Laboratory of Structural Proteomics


Institute for Protein Research

Osaka University

3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN

FAX (from abroad) +81-6-6879-8599


Associate Professor :                Takahisa IKEGAMI, Ph.D.

E-mail :                                         tiik@protein.osaka-u.ac.jp


The group is studying biomolecules such as proteins, nucleic acids, and lipids mainly by two methods, X-ray crystallography and nuclear magnetic resonance (NMR).


1. Nuclear Magnetic Resonance

NMR is a useful tool for the analyses of protein structures and dynamics with atomic resolutions. This group determines the three-dimensional structures of proteins using NMR, studies dynamics of proteins, and develops methodology of related NMR techniques.


2. Determination of Protein Structures

It has been more and more important to describe biological functions in terms of the three-dimensional structures of associated proteins. At least three methods are known to determine structures with the atomic coordinates: X-ray crystallography, electron-microscopy, and NMR. NMR is characteristic in a point that it can analyze the structures of biomolecules in solution states, providing data that reflect more natural conditions. Therefore, NMR allows for the analyses of proteins containing a lot of flexible regions, for which crystallizations are generally difficult. Although it is considered that the procedures of determining the structures of small proteins (M.W. < 30 kDa) by NMR have mostly become protocols, a lot of problems have to be practically solved when flexible and large proteins (M.W. > 40 kDa), such as ones containing multi-domains inside, are targeted.


3. Analyses of Protein Dynamics

NMR is also suitable for detection of flexibility, providing information as to which parts of proteins fluctuate in solutions. The fact that NMR yields dynamic structures can distinguish NMR from X-ray crystallography, which normally gives static structures with higher resolutions. A lot of biological functions are related to protein-motions. In particular, slow dynamics occurring in a time range of microsecond to millisecond are very important to biological functions. Since much faster motions ranging from picosecond to nanosecond have been mainly analyzed by NMR so far, new parameters representing slow dynamics are expected to elucidate new characters of proteins as well as mechanisms of protein folding/unfolding and protein-protein associations.


4. Development of NMR Methodology

Further developments of NMR methodology to facilitate the above-mentioned studies are also important tasks. For example, new methods for structure determination of much larger proteins with molecular weights of > 40 kDa and for observation of slow dynamics by NMR should be developed more.

Fig. 1

The super-conducting-magnet in a 600 MHz nuclear magnetic resonance (NMR). A cooling medium, liquid helium, is just being transferred to the magnet to keep the temperature of the super-conducting coils at 4 K. The magnet functions like a Dewar thermos vessel, in which a phase of liquid helium containing the coils is surrounded by that of liquid nitrogen.

Fig. 2

The top part of an 800 MHz NMR magnet. A solution sample stuffed at the bottom of a glass tube is just being placed in the magnet.

Fig. 3

The spectrometer part of an NMR. It generates radio-frequency waves in forms of pulses, emits them to the sample in the magnet, processes the signals having returned back from the sample, and saves these data.

Fig. 4

A two-dimensional NMR spectrum of a protein. The spectrum is referred to as 1H-15N heteronuclear single quantum correlation (HSQC), in which each peak corresponds to the 1H and 15N resonances of the amide group in an amino acid. These kinds of spectra imply the stabilities in conformations of proteins.

The 1H-15N pulse sequences (Bruker) for the participants in JASS'03 NMR-Winter-School (2004/Jan./22nd).