ICFA Future Light Source Workshop, 2 March 2010, Stanford ... · 3/2/2010  · N-GAT. Clathrin...

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2.5 GeV PF Science with Future Hard X- ray Sources: Exploration of Protein Universe ICFA Future Light Source Workshop, 2 March 2010, Stanford 6.5GeV PF-AR 7 GeV & 4 GeV KEK-B ring (Super KEK-B & KEK-X ) cERL ERL Soichi Wakatsuki Photon Factory IMSS, KEK

Transcript of ICFA Future Light Source Workshop, 2 March 2010, Stanford ... · 3/2/2010  · N-GAT. Clathrin...

  • 2.5 GeV PF

    Science with Future Hard X-ray Sources: Exploration of

    Protein Universe

    ICFA Future Light Source Workshop, 2 March 2010, Stanford

    6.5GeV PF-AR

    7 GeV & 4 GeV KEK-B ring (⇒ Super KEK-B & KEK-X )

    cERLERL

    Soichi WakatsukiPhoton FactoryIMSS, KEK

  • Role of Structural Biology

    Medicine, drug design(industrial applications)

    Biology(Basic research)

    DNA→mRNA→Genome

    Molecular machines(ribosomes, enzymes)Information network

    Signal transduction

    Atomic resolution analysis○Protein structure and dynamics○Interactions between molecular machines

    Protein transport

    Proteins

    Ribosome

    Translation

    Transcription

  • Nobel Award in Chemistry, 2009

    • Ribosome structures• Prof. Ada Yonath was a user of the Weissenberg Camera

    with large IPs developed by Prof. Sakabe, Photon Factory for 10 years from 1987– Symposium of Target Protein Resarch Program March in Tokyo,

    on 5th, 2010– Photon Factory Symposium in Tsukuba on March 9, 2010

    http://www.kek.jp/ja/news/topics/2009/NobelYonath.html

    Harms et al., Cell, 107, 679-88 (2001)

    http://www.weizmann.ac.il/sb/faculty_pages/Yonath/HarmsCELL2001.pdf�http://www.weizmann.ac.il/sb/faculty_pages/Yonath/HarmsCELL2001.pdf�http://www.weizmann.ac.il/sb/faculty_pages/Yonath/HarmsCELL2001.pdf�

  • The Worldwide Protein Data Bank (wwPDB) http://www.wwpdb.org/index.html

    David S. Goodsell, Scripps Institute

    >60,000 entries and growing!

  • How large is the protein universe?• How many genes?

    – Meta genomes --- J. Craig Venter Institute's Global Ocean Sampling Expedition

    – Human microbiomes (Gill, et.al. David Relman, Stanford, Science 2006)

    – Emerging infectious diseases• Splicing variants – exon: cut and paste• Non-coding RNA: largely uncharted• Protein-protein, protein-carbohydrate, protein-

    lipid, protein-nucleic acid interactions

    • Posttranslational modifications

  • From atomic structures toIn situ observation of biological nano machines for cell/tissue level understanding

    Understanding of self-organizing biomolecularnano machines using SR X-ray nano beam

    Signal transduction through membrane

    proteins in the lipid raftFlagellin formation

    Namba and coworkers

    Extraordinarily large Vault complexTanaka et al. (2009) Science

    67nmLipid raft

  • What do we want to know?• Large complexes: real time, real place

    (organelle/cell/tissue), at atomic resolution• Dynamics of multicomponent complexes:

    hierarchical structure• Imaging: 5 nm or better spatial resolution to

    discriminate inside/outside of membranes.• Imaging with chemical speciation is not sufficient:

    spectroscopy required for certain components which include metal proteins

    • Structural changes at the membrane surface: lipid rafts with membrane protein complexes: can time-resolved GISAXS be the solution?

  • Figure by David S. Goodsell, Scripps Institute

    View of a eukaryotic cell

    COLORS: proteins in blue, ribosomes in magenta, DNA and RNA in red and orange, lipids in yellow, and carbohydrates in green.

    http://www.scripps.edu/mb/goodsell/

    •Red boxes: about ~50 nm by ~100 nm.•Imaging needs better than 5 nm resolution.•COHERENT BEAM: X-ray photon correlation spectroscopy (XPCS) to study the dynamics?

