Yuji Sugita

RIKEN Cluster for Pioneering Research,  Japan

RIKEN Center for Biosystems Dynamics Research, Japan

RIKEN Center for Computational Science, Japan

Talk Title: Protein functions in crowded cellular environments

Abstract: Inside of the cell is highly crowded with proteins, RNAs, their complexes, and various metabolites. How proteins can maintain conformational stability and properly function in crowded cellular environments is a fundamental question in molecular and cellular biology. To answer the question using computer simulations, Extensive molecular dynamics (MD) simulations with multi-scale molecular models that include atomistic, coarse-grained (CG), and hybrid QM/MM models are useful. For this purpose, our group has developed multi-scale MD software, GENESIS, and optimized it to supercomputers like Fugaku. 

After introducing our computational methods and software developments, I will introduce several application studies related to crowded cellular environments. In each simulation, we utilized the most suitable molecular models (either atomistic, CG, or QM/MM) and carried out extensive simulations using supercomputers like K computer, Fugaku, or Anton2. These simulations highlight the importance of conformational flexibilities of proteins and non-specific molecular interactions in biological functions in cellular environments.

Zhi Qi

Peking University 

Talk title: Deciphering the molecular mechanism of DNA-protein interactive co-condensation

Wei Han

Hong Kong Baptist University

Talk title: Bridging Atomic Details and Overall Kinetics: A Multiscale Computational Approach to Understand Peptide Self-Assembly

Yu Li

The Chinese University of Hong Kong

Talk title: RNA structure prediction with deep learning

Haibin Su

The Hong Kong University of Science and Technology

Talk title: Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins

Qianyuan Tang

Hong Kong Baptist University 

Talk title: Unravelling Protein Dynamics through Analysis of AlphaFold Prediction Error

Lizhe Zhu

The Chinese University of Hong Kong, Shenzhen

Talk title: Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching

Xiangze Zeng

Hong Kong Baptist University 

Talk title: From the Single-Chain Behavior to Phase Behavior of Intrinsically Disordered Proteins