English

Biological Soft Matter Group

We use a soft matter physics approach to cell-mimicking systems so that we can understand the physical principles of biological systems. Living cells are a form of self-assembled soft matter. Lipid bilayer membranes are essential components of living organisms. We i) construct artificial lipid vesicles which produce cellular dynamics, such as endocytosis and autophagy, ii) elucidate the association of biological and nonbiological nano-materials on membrane surfaces, and iii) conduct quantitative analyses based on condensed soft matter physics.




Members
Hamada, Tsutomu (Associate Professor, PI)    [E-mail]t-hamada_at_jaist.ac.jp
Nagai, Ken (Assistant Professor)
Mizuno, Shino (Research assistant)
Nakade, Akiko (Research assistant)
Shigyo, Kazuki (Graduate student)
Ishii, Takero (Graduate student)



Recent research funds
Grant-in-aid for Scientific Research, Innovative Areas, MEXT, 2013-2014, 4,900,000JPY
Grant-in-aid for Scientific Research, Innovative Areas, MEXT, 2012-2013, 5,700,000JPY
Grant-in-aid for Scientific Research, Young Scientist (B), JSPS, 2011-2013, 3,300,000JPY
Grant-in-aid for Scientific Research, Priority Areas, MEXT, 2009-2010, 6,600,000JPY

Selected publications
"Size-dependent partitioning of nano/micro-particles mediated by membrane lateral heterogeneity" T. Hamada, et al, J. Am. Chem. Soc., 134, 13990-13996 (2012). doi
"Membrane disc and sphere: controllable mesoscopic structures for the capture and release of a targeted object" T. Hamada, et al, J. Am. Chem. Soc., 132, 10528-10532 (2010). doi
"Rhythmic pore dynamics in a shrinking lipid vesicle" T. Hamada, et al, Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 80, 051921 (2009). doi

Publications

2014
"Endo- and Exocytic Budding Transformation of Slow-Diffusing Membrane Domains Induced by Alzheimer’s Amyloid Beta"
Masamune Morita, Tsutomu Hamada,* Mun'delanji C. Vestergaard, Masahiro Takagi
Phys. Chem. Chem. Phys., in press (2014). doi
2013
41.
"Entry of a cationic lytic-type peptide into the cytoplasm via endocytosis-dependent and -independent pathways in human glioma U251 cells"
Koji Ohara, Masayuki Kohno, Tsutomu Hamada, Koji Kawakami
Peptides, 50, 28-35 (2013). doi
40.
"Dynamical formation of lipid bilayer vesicles from lipid-coated droplets across a planar monolayer at an oil/water interface"
Hiroaki Ito, Toru Yamanaka, Shou Kato, Tsutomu Hamada, Masahiro Takagi, Masatoshi Ichikawa and Kenichi Yoshikawa
Soft Matter, 9, 9539-9547 (2013). doi
Cover art
39.
"The effect of oxysterols on the interaction of Alzheimer's amyloid beta with model membranes"
Huong Thi Thanh Phan, Takahiro Hata, Masamune Morita, Tsuyoshi Yoda, Tsutomu Hamada, Mun'delanji C Vestergaard and Masahiro Takagi
Biochim. Biophys. Acta, Biomembr., 1828, 2487-2495 (2013). doi
38.
"Dynamic Morphological Changes Induced By GM1 and Protein Interactions on the Surface of Cell-Sized Liposomes"
Shruti Dhingra, Masamune Morita, Tsuyoshi Yoda, Mun'delanji C. Vestergaard, Tsutomu Hamada and Masahiro Takagi
Materials, 6, 2522-2533 (2013). doi
37.
"Antimicrobial activity and mechanism of action of a novel cationic α-helical dodecapeptide, a partial sequence of cyanate lyase from rice"
Norihiro Takei, Nobuteru Takahashi, Tomohiro Takayanagi, Atsuo Ikeda, Masahiro Takagi, Tsutomu Hamada, Eiichi Saitoh, Akihito Ochiai, Takaaki Tanaka, Masayuki Taniguchi
Peptides, 42, 55?62 (2013). doi
36.
"Membrane fusion and vesicular transformation induced by Alzheimer's Amyloid beta"
Mun'delanji C. Vestergaard, Masamune Morita, Tsutomu Hamada, Masahiro Takagi
Biochim. Biophys. Acta, Biomembr., 1828, 1314?1321 (2013). doi
2012
35.
"Ion Permeation by a Folded Multiblock Amphiphilic Oligomer Achieved by Hierarchical Construction of Self-Assembled Nanopores "
Takahiro Muraoka, Tatsuya Shima, Tsutomu Hamada, Masamune Morita, Masahiro Takagi, Kazuhito V. Tabata, Hiroyuki Noji, and Kazushi Kinbara
J. Am. Chem. Soc., 134, 19788?19794 (2012). doi
34.
"Cell-Sized Liposomes and Droplets: Real-World Modeling of Living Cells"
Tsutomu Hamada*, Kenichi Yoshikawa
Materials, 5, 2292-2305 (2012). doi (open access)

