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タイトル: Free-energy function for discriminating the native fold of a protein from misfolded decoys.
著者: Yasuda, Satoshi
Yoshidome, Takashi
Harano, Yuichi
Roth, Roland
Oshima, Hiraku
Oda, Koji
Sugita, Yuji
Ikeguchi, Mitsunori
Kinoshita, Masahiro  kyouindb  KAKEN_id
著者名の別形: 木下, 正弘
キーワード: protein folding
structure prediction
decoy recognition
hydration entropy
dehydration
molecular liquid
integral equation theory
morphometric approach
発行日: 9-May-2011
出版者: wiley
誌名: Proteins : structure, function, and genetics
巻: 79
号: 7
開始ページ: 2161
終了ページ: 2171
抄録: In this study, free-energy function (FEF) for discriminating the native fold of a protein from misfolded decoys was investigated. It is a physics-based function using an all-atom model, which comprises the hydration entropy (HE) and the total dehydration penalty (TDP). The HE is calculated using a hybrid of a statistical-mechanical theory applied to a molecular model for water and the morphometric approach. The energetic component is suitably taken into account in a simple manner as the TDP. On the basis of the results from a careful test of the FEF, which have been performed for 118 proteins in representative decoy sets, we show that its performance is distinctly superior to that of any other function. The FEF varies largely from model to model for the candidate models for the native structure (NS) obtained from nuclear magnetic resonance experiments, but we can find models or a model for which the FEF becomes lower than for any of the decoy structures. A decoy set is not suited to the test of a free-energy or potential function in cases where a protein isolated from a protein complex is considered and the structure in the complex is used as the model NS of the isolated protein without any change or where portions of the terminus sides of a protein are removed and the percentage of the secondary structures lost due to the removal is significantly high. As these findings are made possible, we can assume that our FEF precisely captures the features of the true NS.
著作権等: This is the peer reviewed version of the following article: Yasuda, S., Yoshidome, T., Harano, Y., Roth, R., Oshima, H., Oda, K., Sugita, Y., Ikeguchi, M. and Kinoshita, M. (2011), Free-energy function for discriminating the native fold of a protein from misfolded decoys. Proteins, 79: 2161–2171, which has been published in final form at http://dx.doi.org/10.1002/prot.23036
This is not the published version. Please cite only the published version. この論文は出版社版でありません。引用の際には出版社版をご確認ご利用ください。
URI: http://hdl.handle.net/2433/197178
DOI(出版社版): 10.1002/prot.23036
PubMed ID: 21557318
出現コレクション:学術雑誌掲載論文等

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