Electrostatic Interactions That Determine the Rate of Pseudorotation Processes in Oxyphosphorane Intermediates: Implications with Respect to the Roles of Metal Ions in the Enzymatic Cleavage of RNA.
The enzymatic cleavage of RNA takes place via a cyclic pentacoordinate oxyphosphorane intermediate/transition state. We carried out ab initio investigations on the neutral cyclic oxyphosphorane, which exists as a stable intermediate. As a consequence of the conformational preferences of the pentacoordinate trigonal bipyramidal intermediates, the rotation of the P-OH bonds is strongly coupled with the reaction coordinate for the pseudorotation process. In addition, the neutral PF(4)OH species has a higher barrier to pseudorotation than the corresponding anionic species PF(4)O(-). These findings are related to the positive charge of the hydrogen atoms on the equatorial oxygens in the trigonal bipyramidal structures: the hydrogen atoms preferably adopt eclipsed positions relative to the axial ligands. Fixing the cationic species in these regions causes an increase in the barrier heights for pseudorotation processes and, thus, prevents isomerization by pseudorotation. Consequently, metal coordination in the double-metal ion mechanism for enzymatic cleavage of RNA should serve to exclusively stabilize the trigonal bipyramidal intermediate/transition state for the in-line attack and departure process.
Uchimaru
Tadafumi
T
National Institute of Materials and Chemical Research, National Institute of Bioscience and Human Technology, Agency of Industrial Science and Technology, MITI, and Institute of Applied Biochemistry, University of Tsukuba, Tsukuba Science City, 305 Japan.
Uebayasi
Masami
M
Hirose
Takuji
T
Tsuzuki
Seiji
S
Yliniemelä
Ari
A
Tanabe
Kazutoshi
K
Taira
Kazunari
K