Analysis of the cellulase protein structure to understanding the binding site of endo- and exo-glucanase
|關鍵字:||纖維素;纖維分解酵素;結合位置;蛋白質接觸數目模型;Cellulose;Cellulase;binding site;WCN model|
重要的角色。然而纖維分解酵素是一群水解酵素，可將不具溶解性纖維素的β-1,4鍵水解而分解成單糖。近年纖維分解酵素陸續依蛋白質序列相似度被分成118個家族，主要的酵素包括內切型纖維素分解酵素（endo-β-1,4-glucanase ) EC 184.108.40.206和外切型纖維素分解酵素（exo-β-1,4-glucanase ）EC 220.127.116.11。這兩類酵素若在同家族中作用機制和三級結構上據有相似性。到目前為止，被發現的纖維素分解酵素大都被分離且純化，且除了酵素的氨基酸序列，生化特性和作用機轉大部份已被分析討論出來，但卻還沒有可以利用三級結構來分辨內切型級外切型纖維素分解酵素的方法。所以為了達成辨認纖維素分解酵素的目的，我們思考是否能利用結合位置來作區分的橋梁，以至於必須先分析纖維素分解酵素結合位置。我們應用了已被開發的方法“蛋白質接觸數目模型”來分析是否能預測酵素的結合位置，然而我們的結果提供了利用蛋白質接觸數目模型對於預測結合位置是有幫助的。更進一步而言，我們也許在未來預測結合位置上提供發展新而有效方法並朝著能辨別纖維素分解酵素的目的。|
Cellulose is a well-known biomass energy and plays an important role due to its abundance source to be used for producing commercially industrial products in the world. However, cellulase (Glycoside hydrolases) is referring to a class of enzymesthat hydrolyses the β-1, 4-glycosidic linkages of cellulose. And it has already been classified more than 118 families on amino acid sequence similarities that have been proposed so far, and traditionally divided into two classes denominated “endoglucanase” (EC 18.104.22.168) and “exo-glucanase” (EC 22.214.171.124). Both of them utilize the same catalytic mechanisms, and have overall similar structures. In spite of considerable structure of cellulase − function information, mechanistic studies, and catalytic site simulations seems to be well understood in recent works, there is still way to distinguish the structures between endo- and exo-glucanase being researched up to now. Therefore, in order to identify the structures of cellulase, we apply a computational method that had been developed, WCN (Weighted Contact Number) model to analyze the dynamic properties of cellulase. It means that the atom’s thermal fluctuations are in reverse proportion to the protein contact number of this atom, and a residue with lower flexibility is also more compact in proteins. Thus, through WCN model, would be helpful in binding site prediction. In summary, the fundamental purpose in this work is to realize and analyze binding site of cellulase then maybe we can recognize endo-glucanase and exo-glucanase in further. Our results provide information of cellulase protein binding site prediction. Furthermore, we can get more useful and powerful studies by using the method that we applied in the future.
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