工业蛋白质理性设计与应用

作为合成生物学与绿色生物制造等领域的底层核心技术,蛋白理性设计可有效解决天然功能元件性能不足等共性挑战,创制高性能人工酶元件。值此天津工业生物研究所(Tianjin Institute of Industrial Biotechnology, TIB)创立10周年之际,文中回顾了研究所在工业蛋白理性设计领域的系列重要工作进展。从酶设计方法学研究、新酶反应设计到生物催化应用等方面进行了分析讨论,并展望了本领域未来发展方向。望借此搭建学术界和产业界与酶理性设计的桥梁,促进新技术、新策略的开发应用,加速融合人工酶的基础研究与产业应用,推动我国生物制造领域的科技创新升级。     

融合酶的设计和应用研究进展

酶的分子改造和重新设计是解决酶催化工业应用瓶颈的重要途径。基于融合蛋白设计的融合酶技术是分子酶工程的一个研究热点,已逐渐应用于多功能酶和酶靠近效应的构建与控制研究中,显示出重要的理论和应用研究价值。文中对近年来融合酶的分子设计策略和应用研究的进展进行了综述。首先介绍了融合酶的概念和特点,并对最近研究中出现的融合酶构建策略进行了归纳总结,重点阐述了不同种类连接肽对融合酶的影响及其可能机理。同时,对目前融合酶的应用研究进行了归纳和讨论。最后,结合本实验室的研究,指出了融合酶领域的关键问题并对其发展方向进行了探讨和展望。     

工业酶蛋白研究的重要进展

作为生物催化剂的核心,工业酶的研究在近年来取得了许多重要的进展,特别是具有重要意义的新酶发现、酶家族研究、酶的分子改造等领域出现了许多突破性的进展。     

酶分子化学修饰研究进展

酶是高效生物催化剂,在工业和临床医药上应用广泛。但由于酶是蛋白质,稳定性差,且在生物体内有较强的免疫原性,因而严重制约了其应用。对酶分子进行化学修饰是提高其稳定性和降低免疫原性的有效途径。简要介绍几种改进酶催化特性的方法、酶分子修饰效果的分析与评价、酶通过化学修饰获得的新性质及其原理、酶化学修饰的研究动态等。     

漆酶及其应用的研究进展

漆酶是一种含铜的多酚氧化酶,白腐真菌普遍能分泌该酶.有氧条件下,漆酶能催化多种高分子化合物降解,利用该性质漆酶已经广泛应用于生物制浆、污染物生物降解、生物漂白等领域.介绍了目前漆酶在农业和工业各个领域中的应用.     

酶的分子定向进化及其应用

酶的分子定向进化是20世纪90年代初兴起的一种蛋白质工程的新策略,是一种在生物体外模拟自然进化过程的、具有一定目的性的快速改造蛋A质的方法.该方法引起了生物催化技术领域的又一次革命.目前分子定向进化技术已被广泛应用于工业、农业及制药业等的相关领域.本文详细综述了酶的分子定向进化的概念、过程、基本策略及其核心技术,并着重介绍了酶的分子定向进化技术在提高酶的活力、稳定性、底物特异性和对映体选择性等几方面的应用及取得的相关成果.     

微生物酶工程：绿色生物制造的基石

酶工程是酶学与工程科学融合的综合性科学技术,新酶的发掘、对酶的结构与功能的认知及酶的改造是合成生物学、生物制造技术的重要科学与技术基础。在合成生物学的发展方兴未艾的今天,酶工程更是不可或缺的研究领域。     

酶祖先序列重建与定向进化

酶祖先序列重建是指通过计算机算法推导来自灭绝生物的祖先酶的氨基酸序列的技术。通常可分为6个步骤,依次为现代酶的核酸/氨基酸序列收集、多序列比对、系统发育树构建、祖先酶序列的计算机推测、基因克隆、酶学性质表征。该方法广泛应用于研究分子在行星时间尺度上对环境条件不断变化的适应性和进化机制。随着酶在生物催化领域中扮演越来越重要的角色,该方法逐渐成为研究酶序列、结构和功能关系的有力手段。同时,祖先酶大多具有温度稳定性、突变稳定性等特性,使其成为进一步定向进化的理想蛋白质支架。文中综述了酶祖先序列重建的计算机算法、应用和常用计算机软件,并结合最新研究进展,展望其在酶定向进化领域中的应用前景。     