33.
"Size-dependent partitioning of nano/micro-particles mediated by membrane lateral heterogeneity"
Tsutomu Hamada, Masamune Morita, Makiyo Miyakawa, Ryoko Sugimoto, Mun'delanji C. Vestergaard, Masahiro Takagi
J. Am. Chem. Soc., 134, 13990?13996 (2012). doi

32.
"Thermo-induced vesicular dynamics of membranes containing cholesterol derivatives"
Tsuyoshi Yoda, Mun'delanji C. Vestergaard, Tsutomu Hamada, Le Phuc T Minh, Masahiro Takagi
Lipids, 47, 813-820 (2012). doi
31.
"Selective localization of Alzheimer's amyloid beta in membrane lateral compartments"
Masamune Morita, Tsutomu Hamada*, Yuiko Tendo, Takahiro Hata, Mun'delanji C. Vestergaard, Masahiro Takagi
Soft Matter, 8, 2816-2819 (2012). doi
30.
"Physicochemical profiling of surfactant-induced membrane dynamics in a cell-sized liposome"
Tsutomu Hamada, Hideyuki Hagihara, Masamune Morita, Mun'delanji C. Vestergaard, Yoshio Tsujino, Masahiro Takagi
J. Phys. Chem. Lett., 3, 430-435 (2012). doi
»Slide share
2011
29.
"Lateral phase separation in tense membranes"
Tsutomu Hamada*, Yuko Kishimoto, Takeshi Nagasaki, Masahiro Takagi
Soft Matter, 7, 9061-9068 (2011). doi
Virtual Journal of Biological Physics Research, Vol.22, Issue 7
28.
"Photochemical control of membrane raft organization"
Tsutomu Hamada*, Ryoko Sugimoto, Takeshi Nagasaki, and Masahiro Takagi
Soft Matter, 7, 220-224 (2011). doi
»PDF (JAIST Repository)
»Movie of photo-induced reversible phase separation 1 (in real speed)
»Movie of photo-induced reversible phase separation 2 (in real speed)
27.
"The Effect of Oxycholesterols on Thermo-sensitivity of Lipid Vesicles"
Mun'delanji C. Vestergaard, Tsuyoshi Yoda, Tsutomu Hamada, Yoko Akazawa-Ogawa, Yasukazu Yoshida, Masahiro Takagi
Biochim. Biophys. Acta, Biomembr., 1808, 2245-2251 (2011). doi
26.
"A Possible Mechanism of Cholesteryl Glucoside Formation Involved in Heat Shock Response in the Animal Cell Membrane"
Hisako Akiyama, Tsutomu Hamada, Yasuko Nagatsuka, Susumu Kobayashi, Yoshio Hirabayashi, Kimiko Murakami-Murofushi
Cytologia, 76, 19-25 (2011). doi
25.
"Mimicking Multipass Transmembrane Proteins: Synthesis, Assembly and Folding of Alternating Amphiphilic Multiblock Molecules in Liposomal Membranes"
Takahiro Muraoka, Tatsuya Shima, Tsutomu Hamada, Masamune Morita, Masahiro Takagi, and Kazushi Kinbara
Chem. Comm., 47, 194-196 (2011). doi
2010
24.
"Membrane disc and sphere: controllable mesoscopic structures for the capture and release of a targeted object"
Tsutomu Hamada, Ryoko Sugimoto, Mun’delanji Vestergaard, Takeshi Nagasaki, and Masahiro Takagi
J. Am. Chem. Soc., 132, 10528-10532 (2010). doi
»Movie of membrane closing dynamics (in real speed)
»Movie of membrane opening dynamics (in real speed)
»Movie of membrane edge fluctuation (in real speed)
»Movie of the capture and release of a colloidal particle (in real speed)