  • Protein-protein interaction network

    Taken from Rua et al., Nature 2005

  • Nucleus

    Endoplasmic Reticulum

    TGN

    Plasma Membrane

    Protein glycosylation

    Golgi apparatus

    Endocyticpathway

    Autophagic pathway

    Lysosome

    Clathrin Coated Vesicle Early Endosome

    Late Endosome

    Autolysosome

    Secretory Vesicles

    Systems Structural BiologyPosttranslational modification and transport

    GGA

    Melanosome

  • Transport in nueronsFrom N. Hirokawa, J. of Neuroscience, 2006

    KIF1A: single headed motor, Nitta, Hirokawa et al., Science 2004, 305, 678 – 683, Data collected on PF-BL6A & 19ID APSOgawa, et al., Cell, 2004

    Double headed kinesin

    1~2 µm/sec8 nm step

    ~0.5 µm

    N. Hirokawa, Univ of Tokyo Med School

  • Endocytosis of toxin -> Drug delivery

    David S. Goodsell, Scripps Institute, http://www.scripps.edu/mb/goodsell/

    Clathrin movie by Allison Bruce, Harvard http://www.hms.harvard.edu/news/clathrin/

  • TGN membrane

    GAE

    Hinge region

    GAT

    Accessory protein

    Lumen

    N-GAT

    Clathrin terminal domain

    Clathrin

    clathrin box

    cargo protein

    M6PR

    VHS

    ARF-GTP

    MPR

    Human GGA: a new class of adaptor proteins

    Auto-inhibition

    Competition with AP-1

    ① Shiba et al. Nature 415,937-941, 2002Shiba et al., Traffic, vol. 5, 437-448, 2004

    ② Shiba et al., Nature Structural Biology, 10 386-393, 2003Shiba et al., J. Biol. Chem. 279, 7105-11279, 2004Kawasaki et al., Genes to Cells, 10, 639–654, 2005Yogosawa et al., BBRC, 350, 82-90, 2006

    ③ Nogi et al. Nature Structural Biology, 9, 527-531, 2002Inoue et al. Traffic, 8, 904-913, 2007

    33 nm

    50 nm

  • EGFP-Arf6 MKLP1 β-tubulin

    Cytokinesis needs lots of new membranes

    Tubulin

    Cleavage furrow

    midbody

    Colocalization of MKLP1 & Arf6 in midbody

    Cytokinesis seen with EGFP-FIP3 and mCherry-Rab11

  • 微小管microtubules

    MKLP1

    Exocyst complex

    Cyk4

    Arf6 Arf6

    細胞膜 Plasma membrane

    分裂溝Cleavage furrow

    + -+-

    +-

    Rab11

    FIP3Rab11

    Fusion

  • BAR domain

    Homology

    N-terminal C-terminal

    1 108 121 321 342

    80%Arfaptin1

    Arfaptin2

    BAR (Bin/Amphiphycin/Rvs)

    domain: a module that is involved

    in dimerization, membrane

    binding and curvature-sensing.

    Arfaptin/POR function in membrane trafficking

    Taken from Wang et al., Structure, 2008

  • Time lapse images

    Arfaptin2 & Arl1

    Arl1/Arfaptin tubulationmovie part 1 by Yuko

    Tsukihara (Meta Corporation Japan)

    Arl1/Arfaptin tubulationmovie part 2 by Yuko

    Tsukihara (Meta Corporation Japan)

  • K6

    K11

    K27K29

    K33

    K48

    K63

    N

    C

    K6

    K11

    K27K29

    K33

    K48

    K63

    N

    C

    Ubiquitin (Ub): ubiquitous protein modifier with only 76 amino acid residues, 27000 papers published to date

    Can connect Ub to another Ub using 7 (now 8) different ways

    How are specific linkages recognized for signaling?

