Side-chain dynamics analysis of KE07 series |
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| Institution: | 1. Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France;2. University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France;3. KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium;1. Department of Food Science and Technology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran;2. Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran;3. Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran |
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| Abstract: | The significant improvement of KE07 series in catalytic activities shows the great success of computational design approaches combined with directed evolution in protein design. Understanding the protein dynamics in the evolutionary optimization process of computationally designed enzyme will provide profound implication to study enzyme function and guide protein design. Here, side chain squared generalized order parameters and entropy of each protein are calculated using 50 ns molecular dynamics simulation data in both apo and bound states. Our results show a correlation between the increase of side chain motion amplitude and catalytic efficiency. By analyzing the relationship between these two values, we find side chain squared generalized order parameter is linearly related to side chain entropy, which indicates the computationally designed KE07 series have similar dynamics property with natural enzymes. |
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| Keywords: | Molecular dynamics Conformational entropy Generalized order parameter Protein design |
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