Spontaneous adjustment mechanism in an RNA-binding protein: Cooperation between energetic stabilization and target Search Enhancement

Ikuo Kurisaki*, Hirofumi Watanabe, Shigenori Tanaka

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

We propose a novel concept associated with the relationship between structure and function in biomolecular systems. We performed a 75 nanoseconds molecular dynamics (MD) simulation for an RNA-binding protein, neuro-oncological ventral antigen (NOVA), and examined its physico-chemical properties. NOVA dissociated from the NOVA-RNA complex showed a large conformational change: formation of intra-molecular hydrogen bonds between the C-terminal region and the loop structure located at the middle of amino acid sequence. The free energy analysis suggests that the deformed structure is more stabilized in macromolecular crowding environment where the dielectric constant is smaller than 5. The solvent accessible surface area (SASA) analysis indicates that NOVA enhances the efficiency of association with RNA by changing the relative SASA for the target sequence in RNA molecules. Based on the obtained results, we propose a novel concept of spontaneous adjustment mechanism to explain the structural and energetic changes observed for NOVA in the free state.

Original languageEnglish
Pages (from-to)1547-1552
Number of pages6
JournalProtein and Peptide Letters
Volume17
Issue number12
DOIs
Publication statusPublished - 2010 Dec
Externally publishedYes

Keywords

  • K homology (KH) domain
  • Molecular dynamics (MD)
  • Neuro-oncological ventral antigen (NOVA)
  • Relationship between structure and function
  • RNA-binding protein (RBP)
  • Stabilization of protein.

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry

Fingerprint

Dive into the research topics of 'Spontaneous adjustment mechanism in an RNA-binding protein: Cooperation between energetic stabilization and target Search Enhancement'. Together they form a unique fingerprint.

Cite this