Electronic structure calculations on K^+ ion channel protein

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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.