Yuji Sugita (RIKEN), Takaharu Mori (RIKEN)
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"
Yuji Sugita (RIKEN), Masaki Yamamoto (RIKEN), Genji Kurisu (Osaka Univ.)
(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"
Yuji Sugita (RIKEN), Kohei Tsumoto (The University of Tokyo)
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 Univ.)
"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"
Miho Yanagisawa (Tokyo University of Agriculture and Technology), Isseki Yu (RIKEN)
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 Univ.)
"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 Univ. of Science)
"Anomalous diffusion in heterogeneous environments"
Hideyasu Okamura1, Takanori Kigawa1,2 (1RIKEN QBiC, 2Department of Computer Science, Tokyo Institute of Technology)
"NMR relaxation analysis of the protein under macromolecular crowding environment"
Isseki Yu1,2, Po-Hung Wang2, Michael Feig3, Yuji Sugita1,2 (1RIKEN iTHES, 2RIKEN Theoretical Molecular Science Lab., 3Michigan State Univ.)
"Dynamics of Proteins and Metabolites in Cellular Crowding Environment: Theoretical Study with All-atom Molecular Dynamics Simulation"
Kang Kim (Osaka University), Kiyoshi Yagi (RIKEN), Toshifumi Mori (IMS)
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(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”
Yuji Sugita (RIKEN), Kiyoshi Yagi (RIKEN)
Yuji Sugita (RIKEN), Yutaka Ito (Tokyo Metropolitan University)
In living cells, a variety of soluble macromolecules exist in a very crowded environment. Recent advancements in in situ observations by NMR and in large scale simulations using K computer have been contributing to investigate the various effects perturbing proteins' structures, dynamics and folding stabilities as well as the mechanisms permitting proteins to find their binding partners efficiently under the macromolecular crowding. In this symposium, we would overview the recent progresses and discuss future perspectives of the biophysical researches under intracellular environments in the field of life science.
(Speakers)
Gary J. Pielak (University of North Carolina)
"Intermolecular Quinary Interactions Modulate Protein Stability in Living Cells"
Hideyasu Okamura, Takanori Kigawa (QBiC, RIKEN)
"NMR relaxation analysis of the protein under macromolecular crowding environment"
Kohsuke Inomata (Quantitative Biology Center (QBiC), RIKEN)
"In-cell NMR analysis for protein conformational diversity in a cell"
Teppei Ikeya, Jin Inoue, Yutaka Ito (Tokyo Metropolitan University)
"Dynamics of intrinsically disordered proteins in living cells"
Michael Feig, Yildirim Asli (Michigan State University)
"Combining Structure with Genomics"
Yuji Sugita (RIKEN), Takaharu Mori (RIKEN)
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Proteins, nucleic acids, lipids, and carbohydrate are major components of biological systems. To explore molecular dynamics of those complexes such as protein-membrane and cytoplasmic systems by computer simulations, realistic representation of molecules, reliable force-field parameters, and advanced techniques for whole structure modeling are required. The aim of this workshop is to offer an opportunity to exchange and share ideas from recent studies focusing on "Realistic modeling and simulations of biomolecular systems".
Alexander D. MacKerell, Jr. (University of Maryland, USA)
"A Polarizable Force Field for Biological Macromolecules based on the Classical Drude Oscillator Model"
Wonpil Im (University of Kansas, USA)
"Biomolecular Modeling and Simulation using CHARMM-GUI"
Michael Feig (Michigan State University, USA)
"Chromosomal Dynamics and Correlations between Gene Location and Protein Function from Experimentally-Driven Models of Bacterial Nucleoids"
Isseki Yu (Theoretical Molecular Science Laboratory, RIKEN)
"Dynamics and Interactions of Macromolecules in the Cytoplasm of Mycoplasma Genitalium: All-atom Molecular Dynamics Study"
Yuji Sugita (RIKEN), Yuko Okamoto (Nagoya University)
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After ICMS2013, we would like to hold a one-day workshop on molecular simulations on biophysics and biochemistry. Here we invite 7 professors (all of them are the invited speakers of ICMS2013) and 6 young researchers in Japan. At workshop, we hope to have fruitful discussion about both simulation applications and methodological developments in this field.
Yuji Sugita (RIKEN), Shoji Takada (Kyoto University), Koichi Takahashi (RIKEN), Michael Feig (Michigan State University)
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The overall aim of this workshop is to bring together a mix of computational and experimental researchers to discuss current challenges in developing comprehensive views of cellular environments. More specifically, there are three main themes: 1) What are the biophysical consequences of cellular environments on protein stability and dynamics beyond simple volume exclusion effects? 2) What are the details of the structure and dynamics of genomic DNA and its transcriptional regulation? 3) How can we develop realistic structural and dynamic models of interacting biomolecules at cellular levels? In this workshop, we invite 20 researchers from abroad and from Japan and would like to have fruitful discussion about this new research topics.
