分子研研究会
日韓生体分子科学セミナー	  −実験とシミュレーション
6th Japan-Korea Seminars on Biomolecular Science:Experiments and Simulation

Okazaki Conference Center
Institute for Molecular Science
Nov. 25 – 27, 2013

November 25 (Mon)【Chair: Yuji Furutani (IMS)】
10:00-10:25
Akihito Ishizaki (IMS)QUANTUM DYNAMIC ASPECTS IN PHOTOSYNTHETIC LIGHT HARVESTING – OLD ROOTS,NEW SHOOTS

10:25-10:50

Young Min Rhee (POSTECH)

10:50-11:10

coffee break

INTERPOLATED MECHANICS / MOLECULAR MECHANICS STUDIES ON THEDYNAMICS OF
FLUORESCENT PROTEINS【Chair: Shigetoshi Aono (IMS)】
11:10-11:35
Yuji Furutani (IMS)STIMULUS-INDUCEDION-PUMP PROTEINS

11:35-12:00

12:00-13:30

DIFFERENCE

FTIR

SPECTROSCOPYON

ION-CHANNALAND

Osami Shoji (Nagoya Univ.)

GASEOUS ALKANE HYDROXYLATION CATALYZED BY CYTOCHROME P450BM3 BY TRICKINGITS SUBSTRATE RECOGNITION USING DECOY MOLECULES

lunch【Chair: Young Min Rhee (POSTECH)】
13:30-13:55
Jinwoo Lee (Kwangwoon Univ.)

A NOVEL APPROACH TO NON-EQUILIBRIUM THERMODYNAMICS

13:55-14:20

Nam Ki Lee (POSTECH)

14:20-14:45

Naoyuki Inagaki (Nara Inst. of Sci. & Tech.)14:45-15:05

coffee break

SINGLE-VESICLE FRET ASSAY FOR THE NEUROTOXICITY OF Α-SYNUCLEIN OLIGOMERSIN PARKINSON'S DISEASE: INHIBITING NEURONAL SNARE-MEDIATED VESICLE FUSION
SIGNAL-FORCE TRANSDUCTION IN AXON OUTGROWTH AND GUIDANCE【Chair: Yuji Furutani (IMS)】
15:05-15:30
Jaehoon Yu (Seoul National Univ.)

A PEPTIDE MIMETIC OF APOLIPOPROTEIN A-I THAT CONTAINS 2-NAPHTHYLALAMINERESIDUES ENHANCES CHOLESTEROL EFFLUX AND SEQUESTERS OXIDIZED LDL FROM
MACROPHAGE CELLS

15:30-15:55

Changbong Hyeon (KIAS)

15:55-16:20

Chaok Seok (Seoul National Univ.)

16:20-16:40

coffee break

UREA-INDUCED DENATURATION OF RNAGALAXY 2013 TESTED ON RECENT COMMUNITY-WIDE PREDICTION EXPERIMENTS【Chair: Hisashi Okumura (IMS)】
16:40-16:55
Balachandran Manavalan (KIAS)RANDOM FOREST-BASED PROTEIN MODEL QUALITY ASSESSMENT (RFMQA) USINGSTRUCTURAL FEATURES AND POTENTIAL ENERGY TERMSR

16:55-17:10
17:10-17:25
17:25-17:40

18:00-

Takumi Yamaguchi (IMS)

PARAMAGNETISM-ASSISTED NMR EVALUATION OF MOLECULAR DYNAMICS SIMULATIONSFOR CONFORMAIONAL CHARACTERIZATION OF OLIGOSACCHAIRDESTadashi Satoh (Nagoya City Univ. & JST PRESTO)STRUCTURAL BASIS FOR PROTEASOME FORMATION MEDIATED BY ASSEMBLY CHAPERONE
NAS2Min-Kyu Kim (KIOST)CRYSTAL STRUCTURES OF COLD-ACTIVE β-MANNANASE AND ITS MANNOPENTAOSECOMPLEXE FROM ANTARCTIC SPRINGTAIL, Cryptopygus antarcticus

Free Discussion/Mixer

November 26 (Tue)【Chair: Jooyoung Lee (KIAS)】
9:30-9:55
Julian Lee (Soongsil Univ.)

EXACT PARTITION FUNCTION ZEROS OF THE WAKO-SAITÔ-MUÑOZ-EATON PROTEIN MODEL

9:55-10:20
10:20-10:40

Fumio Hirata (Ritsumeikan Univ.)

ROLE OF WATER TO CONVERT "NON-BIOLOGICAL" FLUCTUATION TO THE "BIOLOGICAL"
ONE

coffee break【Chair: Seokmin Shin (Seoul National Univ.)】
10:40-11:05
Jooyoung Lee (KIAS)

HIGH-ACCURACY PROTEIN STRUCTURE MODELING AND ITS APPLICATION TO MOLECULARREPLACEMENT OF CRYSTAL PHASING

11:05-11:30
11:30-11:55

11:55-13:30

Hisashi Okumura (IMS)REPLICA-PERMUTATION METHOD FOR PROTEIN SIMULATIONS AND PRESSURE-INDUCEDDENATURATIONSun Choi (Ewha Womans Univ.)

