Automated docking to explore subsite binding by glycoside hydrolase family 6 cellobiohydrolases and endoglucanases |
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Authors: | Mertz Blake Hill Anthony D Mulakala Chandrika Reilly Peter J |
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Institution: | Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA. |
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Abstract: | Cellooligosaccharides were computationally docked using AutoDock into the active sites of the glycoside hydrolase Family 6 enzymes Hypocrea jecorina (formerly Trichoderma reesei) cellobiohydrolase and Thermobifida fusca endoglucanase. Subsite -2 exerts the greatest intermolecular energy in binding beta-glucosyl residues, with energies progressively decreasing to either side. Cumulative forces imparting processivity exerted by these two enzymes are significantly less than by the equivalent glycoside hydrolase Family 7 enzymes studied previously. Putative subsites -4, -3, +3, and +4 exist in H. jecorina cellobiohydrolase, along with putative subsites -4, -3, and +3 in T. fusca endoglucanase, but they are less important than subsites -2, -1, +1, and +2. In general, binding adds 3-7 kcal/mol to ligand intramolecular energies because of twisting of scissile glycosidic bonds. Distortion of beta-glucosyl residues to the (2)S(O) conformation by binding in subsite -1 adds approximately 7 kcal/mol to substrate intramolecular energies. |
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Keywords: | AutoDock automated docking cellobiohydrolase endoglucanase glycoside hydrolase Family 6 Hypocrea jecorina Thermobifida fusca Trichoderma reesei |
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