    7 lysines of ubiquitin

  • K6

    K11

    K27K29

    K33

    K48

    K63

    N

    C

    K6

    K11

    K27K29

    K33

    K48

    K63

    N

    C

    Protein

    Ub

    Mono-ubiquitylation

    Poly-ubiquitylation

    Endocytosis

    DNA repair

    Protein

    Ub

    Protein

    Ub

    Protein degradationUb

    Ub

    Ub

    UbUb

    Ub

    K48-linked

    K63-linked

    Main functions

    7 lysines of ubiquitin Protein

    Ub DNA transcriptionUb Ub Ub Linear

    Linear-ubiquitylation and NEMO (Rahighi, et al., Wakatsuki, Dikic, Cell 2009; Tokunaga et al., Iwai, Nature Cell Biol., 2009)

    Polyubiquitin: linkage specificity vs. function

    DNA transcriptionVesicle transport

  • 7 lysines, K48, K63 and Linear

    Lange et al.,

    Science 2008

    Taken from Dikic, Wakatsuki, Walter, Nat. Rev. Mol. Cell Biol., in press

  • Ubiquitin binding domain of NEMO (UBAN) specifically recognizes linear-diubiquitin

    SPR measurement of NEMO-UBAN/diubiquitin dissociation constant: 1.6 µM

    CC1 HLX2 CC2 LZ ZF58 96 187 202 243 250 314 336 390 410

    1 412HLX1

    250 338UBAN

    289

    285

  • Model of Ub signaling in the NF-κB pathwayNew paradigm in ubiquitin signaling in the NF-κBpathway: linear ubiquitin recognition

    Plasma membrane

    Degradation of IκBα

    Nucleus

    Into nucleus

    Liner polyUbIKK complexes

    LUBAC linear Ub ligase

    Immune response,

    inflammation, apoptosis, cancer etc.

    Cytokines

  • N

    CC

    N

    Ubdistal Ubdistal

    UbproximalUbproximal

    Rahighi et al., Cell, March 2009 2:2

    Lo et al., Molecular Cell, January 2009 2:1

    Yoshimura et al., FEBS Lett, September 2009 2:1

    Crystallographic controversy NEMO: diUbiquitin =2:1 vs 2:2NEEDS MUCH BETTER METHOD TO RESOLVE THIS!

  • (A) (B)(D)

    IKKα

    IKKβ

    Substrate

    Substrate

    K

    K

    (C)

    NEMO is a long alpha helical dimer

    How does Ub binding activate IKKα and IKKβ?

    A) Rushe M., et al., Structure (2008)

    B) Bagneris C., et al., Mol. Cell (2008)

    C) Current work, Rahighi, Ikeda et al., S. Wakatsuki, Ivan Dikic, Cell (2009)

    D) Cordier F., et al., J. Mol. Biol. (2008)

    Eli Lilly and Companynow has the structures of IKKα and IKKβ!!!

  • Plethora of ubiquitin chains may lead to

    numerous biological signals ⇒ New ubiquitin world

    Lys 48/Lys 29

    Taken from Ikeda & Dikic, EMBO Reports, 9, 536-542 (2008)

    Linear!

    Tokunaga, Iwai et al., NCB, 2009

    Kim et al, JBC 2007

    Tatham et al, NCB 2008

    Previously: 7x7x7x7x7 = 16807

    With linear: 8x8x8x8x8 = 32768

  • (A) (B)(D)

    IKKα

    IKKβ

    Substrate

    Substrate

    K

    K

    (C)

    Time resolved solution structural analyses of posttranslational modifications & complex formation

    Accelerate developments of drugs

    Imaging localization of protein complexes with high resolution and contrast

    Structural studies of polyubiquitin synthesis & recognitionIn vivo analysis of drug delivery and signal transduction

    Analysis of receptors upon agonist binding

    Macroscopic structural changes ⇔ function

    SAXS

    Protein CrystallographyRahighi et al., Cell 2009

    SR X-ray tomographyFigure by C. Larabell

    Neutron reflectivityGI-SANS & GI-SAXS

    NF-kB pathway

    New Ubiquitin World with Accelerator Technologies

    KEK-X

    Hierarchical structure of

    ubiquitin recognition

  • Roadmap of protein crystallography beamlines in JapanExamples A: membrane proteins, B: enzymes without heavy atom lables

