International Conference on Stracturak Genomics 2013

Scientific Program

Satellite Workshops (* tentative titles)     29th July, 2013

0a Biopharmaceuticals and protein manipulation sponsored by Bioconjugate project of Hokkaido University
Place :Plaza Hall, Keio Plaza Hotel
July 29, 2013
Plaza Hall, Keio Plaza Hotel
9:00 am Opening remarks
Katsumi Maenaka (Hokkaido University, Japan)
9:05 - 11:40 am

9:05 am

9:30 am

9:55 am

10:20 am

10:45 am

11:10 am

11:35 am
Chair : Yoshikazu Tanaka (Hokkaido University, Japan)
Toyoyuki Ose (Hokkaido University, Japan)

Session 1
Masashi Sonoyama (Gunma University, Kiryu, Japan)
Development of partially fluorinated phospholipids as materials for membrane protein research
Shohei Koide (The University of Chicago, Chicago, IL, USA)
Structure-guided directed evolution

Session 2
Pamela Bjorkman (California Institute of Technology, CA, USA)
The Protein Expression Center at Caltech
Edward N. Baker (University of Auckland, Auckland, New Zealand)
Horses for courses: Choosing appropriate expression hosts for production of recombinant proteins
David Stuart (University of Oxford, Oxford, UK)
Making virus capsids and tricky cell surface proteins in eukaryotic cells, and aspects of their use for vaccine and pharmaceutical discovery.

Session 3
Shigeyuki Yokoyama (RIKEN Structural Biology Laboratory, Yokohama, Japan)
Cell-free synthesis of protein complexes and integral membrane proteins for structural biology
Dr. Matthias Harbers (CellFree Sciences Co., Ltd., Ehime, Japan)
A universal protein expression platform for structural genomics
12:00 am Closed
1. Development of partially fluorinated phospholipids as materials for membrane protein research

Masashi Sonoyama
Division of Molecular Science, Faculty of Science and Technology, Gunma University

We have been developing novel partially fluorinated phospholipids, phospholipids whose hydrogen atoms in the terminal segment of the acyl chain are substituted to fluorine atoms. I will talk about some interesting physical properties of lipid membrane of a novel partially fluorinated phosphatidylcholine ant a successful application to a membrane protein bacteriorhodopsin.

2. Structure-guided directed evolution

Shohei Koide
Department of Biochemistry and Molecular Biology, The University of Chicago

Directed evolution is a powerful technology for manipulating and creating protein function, and it is applicable to diverse protein systems. I will describe technological aspects important for establishing a directed evolution project and illustrate how integrating structural biology accelerates such a project.

3. The Protein Expression Center at Caltech

Pamela Bjorkman
California Institute of Technology, CA, USA

High throughput protein expression is required for structural and biochemical studies in many laboratories. For example, we need large quantities of purified broadly neutralizing antibodies and their HIV-1 antigens for X-ray crystallography as well as for in vitro and in vivo experiments. Academic laboratories rarely have the expertise to assemble the most up-to-date and efficient expression systems for producing proteins. However the Caltech Protein Expression Center (PEC) has over 15 years of experience producing and purifying proteins for the Caltech community and many outside users. I will describe some of the methods we use to optimize protein expression and purification.

4. Horses for courses: Choosing appropriate expression hosts for production of recombinant proteins

Edward Baker, Ghader Bashiri and James Dickson
School of Biological Sciences, University of Auckland

One of the major bottlenecks in the structural and functional characterization of proteins lies in the expression of correctly-folded soluble proteins. This problem can be greatly reduced by the choice of a suitable expression host. We work on two classes of proteins that are of interest for drug design: human kinases implicated in cancer and proteins from Mycobacterium tuberculosis, the cause of TB. For expressing human kinases we routinely use expression in baculovirus-Sf9 insect cells; using the MultiBac system developed by Berger et al. [1] protein complexes comprising many subunits can be readily expressed. Our expression of the human phosphoinositide 3-kinase (PI3K) will be used as an example in which high levels of fully-active protein can be readily expressed. For proteins from Mycobacterium tuberculosis, we encountered severe solubility problems when expressing in E. coli. To overcome this we have developed a very convenient set of vectors for expression in Mycobacterium smegmatis [2], which has the advantage of having similar chaperones, cofactors etc. as M. tuberculosis, but is non-pathogenic and much faster-growing, and suitable for expression of selenomethionyl derivatives.

