2011 Fiscal Year Final Research Report
Developing a method for predicting protein structure based on physical chemistry of liquid
| Project/Area Number |
20700267
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Single-year Grants |
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| Research Field |
Bioinformatics/Life informatics
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| Research Institution | Osaka University (2009-2011)
Tokyo Institute of Technology (2008) |
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Principal Investigator |
HARANO Yuichi 大阪大学, 蛋白質研究所, 特任准教授 (60456259)
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| Project Period (FY) |
2008 – 2011
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| Keywords | タンパク質 / 立体構造予測 / 溶液化学 / 溶媒和エントロピー |
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| Research Abstract |
We predicted protein structure using our recently developed free energy function for describing protein stability, which was focused on solvation thermodynamics. The function is combined with the current most reliable sampling methods, i. e., fragment assembly(FA) and comparative modeling(CM). The prediction was tested using 11 small proteins for which high-resolution crystal structures were available. Fairly accurate models with average Cαroot mean square deviation(RMSD)~ 2. 0 A were successfully obtained for all cases. The exhaustive sampling by coarse-grained normal mode analysis around the native structures reveals that our function has a linear correlation with RMSDs<3. 0A. These results suggest that the function is quite reliable for the protein structure prediction while the sampling method remains one of the its major limiting factors in it.
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