    & C: virus crystals

    Size

    of c

    ryst

    al

    > 200μm

    1μm

    B

    Size

    of c

    ryst

    al

    A

    CAR-NE3A

    BL-5AAR-NW12A

    BL-17A

    BL-1A

    PF

    BL-6A

    SAGABL-7

    SPring-8

    BL44XU(Osaka Univ)

    BL41XU

    BL32XU

    BL38B1 BL26B1/2

    (RIKEN)

  • •Yearly budget: 5.5 billion yen, US$ 44.5M (includes 30% overhead)•43 teams selected on 15 June 2007 & 2 new teams joined in 2009•So far, papers in Nature 13, Science 2, Cell 7•KEK: Vesicle transport & Structural Analysis Core

    Structural Analysis Core

    Microfocus (SP8) & long λ SAD(PF)

    Protein Production Core

    Informatics Core

    Functional Control Core

    (140K compounds Chem. Library)

    Medical importance/relevance

    Fundamental Biology

    Food and environmentTargets:

    Target Protein Project (5 years: 2007-2011)

    5 yr term 7 6 5

    3 yr term 5 4 6

    5 yr 1 1 (X-ray) 1 13 yr 3 2 (NMR) 0 1

    http://www.tanpaku.org/e_index.php

  • Extremely large complex, Vault(Tsukihara Group, Science 2009)

    • Structure determined at 3.5 Å reslution with 39-fold symmetry• MVP(major vault protein) alone is 99kDa x 78 copies = 7.7 MDa• SPring-8 BL44XU Osaka Univ. Beam Line

  • Vault crystal (Tsukihara et al., Science 2009, SPring-8 BL44XU)

    Photographs of vault crystal. The crystal was about 0.70 mm x 0.15 mm x0.03 mm, and belongs to the space group C2, with cell dimensions of a = 702.2 Å, b = 383.8 Å, c = 598.5 Å, and β = 124.7°.

    10,000 x 4000 x 500 = 2 x 1010 unit cells

  • How many unit cells in micro/nano crystals do we need for structure determination?

    Unit cell dimension

    Crystal size (micro cube)

    30Å 40Å 50Å 100Å 200Å 300Å 500Å 800Å

    300 1.0E+15 4.0E+14 2.0E+14 3.0E+13 3.0E+12 1.0E+12 2.0E+11 5.0E+10

    200 3.0E+14 1.0E+14 6.0E+13 8.0E+12 1.0E+12 3.0E+11 6.0E+10 2.0E+10

    100 4.0E+13 2.0E+13 8.0E+12 1.0E+12 1.0E+11 4.0E+10 8.0E+09 2.0E+09

    50 5.0E+12 2.0E+12 1.0E+12 1.0E+11 2.0E+10 5.0E+09 1.0E+09 2.0E+08

    30 1.0E+12 4.0E+11 2.0E+11 3.0E+10 3.0E+09 1.0E+09 2.0E+08 5.0E+07

    20 3.0E+11 1.0E+11 6.0E+10 8.0E+09 1.0E+09 3.0E+08 6.0E+07 2.0E+07

    10 4.0E+10 2.0E+10 8.0E+09 1.0E+09 1.0E+08 4.0E+07 8.0E+06 2.0E+06

    5 5.0E+09 2.0E+09 1.0E+09 1.0E+08 2.0E+07 5.0E+06 1.0E+06 2.0E+05

    4 2.0E+09 1.0E+09 5.0E+08 6.0E+07 8.0E+06 2.0E+06 5.0E+05 1.0E+05

    3 1.0E+09 4.0E+08 2.0E+08 3.0E+07 3.0E+06 1.0E+06 2.0E+05 5.0E+04

    2 3.0E+08 1.0E+08 6.0E+07 8.0E+06 1.0E+06 3.0E+05 6.0E+04 2.0E+04

    1 4.0E+07 2.0E+07 8.0E+06 1.0E+06 1.0E+05 4.0E+04 8.0E+03 2.0E+03

    Numbers of “cubic shape” unit cells in cubic shape crystals. Colored according to the number of unit cells contained in crystals: more than 108 copies in green, 107

    pink, & 106 copies yellow. (by Masaki Yamamoto, Harima RIKEN/SPring-8)

  • Micro crystals of cypovirus polyhedraby Peter Metcalf et al.