1. Berger, I., Fitzgerald, D.J. and Richmond, T.J. (2004). Nature Biotechnol. 22, 1583-1587.
2. Goldstone, R.M., Moreland, N.J., Bashiri, G., Baker, E.N. and Lott, J.S. (2008). Protein Expr. Purif. 57, 81-87.
Making virus capsids and tricky cell surface proteins in eukaryotic cells, and aspects of their use for vaccine and pharmaceutical discovery.

David Stuart
University of Oxford, Oxford, UK

I will outline some of the current methods developed and used in Oxford for making proteins and assembled complexes in human and insect cells, with a particular focus on capsids of small RNA viruses and cell surface proteins. I will also briefly suggest how these methods, together with new downstream experimental and in silico methods might inform vaccine and drug discovery more effectively than in the past.

6. Cell-free synthesis of protein complexes and integral membrane proteins for structural biology

Shigeyuki Yokoyama
RIKEN Structural Biology Laboratory

Cell-free protein synthesis is advantageous to structural biology. We have established protein preparation techniques using the Escherichia coli cell-free protein synthesis system for large-scale expression of difficult targets suitable for structure determination by X-ray crystallography. The quantity and the quality of the cell-free expressed proteins were generally better than those of the proteins expressed in conventional cell-based systems, because various parameters can be more precisely controlled. First, cell-free protein synthesis is suitable for the co-expression of two or more components of the target protein complexes. Protein complexes, including heterodimers of functional domains from mammalian membrane and cytosolic proteins, have been synthesized and their crystal structures have been determined. Second, cell-free protein synthesis in the presence of detergents and/or lipids is suitable for expression of integral membrane proteins. Microbial rhodopsins were prepared by the cell-free methods and crystallized by the lipidic cubic phase method. Their crystal structures have been solved by X-ray crystallography. Furthermore, human GPCRs were prepared by the cell-free method, and their ligand binding activities indicated that these cell-free synthesized GPCRs were functional. Monoclonal antibodies were raised against the cell-free synthesized GPCRs, some of which exhibited tertiary structure-dependent binding to the antigens. These antibodies are expected to be useful for crystallization of the GPCRs as well as for development of antibody drugs. Third, cell-free techniques are useful for incorporation of non-standard amino acids site-specifically into proteins, which has been applied to preparation of nucleosome core particles having epigenetic modifications of histones.

7. A universal protein expression platform for structural genomics

Matthias Harbers
Cell Free Sciences

When the human genome project started, Japan decided to put additional efforts on the analysis of the transcriptome. This led to large cDNA clone resources, a strong contribution the structural genomics, and the development of new technologies. Among those technologies, cell-free protein synthesis approaches were established for the expression of a wide range of proteins. The wheat germ cell-free protein expression system developed at Ehime University and marketed by CellFree Sciences is for example used to express some 14,000 human proteins for analysis. The expression system can be fully automated for high-throughput screening and is scalable produce mg amounts of protein. As of today, the wheat germ cell-free protein synthesis system is used as one of the universal protein expression platforms in structural genomics and other applications requiring a large number of different proteins.

