演題概要

基盤セッション

第1日　5月15日（月）　10:00～10:18　A会場（特別会議場）

1A-O-1000　　PDF

静電および疎水性相互作用を考慮した気相粗視化分子シミュレーション法の開発

(¹産総研・ ²横市大院生命医・ ³京大院理)
^o七種和美^1,2・ 明石知子²・ 渕上壮太郎³

Ion mobility mass spectrometry (IM-MS) can provide not only mass but also collision cross section (CCS) of biomolecules. In our previous studies, we characterized biomolecular complexes using IM-MS and all-atom molecular dynamics simulation. In this study, to reduce computational cost and to enable simple and rapid calculations, we constructed a method of coarse-grained molecular dynamics simulations with electrostatic and hydrophobic interactions, and applied the developed method to a model protein complex, avidin. The structural ensemble obtained by the optimal interaction strengths gave CCS values in the range of 3590-3770 Ų, within which the experimental value of 3640 Ų is comprised. Now, we are trying to simulate other protein complexes with/without intrinsically disordered region, Swi5-Sfr1/Swi5-Sfr1C using the optimal interaction strengths.