Yuji Sugita (RIKEN), Koichi Takahashi (RIKEN)
cellular nucleus is also a crowded environment where long DNA chains are packed with high densities. Recently, the high packed DNA structures with DNA binding proteins have been investigated using X-ray crystallography, cyoelectron microscopy, and small-angle X-ray scattering (SAXS). These updated experimental information encourages multi-scale computational modeling of nucleosomes or chromatin fibers. In the symposium, both experimental and computational scientists show the latest data and discuss about the structures and dynamics of genomic DNA in chromosome or nucleus.
(Speakers)
Hidetoshi Kono, Yoshiteru Yonetani, Jinzen Ikebe, Shun Sakuraba, Hisashi Ishida (Molecular Modeling and Simulation, JAEA)
"Free Energy Profile for Nucleosomal DNA unwrapping"
Hitoshi Kurumizaka (Waseda University, Faculty of Science and Engineering)
"Structural versatility of nucleosomes in higher order chromatin"
Shoji Takada (Department of Biophysics, Graduate School of Science, Kyoto University)
"Structure of model chromatin and dynamics of transcription factors studied by coarse-grained simulations"
Kazuhiro Maeshima (National Institute of Genetics)
"How is nucleosome fiber organized in the cell?"
Kazunari Kaizu, Koichi Takahashi (Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center (QBiC))
「Diffusion-controlled reaction rate-laws in intracellular environment with molecular crowding: A single-particle- level simulation study」
Mitsunori Ikeguchi (Yokohama City Univ.), Yuji Sugita(RIKEN)
While K supercomputer just starts working recently, the design of next-generation super computers also begins. Although in the next-generation super computers, computer architectures will dramati- cally change, what science will be done using the next super computers is important. Therefore, based on the report of future HPCI systems in MEXT, large-scale computational protein science is discussed.
(Speakers)
Mitsunori Ikeguchi (Yokohama City Univ.)
"Computational protein science in ExaFlops era"
Yuji Sugita (RIKEN)
"Molecular dynamics simulations under cellular environments"
Noriyuki Yoshii (Nagoya Univ.)
"Protein science by the large-scale molecular dynamics calculation using the next-generation supercomputers"
Takefumi Yamashita (Univ. of Tokyo)
"Drug Design Assisted by All-Atom Molecular Dynamics Simulations:An Outlook for the ExaFlops Era"
Yuji Mochizuki (Rikkyo Univ., Univ. of Tokyo)
"Computational protein science in ExaFlops era"
Yoshiki Yamaguchi (RIKEN), Yuji Sugita (RIKEN), Suyong Re (RIKEN)
RIKEN official site
(Speakers)
Yuji Sugita (RIKEN)
"Opening Remarks"
Yoshiki Yamaguchi (RIKEN)
"Structural glycobiology overview"
Kazuo Yamamoto (The University of Tokyo)
"Role of malectin in protein quality control"
Wonpil Im（Center for Bioinformatics, The University of Kansas）
"Toward Glycan Structure Modeling and Simulation"
Suyong Re (RIKEN)
"Structure prediction of glycans using replica-exchange molecular dynamics simulation"
Seiko Flora Kinoshita (Soka University)
"Development of tools to aid in glycan profiling analysis"
Shinobu Kitazume (RIKEN)
"How glycosylation regulates amyloid β production?"
Hiromune Ando (Gifu University, iCeMS Kyoto University)
"One step toward dynamic raft science: Developing ganglioside probes for
single molecule imaging in living cell membrane"
Akinori Kidera (Yokohama City Univ.), Yuji Sugita (RIKEN)
K computer (the ten Peta FLOPS supercomputer installed in Kobe) provides an enormous enhancement of the capability in computational life science. This symposium intends to bring forth the possibility of supercomputing in life science fully utilizing K computer. Particularly, it focuses on the multi-scale descriptions of molecular networks and cellular dynamics by integrating the molecular and the cellular simulation methods.
(Speakers)
Michael Feig (Michigan State University)
"Dynamics and stability of proteins in cellular environments"
Koichi Takahashi1,2,3 (1RIKEN QBiC, 2Keio Inst. Adv. Biosci., 3Osaka Univ. Grad. Sch. Front. Biosci.)
"How supercomputing can help change cell biology"
Hideo Yokota1,2, Yasuhiro Sunaga2, Sigeho Noda3 (1ASI, Riken, 2iSLIM, Riken, 3ACCC, Riken)
"Development of the cell simulator in consideration of space"
Yoshinori Tamada1, Teppei Shimamura2, Rui Yamaguchi2, Atsushi Niida2, Ayumu Saito2, Yuto Kataoka1,2, Seiya Imoto2, Masao Nagasaki3, Satoru Miyano1,4 (1Grad. Sch. Info. Sci. Tech., Univ. Tokyo, 2Inst. Med. Sci., Univ. Tokyo, 3Tohoku Med. Megabank, Tohoku Univ., 4CSRP, RIKEN)
"Large scale gene network estimation with K computer"
Ryo Yoshida (The Institute of Statistical Mathematics, Research Organization of Information and Systems)
"Biological system modeling and data assimilation"
