Oliveira Osmair V, Freitas Luiz C G, Straatsma T P, Lins Roberto D
Pacific Northwest National Laboratory, Richland, WA 99352, USA.
J Mol Recognit. 2009 Jan-Feb;22(1):38-45. doi: 10.1002/jmr.925.
Molecular docking and molecular dynamics (MD) simulations were used to investigate the binding of a cellodextrin chain in a crystal-like conformation to the carbohydrate-binding module (CBM) of Cel9A from Thermobifida fusca. The fiber was found to bind to the CBM in a single and well-defined configuration in-line with the catalytic cleft, supporting the hypothesis that this CBM plays a role in the catalysis by feeding the catalytic domain (CD) with a polysaccharide chain. The results also expand the current known list of residues involved in the binding. The polysaccharide-protein attachment is shown to be mediated by five amine/amide-containing residues. E478 and E559 were found not to interact directly with the sugar chain; instead they seem to be responsible to stabilize the binding motif via hydrogen bonds.
利用分子对接和分子动力学（MD）模拟研究了呈晶体样构象的纤维二糖链与嗜热栖热放线菌Cel9A的碳水化合物结合模块（CBM）的结合情况。发现该纤维以单一且明确的构型与CBM结合，与催化裂隙对齐，这支持了该CBM通过向催化结构域（CD）提供多糖链而在催化过程中发挥作用的假说。研究结果还扩充了目前已知的参与结合的残基列表。多糖 - 蛋白质附着显示由五个含胺/酰胺的残基介导。发现E478和E559不直接与糖链相互作用；相反，它们似乎通过氢键负责稳定结合基序。
