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从纤维素酶的延伸性研究中揭示的驱动延伸性多糖易位的碳水化合物-蛋白质相互作用。

Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity.

机构信息

National Bioenergy Center and ‡Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States.

出版信息

J Am Chem Soc. 2014 Jun 18;136(24):8810-9. doi: 10.1021/ja504074g. Epub 2014 Jun 6.

Abstract

Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.

摘要

碳水化合物聚合物通过蛋白质隧道和裂隙的转移是多糖合成酶、糖苷水解酶和碳水化合物结合模块等蛋白质中普遍存在的生化现象。尽管通过晶体学和光谱学长期以来一直研究了蛋白质中碳水化合物聚合物结合的静态快照,但多糖链连续性的分子细节尚未阐明。在这里,我们通过模拟研究了糖苷水解酶家族 7 纤维素酶在酶的连续循环过程中如何通过二糖单位转移纤维素链。我们的结果表明,这些在生物学和工业上都很重要的酶采用两步机制进行链穿线,以形成迈克尔is 复合物,并且链穿线的自由能障碍明显低于水解障碍。结合以前的研究,我们的发现表明,酶促纤维素降解的限速步骤是糖基化反应,而不是链连续性。基于模拟,我们发现,在 GH7 纤维素酶中保守的、与 GH7 内切葡聚糖酶中没有的极性残基之间的强静电相互作用,为多糖链转移提供了热力学驱动力。此外,我们还考虑了广泛存在于碳水化合物活性酶中的芳香族碳水化合物相互作用的作用,这些相互作用长期以来一直与连续性有关。我们的分析表明,这些芳香族残基的主要作用是提供隧道形状并将碳水化合物链引导至活性位点。更广泛地说,这项工作阐明了在通过与催化偶联的链转移机制合成或解聚多糖的碳水化合物活性酶中常见蛋白质基序的作用。

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