0b Drug Discovery and Structural Life Science sponsored by platform for drug discovery, bioinformatics, and structural life science (MEXT)
Place :Plaza Hall, Keio Plaza Hotel
July 29, 2013
Plaza Hall, Keio Plaza Hotel
1:00 pmOpening remarks
Soichi Wakatsuki
(Stanford University, USA)
1:10 - 2:00 pm

1:10 pm
1:35 pm
Session 1 – Small molecule screening
Chair : Tsuyoshi Inoue (Osaka University, Osaka, Japan)
Aled Edwards (University of Toronto, Toronto, Canada)
Kouhei Tsumoto(University of Tokyo, Tokyo, Japan)
2:00 - 2:50 pm

2:00 pm

2:25 am
Session 2: Biologics and vaccine
Chair : Junichi Takagi (Osaka University, Osaka, Japan)
Ian Wilson (The Scripps Research Institute, La Jolla, CA, USA)
Broad Neutralization of Influenza Viruses and Implications for a Universal Vaccine and Therapy
Hiroshi Kida (Hokkaido University, Sapporo, Japan)
For the control of avian influenza and preparedness for pandemic influenza
2:50 - 4:10 pm

2:50 pm

3:15 pm
Session 3: Bioinformatics and SBDD Chair : Haruki Nakamura (Osaka University, Osaka, Japan)
Prof. Julian Gough (Univ. Bristol, UK)
Genome4d : Linking Structure, Function and SNP Analysis
Akira R. Kinjo (Osaka University, Osaka, Japan)
Composite structural motifs of binding sites of proteins for annotating functional differences
3. Broad Neutralization of Influenza Viruses and Implications for a Universal Vaccine and Therapy

Ian A. Wilson, D.Sc.
Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute

The major surface antigen, the hemagglutinin (HA), of influenza virus is the main target of neutralizing antibodies. However, most antibodies are strain-specific and protect only against highly related strains within the same subtype. Recently, a number of antibodies have been found that are much broader and neutralize across subtypes and groups of influenza A, as well as influenza B, viruses through binding to functionally conserved sites. We have determined x-ray and EM structures of broadly neutralizing antibodies with the HA and have identified highly conserved sites in the HA fusion domain (stem) in influenza A (1,2) as well as influenza B (3.) We have also structurally characterized antibodies that bind to the conserved receptor binding site and protect against different strains and subtypes (e.g. (4), (5)). The identification and characterization of these exciting new antibodies (6) provide new opportunities for structure-assisted vaccine design as well as potential therapeutics that afford greater protection against influenza viruses.

1Ekiert et al. (2009) Antibody recognition of a highly conserved influenza virus epitope. Science 324:246-251.
2Ekiert et al. (2011) A highly conserved neutralizing epitope on group 2 influenza A viruses. Science 333:843-50.
3Dreyfus et al. (2012) Highly conserved protective epitopes on influenza B viruses. Science 337:1343-1348.
4Ekiert et al. (2012) Cross-neutralization of influenza A viruses mediated by a single antibody loop. Nature 489:526-532
5Xu et al. (2013) A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin. Nat. Struct. Mol. Biol. 20:363-370
6Laursen and Wilson (2013) Broadly neutralizing antibodies against influenza viruses. Antiviral Res. 98:476-83.

4. For the control of avian influenza and preparedness for pandemic influenza

Hiroshi Kida
Research Center for Zoonosis Control, Hokkaido University

Highly pathogenic avian influenza virus (HPAIV) causes lethal infection in chickens. HPAIV is generated when a nonpathogenic virus brought by migratory birds from nesting lakes in the north is transmitted to chickens via domestic ducks, geese, quails, etc. and acquires pathogenicity for chickens with repeated multiple infections in the chicken population. Now H5N1 HPAIV has spread to 62 countries in Eurasia and Africa. The other serious concern is the fact that cumulative number of confirmed human cases for the H5N1 virus infection, 2003-2013 is 630 including 375 deaths as of 4 June 2013. Emerging outbreak of human infections with H7N9 avian influenza A virus low pathogenic for chicken occurred in China in February to May in 2013. So far the total number of cases stands at 132 infections, including 37 deaths as of the end of June 2013. In May, a human case of H6N1 influenza virus infection was found in Taiwan.
It is now believed that each of the past 4 pandemic influenza viruses are the reassortants between avian influenza viruses and the preceding human strains. We have shown that pigs are susceptible to each of avian and mammalian influenza viruses, generating reassortants that acquire human receptor specificity. Since each of the subtypes of influenza A virus perpetuates among migratory ducks and their nesting lake water in nature and avian viruses of any subtype can contribute genes in the generation of reassortants in pigs, none of the 16 HA and 9 NA subtypes can be ruled out as potential candidates for future pandemic strains.
We have carried out global surveillance study of avian influenza and influenza virus isolates of 72 combinations of HA and NA subtypes have been isolated from fecal samples of ducks. So far, 72 other combinations have been generated by the genetic reassortment procedure in chicken embryos. Thus, 246 non-pathogenic avian influenza virus strains of 144 combinations of HA and NA subtypes have been stocked for vaccine strain candidates and diagnostic use. Their pathogenicity, antigenicity, genetic information and yield in chicken embryo have been analyzed and registered in the database opened at web site (
It is strongly stressed that HPAI must be completely controlled in avian species by the “stamping-out policy without misuse of vaccine” and that drastic improvement of vaccine for the control of seasonal influenza in humans is of crucial importance in order to assure the effective preparedness for the emergence of pandemic influenza.