    • Structure at 2 Å resolution(Peter Metcalf group, Nature 2007, data collected at Swiss Light Source, presented in AsCA 2009, Beijing)

    • Very robust crystals:dissolve only above pH10

    • a=b=c= 103 Å, 1 micron cube crystal ⇒ contains 106unit cells ⇒ 100 repeats along each axis

  • Laue function of micro crystalsLimit 10 x 10 x 10 = 1000 ?

    Laue

    func

    tion

    For Na = 10

    • Intense micro/submicro beam with low divergence (0.1 mrad or lower in H direction)

    • Stability ~10-3: with the next generation PADs, each reflection might see the beam for 1~10 msec

  • Target Protein Research Project (MEXT) Microbeam Beamline BL32XU

    Achieved beam size (2009/11/27) by SPRing-8

    -3 -2 -1 0 1 2 30.0

    0.2

    0.4

    0.6

    0.8

    1.0

    Inte

    nsity

    / ar

    b. u

    nit

    Position / um-3 -2 -1 0 1 2 3

    0.0

    0.2

    0.4

    0.6

    0.8

    1.0

    Inte

    nsity

    / ar

    rb. u

    nit

    Position / um

    Focused photon flux : 5.7x1010 photons/secDivergence: 0.5 mrad (H) x 0.009 mrad (V)

    Horizontal beam profile Vertical beam profile

    FWHM0.69 µm

    FWHM0.78 µm

    SP8

  • Facility Beamline Vert(µm)

    Width(µm)

    Flux (phs/sec)Flux density

    (phs/sec/µm2)

    APS 23-ID-B 4 µmφ 4.0E+10 3.2E+09ESRF ID23-2 7.5 5 4.0E+11 1.1E+10

    SLS X06SA 25 5 1.0E+12 8.0E+09

    X10SA 50 5 1.0E+12 4.0E+09

    SPring-8 BL32XU 1.1 1.0 6.2E+10 5.6E+1019.3 7.2 6.7E+12 4.8E+10

    http://biosync.rcsb.org/international.html(as of Nov 20th, 2009)

    Microfocus beamlines around the world

    SP8

    http://biosync.rcsb.org/international.html�

  • Crystal size and diffracting powerTaken from Acta Cryst. (2008), D64, 158-166

    ◆ Protein crystals

    □ Organic small molecule crystals

    cryst32

    cell000 )/( VVFS ××= λ

    ※2Å data collected from a 2µm lysozyme crystal

    SPring-8 BL32XU

    Diffracting power

    SP8

    20 µmLysozyme crystal

  • Sample Thermolysin 1 Thermolysin 2

    Laser trapping(λ = 1064nm)

    760mW, 1min.

    none 760mW, 1min.

    none

    Data Collection Statistics

    Resolution (Å) 50 - 2.08 (2.15 – 2.08)

    Space group P6122

    Cell dim: a,c (Å) 92.7, 129.3 92.8, 129.3 92.6, 129.4 92.7, 129.3

    Mosaicity (º) 0.127 0.100 0.168 0.174

    I 403 (153) 460 (179) 539 (196) 725 (263)

    I / σ( I ) 44.7 (17.9) 45.9 (18.6) 46.0 (17.6) 52.9 (21.5)Multipicity 10.4 (9.9) 10.4 (9.9) 10.5 (10.0) 10.4 (10.1)

    Comp. (%) 99.6 (99.3) 99.5 (98.6) 98.9 (96.6) 99.0 (97.8)

    R merge (%) 8.7 (15.6) 8.6 (14.8) 8.1 (15.2) 7.6 (14.1)

    Structure Refinement Statistics

    R factor (%) 17.8 18.0 17.5 17.6

    R free (%) 21.1 22.9 20.6 21.3

    Ave. B (Å2) 9.88 9.43 9.87 10.26

    R.m.s. dev. (Å) 0.031 0.033

    50µm

    Laser TrappedPoint760mW, 1min

    X-ray ExposedPoints

    1064nmYAG Laser

    microscope

    1064nmYAG Laser

    XYZManipulator

    XYZManipulator

    Lensed FiberProbes

    CrystalSolution

    3D manipulation of lysozyme crystal(Laser power = 25mW x 2)

