MASAYUKI IRISA

MASAYUKI IRISA

Kyushu Institute of Technology, Japan



Biography

Masayuki Irisa completed a doctoral program of Kyoto University without degree and got his Ph.D. by way of dissertation at the age of 32 years from Osaka University. He is an Associate Professor in department of Bioscience and Bioinformatics, faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, which belongs to a national university corporation, JAPAN. He has been serving as a teacher and a researcher in the Kyushu Institute of Technology for 20 years.

Abstract

I. Onishi, S. Sunaba, N. Yoshida, F. Hirata, M. Irisa
 
1 Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka 820-8502 (Kyushu Institute of Technology, JAPAN)
2Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka 820-8502 (Kyushu Institute of Technology, JAPAN)
3Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395 (Kyushu University, JAPAN)
4Department of Chemistry, Toyota Riken, Aichi 480-1192 (Toyota Riken, JAPAN) and  
Institute for Molecular Science, Okazaki 444-8585 (Institute for Molecular Science, JAPAN)
 5Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka 820-8502 (Kyushu Institute of Technology, JAPAN)
 
 
Abstract (not more than 300 words)
 
The role of Mg2+  ions in DNA hydrolysis by homodimeric restriction enzyme EcoRV was elucidated based on the 3D-RISM-KH theory and the MD simulation. From an analysis of the spatial distribution of Mg2+  in an active site using 3D-RISM-KH, we identified a new position for Mg2+  in the X-ray EcoRV-DNA complex structure (1rvb), which turns out to play a crucial role in the reaction. We refer to the position as site IV†. Site IV† is almost the same position as that of a Ca2+ ion in the superimposed active-site structure of X-ray PvuII-DNA complex (1f0o). The 3D-RSIM-KH was also used to locate the position of water molecules including the water nucleophile at the active site. MD simulations were carried out with the initial structure having two Mg2 +  ions at site IV† and at site I*, experimentally identified by Horton et al., to find a stable complex structure in which rearrangement of the DNA fragment occurred to orient the scissile bond direction toward the water nucleophile. The equilibrium active-site structure of EcoRV-DNA complex obtained in MD simulation was similar to the superimposed structure of X-ray BamHI-DNA complex (2bam). In the active-site structure, two metal ions have the same position as that of 2bam, and the scissile phosphate is twisted to orient the scissile bond toward the water nucleophile as is the case in 2bam. We propose the equilibrium active-site structure obtained in this study as a precursor of the hydrolysis reaction of EcoRV.
 
Keywords—3D-RISM-KH, Molecular Dynamics, EcoRV, restriction enzyme, DNA hydrolysis, Mg2+ ion