************第３９回尾張コンプレックスセミナー*************

Title　： COMPUTER SIMULATION STUDY ON MOLECLURA
          RECOGNITION MECHANISM OF AN RNA-BINDING
          PROTEIN

Speaker ：　Ikuo Kurisaki (Research Organization of Science and
               Engineering, Ritsumeikan University, post doctoral
               fellow)

Date　：　Mon. December 13th, 1:30 pm

Abstract：
RNA-binding proteins (RBPs) play roles in RNA metabolism in the
cell. RBPs express their functions when they bind their target RNAs
recognizing specific sequences and/or shapes. 1000 of 3D structure
of RBP were resolved and the molecular recognition mechanism has
been revealed based on protein structure of RBP-RNA complex.
Furthermore, computer simulations have been employed to obtain
deeper insight into the issue from the aspect of physico-chemical
properties. In this seminar, I will present the molecular dynamics
simulation study and electronic state calculation with fragment
molecular orbital based quantum mechanics (FMO-QM) calculation
for one of RNA-binding protein, NOVA which have canonical RNA-
binding domain, KH-domain. The summary of each study was shown
below.

[1] Molecular recognition would be tightly associated with electronic
state of the molecules. We calculated the electronic state of whole
RBP and RNA employing FMO-QM calculation and analyzed the
change of electronic state upon the complex formation. By
comprehensively visualizing the change of inter-fragment interaction
energy upon the RBP-RNA inter-molecular interactions, we
examined the relation between RBP structure and change of
electronic state.

[2] The statistic study on 3D structure of RBPs revealed that
non-polar residue doublet (e.g. Ile-Ile doublet) were familiar
components of RNA-binding interface [Kim et al., Nucleic Acid Res.,
34, 6450-6460 (2006)]. We performed molecular modeling to
prepare RNA-mutated structure and estimate binding free energy
for both wild type and the mutants. We examined the contribution
of seemingly weak interactions on RNA base recognition.

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