5. Genome4d: Linking Structure, Function and SNP Analysis

Blundell, T.L. (Cambridge University), Gough, J. (Bristol University), Jones, D.T. (University College London), Murzin, A.G. (MRC Laboratory for Molecular Biology), Orengo, C. (University College London), Sternberg, M.J. (Imperial College London)

Over the past year we have established the Genome3D[1] resource/website ( providing integrated structural predictions for genome sequences by combining multiple independent predictors for enhanced confidence. We are now planning to move forward from Genome3d to Genome4d by adding another important dimension – function – and provide consensus predictions of protein functions and functional sites. Our protein level viewpoint will be enhanced by a functionally oriented residue-level view within its structural context. Data in Genome4D will underpin our annotation of genetic variations affecting amino acid residues in animals and plants by mapping them to 3D structures and examining their effect on functional properties. Complementary methods will be combined into a meta-predictor of whether genetic variations are likely to alter phenotype through effects on structural and functional sites

[1] Lewis, T.E., Sillitoe, I., Andreeva, A., Blundell, T.L, Buchan, D.W., Chothia, C., Cuff, A., Dana, J.M., Filippis, I., Gough, J., Hunter, S., Jones, D.T., Kelley, L.A., Kleywegt, G.J., Minneci, F., Mitchell, A., Murzin, A.G., Ochoa-Montano, B., Rackham, O.J., Smith, J., Sternberg, M.J., Velankar, S., Yeats, C., Orengo, C. (2013) Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucl. Acids Res. 41, D499-D507.

6. Composite structural motifs of binding sites of proteins for annotating functional differences

Akira R. Kinjo
Institute for Protein Research, Osaka University

We define composite structural motifs by classifying and integrating the results of exhaustive all-against-all comparison of binding site structures of small molecules, proteins and nucleic acids in proteins. It is shown that subtle differences in biological functions among homologous proteins can be annotated in terms of differences in composite structural motifs. We demonstrate how detailed and abundant structural information (at atomic resolution) may be usefully exploited for functional annotation by focusing on the differences of functional sites, rather than their mere similarity.

1. RT-PCR based screening with Differential Scanning Fluorimetry (DSF)

Structural Genomics Consortium (SGC) has established a platform to characterize large numbers of purified proteins (Vedadi et al. 2010; PMID: 20466062). This platform includes screening for ligands in a 384-well format using thermal shift assays. Differential scanning fluorimetry (DSF) and differential static light scattering (DSLS) are two thermal shift assays which have been optimized for screening in 384-well format (Vedadi et al. 2006, PMID: 17035505; Niesen et al. 2007, PMID: 17853878). It has been shown that identified ligands improve crystallization, crystal quality and increase the rate of success in protein structure determination. Coupled with high-resolution X-ray crystallography and structure-guided methods, the platform can also be used toward the development of potent and selective inhibitors (chemical probes) through screening families of proteins against a variety of chemical series and focused chemical libraries.

International Conference on Structural Genomics (ICSG) offers a one-day DSF training workshop that aims to provide an opportunity for interested scientists to learn how to implement this technique.

