The Mass Spectrometry society of Japan - The 71st Annual Conference on Mass Spectrometry, Japan
Japanese

Abstract

Table of contents

Timetable

Plenary Lecture

Symposium Sessions (Day1, Day2, Day3)

Basic Sessions (Day1, Day2, Day3)

Young Researchers' Sessions (Day1, Day2, Day3)

Poster Presentations (Day1, Day2, Day3)

Special Evening Sessions

Corporate Program

Basic Sessions

Day 1, May 15（Mon.）　10:00-10:18　Room A (Special Conference Room)

1A-O-1000　　PDF

Development of the method for gas phase coarse-grained molecular dynamics simulation including electrostatic and hydrophobic interactions

(1AIST, 2Yokohama City Univ., 3Kyoto Univ.)
oKazumi Saikusa1,2, Satoko Akashi2, Sotaro Fuchigami3

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 Å2, within which the experimental value of 3640 Å2 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.