纳米材料固定化酶的研究进展

近年来,纳米技术为酶固定化提供了多种纳米级材料,纳米材料固定化酶不仅具有高的酶负载量,而且具有良好的酶稳定性。本文基于纳米材料固定化酶,对纳米材料的种类进行了总结,分析了纳米材料对固定化酶性能的影响,并介绍了纳米级固定化方法及纳米材料固定化酶在生物转化、生物传感器、生物燃料电池等领域的应用。     

工业酶结构与功能的构效关系

工业酶是绿色生物制造的"芯片",支撑着下游数十倍甚至百倍的产业。解析工业酶结构与功能关系是对其设计改造并应用于工业生产的基础。近年来随着蛋白结构解析技术和计算模拟技术的发展,酶结构与功能的构效关系得到更加深刻的认识,使得酶理性设计,甚至是从头设计成为可能。文中围绕酶结构的可塑性及其催化功能的多样性,综述工业酶结构与功能构效关系的研究进展及应用,并展望该领域的未来发展前景。     

工业蛋白质构效关系的计算生物学解析

工业催化用酶已经成为现代生物制造技术的核心"芯片"。不断设计和研发新型高效的酶催化剂是发展工业生物技术的关键。工业催化剂创新设计的科学基础是对酶与底物的相互作用、结构与功能关系及其调控机制的深入剖析。随着生物信息学和智能计算技术的发展,可以通过计算的方法解析酶的催化反应机理,进而对其结构的特定区域进行理性重构,实现酶催化性能的定向设计与改造,促进其工业应用。聚焦工业酶结构-功能关系解析的计算模拟和理性设计,已成为工业酶高效创制改造不可或缺的关键技术。本文就各种计算方法和设计策略以及未来发展趋势进行简要介绍和讨论。     

Expression cloned cDNA for 10-deacetylbaccatin III-10-O-acetyltransferase in Escherichia coli: a comparative study of three fusion systems

10-Deacetylbaccatin III-10-O-acetyltransferase (10-DABT) catalyzes the formation of baccatin III, which is an immediate diterpenoid precursor of Taxol. A cDNA encoding 10-DABT was cloned from Taxus baccata by using RT-PCR and screening a cDNA library. A study of its heterologous overexpression in Escherichia coli was carried out. To get high-level expression of recombinant enzyme, three kinds of IPTG inducible fusion expression systems (with glutathione S-transferase (GST), hexahistidine (6x His), and biotinylated tag) were used, and results of expression were compared. Fusion 10-DABT with different tags was expressed with diverse expression levels and solubility in the three systems. Optimum IPTG concentration, temperature, and inducing time for producing recombinant enzymes were found. Under higher IPTG concentration (up to 1 mM), the highest level of expression for fusion protein was obtained in the 6x His fusion system with phage T5 promoter, but expressed products were only partially soluble. With lower IPTG concentration (less than 0.5 mM), the highest expression was detected in the GST fusion system with tac promoter, and the lowest level of expression appeared in the biotinylated fusion system. The expression level in the latter system did not differ dramatically with a range of different inducer concentrations. GST and 6x His fusion proteins were mainly soluble in aqueous solutions and Triton X-100 improved the solubility of biotinylated fusion proteins (inferring this protein is membrane-associated). Fusion proteins could only be partially purified by a single affinity chromatography step for all three systems. Glutathione-coupled matrix and streptavidin-conjugated resin have higher specificity than Ni-NTA resin, and elution conditions were shown to affect enzyme activity. Three kinds of recombinant 10-DABT with different tags showed enzyme activity, but total enzyme activity was lost as a result of the affinity chromatography step. Thrombin and Factor Xa could be used for site-specific cleavage of fusion proteins, but the incubation temperature affected enzyme activity of recombinant enzymes.     

生物质多糖的高效降解与降解酶（系）的精确定制

自然界中多糖类生物质资源十分丰富,然而其复杂的抗降解屏障限制了生物转化的进程.近年来,随着生物质多糖结构的快速解析以及大量多糖降解酶的鉴定研究,针对不同底物结构或产物需求,仿制高效微生物多糖代谢途径,精确定制多糖降解酶系,促进生物质高效转化已成为可能.本文分析中性多糖(纤维素和木聚糖)、碱性多糖(几丁质和壳聚糖)以及酸性多糖(褐藻胶)的精细结构组成与基团性质,总结3类多糖主要降解酶的活性架构特征及其底物精确结合模式.文章还阐述蛋白质工程设计与定制策略,针对酶分子不同功能区的分析,可为酶分子的功能快速设计与改造提供靶点,以获得适宜于工业应用的高效酶分子,此外,根据微生物胞外降解酶系的降解次序与协同关系,可基于应用需求精确定制复杂多糖降解酶系,实现生物质的高效与高值降解转化.     