Organizer :Dr. Masoud Vedadi (University of Toronto).
Place :Biology room, Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University.
Capacity : 10-15
RT-PCR based screening with Differential Scanning Fluorimetry (DSF) workshop schedule July 29, 2013
9:00 AMIntroduction
9:20 AMMethods and applications
9:50 AMModel experiments and screening
10:30 AM – 12:00 PMData analysis

2. Automated Methods for Macromolecular Crystallography

This workshop will have a half-day of lectures on the latest developments in structure solution, model-building, refinement, and model completion with examples from the Phenix , LAFIRE and HKL3000 software packages. The second half day will consist of installation of software on each student's computer and hands-on group and individual tutorials in how to make the best use of these programs for solving macromolecular structures.

Organizers : Dr. Paul Adams (Lawrence Berkeley National Laboratory), Dr. Thomas Terwilliger (Los Alamos National Laboratory), Dr. Min Yao (Hokkaido University), Dr. Wladek Minor (University of Virginia), Li-Wei Hung (Los Alamos National Laboratory)
Place :#302, Science Bldg.5, 3rd floor, Graduate School of Science,Hokkaido University MAP
Automated Methods for Macromolecular Crystallography workshop schedule July 29, 2013
9:00 AMRefinement and validation (Paul Adams)
9:50 AMModel completion (Min Yao)
10:40 AMBreak and set-up of software on individual computers
11:00 AMFrom images to models (Wladek Minor)
11:15 AMAutomation of structure determination (Tom Terwilliger)
12:00 PMLunch
1:00 - 4:00 PMParallel sessions:
Individual and small group sessions with your data
(Wladek Minor, Paul Adams, Min Yao, Tom Terwilliger, Li-Wei Hung)
1:00 - 2:00 PMGroup Hands-on Tutorials
Data quality analysis, structure solution, and ligand fitting (Tom Terwilliger, Li-Wei Hung)
2:00 - 3:00 PMGroup Hands-on Tutorials
Model completion (Min Yao)
3:00 - 4:00 PM Group Hands-on Tutorials
Refinement and validation (Paul Adams)
3.Advances in Automated Analysis and Validation of Protein Structures
Organizers : Dr. Gaetano Montelione (Rutgers University); Dr. Thomas Szyperski (State University of New York); Dr. John Markley (University of Wisconsin); Dr. Fuyuhiko Inagaki (Hokkaido University)
Place :Seminar Room, Facuilty of Pharmaceutical Sciences, Hokkaido University MAP
Email for application :Please send your name and your contact information, such as affiliation to email address in advance. When you send email to us, if there is no replies, please contact us again.
Advances in Automated Analysis and Validation of Protein Structures workshop schedule July 29, 2013
9:00 AMNew approaches to automation in protein NMR spectroscopy from the National Magnetic Resonance Facility at Madison (John Markley)
9:45 AMDisMeta - a Meta Server for Construct Design and Optimization (Janet Huang)
10:15 AMHigh-throughput NMR protein sample production at NESG (Rong Xiao)
10:45 AMCoffee Break
11:00 AMParamagnetic lanthanide probe for drug screening (Fuyuhiro Inagaki)
11:30 AMOlivia, a useful platform for NMR spectral analysis and structure determination (Masahi Yokochi)
12:00 PMLunch
1:00 PMNortheast Structural Genomics Consortium NMR Wiki (Thomas Szyperski)
1:30 PMHighly automated and secure pipelines to study and validate NMR structures and complexes of biomolecules performed by a stand-alone cloud computing platform using virtual machine servers (Naohiro Kobayashi)
2:00 PMQuality assessment of protein NMR structures (Gaetano Montelione)
2:30 - 3:00 PMGeneral discussion on advances in the field
4. Interaction Analyses.SPR, ITC, DSC for drug developments.

ITC and DSC training workshop in front of the instruments (half a day) with seminars. Basic principles, application examples, handling and data implementation etc. of these techniques will be overviewed.