    Test for damage on sample

    Development of Micro-crystal handling with laser tweezers being developed by SPring-8

    Crystal tweezers with fiber laser optics

    50µm

    SP8

  • PF-AR NW14A: ERATO Project (~2009): Dynamics studies with 100 ps time resolution for innovation in materials and biological sciences

    Tokyo Institute of Technology, ERATO (JST) S. Koshihara、KEK・PF Shin-ichi Adachi

    Laser driven shock waves through CdS single crystal

    Dynamics of ligand migration in protein crystal

    Solution photo reaction

    Laser induced spin crossover

    reaction

  • 39

    AcetylcholinesteraseProf. Joel Sussman et al.

    Weizmann Institute, Israel50,000 hydrolysis reactions per second, i.e. 20 µsec/event

    So far, it has not been possible to observe the protein breezing motion in the crystal despite numerous efforts including Laue experiments. -> Need to do time-resolved SAXS at one micro sec or faster time resolution with light cleavable cage compound.

    http://www.weizmann.ac.il/sb/faculty_pages/Sussman/images/big_wh_ray01.gif�

  • Single molecule structure determination with hard x-ray FEL

    • Radiation damage: avoidable if X-ray photons are as short as several fsec (?)

    • How to average coherent diffraction images (fundamentally different from crystallography where averaging is done by the crystal). Determination of orientation of the molecule crucial

    • How many water molecules are allowed to be attached to the proteins?

    • How many lipids need to be there for membrane proteins to stay in the active form when electron-sprayed?

    • Conformations of the single molecules (complexes) in the beam have to be the same for all the images to be used for structure determination – rather difficult

  • Dikic, Wakatsuki, Walter, Nature Review Molecular Cell Biology, 2009

    Drug design targets: can we freeze the complexes?

    Targeting ubiquitin itself with ubistatins: Verma et al, R.W. King, Science, 2004

  • Ultimate storage ring and/or ERL• Ultimate protein crystallography: nano crystals

    with million or fewer copies

    • Coherent diffraction of organelles/cells and other large structures such as chromosomes

    • X-ray microscopy/tomography: finding new organelles or distribution thereof.

    • XPCS of subcellular regions for dynamics• Grazing incidence SAXS to study structure and

    dynamics of membrane proteins/lipid rafts

  • Understanding hierarchical structure/function using CDI, crystallography, SAXS, GISAXS, EM, NMR, etc.

    Small Angle X-ray Scattering

    Diffraction image Reconstructed yeast cell(by C. Jacobsen, Stony Brook)

    Imaging needs 5 nm or better resolution to see inside/outside of membranes

    Signature with metal incorporation (eg. 3-iodo-L-tyrosine) into different proteins

    Adapter protein GGA Clathrine

    Motor protein on microtubule

    Ribosome

  • Preliminary Design of 5GeV ERL

    XFEL-O

  • KEK-X Project with the upgrade of KEKB to Super KEKBLER

    PF-AR 7 GeVinjection and top-up operation?

    LER

    HER

    HER

  • Preliminary plan ofLER West-Symmetry Point Experimental hall

    150m x 30m = 4500 m2

    ID26

    ID28

    ID30

    ID32

    ID34

  • Preliminary calculation for LERSpectra of ID27A SX &HX beam lines

  • Global Ocean Sampling Expedition

    • Sorcerer II of Craig Ventor Institute• GOS analysis identified some 6.12 million

    proteins from 7.7 million newly discovered sequences

  • Human microbiomes• Within the body of a healthy adult,

    microbial cells are estimated to outnumber human cells by a factor of ten to one.

    • Human gut: 1000 microbiomes, 1x1014cells, 1 kg per person, but so far only 40 species have been characterized.

