Workshops2017-2021

The EU-ASEAN High-Performance Computing (HPC) Virtual School 2021: System Design and HPC Applications is a hands-on virtual curriculum taught by foremost international experts in HPC technology. It is hosted by National Science and Technology Development Agency (NSTDA) Supercomputer Center (ThaiSC), Thailand.

Day 3, 09.00 – 13.00

Module 5

“Large-scale Sequence Analysis with Alignment and Phylogenetic Trees”
Dr. Sebastian Maurer-Stroh
Executive Director, Bioinformatics Institute (BII), Singapore

“Molecular Dynamics: Understanding structure-function-dynamics relationships”
Dr. Yuji Sugita
Team Leader, Computational Biophysics Research Team, RIKEN R-CCS
Dr Chigusa Kobayashi

official site

Recent advances in experimental and theoretical techniques have enabled us to understand detailed mechanisms of gene expression. Since conventional approaches in vitro are usually not enough to fully understand them, integrative approaches combining various techniques are essential to reveal dynamic structures of proteins and DNA in the cell at the molecular level. In this symposium, we discuss how hybrid approaches using the X-ray crystallography, cryo-electron microscopy, single-molecule imaging, and molecular simulations can contribute to the integrative understandings of genome functions.

(Speakers)

Kazuhiro Maeshima, Kayo Hibino, Ryosuke Nagashima (Genome Dynamics Laboratory, National Institute of Genetics)
“Chromatin dynamics and transcription”

Kayo Nozawa (The University of Tokyo, Institute for Quantitative Biosciences)
“Structural and functional basis of the Mediator complex in the eukaryotic transcriptional system”

Shun-ichi Sekine (RIKEN BDR)
“Structural basis of nucleosome transcription by RNA polymerase II”

Takaharu Mori¹, Haruhiko Ehara², Shun-ichi Sekine², Yuji Sugita^1,3,4 (¹RIKEN Theor. Mol. Sci. Lab., ²RIKEN BDR (Yokohama), ³RIKEN BDR (Kobe), ⁴RIKEN R-CCS)
“Dynamic structures of the RNA polymerase II elongation complex by cryo-EM and MD approaches”

Cheng Tan, Shoji Takada (Kyoto University)
“Allostery of Nucleosomal DNA for Transcription Factor Binding”

Hiroaki Yokota (Biophotonics Lab., Grad. Sch. Creation New Photon. Indust.)
“Single-molecule imaging of a non-hexameric Escherichia coli helicase UvrD mutant lacking C-terminal residues”

Recent progress of supercomputers have allowed us to study large biological systems, such as biological membrane, membrane proteins, crowding in the cytoplasm, virus, nucleosome, and chromatin, by computer simulations. In these simulations, it is essential to investigate interactions between multiple biomolecules for understanding biological functions in cellular environments. We show new insight obtained by computer simulations and discuss collaboration with experiments

(Speakers)

Charles L. Brooks III (Univ. of Michigan)
“Exploring free energy landscapes in pH, chemical and sequence spaces”

Giovanni Bruno Brandani, Shoji Takada (Grad. Sch. Sci., Kyoto Univ.)
“Insights into nucleosome dynamics from coarse-grained simulations”

Michael Feig (Michigan State Univ.)
“Crowding in the cellular context: Tales of Clusters and Dynamics”

Sangjae Seo, Huihui Liu, Wataru Shinoda (Grad. Sch. Eng., Nagoya Univ.)
“Coarse-grained molecular dynamics study for protein-lipid complexes”

Wonpil Im (Lehigh Univ)
“Bacterial Outer Membranes and Interactions with Membrane Proteins”

Yuji Sugita (RIKEN)
“Protein-protein and protein-ligand interaction in cellular environments”

(Speakers)

Sep 26

Shun-ichi Sekine (RIKEN BDR)
“Structural basis of chromatin transcription by RNA polymerase II”

Akihiro Kawamoto (IPR, Osaka Univ.)
“Dynamic and Functional states of protein structure revealed by CryoEM”

Radostin Danev (Grad. Sch. of Med., Univ. of Tokyo)
“Cryo-EM with and without phase plates”

Kunio Hirata (RIKEN/SPring-8 Center)
“Qualitative change of structural information provided by quantitative change in data collection”

Eiki Yamashita (IPR, Osaka Univ)
“Structural basis for selective binding of export cargoes by exportin-5”

Hitoshi Kurumizaka (IQB, Univ. of Tokyo)
“Dynamic structural biology for chromatin”

Shoji Takada (Grad. Sch. Sci., Kyoto Univ.)
“Dynamic structure of nucleosomes and transcription regulation: Molecular simulation approach”

Gert-Jan Bekker(IPR, Osaka Univ.)
“Flexible docking and affinity calculation between CDK2 and its inhibitor using multicanonical MD”

Takaharu Mori (RIKEN)
“Structure refinement of large biomolecular systems by cryo-EM flexible fitting”