Cited by 11
23.
"Biomimetic microdroplet membrane interface: detection of the lateral localization of amyloid beta peptides"
Tsutomu Hamada, Masamune Morita, Yuko Kishimoto, Yuuki Komatsu, Mun'delanji Vestergaard, Masahiro Takagi
J. Phys. Chem. Lett., 1, 170-173 (2010). doi

Cited by 9
22.
"Dynamic response of a cholesterol-containing model membrane to oxidative stress"
Tsuyoshi Yoda, Mun'delanji C. Vestergaard, Yoko Akazawa-Ogawa, Yasukazu Yoshida, Tsutomu Hamada*, Masahiro Takagi
Chem. Lett., 39, 1273-1274 (2010).
»PDF (Open Access)
Cited by 3
21.
"Real-time observation of model-membrane dynamics induced by Alzheimer's amyloid beta"
Masamune Morita, Mun’delanji Vestergaard, Tsutomu Hamada, Masahiro Takagi
Biophys. Chem., 147, 81-86 (2010). doi
Cited by 12
20.
"Cholesterol, Lipids, Amyloid Beta, and Alzheimer's"
Mun’delanji Vestergaard, Tsutomu Hamada, Masamune Morita, Masahiro Takagi
Curr. Alzheimer Res., 7, 262-270 (2010). Abstract
Cited by 3
2009
19.
"Rhythmic pore dynamics in a shrinking lipid vesicle"
Tsutomu Hamada*, Yuichi Hirabayashi, Takao Ohta, Masahiro Takagi
Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 80, 051921 (2009). doi
Virtual Journal of Biological Physics Research, Vol.18, Issue 11
»PDF (JAIST Repository)
»Movie of rhythmic-pore shrinkage
»Movie of continuous-pore shrinkage

Cited by 9
18.
"Dynamic behaviors of giant liposomes in desired osmotic pressures"
Masae Ohno, Tsutomu Hamada, Kingo Takiguchi, Michio Homma
Langmuir, 25, 11680-11685 (2009). doi
Cited by 9
17.
"Reversible Control of Exo- and Endo-Budding Transitions in a Photosensitive Lipid Membrane"
Ken-ichi Ishii, Tsutomu Hamada*, Masaomi Hatakeyama, Ryoko Sugimoto, Takeshi Nagasaki, Masahiro Takagi
ChemBioChem, 10, 251-256 (2009). doi
»Movie files are available

Cited by 23
16.
"Artificial-cellular computing"
Shin-ichiro M. Nomura, Tsutomu Hamada
Int. J. Unconv. Comput., 5, 87-102 (2009). Abstract
Cited by 0
15.
"The conjugation of diphtheria toxin T domain to poly(ethylenimine)based vectors forenhanced endosomal escape during gene transfection"
Shinji Kakimoto, Tsutomu Hamada, Yuuki Komatsu, Masahiro Takagi, Toshizumi Tanabe, Hideki Azuma, Seiji Shinkai, and Takeshi Nagasaki
Biomaterials, 30, 402-408 (2009). doi
Cited by 9
2008
14.
"Construction of asymmetric cell-sized lipid vesicles from lipid-coated water-in-oil micro-droplets"
Tsutomu Hamada, Yoko Miura, Yuuki Komatsu, Yuko Kishimoto, Mun’delanji Vestergaard, Masahiro Takagi
J. Phys. Chem. B, 112, 14678-14681 (2008). doi

