2003 Fiscal Year Final Research Report Summary
Electronic structure calculations on K^+ ion channel protein
| Project/Area Number |
14540482
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Physical chemistry
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| Research Institution | National Institute of Advanced Industrial Science and Technology (AIST) |
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Principal Investigator |
KITAURA Kazuo AIST, RICS, principal researcher, 計算科学研究部門, 総括研究員 (30132723)
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| Co-Investigator(Kenkyū-buntansha) |
UEBAYASI Masami AIST, IBRF, chief researcher, 生物機能工学研究部門, 主任研究員 (70356559)
KOMEIJI Yuto AIST, RICS, chief researcher, 計算科学研究部門, 主任研究員 (30357032)
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| Project Period (FY) |
2002 – 2003
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| Keywords | MO calculation of protein / channel protein / fragment MO method / potassium ion channel / large scale MO calculations |
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| Research Abstract |
We have developed a fragment-based molecular orbital method(FMO) for electronic structure calculations of large molecules such as proteins. We applied this method to K+ ion channel proteins to elucidate the permeation mechanism. For large scale calculations, we improved the FMO method to improve efficiency of parallel processing on PC clusters. The FMO codes developed in this project was interfaced with GAMESS. Using the program we performed the FMO calculations of the whole channel protein consisting of 5,902 atoms at the RHF/STO-3G level. The computational time (elapsed time) was 13 hours and 12 minutes on a ten Pentium IV personal computers connected with 100-base network.
The calculated result showed that the net charge of K+ ions in the channel was changed from +1 to +0.54-+0.61 and the repulsion between the ions was largely reduced. The charge transfers mainly occurred form the thr75 and tyr78 residues to the K+ ions. The thy75 and tyr78 residues were polarized by the K+ ions and -0.09 and -0.04 charges were induced on the carbonyl oxygen atoms, respectively. An interaction energy analysis based on the FMO method revealed that the induced charges also stabilize the K+ ions in the channel.
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