Optimization protocols and improved strategies of cross-linked enzyme aggregates technology: current development and future challenges

Cross-linked enzyme aggregate (CLEA) technology has been regarded as an effective carrier-free immobilization method. This method is very attractive due to its simplicity and robustness, as well as for the possibility of using the crude enzyme extract and the opportunity to co-immobilize multiple different enzymes. The resulting CLEAs generally exhibit high catalyst productivities, improved storage and operational stability and are easy to recycle. Nowadays, although the technology has been applied to various enzymes, some undesirable properties have limited its further application. To overcome these limitations, novel strategies have been developing in recent years. This mini-review focuses on process optimization, new improved strategies and the latest advances on CLEAs technology.     

Microinjection of arginase into enzyme-deficient cells with the isolated glycoproteins of Sendai virus as fusogen

A method of introducing enzymes into the cytoplasm of fibroblasts in culture is described. Erythrocytes obtained from normal and arginase-deficient individuals were loaded with arginase in vitro and fused to arginase-deficient mouse and human fibroblasts. Erythrocyte ghost-fibroblast fusion was quantified by a 14C-radioactive assay for arginase in solubilized fibroblasts. Fusion was successfully induced by Sendai virus and also by the isolated glycoproteins of Sendai virus. After fusion the arginase activity associated with the Fibroblasts was 700--1500 U of arginase/mg of cell protein; this enzyme activity was 5- to 10-times higher than that normally found in the fibroblasts. The enrichment in arginase activity indicated that between four and ten ghosts had fused per fibroblast. The use of isolated viral proteins to mediate the transfer of enzymes into cells in vivo might alleviate clinical complications inherent in the use of whole virions. The enzyme replacement technique described in this report for a hyperargininemic model cell system should be applicable to the group of inborn errors of metabolism characterized by deficiency of an enzyme normally localized in the cytoplasmic compartment of cells.     

酶分子设计常用策略和进展

酶分子的生物学功能很大程度上是由其三维空间结构和所处溶剂环境共同决定的。因此,优化酶分子的结构性质以及探索其性质最优的溶剂环境是改善酶分子功能以及进行理性设计的一个可行途径。从实际应用的角度来看,分子设计方法可以为酶工程提供一种有效的解决方案。目前,酶分子设计有两个重要的研究方向,包括提高酶分子的催化活力和优化其稳定性。同时,对酶分子设计方法的研究也有助于对蛋白质生物学机理的探索。在近些年的学术界酶分子设计案例中,生物信息学方法得到广泛的应用。本文系统地总结基于生物信息学的酶分子设计方法的背景、策略和一些经典案例。     

Evaluation of a novel bifunctional xylanase–cellulase constructed by gene fusion

An artificial bifunctional enzyme, xylanase–cellulase, has been prepared by gene fusion. Three chimeric genes were constructed that encoded fusion proteins of different lengths. The fusion proteins exhibited both xylanase (XynX) and cellulase (Cel5Z::Ω) activity when cel5Z::Ω was fused downstream of xynX, but not when xynX was fused downstream of cel5Z::Ω. Activities of bifunctional enzymes decreased when a shorter xylanase peptide was fused. Three fusion enzymes were purified, and the molecular weights of the enzymes were estimated by CMC-SDS-PAGE and XYN-SDS-PAGE to be 149, 129, and 87 kDa, respectively. The fusion enzymes displayed optimum cellulase activity at pH 8.0 and 50 °C and optimum xylanase activity at pH 8.0 and 70 °C.     

嗜热酶的耐热机理

酶蛋白在高温下的不稳定性是影响其广泛应用的主要瓶颈,嗜热酶因为独特的性质而被作为热稳定研究的极好材料。了解嗜热酶的热稳定性机制,对于采用酶工程定向设计、改造酶具有重要的意义。嗜热酶的热稳定性并不是由单一因素决定的,氨基酸组成、氢键、离子对、二硫键等都是影响嗜热酶热稳定性的重要因素。相对于嗜温酶,嗜热酶更多地采用寡聚体的形式。