Laboratory of Bio-Functionl Molecular Design

Hiroshi Nakajima (Professor)




1. Current Research and Principal Research Interests

We have focused on development of novel biomaterials based on coordination and electro- chemistry, which include artificial metallo-enzymes, stimuli responsible nano-carriers, electrochemical signal transduction with proteins and so on. Characterization of a novel signal transducer protein, particularly a transcriptional regulator, is also a target in our research, aiming at the exploitation of its functional mechanism to a future signal transduction system. In light of the practical application of proteins as a durable molecular material, we are interested in the functional transformation of proteins from thermophiles by making use of genetic techniques and chemical modification. The followings are some research projects on going in our research group.

Application of a signal transducer protein as a sensing module of electrochemical bio-sensor. A transcriptional regulator is a member of signal transducer proteins which specifically sense an environmental stress to treat it by regulating activity of appropriate proteins at the transcriptional level. In biological systems, various transcriptional regulators have evolved to respond to all kinds of stresses not only chemical substances but also physical stimuli such as light, heat, and osmotic pressure. In general, the stress detection by the transcriptional regulators is highly sensitive and specific, which are essential to eliminate the stresses and retain homeostasis of living cells. Meanwhile, these properties appear attractive in light of constructing a novel bio-based sensor device. In order to realize such biosensor, we are focusing to construct an electrochemical system to transduce the readout of a transcriptional regulator to an electronic signal. The figure below shows a recent achievement in this research project. For more details, please visit the home page of our research group.

Alteration in the binding affinity of CO-dependent transcriptional regulator (the intrinsic readout of the regulator) is transduced to modulation in the electron transfer rate between two electron transfer proteins.



Cytohrome c552 from Thermus thermophirus. A frequently used protein in our research project

Creation of thermally tolerant peroxidase transforming a protein from thermophilic bacterium Proteins are generally considered to be fragile under conditions other than room temperature and near neutral aqueous solution and readily lose their functions.  This is because proteins familiar to us derive from cells that work in the environment moderate to our cells.  Proteins produced in microorganisms which grow (as viewed from us) in harsh environments, however, has excellent properties to be tolerant to the environment.  Using such proteins, we are trying to create an artificial enzyme and nano-carrier which shows sufficient thermal stability required on practical use. For more details, please visit the home page of our research group.


Characterization of Transcriptional regulator of nitrogenase, another pathway to understand nitrogenase In present days, artificial nitrogen fixation (reduction of nitrogen in the air to ammonia) reaches approximately to 10% of whole ecosystem (Ref. 1), which is essential for the production activities of the human race. Most of them have been demanded by the Haber process. In light of energy saving for material production, development of alternative processes that do not require high temperature and high pressure would become a more and more important issue. Among several challenges to realize such processes, use of bacteria that produce nitrogenase (a nitrogen-fixing enzyme) as biomass is counted to be a strong candidate. However, there are several big problems before putting it into practical use. One of them is to understand what growing environment maximizes ability of bacterial nitrogen fixation.

Detailed characterization of the nitrogenase would be a conventional method to understand suitable conditions to maximize the nitrogenase function. Meanwhile, our have taken another approach to do so: functional characterization of the transcriptional regulator of nitrogenase. Recent achievements are schematized in the left-hand. For more details, please visit the home page of our research group.




2. Selected Publications

1.     Miura Y., Yoshimitsu K., Takatani N., Watanabe Y., Nakajima H., Effect of Nitric Oxide on VnfA, a transcriptional activator of nitrogenase-2, in Azotobacter vinelandii. J. Biochem. 157, 365-375, 2015.

2.     Rabindra KB., Nakajima H., Jitumani R., Watanabe Y., Mazumdar S., Thermodynamic effects of the alteration of the axial ligand on the unfolding of the thermostable cytochrome c. Biochemistry, 52, 1373-1384, 2013.

3.     Ibrahim Sk. Md., Nakajima H., Ramanathan K., Takatani N., Ohta T., Naruta Y., Watanabe Y., Cytochrome c552 from Thermus Thermophilus Engineered for Facile Conversion of the Prosthetic Group. Biochemistry, 50, 9826-9835, 2011.

4.     Nakajima H., Takatani N., Yoshimitsu K., Itoh M., Aono S., Takahashi Y., Watanabe Y., The role of Fe-S cluster in the sensory domain of nitrogenase transcriptional activator VnfA Azotobacter vinelandii. FEBS J., 277, 817-832, 2010.

5.     Rosenberger N., Studer A., Takatani N., Nakajima H., Watanabe Y., Azurin–Poly(N-isopropylacrylamide) Conjugates by Site-Directed Mutagenesis and their Temperature Dependent Behavior in Electron Transfer Processes. Angew. Chem. Int. Ed., 48, 1946-1949, 2009.

6.     Nakajima H., Ichikawa Y., Satake Y., Takatani N., Manna SK., Rajbongshi J., Mazumdar S., Watanabe Y., Engineering of Thermus thermophilus Cytochrome c552: Thermally Tolerant Artificial Peroxidase. ChemBioChem, 9, 2954-2957, 2008.

7.     Tokita Y., Shimura J., Nakajima H., Goto Y., Watanabe Y., Mechanism of Intermolecular electron Transfer in the Photoexcited Zn-Substituted Cytochrome c: Theoretical and Experimental Perspective. J. Am. Chem. Soc., 130, 5302-5310, 2008.

8.     Satake Y., Abe S., Okazaki S., Ban N., Hikage T., Ueno T., Nakajima H., Suzuki A., Yamane T., Nishiyama H., and Watanabe Y., Incorporation of a phebox rhodium complex into apo-myoglobin affords a stable organometallic protein showing unprecedented arrangement of the complex in the cavity. Organometallics, 26, 4904-4908, 2007.

9.     Watanabe Y., Nakajima H., Ueno T., Reactivities of oxo and peroxo intermediates studied by hemoprotein mutants. Acc Chem Res, 40, 554-562, 2007.

10.   Ichikawa Y., Nakajima H., Watanabe Y., Characterization of peroxide bound heme species generated in reaction of thermally tolerant cytochrome c552 with hydrogen peroxide. ChemBioChem, 7, 1582-1589, 2006.