Organizers : Tomoya Mitani (GE Healthcare Japan) ; Dr. Takashi Saitoh (Hokkaido University)
Place : Room E302, Screening room, Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University
Time : 1:00 - 4:00 PM
Capacity : 10-20
13:00-13:30introduction of Biacore, itc and DSC (seminar)
13:30- Biacore T200 Hands-On:kinetics experiment setup & start(ProteinA-IgG)
14:00auto ITC Hands-On : experiment setup & start (EDTA-CaCl2)
15:00- 15:15DSC software demo
15:15- Biacre/ITC data evaluation
5. In silico (virtual) screening

Screening for finding hit compounds to be developed further is an important process at the early stage of drug discovery. In silico (virtual) screening makes it possible to obtain hit compounds by a much smaller number of experiments than high throughput screening. Participants in this workshop will learn how to perform in silico drug screening using myPresto which is a free software for structure guided drug developments (JBIC, AIST : Fukunishi et al (2005) J. Mol. Graph. Model. 24,34-45.) and MF myPresto which is a commercial software with a graphic user interface developed by Fiatlux corporation. MF myPresto makes it easier to perform in silico screening using myPresto. Preparations of docking simulations, submitting simulation jobs, ranking compounds with multiple target screening (MTS) method, and obtaining catalog codes for ordering compounds will be demonstrated.

Organizers : Dr. Kota Kodama (Hokkaido University) ;
Dr. Hironori K. Nakamura (Biomodeling Research Co., Ltd.) ; Dr. Takanori Matsumaru (Hokkaido University) ; Dr. Hideo Fukuhara (Hokkaido University).
Place :Room 4, Conference Hall, Hokkaido University MAP
Time : 10:00 - afternoon
Capacity : 10-20

Main Program

Monday, 29 July

Registration B1 Plaza Hall

15:00 -

Vendor Booths / Setting up posters       3F Miyabi and Ohgi Room


Welcome and Introductory Remarks B1 Plaza Hall

Katsumi Maenaka (Hokkaido University, Japan)


Opening lectures B1 Plaza Hall

Chair : Thomas Terwilliger (Los Alamos National Laboratory, USA),

Kosuke Morikawa (International Institute for Advanced Studies, Japan)

17:15 - 17:45

S001 David Stuart (University of Oxford, UK)

17:45 - 18:15

S002 So Iwata (Kyoto University, Japan)
Pipeline for Mammalian Membrane-Protein Structures

18:15 - 18:45

S003 Wayne Hendrickson (Columbia University, USA)
Membrane Protein Structures Determined from Multi-crystal SAD Analyses


Welcome Reception 2F Eminence Hall

Tuesday, 30 July

Session 1 B1 Plaza Hall

Advances in protein preparation, characterization, crystallization, and EM : sponsored by Grant-in-Aid for Scientific Research on Innovative Areas, "Structural Cell Biology"

Chair : Wladek Minor (University of Virginia, USA),

Nobuhisa Watanabe (Nagoya University, Japan)

9:00 - 9:15

P107 Chikara Sato (AIST, Japan)
3D transmission electron microscopy of membrane proteins and direct observation of cells, tissues and crystals in solution using ASEM.

9:15 - 9:30

P084 Kenji Iwasaki (Osaka University, Japan)
in vivo (in cell) crystal structural analysis using EM

9:30 - 9:50

S005 Toshiya Senda (High Energy Accelerator Research Organization, Japan)
Crystal quality improvement with cryoprotectants

9:50 - 10:15

S006 Shohei Koide (The University of Chicago, USA)
Accelerating structural and functional studies of macromolecules using synthetic binding proteins

10:15 - 10:40

S007 Carol Robinson (University of Oxford, UK)
Membrane proteins and their complexes – insights from mass spectrometry


Break / Vendor Booths 3F Miyabi and Ohgi Room


Session 2 B1 Plaza Hall

Structural Life Science I: Membrane and Cell Surface Proteins

Chair : John Markley (University of Wisconsin, USA),

Toshiyuki Shimizu (University of Tokyo, Japan)