    • Many sequencing projects in Asia, US, and Europe:– The NIH Roadmap Initiative now includes

    a Human Microbiome Project (HMP,http://nihroadmap.nih.gov/hmp)

  • Acknowledgements Part 1Photon Factory, IMSS, KEKRyuichi Kato (talk on Wed PM)

    Noriyuki Igarashi

    Masahiko Hiraki

    Masato Kawasaki

    Naohiro Matsugaki

    Yusuke Yamada

    Leonard M. Chavas

    Hisayoshi Makio (MKLP1/Arf6)

    Norio Kudo

    Kentaro Ihara

    Tamami Uejima

    Simin Rahighi (NEMO/Ub)

    Seiji Okazaki

    Kensuke Nakamura (Arl1/Arfaptin)

    Ken Ohkubo

    Accelerator Lab, KEKDivision VII Light Source

    RIKEN M. Yamamoto

    G. Ueno

    K. Hirata

    A. Nisawa

    Y. Kawano

    T. Hikima

    H. Murakami

    D. Maeda

    T. Tanaka

    H. Kitamura

    JASRIStructure Biology G.

    T. Kumasaka

    N. Shimizu

    K. Hasegawa

    S. Baba

    Light Source &Optics Div.

    S. Goto

    H. Ohashi

    K. Takeshita

    S. Takahashi

    H. Yamazaki

    T. Takeuchi

    H. Yumoto

    Control & Computer Div.

    T. Ohata

    Y. Furukawa

    T. Matsushita

  • Acknowledgements II

    Osaka UniversityAtsushi NakagawaMamoru Suzuki

    Nagoya University

    Nobuhisa Watanabe

    Financial Supports

    Protein 3000 Project (MEXT)

    Development of Systems and Technology for Advanced Measurement and Analysis (JST)

    Vesicle transport: Kazuhisa Nakayama, Kyoto Univ, Pharm. Dept

    Hokkaido UniversityIsao Tanaka

    Kyoto UniversityKunio Miki

    Target Protein Research Program (MEXT)

    Astellas Pharmaceutical Inc.

    Thank you for your attention!Grand-in-Aid for Young Scientists (B) 18770098 (MEXT)

    Linear Ub: Ivan Dikic & Fumiyo Ikeda, Goethe Univ, Frankfurt

    Slide Number 1Slide Number 2Nobel Award in Chemistry, 2009Slide Number 4How large is the protein universe?Slide Number 6What do we want to know?Slide Number 8Protein-protein interaction networkSlide Number 10Transport in nueronsSlide Number 12Slide Number 13Slide Number 14Slide Number 15Slide Number 16Time lapse imagesSlide Number 18Slide Number 197 lysines, K48, K63 and LinearSlide Number 21Slide Number 22Slide Number 23Slide Number 24Plethora of ubiquitin chains may lead to numerous biological signals ⇒ New ubiquitin world Slide Number 26Slide Number 27Slide Number 28Extremely large complex, Vault� (Tsukihara Group, Science 2009)�Vault crystal (Tsukihara et al., Science 2009, SPring-8 BL44XU)How many unit cells in micro/nano crystals do we need for structure determination?Micro crystals of cypovirus polyhedra�by Peter Metcalf et al.Laue function of micro crystalsTarget Protein Research Project (MEXT) �Microbeam Beamline BL32XU�Achieved beam size (2009/11/27) by SPRing-8Microfocus beamlines around the worldCrystal size and diffracting powerDevelopment of Micro-crystal handling �with laser tweezers being developed by SPring-8PF-AR NW14A: ERATO Project (~2009): Dynamics studies with 100 ps time resolution for innovation in materials and biological sciences�Tokyo Institute of Technology, ERATO (JST) S. Koshihara、KEK・PF Shin-ichi AdachiAcetylcholinesterase�Prof. Joel Sussman et al.�Weizmann Institute, IsraelSingle molecule structure determination with hard x-ray FELDrug design targets: can we freeze the complexes?Ultimate storage ring and/or ERLSlide Number 43Preliminary Design of 5GeV ERLSlide Number 45Preliminary plan of�LER West-Symmetry Point Experimental hallPreliminary calculation for LER�Spectra of ID27A SX &HX beam linesGlobal Ocean Sampling ExpeditionHuman microbiomesAcknowledgements Part 1Acknowledgements II