Workshops2012 –

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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”

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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”

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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.

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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.

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」

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”

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”

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”