11:10 - 11:35

S008 Ian A. Wilson (The Scripps Research Institute, USA)
An Integrative Approach to Characterizing Broadly Neutralizing Antibodies to the HIV-1 Glycan Shield

11:35 - 12:00

S009 Yvonne Jones (University of Oxford, UK)
Surface Assemblies in Cell Guidance Signalling Systems

12:00 - 12:25

S010 Pamela Bjorkman (California Institute of Technology, USA)
Overcoming HIV Pathways for Escape using Rationally-Designed Anti-HIV Antibodies


Luncheon seminars / GE Healthcare B1 Plaza Hall

Monitoring higher order structural integrity in biotherapeutic development using SPR, DSC and 2D-DIGE


Break / Vendor Booths 3F Miyabi and Ohgi Room


Session 3 B1 Plaza Hall

Infectious Disease Research: Viral and Parasitic Diseases

Chair : Keith Hodgson (Stanford University, USA)

Toshiya Senda (High Energy Accelerator Research Organization, Japan)

14:45 -15:10

S011 Edward N. Baker (University of Auckland, New Zealand)
Discovering post-translational modifications in bacterial cell surface adhesins

15:10 -15:35

S012 Peter J. Myler (Seattle Biomedical Research Institute, USA)
Structural Genomics of Infectious Disease: the next 500 structures

15:35 - 16:00

S013 Andrzej Joachimiak (Argonne National Laboratory, USA)
Structural Genomics Approach to Antibiotic Resistance

16:00 - 16:25

S014 Zihe Rao (Tsinghua University, China)
Structural genomics of Picornavirus


Break / Vendor Booths 3F Miyabi and Ohgi Room


Session 4 B1 Plaza Hall

Automated and Advanced Techniques for X-ray crystallography and NMR sponsored by Grant-in-Aid for Scientific Research on Innovative Areas, "Transient Macromolecular Complexes"

Chair : Hideo Akutsu (Osaka University, Japan)

Koichi Kato (National Institutes of Natural Sciences, Japan)

16:55 - 17:20

S015 Thomas Terwilliger (Los Alamos National Laboratory, USA)
Molecular replacement and model-building using distant homology models as templates

17:20 - 17:45

S016 Gaetano Montelione (Rutgers University. USA)
Targeting protein-protein interaction networks: Development of NMR technologies for structural analysis of protein complexes

17:45 - 18:10

S017 Ichio Shimada (The University of Tokyo, Japan)
Functional Equilibrium of Membrane Proteins

18:10 - 18:35

S018 Thomas Szyperski (University at Buffalo, USA)
Development and Application of New Methods for NMR-based Structural Genomics


Poster Session 1 3F Miyabi and Ohgi Room

Wednesday, 31 July

Session 5 B1 Plaza Hall

Structural Life Science II

Chair : Osamu Nureki (University of Tokyo, Japan),

Genji Kurisu (Osaka University, Japan)


S019 Shigeyuki Yokoyama (RIKEN Systems and Structural Biology Center, Japan)
Crystallographic Studies on Specific Aminoacylation of tRNA and Genetic Code Expansion

9:25 - 9:50

S020 Joel L. Sussman (Weizmann Institute of Science, Israel)
Cholinesterases: From 3D Structure to Dynamics

9:50 - 10:15

S021 Yunyu Shi (University of Science and Technology of China, China)
PHD finger with versatile structure and function in epigenetic regulation

10:15 - 10:40

S022 Jennifer Martin (The University of Queensland, Australia)
Complementary Approaches Targeting DSB Enzymes for Anti-Virulence Drug Discovery

10:40 - 11:05

S023 Cheryl Arrowsmith (University of Toronto, Canada)
Structural and chemical biology approaches to study protein methylation signaling networks

11:05 - 11:20

P089 Katsumi Imada (Osaka University, Japan)
Common architecture of the soluble components of bacterial flagellar type III secretion system and F/V-type ATPases


Luncheon seminarsB1 Plaza Hall

Anton Paar
Nano Structure Analysis for Pharmaceutical materials using Advenced Small Angle X-ray Scattering

