時間：2026-07-03(五) 15:20 pm

講題：Molecular Modeling of Viral Envelope Architecture:Applications of the SPICA Coarse-Grained Force Field to Protein–Lipid Assemblies

講者 :  Prof. Wataru Shinoda

服務單位：Research Institute for Interdisciplinary Science (RIIS), Okayama University , Department of Chemistry, School of Science, Okayama University  

地點：4樓創意講堂

主持人：邱繼正教授

摘要：

          Biological membranes form functional architectures through a delicate balance of protein–protein, protein–lipid, and lipid–lipid interactions. Capturing such mesoscale organization at molecular resolution remains challenging because the relevant length and time scales often lie beyond the reach of routine all-atom molecular dynamics simulations. This presentation highlights recent developments and applications of the SPICA coarse-grained force field for studying large protein–lipid assemblies.

          The first part introduces the SPICA protein model, developed to be compatible with SPICA lipid and solvent models and to reproduce key thermodynamic and structural properties of proteins in aqueous and membrane environments. Recent improvements, including secondary-structuredependent backbone interactions and expanded protein–lipid interaction parameters, further extend its applicability to diverse protein systems and lipid compositions.

          Two viral envelope systems are then discussed as representative applications. In the hepatitis B virus model, coarse-grained simulations of the envelope–capsid complex reproduced experimental electron density profiles and revealed molecular interactions among capsid spikes, envelope S proteins, and lipids. In the SARS-CoV-2 envelope study, systematic bicelle-to-vesicle simulations showed that the formation of a closed envelope with the correct topology requires cooperative M–S protein contacts, together with M–lipid and S–lipid interactions.

          Together, these studies demonstrate how chemically specific coarse-grained simulations can connect local molecular interactions to large-scale membrane organization, providing a useful framework for analyzing viral envelopes and related protein–lipid assemblies.

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