Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems
November 18 (Thu) – 19 (Fri), 2021
Online using Zoom
November 18 (Thu) – 19 (Fri), 2021
Online using Zoom
General Information
Understanding of the relationships between structure, dynamics, and function of various biomolecules is essential in molecular and cellular biology. Membrane proteins and other complex, large systems are major research targets in terms of their biological importance as well as their roles in drug developments. To get deeper understandings of these systems, computer simulations, such as molecular dynamics (MD) simulations, and structural analysis using cryo-ET/EM are popular tools. In this workshop, we invite experts from these two research areas and discuss the latest research topics and possibilities of future collaborations.
Scientific Program
November 18 (Thu) |
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|---|---|
| (CET) 08:00 – 08:05, (CST) 15:00 – 15:05, (JST) 16:00 – 16:05 | Opening Remarks by Chen Song (Peking University, China) |
| Session 1 | Simulations of Membrane Proteins (Chair: Chen Song (Peking University, China)) |
| (CET) 08:05 – 08:35, (CST) 15:05 – 15:35, (JST) 16:05 – 16:35 | Toby Allen (RMIT University, Australia) |
| Simulations of potassium channel activation, inactivation and modulation. | |
| (CET) 08:35 – 09:05, (CST) 15:35 – 16:05, (JST) 16:35 – 17:05 | Kei-ichi Okazaki (Institute for Molecular Science, Japan) |
| Multiscale simulations of conformational dynamics of transporter and membrane-remodeling proteins in function. | |
| (CET) 09:05 – 09:35, (CST) 16:05 – 16:35, (JST) 17:05 – 17:35 | Ben Corry (Australian National University, Australia) |
| Simulating the interaction between mechanosensitive Piezo channels and their membrane environment. | |
| (CET) 09:35 – 10:05, (CST) 16:35 – 17:05, (JST) 17:35 – 18:05 | Bert de Groot (Max Planck Institute for Biophysical Chemistry, Germany) |
| The molecular dynamics of potassium channel permeation, selectivity and gating. | |
| << Break >> | |
| Session 2 | Simulations and Cryo-ET/EM of Large Biomolecules (Chair: Hai-Guang Liu (Beijing Computational Science Research Center, China)) |
| (CET) 10:20 – 10:50, (CST) 17:20 – 17:50, (JST) 18:20 – 18:50 | Masahide Kikkawa (University of Tokyo, Japan) |
| Combination of cryo-EM ang genetics to study cilia/flagella. | |
| (CET) 10:50 – 11:20, (CST) 17:50 – 18:20, (JST) 18:50 – 19:20 | Sai Li (Tsinghua University, China) |
| In-situ architecture and neutralization mechanism of SARS-CoV-2. | |
| (CET) 11:20 – 11:50, (CST) 18:20 – 18:50, (JST) 19:20 – 19:50 | Joanna Trylska (Warsaw University, Poland) |
| Macromolecular crowding affects diffusion and dynamics of the hepatitis C virus protease. | |
November 19 (Friday) |
|
| Session 3 | Simulations and Cryo-ET/EM of Large Biomolecules (Chair: Shoji Takada (Kyoto University, Japan)) |
| (CET) 08:00 – 08:30, (CST) 15:00 – 15:30, (JST) 16:00 – 16:30 | Atsunori Oshima (Nagoya University, Japan) |
| Structural biology of gap junction family proteins. | |
| (CET) 08:30 – 09:00, (CST) 15:30 – 16:00, (JST) 16:30 – 17:00 | Zhenli Xu (Shanghai Jiao Tong University, China) |
| Random batch Ewald method for high-scalable MD simulations. | |
| (CET) 09:00 – 09:30, (CST) 16:00 – 16:30, (JST) 17:00 – 17:30 | Syma Khalid (University of Oxford, UK) |
| MD simulations of the Mla complex initiated from a new cryoEM structure. | |
| << Break >> | |
| Session 4 | Enhanced Sampling Simulations (Chair: Yuji Sugita (RIKEN, Japan)) |
| (CET) 09:45 – 10:15, (CST) 16:45 – 17:15, (JST) 17:45 – 18:15 | Yuko Okamoto (Nagoya University, Japan) |
| Generalized-ensemble simulations of biomolecular systems. | |
| (CET) 10:15 – 10:45, (CST) 17:15 – 17:45, (JST) 18:15 – 18:45 | Xin Zhou (University of Chinese Academy of Sciences, China) |
| High Efficient Sampling of Proteins via Adaptive Multiscale Simulations. | |
| (CET) 10:45 – 11:15, (CST) 17:45 – 18:15, (JST) 18:45 – 19:15 | Akio Kitao (Tokyo Institute of Technology, Japan) |
| PaCS-MD/MSM to investigate protein motions and association/dissociation of protein complexes. | |
| (CET) 11:15 – 11:20, (CST) 18:15 – 18:20, (JST) 19:15 – 19:20 | Closing Remarks by Yuji Sugita (RIKEN, Japan) |
Registration
The workshop is open to anyone registered at
https://www.wjx.cn/vj/OtareMG.aspx and is free of charge.
The deadline for the registration is November 17, 2021.
Once registered, you will receive the link to the Zoom meeting a few days before the workshop. Please do not distribute the Zoom link you receive, instead every attendee must register at this page to get the link. Recoding the workshop talks are prohibited. By registering at this page, you are supposed to agree with the above statements.
Organizing Committee
Chen Song Center for Quantitative Biology, Peking UniversityYuji Sugita RIKEN CPR, BDR, and R-CCS
Shoji Takada Department of Biophysics, Kyoto University
For any questions regarding the workshop, please send an email to Prof. Chen Song (c.song[at]pku.edu.cn) or Dr. Yuji Sugita (sugita[at]riken.jp) or Prof. Shoji Takada (takada[at]biophys.kyoto-u.ac.jp).
Acknowledgement
The workshop is supported by the MOST-RIKEN international collaboration grant (2021YFE0108100) as well as Program for Promoting Researches on the Supercomputer Fugaku (JPMXP1020200101). The top figure on the homepage was designed by Dr. Ai Niitsu (RIKEN).