Douglas Instruments
Seeding Strategies for "Random" Crystal Screening and Crystal Optimization

Introduction of ProCube service, a recombinant protein providing from silkworm-baculoviruses platform

A single crystal X-ray analysis system equipped with a newly developed pixel array detector


Vendor Booths 3F Miyabi and Ohgi Room


Poster Session 2 3F Miyabi and Ohgi Room


Session 6 B1 Plaza Hall

Structural Genomics and Drug Discovery

Chair : Paul Adams (Lawrence Berkeley National Laboratory, USA),

Min Yao (Hokkaido University, Japan)

15:00 - 15:25

S024 Aled Edwards (University of Toronto, Canada)
Structure-based discovery of chemical probes to enable epigenetics research and drug discovery

15:25 - 15:50

S025 James C. Sacchettini (Texas A&M University, College Station, USA)
Combining Antimicrobial Drug Discovery and Structural Genomics

15:50 - 16:15

S026 Stephen Burley (Rutgers University, USA)
Worldwide Protein Data Bank (wwPDB): Ensuring a freely accessible, singular archive of high quality macromolecular structure information

16:15 - 16:40

S027 Kenji Mizuguchi (NIBIO, Japan)
Data integration and protein network analysis for early stage drug discovery

16:40 - 16:55

P144 Ethan A. Merritt (University of Washington – Seattle, USA)
Use of key structural features to identify protein kinases vulnerable as targets for anti-protozoan drug development

16:55 - 17:10

S028 Tamar Unger (The Weizmann Institute of Science, Israel)
Gene Manipulation and Protein Expression for Therapeutic Studies




Session 7 B1 Plaza Hall

Hybrid Methods, Macromolecular Complexes, XFEL

Chair : Soichi Wakatsuki (Stanford University, USA)

Atsushi Nakagawa (Osaka University, Japan)

17:30 - 17:55

S029 Michael Rout (The Rockefeller university, USA)
The Architecture and Mechanism of the Nuclear Pore Complex

17:55 - 18:20

S030 Ilme Schlichting (MPI Heidelberg, Germany)
Structure determination using free-electron lasers

18:20 - 18:45

S031 Petra Fromme (Arizona State University, USA)
Femtosecond nanocrystallography opens a new Era for Structural Biology


Banquet 2F Eminence Hall

Thursday, 1 August

Session 8 B1 Plaza Hall

Structural Life Science IV sponsored by Grant-in-Aid for Scientific Research on Innovative Areas, "Intrinsically Disordered Protein"

Chair : Fuyuhiko Inagaki (Hokkaido University, Japan)

Koichiro Ishimori (Hokkaido University, Japan)

9:00 - 9:15

P015 / P009 Yusuke Sato (University of Tokyo, Japan)
Structural Basis for specific cleavage of Met1- and Lys63-linked polyubiquitin chains by the USP domain of CYLD

9:15 - 9:30

P039 /P040 Umeharu Ohto (University of Tokyo, Japan)
Structural basis for species-specific endotoxin recognition by TLR4/MD-2

9:30 - 9:45

P007 Tadashi Satoh (Nagoya City University, Japan)
Mechanistic insights into the proteasome orchestration by a proteasome assembly chaperone Nas2

9:45 - 10:10

S032 Mamoru Sato (Yokohama City University, Japan)
Protein Dynamics Investigated by SAXS and MD Simulation

10:10 - 10:35

S033 Hiroaki Suga (The University of Tokyo, Japan)
Natural Product-Inspired Peptide Discovery Accelerated by the RaPID System

10:35 - 11:00

S034 Katrin Rittinger (MRC National Institute for Medical Research in London, UK)
Mechanism of linear ubiquitin chain synthesis by the E3 ligase complex LUBAC


Closing Lecture B1 Plaza Hall

S035 Junichi Takagi (Osaka University, Japan)
Expanding the Structural Genomics to Structural Life Science: Not just to answer, but to ask new biological questions


Closing Remarks B1 Plaza Hall

         Katsumi Maenaka (Hokkaido University, Japan)



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