On the Prediction of Folding Nuclei in Globular Proteins |
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Authors: | S O Garbuzynskiy A V Finkelstein O V Galzitskaya |
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Institution: | (1) Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia |
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Abstract: | An approach to predicting folding nuclei in globular proteins with known three-dimensional structures is proposed. This approach is based on the pinpointing of the lowest saddle points on the barrier between the unfolded state and native structure on the free-energy landscape of a protein chain; the proposed technique uses the dynamic programming method. A comparison of calculation results with experimental data on the folding nuclei of 21 proteins shows that the model provides good Φ value predictions for protein structures determined by X-ray analysis and, less successfully, in structures determined by nuclear magnetic resonance. Consideration of the whole ensemble of transition states provides a better prediction of folding nuclei than consideration of only transition states with lowest free energies. In addition, we predict the location of folding nuclei in three-dimensional structures of some proteins whose folding kinetics is being studied, but there is no experimental evidence concerning their folding nuclei. |
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Keywords: | protein folding atom-atom contacts folding nucleus folding rate transition state dynamic programming |
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