Protein assembly and crowding simulations |
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| Institution: | 1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA;2. Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;3. Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;4. Computational Biophysics Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;1. Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China;2. Department of Intensive Care Unit, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China;1. RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;2. RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;3. Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan;4. RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;1. Physics Department, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy;2. Istituto Pasteur – Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro, 5 I-00185 Roma, Italy |
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| Abstract: | Proteins encounter frequent molecular interactions in biological environments. Computer simulations have become an increasingly important tool in providing mechanistic insights into how such interactions in vivo relate to their biological function. The review here focuses on simulations describing protein assembly and molecular crowding effects as two important aspects that are distinguished mainly by how specific and long-lived protein contacts are. On the topic of crowding, recent simulations have provided new insights into how crowding affects protein folding and stability, modulates enzyme activity, and affects diffusive properties. Recent studies of assembly processes focus on assembly pathways, especially for virus capsids, amyloid aggregation pathways, and the role of multivalent interactions leading to phase separation. Also, discussed are technical challenges in achieving increasingly realistic simulations of interactions in cellular environments. |
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