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| 総合実験棟Multidisciplinary Research Center 1F |
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Masaru Kawakami Associate Professor
School of Materials Science（Department of Materials Science・New Materials Design and Synthesis）
■Degrees
BS from Kobe University (1994)
MS from Kobe University (1996)
Ph.D. from Kobe University (1999)
■Professional Career
JSPS (Japan Society for the Promotion of Science) Fellow (DC1) (1996-1999)
Lecturer at Kobe University (1999-2000)
JSPS PostDoctoral Fellow (2000-2003)
Visiting Researcher at University of Leeds (2002-2003)
UK, EPSRC Postdoctoral Research Fellow (2003-2006)
(at The Astbury Centre for Structural Biology and
at Molecular Nanoscape Physics, University of Leeds)
JST PRESTO "Life Phenomena and Measurement Analysis" researcher (2006-2010)
Lecturer at JAIST, School of Materials Science (2006-2011)
Associate Professor at JAIST, School of Materials Science (2011-)
■Specialties
Biophysics, Single Molecule Measurement, Protein Folding,Structural Biology
■Research Keywords
Atomic Force Microscopy, Single Molecule Dynamics, Protein Folding
■Research Interests
Single Molecule Dynamics of Biomolecules with AFM
In order to understand the phenomenon of life, the elucidation ofthe function of each biomolecule is of great importance. Thefunctions of protein molecules, which play essential roles in the cell, have been studied intensively. To carry out their biological function, most protein molecules have to fold into a unique and highly-ordered structure and consequently much work has involved the determination of the three dimensional structures of proteins. However, the three-dimensional structure of proteins reveals only the “static” properties of proteins and not the dynamic “fluctuations” of their structures that are so important to their biological function.Until recently, almost all measurements of protein dynamics have been obtained using ensemble measurements. These techniques yield the average properties of the system: information about individual molecules is hidden and rarely populated conformational states, which might be of functional relevance, are extremely difficult to characterise. Techniques which can explore the behaviour of single molecules are, therefore, essential for developing new insights into the relationship between the dynamics and function of proteins.Single molecule techniques such as force mode AFM and optical tweezers have recently been used to investigate the mechanical properties of various kinds of biomolecules, but these techniques are not capable of investigating the “internal” dynamics of molecules.The aim of this study is to develop a novel technique which is capable of measuring the viscoelasticity of a single molecule using the thermally or externally driven motion of an AFM cantilever.Quantitative analysis of single molecule viscoelasticity provides dynamic information on the minor intra-molecular motions of protein molecules, which are expected to be important to their biological function. Using the single molecule viscoelasticity instrumentation, a novel single molecule manipulation technique will be developed that can control the reaction pathway of a singlemolecule leading to the formation of a structure.
The field of structural biology currently relies on computer-generated graphical representations of three-dimensional (3D) structures to conceptualize biomolecules. As the size and complexity of the molecular structure increases, model generation and peer discussions become more difficult. It is even more problematic when discussing protein-protein interactions wherein large surface area contact is considered. A new handleable protein molecular model with a soft and transparent silicone body similar to the molecule's surface has been developed in our laboratory. A full-color printed main chain structure embedded in the silicone body enables users to simultaneously feel the molecular surface, view through the main chain structure, and manually simulate molecular docking. The interactive, hands-on experience deepens the user’s understanding of the complicated 3D protein structure and elucidates ligand binding and protein-protein interactions. This model would be an effective discussion tool for the classroom or laboratory that stimulates inspired learning in this study field.
Press Release from AIP
'Squishy' model shows cell biology
Harmonized supramolecular machinery for motility and its diversity.
Harmonized supramolecular machinery for motility and its diversity.
■Publications
◇Books
- Single Molecule Biophysics: Experiments and Theory，T. Komatsuzaki, M. Kawakami, S. Takahashi, H. Yang , R. J. Silbey, S. A. Rice, A. R. Dinner，John Wiley & Sons Inc.，2012，Vol. 146
- NATO ASI series, Microwave Temperature-jump NMR in Structure, Dynamics and Function of Biological Macromolecules.，Akasaka, K. and Kawakami, M.，IOS Press, Amsterdam.，2001，93
◇Published Papers
- Variation in the mechanical unfolding pathway of p53DBD induced by interaction with p53 N-terminal region or DNA.，Yukinori Taniguchi and Masaru Kawakami*，PLOS ONE，7，11，e49003，2012
- (Highlighted & press released from AIP) A Soft and Transparent Handleable Protein Model，Masaru Kawakami*，Review of Scientific Instruments，83，084303，2012
- (Highlighted article) Prying open single GroES ring complexes by force reveals co-operativity across domains.，Akiko Ikeda-Kobayashi, Yukinori Taniguchi, David J. Brockwell, Emanuele Paci, Isao Sakane, Yasushi Kawata and Masaru Kawakami*，Biophysical Journal，102，8，1961-1968，2012
◇Lectures and Presentations
- Mechanical Unfolding Pathways of Holo-myoglobin Explored by AFM-based Single Molecule Force Spectroscopy，Masaru Kawakami，Indo-Japan Workshop "Recent Advances in Spectroscopy and Microscopy: Fundamentals and Applications to Materials andBiology", School of Chemistry, University of Hyderabad，Hyderabad, India，2012/11/20-21
- Mechanotransduction uncovered by single molecule force spectroscopy，Masaru Kawakami，7th International Conference on High Pressure Bioscience and Biotechnology，Otsu，2012/10/30
- Mechanical Stability of proteins probed by Atomic Force Microscopy，Masaru Kawakami，CNSI-JAIST workshop，CNSI, UCLA，2011/1/13
■Extramural Activities
◇Academic Society Affiliations
- The Biophysical Society of Japan，Regular Member，2007-
- Biophysical Society，Biophysical Society Member，1998-
◇Other Activities
- John Wiley ＆ Sons， Inc．，Co-Editor of "Advances in Chemical Physics" in 2009，2009/01/01 - 2009/12/08
- BBSRC Japan Partnership Award，As a Collaborator on UK side (2004-2006) As a Collaborator on Japan side (2006-2008)，2004/01/01 - 2008/12/31
- BBSRC Japan Partnership Award，As a Collaborator on UK side (2004-2006) As a Collaborator on Japan side (2006-2008)，2004/01/01 - 2008/12/31
■Academic Awards Received
- Kato Memorial BioScience Foundation，Kato Memorial Bioscience，2011
- Best Poster Presentation Award，CEA and QB3，2008
- BBSRC Japan Partnership Award，BBSRC (UK)，2004