Yoshie Harada (IPR, Osaka Univ.)
“Application of NV center to life science measurement”

Sep 27

Takanori Kigawa (RIKEN BDR)
“NMR approaches for protein structure and dynamics in the cellular environment”

Yohei Miyanoiri (IPR, Osaka Univ.)
“SAIL-NMR method for studying structural dynamics of larger proteins”

Hajime Tamaki (IPR, Osaka Univ.)
“Protein structure analysis by combination of NMR data and structure prediction method”

Yasushi Okada (RIKEN BDR/ Univ. of Tokyo)
“Dynamic conformation changes of microtubule by kinesin”

Noriyuki Kodera (WPI NanoLSI, Kanazawa Univ.)
“Integration of high-speed AFM and computational science”

Minoru Kubo (Grad. Sch. Life Sci., Univ. Hyogo)
“Prospects and challenges for time-resolved crystallography at SACLA”

Genji Kurisu (IPR, Osaka Univ.)
“Structural atlus of the dynamic electron transfer complexes around Ferredoxin”

Kazuhiro Abe (CeSPI, Nagoya Univ.)
“A mechanism for the H+ extrusion revealed by the crystal structures of the gastric proton pump”

Understanding of protein-protein interactions in cellular environments is one of the essential research issues in biophysics. To understand them, not only X-ray structures of macromolecules but also various experimental and computational methods are necessary. In particular, recent advance of computer simulations allows us to simulate multiple proteins, nucleic acids, and metabolites simultaneously. We discuss about how to combine those computational studies with experimental measurements.

(Speakers)

Yuji Sugita (RIKEN)
“Specific and non-specific protein-protein interactions in cellular environments”

Sanbo Qin, Huan-Xiang Zhou (Florida State University)
“Atomistic modeling of protein liquid-liquid phase separation”

Michael Feig (MSU, QBiC)
“Nonspecific protein-protein interactions in dense protein solutions and near membranes”

Hiroyuki Mori, Sohei Sakashita, Jun Ito, Eiji Ishii, Yoshinori Akiyama (Inst. Front. Life Med. Sci., Kyoto Univ.)
“Identification and characterization of a translation arrest motif in VemP by systematic mutational analysis”

Yoshitsugu Shiro (Univ. Hyogo)
“NO Dynamics in Cellular System”

Biopolymers such as proteins are present in very high concentrations in cells, which greatly affect the dynamics, structure, and function of them. Although these effects, so-called “macromolecular crowding” has been attracting attention, molecular-level mechanisms are still unknown due to its complexity. At this symposium, we focus on the characteristics of the cellular environment and/or cell-mimicking conditions dominated by macromolecular crowding. Combining experimental, theoretical, and computational approaches, we discuss the influence of macromolecular crowding on diffusion, structural stability, and biological reactivity of DNA or proteins.

Miho Yanagisawa (Tokyo Univ. Agri. Technol.)
“Introduction: the world of macromolecular crowding”

Johtaro Yamamoto (Fac. Adv. Life Sci.)
“Evaluation of molecular crowding based on the rotational and translational diffusion measurement in living cells”

Kei Fujiwara (Dep. Biosci. and Info., Keio University)
“A localization wave of proteins reconstituted in artificial cells with crowding environments”

Yoshihiro Murayama (Tokyo Univ. of Agri. and Tech.)
“Brownian motion in dense DNA solutions”

Takuma Akimoto (Tokyo University of Science)
“Anomalous diffusion in heterogeneous environments”

Hideyasu Okamura¹, Takanori Kigawa^1,2 (¹RIKEN QBiC, ²Department of Computer Science, Tokyo Institute of Technology)
“NMR relaxation analysis of the protein under macromolecular crowding environment”

Isseki Yu^1,2, Po-Hung Wang², Michael Feig³, Yuji Sugita^1,2 (¹RIKEN iTHES, ²RIKEN Theoretical Molecular Science Lab., ³Michigan State University)
“Dynamics of Proteins and Metabolites in Cellular Crowding Environment: Theoretical Study with All-atom Molecular Dynamics Simulation”

→ Official Site

(Speakers)

M. Hatanaka (NAIST)
“Computational study on the mechanism of stereoselectivity for flexible chiral catalytic systems”

S. Koda (IMS)
“A theoretical study of the circadian rhythm of clock proteins: Time-scale hierarchy from picosecond to 24 hours”

H. Nakano (Kyoto University)
“Microscopic understanding of electron transfer reactions at electrode-electrolyte interface: Development of a novel first principle calculation method”

T. Joutsuka (Tohoku University)
“Theoretical Development of Interface Spectroscopy by Molecular Simulation”

R. Harada (University of Tsukuba)
“Developments of Efficient Conformational Sampling Methods for Reproducing / Predicting Biologically Relevant Rare Events”

Y. Matsunaga (RIKEN)
“Linking single-molecule experiment and simulation of protein dynamics by machine learning”