Robotic Path Planning and Protein Complex Modeling Considering Low Frequency Intra-Molecular Loop and Domain Motions

Carlos A. Del Carpio[1] (carlos@aki.che.tohoku.ac.jp)
Pei Qiang[1] (pei@aki.che.tohoku.ac.jp)
Eiichiro Ichiishi[2] (ichiishi@xg7.so-net.ne.jp)
Hideyuki Tsuboi[1] (tsuboi@aki.che.tohoku.ac.jp)
Michihisa Koyama[1] (koyama@aki.che.tohoku.ac.jp)
Nozomu Hatakeyama[1] (hatakeyama@aki.che.tohoku.ac.jp)
Akira Endou[1] (endou@aki.che.tohoku.ac.jp)
Hiromitsu Takaba[1] (takaba@aki.che.tohoku.ac.jp)
Momoji Kubo[1],[3] (momoji@aki.che.tohoku.ac.jp)
Akira Miyamoto[1],[4] (miyamoto@aki.che.tohoku.ac.jp)

[1]Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, 6-6-11-1302 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
[2]Biomedical Engineering Research Organization, Tohoku University, Aoba-ku, Sendai 980-8579, Japan
[3]PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
[4]New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-10 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan


Abstract

A novel algorithm is introduced to deal with intra-molecular motions of loops and domains that undergo proteins at interaction with other proteins. The methodology is based on complex energy landscape sampling and robotic motion planning. Mapping high flexibility regions on the protein underlies the proposed algorithm. This is the first time this type of research has been reported. Application of the methodology to several protein complexes where remarkable backbone rearrangement is observed shows that the new algorithm is able to deal with the problem of change of backbone conformation at protein interaction. We have implemented the module within the system MIAX (Macromolecular interaction assessment computer system) and together with our already reported soft and flexible docking algorithms we have developed a powerful tool for protein function analysis as part of wide genome function evaluation.

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Japanese Society for Bioinformatics