COMPUTER-AIDED DRUG DESIGN AND MOLECULAR MODELING 	  STUDIES FOR THE
DISCOVERY OF COVALENT INHIBITORSlunch【Chair: Sun Choi (Ewha Womans Univ.)】
13:30-13:55
Seokmin Shin (Seoul National Univ.)

UNDERSTANDING AMYLOID FORMATION

13:55-14:20
14:20-14:45

14:45-15:05

Hirofumi Sato (Kyoto Univ.)

MOLECULAR THEORIES OF SOLVATION, FLUCTUATION AND DIFFUSION IN AQUEOUS
SOLUTION

Weontae Lee (Yonsei Univ.)

STRUCTURE AND DYNAMICS OF C-TERMINAL REGULATORY DOMAIN OF Vibrio vulnificus
EXTRACELLULAR METALLOPROTEASE

coffee break【Chair: Kunihiro Kuwajima (SOKENDAI)】
15:05-15:30
Sung-il Yoon (Kangwon National Univ.)

CONSERVED, BUT DISTINCT, ACTIVATION OF TOLL-LIKE RECEPTOR 5 BY FLAGELLIN

15:30-15:55
15:55-16:10
16:10-16:30

Keehyoung Joo (KIAS)NMR STRUCTURE DETERMINATION BY CONFORMATIONAL SPACE ANNEALING

Chihiro Kitatsuji (IMS)

MOLECULAR MECHANISM FOR HEME-MEDIATED INHIBITION OF THE 5-AMINOLEVULINIC
ACID SYNTHASE 1

coffee break【Chair: Koichi Kato (IMS)】
16:30-16:45
Norifumi Muraki (IMS)STRUCTURAL BASIS FOR PROTOCHLOROPHYLLLIDE REDUCTION IN THE CHLOROPHYLL
BIOSYNTHESIS

16:45-17:00

In Suk Joung (KIAS)

A SIMPLE STRUCTURE-BASEDCONFORMATIONAL CHANGES

17:00-17:15

Sim Jun (Soongsil Univ.)

18:00-Banquet

MODELINGFOREXPLORING

GRAPH-THEORY BASED COMPUTATION OF PROTEIN RIGID BLOCKS

MACRO-MOLECULAR

November 27 (Wed)【Chair: Shingo Nagano (Tottori Univ.)】
9:30-9:55
Hironari Kamikubo (Nara Inst. of Sci. & Tech.)

FUNCTIONAL MODIFICATION OF A PROTEIN BY USING ELEMENT IMPLANTATION

9:55-10:20

Shuji Akiyama (IMS)

10:20-10:40

coffee break

KaiC AS CIRCADIAN PACEMAKER OF CYANOBACTERIAL CIRCADIAN CLOCK【Chair: Soo Hyun Eom (GIST)】
10:40-11:05
Genji Kurisu (Osaka Univ.)

STRUCTURAL STUDIES OF THE CYTOPLASMIC DYNEIN MOTOR DOMAIN

11:05-11:30

Koichi Kato (IMS)AN ARCHAEAL HOMOLOG OF PROTEASOME ASSEMBLY CHAPERONEHOMOTETRAMER AND FUNCTIONS AS PROTEASOME ACTIVATOR

11:30-11:55

Sun-Shin Cha (KIOST)

11:55-13:30

lunch

ZINC-BINDING TO THE
EXPERIMENTAL PHASING

SURFACEOF

PROTEINS

AND

ITS

FORMS

APPLICATIONA

TO【Chair: Fumio Hirata (Ritsumeikan Univ.)】
13:30-13:55
Soo Hyun Eom (GIST)

CRYSTAL STRUCTURE OF THE CORE DOMAIN OF HUMAN SWIPROSIN-1, CALCIUM
DEPENDENT ACTIN BUNDLING PROTEIN

13:55-14:20

Kunihiro Kuwajima (SOKENDAI)

14:20-14:45

Shun Hirota (Nara Inst. of Sci. & Tech.)

14:45-15:05

coffee break

IRREVERSIBLE DENATURATION OF Escherichia coli MALTODEXTRIN GLUCOSIDASEOLIGOMERIZATION OF HEME PROTEINS BY DOMAIN SWAPPING【Chair: Shun Hirota (Nara Inst. of Sci. & Tech.)】15:05-15:30
Toshitaka Matsui (Tohoku Univ.)

UNIQUE REACTION MECHANISMS OF IsdG-TYPE HEME DAGRADING ENZYMES FROMPATHOGENIC BACTERIA

15:30-15:55
15:55-16:20

Shingo Nagano (Tottori Univ.)

STRUCTURE AND HEME ACQUISITION MECHANISM OF A HEMOPHORE HasA HAVING
UNUSUAL 5-COORDINATED HEME

Shigetoshi Aono (IMS)STRUCTURALBASISFORTHE
TRANSCRIPTIONALHOMEOSTASIS IN LACTOCOCCUS LACTISREGULATIONOFHEME