications for repurposing photosynthetic systems to enhance photosynthesis.
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Affiliation(s)
- Ruichao Mao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan 430070 Hubei China
| | - Han Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan 430070 Hubei China
| | - Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan 430070 Hubei China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool Liverpool L69 7ZB UK .,Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China Qingdao 266003 China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University Wuhan 430070 Hubei China
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Zhang B, Yin S, Wang Y, Su Z, Bi J. Cost-effective purification process development for chimeric hepatitis B core (HBc) virus-like particles assisted by molecular dynamic simulation. Eng Life Sci 2021; 21:438-452. [PMID: 34140854 PMCID: PMC8182290 DOI: 10.1002/elsc.202000104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Inserting foreign epitopes to hepatitis B core (HBc) virus-like particles (VLPs) could influence the molecular conformation and therefore vary the purification process. In this study, a cost-effective purification process was developed for two chimeric HBc VLPs displaying Epstein-Barr nuclear antigens 1 (EBNA1), and hepatitis C virus (HCV) core. Both chimeric VLPs were expressed in soluble form with high production yields in Escherichia coli. Molecular dynamic (MD) simulation was employed to predict the stability of chimeric VLPs. HCV core-HBc was found to be less stable in water environment compared with EBNA1-HBc, indicating its higher hydrophobicity. Assisting with MD simulation, ammonium sulfate precipitation was optimized to remove host cell proteins with high target protein recovery yields. Moreover, 99% DNA impurities were removed using POROS 50 HQ chromatography. In characterization measurement, we found that inserting HCV core epitope would reduce the ratio of α-helix of HCV core-HBc. This could be another reason on the top of its higher hydrophobicity predicted by MD simulation, causing its less stability. Tertiary structure, transmission electron microscopy, and immunogenicity results indicate that two chimeric VLPs maintained correct VLP structure ensuring its bioactivity after being processed by the developed cost-effective purification approach.
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Affiliation(s)
- Bingyang Zhang
- School of Chemical Engineering & Advanced Materials, Faculty of Engineering, Computer and Mathematical SciencesUniversity of AdelaideAdelaideSAAustralia
| | - Shuang Yin
- School of Chemical Engineering & Advanced Materials, Faculty of Engineering, Computer and Mathematical SciencesUniversity of AdelaideAdelaideSAAustralia
| | - Yingli Wang
- School of Chinese Medicine and Food EngineeringShanxi University of Traditional Chinese MedicineJinzhongShanxi ProvinceP. R. China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process EngineeringChinese Academy of SciencesBeijingP. R. China
| | - Jingxiu Bi
- School of Chemical Engineering & Advanced Materials, Faculty of Engineering, Computer and Mathematical SciencesUniversity of AdelaideAdelaideSAAustralia
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 325] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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Jeong H, Seong BL. Exploiting virus-like particles as innovative vaccines against emerging viral infections. J Microbiol 2017; 55:220-230. [PMID: 28243941 PMCID: PMC7090582 DOI: 10.1007/s12275-017-7058-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 01/20/2023]
Abstract
Emerging viruses pose a major threat to humans and livestock with global public health and economic burdens. Vaccination remains an effective tool to reduce this threat, and yet, the conventional cell culture often fails to produce sufficient vaccine dose. As an alternative to cell-culture based vaccine, virus-like particles (VLPs) are considered as a highpriority vaccine strategy against emerging viruses. VLPs represent highly ordered repetitive structures via macromolecular assemblies of viral proteins. The particulate nature allows efficient uptake into antigen presenting cells stimulating both innate and adaptive immune responses towards enhanced vaccine efficacy. Increasing research activity and translation opportunity necessitate the advances in the design of VLPs and new bioprocessing modalities for efficient and cost-effective production. Herein, we describe major achievements and challenges in this endeavor, with respect to designing strategies to harnessing the immunogenic potential, production platforms, downstream processes, and some exemplary cases in developing VLP-based vaccines.
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Affiliation(s)
- Hotcherl Jeong
- Department of Pharmacy, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Baik Lin Seong
- Department of Biotechnology & Vaccine Translational Research Center, Yonsei University, Seoul, 03722, Republic of Korea.
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Tekewe A, Connors NK, Middelberg APJ, Lua LHL. Design strategies to address the effect of hydrophobic epitope on stability and in vitro assembly of modular virus-like particle. Protein Sci 2016; 25:1507-16. [PMID: 27222486 DOI: 10.1002/pro.2953] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/20/2016] [Indexed: 11/09/2022]
Abstract
Virus-like particles (VLPs) and capsomere subunits have shown promising potential as safe and effective vaccine candidates. They can serve as platforms for the display of foreign epitopes on their surfaces in a modular architecture. Depending on the physicochemical properties of the antigenic modules, modularization may affect the expression, solubility and stability of capsomeres, and VLP assembly. In this study, three module designs of a rotavirus hydrophobic peptide (RV10) were synthesized using synthetic biology. Among the three synthetic modules, modularization of the murine polyomavirus VP1 with a single copy of RV10 flanked by long linkers and charged residues resulted in the expression of stable modular capsomeres. Further employing the approach of module titration of RV10 modules on each capsomere via Escherichia coli co-expression of unmodified VP1 and modular VP1-RV10 successfully translated purified modular capomeres into modular VLPs when assembled in vitro. Our results demonstrate that tailoring the physicochemical properties of modules to enhance modular capsomeres stability is achievable through synthetic biology designs. Combined with module titration strategy to avoid steric hindrance to intercapsomere interactions, this allows bioprocessing of bacterially produced in vitro assembled modular VLPs.
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Affiliation(s)
- Alemu Tekewe
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, Centre for Biomolecular Engineering, St Lucia, Queensland 4072, Australia
| | - Natalie K Connors
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, Centre for Biomolecular Engineering, St Lucia, Queensland 4072, Australia
| | - Anton P J Middelberg
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, Centre for Biomolecular Engineering, St Lucia, Queensland 4072, Australia
| | - Linda H L Lua
- The University of Queensland, UQ Protein Expression Facility, University of Queensland, St Lucia, Queensland 4072, Australia
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Engineering virus-like particles as vaccine platforms. Curr Opin Virol 2016; 18:44-9. [PMID: 27039982 DOI: 10.1016/j.coviro.2016.03.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/11/2016] [Accepted: 03/08/2016] [Indexed: 02/03/2023]
Abstract
Virus-like particles (VLPs) have been utilized as vaccine platforms to increase the immunogenicity of heterologous antigens. A variety of diverse VLP types can serve as vaccine platforms, and research has focused on engineering VLPs to improve their efficacy as vaccines, enhance their stability, and allow for more versatile display of antigens. Here, we review selected VLP vaccine platforms, highlight efforts to improve these platforms through structure-informed rational design, and point to areas of future research that will assist in these efforts.
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