Cited by 23
13.
"Detection of Alzheimer’s amyloid beta aggregation by capturing molecular trails of individual assemblies"
Mun'delanji Vestergaard, Tsutomu Hamada, Masato Saito, Yoshifumi Yajima, Motonori Kudou, Eiichi Tamiya, Masahiro Takagi
Biochem. Biophys. Res. Commun., 377, 725-728 (2008). doi
Cited by 9
12.
"Effect of Phospholipids on conformational structure of bovine pancreatic trypsin inhibitor (BPTI) and its thermolabile mutants"
Naoshige Izumikawa, Shingo Nishikori, Mun'delanji Vestergaard, Tsutomu Hamada, Yoshihisa Hagihara, Noboru Yumoto, Kentaro Shiraki, Masahiro Takagi
Biopolymers, 89, 873-880 (2008). doi
Cited by 1
11.
"Using Model Membranes for the Study of Amyloid beta:Lipid Interactions and Neurotoxicity"
Mun'delanji Vestergaard, Tsutomu Hamada, Masahiro Takagi
Biotechnol. Bioeng., 99, 753-763 (2008). doi
Cited by 23
2007
10.
"Dynamic Processes in Endocytic Transformation of a Raft-Exhibiting Giant Liposome"
Tsutomu Hamada, Yoko Miura, Ken-ichi Ishii, Sumiko Araki, Kenichi Yoshikawa, Mun’delanji Vestergaard, and Masahiro Takagi
J. Phys. Chem. B, 111, 10853-10857 (2007). doi
»Movie of endocytic vesicle formation from a raft

Cited by 36
09.
"Manipulation of Cell-Sized Phospholipid-Coated Microdroplets and Their Use as Biochemical Microreactors"
M. Hase, A. Yamada, T. Hamada, D. Baigl, K. Yoshikawa
Langmuir, 23, 348-352 (2007). doi
Cited by 31
2006
08.
"Spontaneous Transfer of Phospholipid-Coated Oil-in-Oil and Water-in-Oil Micro-Droplets through an Oil/Water Interface"
A. Yamada, T. Yamanaka, T. Hamada, M. Hase, K. Yoshikawa, D. Baigl
Langmuir, 22, 9824-9828 (2006). doi
Cited by 33
07.
"Transporting of a Cell-Sized Phospholipid Vesicle Across Water/Oil Interface"
Masahiko Hase, Ayako Yamada, Tsutomu Hamada, Kenichi Yoshikawa<
Chem. Phys. Lett. 426, 441-444 (2006). doi
Cited by 9
06.
"Domain Growth Kinetics in a Cell-sized Liposome"
Daisuke Saeki, Tsutomu Hamada, Kenichi Yoshikawa
J. Phys. Soc. Jpn., 75, 013602 (2006). doi
»PDF (JAIST Repository)
»Movie files are available
Cited by 17
2005
05.
"Reversible photo-switching in a cell-sized vesicle"
Tsutomu Hamada, Yuko T. Sato, Takeshi Nagasaki, Kenichi Yoshikawa
Langmuir, 21, 7626-7628 (2005). doi
»Movie of prolate-bud transition
»Movie of stomatocyte-prolate transition

Cited by 27
04.
"Folding transition into a loosely collapsed state in plasmid DNA as revealed by single-molecule observation"
Yuko T. Sato, Tsutomu Hamada, Koji Kubo, Ayako Yamada, Tsunao Kishida, Osam Mazda, Kenichi Yoshikawa
FEBS Letters, 579, 3095-3099 (2005). doi
Cited by 12
03.
"Self-running droplet: Emergence of regular motion from nonequilibrium noise"
Yutaka Sumino, Nobuyuki Magome, Tsutomu Hamada, Kenichi Yoshikawa
Phys. Rev. Lett., 94, 068301 (2005). doi
Nature, 433, 693 (2005). news and views
Cited by 120
2004
02.
"Peeling Kinetics of giant multilamellar vesicles on a solid-liquid interface"
Tsutomu Hamada and Kenichi Yoshikawa
Chem. Phys. Lett., 396, 303-307 (2004). doi
»PDF (JAIST Repository)
Cited by 10
2003
01.
"Gene Expression Within Cell-Sized Lipid Vesicles"
S-i. M. Nomura, K. Tsumoto, T. Hamada, K. Akiyoshi, Y. Nakatani, K. Yoshikawa
ChemBioChem, 4, 1172-1175 (2003). doi
Cited by 128
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