1P126 A theoretical study on the fluorescent spectrum of enhanced green fluorescent protein(06.Electronic state,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)
1P126 緑色蛍光タンパク質の蛍光スペクトルに関する理論的研究(06.電子状態,ポスター,日本生物物理学会年会第51回(2013年度))

Yoshihiro Uchida, Masahiro Higashi, Shigehiko Hayashi
2013 Seibutsu Butsuri  
In this research, we investigated selective adhesion of single-stranded DNA binding (SSB) protein onto SWNT surfaces that were wrapped with singlestranded DNA (ssDNA) or double-stranded DNA (dsDNA). DNA-SWNT hybrids were prepared in an aqueous solution prior to the injection of SSB molecules. Atomic force microscopy and electrophoresis revealed that SSB protein adsorbed only to the ssDNA-SWNT hybrids. The results clearly showed that molecular recognition function of SSB protein molecules is
more » ... lable even for the DNA molecules attached on the SWNT surfaces. Further, the data suggested that dsDNA molecules retained their doublestranded structures on the SWNT surfaces although the molecules were sonicated during the sample preparation. 1P123 全反射蛍光顕微鏡によるショウジョウバエ RNAi 酵素複合体 形成の基本過程の解明 Defining fundamental steps in the assembly of Drosophila RNAi enzyme complex by TIRF microscopy siRNAs and Argonaute (Ago) proteins form RNA-induced silencing complexes (RISCs) that silence expression of target mRNAs. Although Drosophila RISC assembly requires the Dicer-2/R2D2 heterodimer and the Hsc70/Hsp90 chaperone machinery, the details remain unclear. Here, by following the assembly of single RISCs, we find that an siRNA bound to Dicer-2/R2D2 associates with Ago2 only transiently. The chaperone machinery extends the dwell time of Dicer-2/R2D2/siRNA on Ago2, in a manner dependent on the 5' phosphate recognition on the siRNA guide strand. We propose that the chaperone machinery acts to support a productive conformation of Ago2, allowing it to load authentic siRNA duplexes. Our results define the molecular basis for the chaperone-assisted assembly of RISC. 1P124 光刺激により自律的に自己組織化する RNA 分子ロボットの 構築 Molecular computers and molecular self-assembled structures have recently attracted attention as sophisticated bio-inspired systems. Although many nanostructures and autonomous molecular computers based on DNA/RNA molecules have been reported up to now, molecular robots integrating the nanostructures and molecular computers have never been developed yet. Here, we propose an autonomously self-assembled RNA molecular robot as an integrated system of molecular computers and nanostructures. In this system, RNA transcription starts by light stimulation as input information, and the RNA molecules autonomously self-assembles into an RNA molecular robot body. We believe that this molecular robot will be applied to molecular robots with more complex functions in the future. 1P125 蛋白質-RNA の複合体立体構造予測 In general, it is difficult to solve the three dimensional (3D) structure of biomolecule complex compared to a monomeric protein. So, the computational 3D structure prediction of complex (often called "docking problem") has been studied. Although 3D structure prediction of proteinprotein complex and protein-compound complex has been investigated by many researchers during decades, there are few studies about proteinnucleic acid complex. Now, we introduce the method to predict 3D structure of protein-RNA complex. Our method is applied to 72 complex structures, its success rate is ~29%, which may be world record in this research area. Moreover, it usually requires within only an hour to acquire result by using a general desktop computer. 1P126 緑色蛍光タンパク質の蛍光スペクトルに関する理論的研究 A theoretical study on the fluorescent spectrum of enhanced green fluorescent protein Fluorescent proteins have played a crucial role in biological imaging and analysis. The fluorescent spectrum is one of the important photophysical properties of fluorescent protein. Here, we talk about a research on the molecular simulation of the spectral shape of fluorescent protein. First, we introduce a method to calculate fluorescent spectra of protein. For this purpose, it is needed to evaluate accurately both excited states of the chromophore and structural fluctuations of the protein. Next, by applying the method to enhanced green fluorescent protein (EGFP), the origin of the spectral shape is discussed. This new method for calculating fluorescent spectrum is useful to develop the functions of fluorescent proteins such as color variant and ion sensor. Appropriate treatment of electrostatic interaction of charged particles is critical for computational study of biomolecular system. We introduced a novel idea, zero-dipole summation[1], which is based on cut-off approach to calculate the electrostatic interactions, but prevents electrically nonneutral states artificially generated by straight truncation. The resulting formula is very simple and does not necessarily need periodic boundary condition, which is often problematic. We discuss the theory, timing, and results of molecular dynamics simulations applied to a membrane protein system and a DNA system. [1] I. Fukuda, et al.
doi:10.2142/biophys.53.s126_5 fatcat:mzzlwq3wkvcpxgd2pxazyct2ta