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浙江大学学报（农业与生命科学版）
浙江大学学报(农业与生命科学版)  2014, Vol. 40 Issue (1): 58-64    DOI: 10.3785/j.issn.1008-9209.2013.06.011
食品科学     
基于理性设计的β-甘露聚糖酶底物亲和力的定向改造
魏喜换1， 王春娟1， 赵梅1， 李剑芳1， 邬敏辰2*
(1.江南大学食品学院,江苏 无锡214122;2.江南大学无锡医学院,江苏 无锡214122)
Directed modification of β-mannanase substrate affinity based on  rational design
Wei Xihuan1, Wang Chunjuan1, Zhao Mei1, Li Jianfang1, Wu Minchen2*
(1. School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; 2. Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu 214122, China)
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摘要： 以宇佐美曲霉（Aspergillus usamii）YL-01-78的5家族β-甘露聚糖酶（AuMan5A）为研究对象，对其底物亲和力的定向改造进行理性设计及定点突变以获取米氏常数Km值较低的突变酶AuMan5AY111F。首先采用同源建模和分子对接模拟等方法预测AuMan5A与甘露二糖对接复合物的空间结构；在此结构上使用PyMol软件统计到距甘露二糖8 以内的38个氨基酸位点。其次对不同来源的、与AuMan5A一级结构序列全同率大于50%的β-甘露聚糖酶进行多序列比对；排除21个保守氨基酸位点，依据17个非保守位点上的氨基酸性质及其所处空间位置，选择AuMan5A中的Tyr111、Phe206和Tyr243作为拟突变氨基酸，将它们分别替换为性质相似的或在其他β-甘露聚糖酶序列中出现频率高的氨基酸，形成一系列拟突变酶。最后采用MM-PBSA法计算AuMan5A及其拟突变酶与甘露二糖的结合自由能（ΔGbind），其中AuMan5AY111F的ΔGbind为-237.7 kJ/mol，较其他酶的ΔGbind均低。基于该理性设计采用大引物PCR技术将AuMan5A基因（Auman5A）中编码Tyr111的密码子TAC突变为编码Phe111的TTC，构建出突变酶基因（Auman5AY111F）。分别将Auman5AY111F和Auman5A在毕赤酵母GS115中进行表达，并对重组表达产物reAuMan5AY111F和reAuMan5A进行分离纯化和动力学常数测定。结果表明：reAuMan5AY111F对瓜尔豆胶的Km值由突变前的3.9 mg/mL降低为2.5 mg/mL；而突变前后酶的Vmax值变化不大。该研究运用多种生物信息学软件对提高AuMan5A底物亲和力进行了理性设计，并通过定点突变证实之，这为β-甘露聚糖酶乃至其他各种酶底物亲和力的定向改造提供了新的技术策略。
Abstract: β-mannanases (endo-β-1,4-D-mannanases, EC 3.2.1.78), which exist widely in various organisms especially in microorganisms, can catalyze the cleavage of internal β-1,4-D-mannosidic linkages of mannan backbones. To date, almost all known β-mannanases have been classified into glycoside hydrolase (GH) families 5, 26 and 113 based on their amino acid sequence alignment and hydrophobic cluster analysis. Recently, they have attracted much attention due to their great potential applications in industrial processes, such as bioleaching pulps, depolymerizing anti-nutritional factors in feedstuffs, extracting oils from leguminous seeds, hydrolyzing mannan-based polymers in hydraulic fracturing of oil and gas wells, and producing mannooligosaccharides. However, most of commercial β-mannanases had some shortages in enzymatic properties, such as lower substrate affinity and poorer tolerance to extreme environments, which hindered the development of β-mannanases.
A GH family 5 β-mannanase (AuMan5A) from Aspergillus usamii  YL-01-78 was used as the object of this study. The directed modification for its substrate affinity was subjected to the rational design and site-directed mutagenesis to gain a mutant enzyme AuMan5AY111F with higher affinity. Firstly, the three-dimensional (3-D) structure of a docked complex of Auman5A with mannobiose was predicted through homology modeling and molecular docking simulation. On the basis of this 3-D structure, 38 amino acid sites in proximity to mannobiose within 8  were located by using the PyMol software. Secondly, the multiple alignment of various β-mannanase sequences was performed, among which each sequence shared more than 50% identity with AuMan5A. According to the properties of amino acids at 17 non-conserved sites and their locations on the 3-D structure of AuMan5A, Tyr111, Phe206 and Tyr243 were selected to be substituted with the similar amino acids and/or high frequency ones in other β-mannanase sequences, respectively, forming a series of mutant enzymes. Lastly, binding free energies (ΔGbind) of various β-mannanases with mannobiose were calculated by using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, respectively. The ΔGbind of AuMan5AY111F was -237.7 kJ/mol, lower than those of other enzymes. Based on the rational design, an AuMan5AY111F-encoding gene, Auman5AY111F, was constructed by mutating a Tyr111-encoding codon (TAC) of the Auman5A into a Phe111-encoding TTC by megaprimer PCR. Then, the Auman5AY111F and Auman5A were expressed in Pichia pastoris GS115, and kinetic parameters of the purified recombinant AuMan5AY111F and AuMan5A (reAuMan5AY111F and reAuMan5A) were determined, respectively. The results displayed that the Km value of reAuMan5AY111F, towards guar gum, dropped to 2.5 mg/mL from 3.9 mg/mL of reAuMan5A, indicating the substrate affinity of reAuMan5A increased correspondingly. While, the Vmax value of reAuMan5A kept almost unchanged after site-directed mutagenesis.
The directed modification of AuMan5A based on the rational design for enhancing its substrate affinity was firstly predicted by using various bioinformatics softwares, and then was confirmed by site-directed mutagenesis. This work provides  a novel technology strategy for the directed modification of substrate affinities of β-mannanases and other enzymes.
出版日期: 2014-01-20
CLC:  Q556+.2  
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魏喜换1
王春娟1
赵梅1
李剑芳1
邬敏辰2*

引用本文:

魏喜换1， 王春娟1， 赵梅1， 李剑芳1， 邬敏辰2*. 基于理性设计的β-甘露聚糖酶底物亲和力的定向改造[J]. 浙江大学学报(农业与生命科学版), 2014, 40(1): 58-64.

Wei Xihuan1, Wang Chunjuan1, Zhao Mei1, Li Jianfang1, Wu Minchen2* . Directed modification of β-mannanase substrate affinity based on  rational design. Journal of Zhejiang University (Agriculture and Life Sciences), 2014, 40(1): 58-64.

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http://www.zjujournals.com/agr/CN/10.3785/j.issn.1008-9209.2013.06.011    或    http://www.zjujournals.com/agr/CN/Y2014/V40/I1/58

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