دورية أكاديمية
Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles.
| العنوان: | Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles. |
|---|---|
| المؤلفون: | Depta PN; Institute of Solids Process Engineering and Particle Technology (SPE), Hamburg University of Technology, 21073 Hamburg, Germany., Dosta M; Institute of Solids Process Engineering and Particle Technology (SPE), Hamburg University of Technology, 21073 Hamburg, Germany.; Boehringer Ingelheim Pharma GmbH & Co Kg., 88400 Biberach an der Riss, Germany., Wenzel W; Institute of Nanotechnology (INT), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany., Kozlowska M; Institute of Nanotechnology (INT), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany., Heinrich S; Institute of Solids Process Engineering and Particle Technology (SPE), Hamburg University of Technology, 21073 Hamburg, Germany. |
| المصدر: | International journal of molecular sciences [Int J Mol Sci] 2022 Nov 24; Vol. 23 (23). Date of Electronic Publication: 2022 Nov 24. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Basel, Switzerland : MDPI, [2000- |
| مواضيع طبية MeSH: | Hepatitis B virus* , Macromolecular Substances*/chemistry , Artificial Virus-Like Particles*/chemistry, Capsid/chemistry ; Capsid Proteins/chemistry ; Hepatitis B Core Antigens |
| مستخلص: | Macromolecular self-assembly is at the basis of many phenomena in material and life sciences that find diverse applications in technology. One example is the formation of virus-like particles (VLPs) that act as stable empty capsids used for drug delivery or vaccine fabrication. Similarly to the capsid of a virus, VLPs are protein assemblies, but their structural formation, stability, and properties are not fully understood, especially as a function of the protein modifications. In this work, we present a data-driven modeling approach for capturing macromolecular self-assembly on scales beyond traditional molecular dynamics (MD), while preserving the chemical specificity. Each macromolecule is abstracted as an anisotropic object and high-dimensional models are formulated to describe interactions between molecules and with the solvent. For this, data-driven protein-protein interaction potentials are derived using a Kriging-based strategy, built on high-throughput MD simulations. Semi-automatic supervised learning is employed in a high performance computing environment and the resulting specialized force-fields enable a significant speed-up to the micrometer and millisecond scale, while maintaining high intermolecular detail. The reported generic framework is applied for the first time to capture the formation of hepatitis B VLPs from the smallest building unit, i.e., the dimer of the core protein HBcAg. Assembly pathways and kinetics are analyzed and compared to the available experimental observations. We demonstrate that VLP self-assembly phenomena and dependencies are now possible to be simulated. The method developed can be used for the parameterization of other macromolecules, enabling a molecular understanding of processes impossible to be attained with other theoretical models. |
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| معلومات مُعتمدة: | HE 4526/19-2 Deutsche Forschungsgemeinschaft; WE1863/30-2 Deutsche Forschungsgemeinschaft; Brigitte-Schlieben-Lange-Programm Ministry of Science, Research and Art of Baden-Württemberg; Acid 44178 High-Performance Computing Center Stuttgart; 491268466 - Open Access Publishing Deutsche Forschungsgemeinschaft (DFG) and Hamburg University of Technology (TUHH) |
| فهرسة مساهمة: | Keywords: capsid formation; hepatitis B VLP; macromolecular self-assembly; molecular discrete element method; multiscale modeling; supervised learning |
| المشرفين على المادة: | 0 (Capsid Proteins) 0 (Hepatitis B Core Antigens) 0 (Macromolecular Substances) |
| تواريخ الأحداث: | Date Created: 20221211 Date Completed: 20221229 Latest Revision: 20221229 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC9740473 |
| DOI: | 10.3390/ijms232314699 |
| PMID: | 36499027 |
| قاعدة البيانات: | MEDLINE |
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