C-1-19
FMO-based electron density analysis
to protein structure refinement
Chiduru Watanabe 1
chiduru@iis.u-tokyo.ac.jp

Kaori Fukuzawa 1,2
kaori.fukuzawa@mizuho-ir.co.jp

Akifumi Kato 2
akifumi.kato@mizuho-ir.co.jp

Shigenori Tanaka 3
tanaka2@kobe-u.ac.jp
1

2

3

4

Yoshio Okiyama 1
okiyama@iis.u-tokyo.ac.jp

Takayuki Tsukamoto 2
takayuki.tsukamoto@mizuho-ir.co.jp

Yuji Mochizuki 1,4
fullmoon@rikkyo.ac.jp

Institute of Industrial Science, The University of Tokyo, 4 -6-1 Komaba, Meguro-ku, Tokyo
153-8505, JapanMizuho Information & Research Institute Inc., 2 -3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo101-8443, Japan
Graduate School of System Informatics, Department of Computational Science, Kobe
University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan
Department of Chemistry & Research Center for Smart Molecules, Faculty of Science, Rikkyo
University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan

Keywords: Electron density, Refinement, Optimization, Fragment molecular orbital (FMO)
method, ABINIT-MP, BioStation
Electron densities obtained by X-ray diffraction analyses for biomolecules determine the nuclearcoordinates with some ambiguities in position of hydrogen atoms, protonation, conformation ofamino acid residues, and orientation of ligand binding, and so on. Optimization using the classicalmolecular mechanics (MM) generally refines the coordinates to obtain the final structures, which
are registered to PDB entry and used to understand functions of biomolecul es. However, the MM
optimization often fails to reproduce the distance of hydrogen bonding and such optimized
structure has inadequate coordinates in the framework of quantum mechanics for example. For
drug discovery using ab initio fragment molecular orbital (FMO) method [1], refinement of thestructure determination is thus needed to evaluate protein-ligand interaction and reaction
mechanism more properly. In this study, we examine an electron density analysis for therefinement by comparing between X-ray and FMO-based electron densities using Crambin protein.
The FMO-based electron densities are prepared as below: First, stating form the high -resolution(0.48Å) X-ray crystal structure of Crambin including hydrogen atoms (PDB -ID: 3NIR), multiple
conformations are obtained by MM and QM optimizations: Next, FMO calculations of these
conformations are carried out to generate FMO-based electron densities at MP2/6-31G* level byusing a development version of BioStation [2] on K-computer. We here reveal position of hydrogenatoms, protonation, and conformation of amino acid by assessing the original X-ray electron
density and the FMO-based ones each other. In addition, the same analysis is performed using thelow-resolution (2.0Å) structure. Finally, we investigate how the optimized conformations based on
low-resolution X-ray electron density, which are used in generally drug design, reproduce theoriginal high-resolution X-ray electron density.
[1] “The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems” ed D. G.
Fedorov and K. Kitaura (Taylor & Francis/ CRC Press, Boca Raton, FL, 200 9).
[2] The calculations and visualization of electron density are performed by a development version ofBioStation (download site; http://www.ciss.iis.u-tokyo.ac.jp/dl/index.php.).
Acknowledgment
This research was supported by the grant for “Strategic Programs for Innovative Research” Field No. 4:
Industrial Innovations from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT)’s“Development and Use of Advanced, High-Performance, General-Purpose Supercomputers Project.”