Simulation Study of RNA-Binding Protein, Pumilio

Ikuo KURISAKIa*, Hirofumi WATANABEb, c and Shigenori TANAKAb, c

aGraduate School of Science and Technology, Kobe University
1-1, Rokkodai, Nada, Kobe 657-8501, Japan
bGraduate School of Human Development and Environment, Kobe University
3-11 Tsurukabuto, Nada, Kobe 657-8501, Japan
cJapan Science and Technology Agency, CREST, Japan

(Received: July 11, 2008; Accepted for publication: February 10, 2009; Advance publication: March 6, 2009)

The RNA-binding proteins (RBPs) can recognize and bind their target RNAs specifically according to RNA sequences and/or 3D structures, and can thus express their functions. One of the RBPs, Pumilio, has an RNA-binding domain, Puf domain, in the C-terminal region, which recognizes the RNA sequence (Figure 1) and the 2' hydroxyl group in ribose. The Puf domain consists of 8 tandem modules (Figure 2) and forms the complexes with RNA containing specific sequences (Figure 3). Further, RNA base mutational experiments suggest that each base in the sequence differs in the contribution to the binding free energy of Puf domain-RNA complex formation. In this study, we employ molecular dynamics (MD) simulation to quantitatively estimate the contribution of each base and amino acid to complex stabilization. We analyze the MD trajectory of Puf domain-RNA complex system and calculate the frequencies of hydrogen bond formation at the Puf domain-RNA interface (Figures 6, 7). We also calculate the enthalpy term of the binding free energy of Puf domain-RNA complex, decompose it into enthalpy per residue (Figure 8), and compare the contributions of each amino acid and RNA base. From these analyses, we conclude that each base does not uniquely contribute to the stabilization of the complex and that amino acid residues around the binding interface are key factors of stabilization in Puf domain.

Keywords: RNA-binding protein, Sequence specific binding, RNA recognition, AMBER, Molecular dynamics simulation, Bio-macromolecule, MM-PBSA

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