Masahiro Sakurai

Thermostabilization of a chimeric enzyme by residue substitutions: four amino acid residues in loop regions are responsible for the thermostability of Thermus thermophilus isopropylmalate dehydrogenase

A chimeric 3-isopropylmalate dehydrogenase, named 2T2M6T, made of parts from an extreme thermophile, Thermus thermophilus, and a mesophile, Bacillus subtilis, was found to be considerably more labile than the T. thermophilus wild-type isopropylmalate dehydrogenase. In order to identify the molecular basis of the thermal stability of the T. thermophilus isopropylmalate dehydrogenase, 11 amino acid residues in the mesophilic portion of the chimera were substituted by the corresponding residues of the T. thermophilus enzyme, and the effects of the side chain substitutions were analyzed by comparing the reaction rate of irreversible heat denaturation and catalytic parameters of the mutant chimeras with those of the original chimera, 2T2M6T. Four single-site mutants were successfully stabilized without any loss of the catalytic function. All these four sites are located in loop regions of the enzyme. Our results strongly suggest the importance of these loop structures to the extreme stability of the T. thermophilus isopropylmalate dehydrogenase.

Electronic properties of graphene and boron-nitride based nanostructured materials

We study the electronic properties of graphene with periodic structural modifications using the local density approximation within the framework of the density functional theory. It is found that the double-layer graphene with nanotube arrays which connect the two sheets seamlessly is a direct-gap semiconductor. Also the single-layer graphene with periodic holes of 24-atomic-site vacancy is found to have a sizable direct fundamental gap as well. These graphene-based materials should be of high importance for nanoelectronics applications in the future. In addition, we study the electronic structure of the superlattice composed of graphene and boron-nitride layers which are stacked alternately. The material is found to be metallic even though each graphene layer is sandwiched by insulating BN layers and is very far from other graphene layers. The material may show interesting electronic properties being different from those of graphene.

Constant-Pressure Molecular-Dynamics Study of Carbon Nanotubes and Electronic Structure of New Phases

The pressure-induced structural phase transition of carbon nanotubes is studied using the constant-pressure tight-binding molecular-dynamics method. We find that an interesting sp2–sp3 hybrid structure, which is considered as a graphitic nanoribbon solid, is obtained from the nanotube solid composed of armchair nanotubes. The sp3-rich phase with anisotropic atomic network is also obtained at elevated pressure and is predicted to have high hardness which is comparable to that of cubic diamond. In contrast, the bundle composed of both armchair and chiral nanotubes transforms into amorphous diamond phase at high pressure. From the electronic-structure study in the framework of the density-functional theory, the nanoribbon solid phase obtained is found to be metallic.

Structure of a loop-deleted variant of 3-isopropylmalate dehydrogenase from Thermus thermophilus: an internal reprieve tolerance mechanism.

A loop-deleted mutant form of 3-isopropylmalate dehydrogenase from Thermus thermophilus was constructed to investigate the relationship between the flexibility of the structure and the thermostability of the enzyme. The structure of the mutant enzyme was determined by X-ray crystallography and was found to be almost the same as that of the native enzyme with a reduced temperature factor. Although the mutant protein had lost the flexible loop, its function and thermostability had remained unchanged. This phenomenon can be explained by an internal reprieve tolerance mechanism.

Pressure-induced Structural Phase Transition of Carbon Nanotubes into New Nanostructured Carbon Solids

We study pressure-induced structural phase transition of carbon nanotubes using the constant-pressure tight-binding molecular-dynamics simulation. The systems studied are nanotube bundles composed of (6,6) armchair nanotube and/or (7,4) chiral nanotube, which are reported to be the nanotubes relatively abundant in experimentally purified sample. We find that the nanotube bundles transforms into a new phase that consist of graphitic ribbons and diamond blocks, “graphitic nanoribbon solid”. It is also found that sp 3 -rich phases obtained from the armchair nanotubes possess an anisotropic network and have high hardness which is comparable to that of cubic diamond. In the case of the bundles containing chiral nanotubes, on the other hand, amorphous diamond phase is obtained. Based on the local-density approximation in the density-functional theory, we also investigate the energetics and electronic structure of some of new carbon phases obtained in the molecular-dynamics study.

Crystallization and preliminary X-ray studies on the hyperstable 3-isopropylmalate dehydrogenase from the thermoacidophilic archaeon Sulfolobus sp. strain 7.

3-Isopropylmalate dehydrogenase from the thermoacidophilic archaeon, Sulfolobus sp. strain 7, has been crystallized by the vapor-diffusion method. The crystals were grown from a solution containing ammonium sulfate, 2-methyl-2,4-pentanediol and magnesium chloride. The crystallization requires 2-methyl-2,4-pentanediol to avoid twinning of the crystals. The crystal belongs to the orthorhombic system with the space group P2221 and unit-cell dimensions a = 67.9, b = 93.3 and c = 134.1 A.