Engineering enzyme access tunnels

Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.     

The state-of-the-art strategies of protein engineering for enzyme stabilization

Enzymes generated by natural recruitment and protein engineering have greatly contribute in various sets of applications. However, their insufficient stability is a bottleneck that limit the rapid development of biocatalysis. Novel approaches based on precise and global structural dissection, advanced gene manipulation, and combination with the multidisciplinary techniques open a new horizon to generate stable enzymes efficiently. Here, we comprehensively introduced emerging advances of protein engineering strategies for enzyme stabilization. Then, we highlighted practical cases to show importance of enzyme stabilization in pharmaceutical and industrial applications. Combining computational enzyme design with molecular evolution will hold considerable promise in this field.     

Enzyme engineering: Reshaping the biocatalytic functions

Enzyme engineering is a powerful tool to fine-tune the enzymes. It is a technique by which the stability, activity, and specificity of the enzymes can be altered. The characteristic properties of an enzyme can be amended by immobilization and protein engineering. Among them, protein engineering is the most promising, as in addition to amending the stability and activity, it is the only way to modulate the specificity and stereoselectivity of enzymes. The current review sheds light on protein engineering and the approaches applied for it on the basis of the degree of knowledge of structure and function of enzymes. Enzymes, which have been engineered are also discussed in detail and categorized on the basis of their respective applications. This will give a better insight into the revolutionary changes brought by protein engineering of enzymes in various industrial and environmental processes.     

生物催化剂发现与改造的研究进展

生物催化是指将酶或生物有机体用于有用的化学转化的过程,在人们对传统化学催化的环境影响抱有忧虑的情况下,生物催化提供了一种有吸引力的选择。在过去的几十年里,对生物催化剂的研究每出现一次大的进步,生物催化的发展就会出现一次高潮。因此,生物催化剂的发现与改造已成为当今研究的热点。宏基因组文库技术的出现克服了许多微生物不可培养的障碍,人们能够从自然资源中获得丰富的潜在的生物催化剂。而基于理性设计的分子改造技术的发展,可以使得人们对潜在的生物催化剂进行快速而有效的改造以满足工业化生产的需求。随着生物催化剂发现与改造的手段不断进步,更多的优良生物催化剂得到了广泛的应用,生物催化在工业生产中也得到了更深入的应用。结合作者的研究工作,总结了生物催化剂发现与改良的一些研究进展,以为获得更多优良的、能够实现工业应用的生物催化剂奠定理论基础。     

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。     

Recent advances in the improvement of enzyme thermostability by structure modification

Abstract

Thermostability is considered to be an important parameter to measure the feasibility of enzymes for industrial applications. Generally, higher thermostability makes an enzyme more competitive and desirable in industry. However, most natural enzymes show poor thermostability, which restricts their application. Protein structure modification is a desirable method to improve enzyme properties. In recent years, tremendous progress has been achieved in protein thermostability engineering. In this review, we provide a systemic overview on the approaches of protein structure modification for the improvement of enzyme thermostability during the last decade. Structure modification approaches, including the introduction of non-covalent interactions and covalent bonds, increase of proline and/or decrease in glycine, reinforcement of subunit–subunit interactions, introduction of glycosylation sites, truncation and cyclization have been highlighted.     

新基因起源：从自然进化到人工设计

生命体系历经40多亿年的自然进化,创造了无数丰富多彩的功能基因,保障了生命体系的传承与繁荣。然而生命体系的自然进化历程极其缓慢,新的功能基因产生需要数百万年时间,无法满足快速发展的工业生产需求。利用合成生物学技术,研究人员可以依据已知的酶催化机理和蛋白质结构进行全新的基因设计与合成,按照工业生产需求快速创造全新的蛋白质催化剂,实现各种自然界生物无法催化的生物化学反应。尽管新基因设计技术展现了激动人心的应用前景,但是目前该技术还存在设计成功率不高、酶催化活性较低、合成成本较高等科技挑战。未来随着合成生物学技术的快速发展,设计、改造、合成和筛选等技术将融合为一体,为新基因设计与创建带来全新的发展机遇。     

Designing enzymes for use in organic solvents.

Enzymes are routinely used in organic solvents where numerous reactions of interest to synthetic and polymer chemists can be performed with high selectivity. Recently, it has become apparent that the catalytic properties of an enzyme can be tailored to a specific catalytic requirement by the use of solvent and protein engineering. The former involves altering the polarity, hydrophobicity, water content, etc., of the organic milieu, while the later applies site-directed mutagenesis to alter the physicochemical properties of the biocatalyst. The dominant effects of organic solvents on enzyme structure and function, and the potential of solvent and protein engineering to design enzymes to function optimally in organic media, are the major foci of this review.     

Post-production modification of industrial enzymes

Industry has an increasing interest in the use of enzymes as environmentally friendly, highly efficient, and specific bio-catalysts. Enzymes have primarily evolved to function in aqueous environments at ambient temperature and pressure. These conditions however do not always correspond with industrial processes or applications, and only a small portion of all known enzymes are therefore suitable for industrial use. Protein engineering can sometimes be applied to convey more desirable properties to enzymes, such as increased stability, but is limited to the 20 naturally occurring amino acids or homologs thereof. Using post-production modification, which has the potential to combine desirable properties from the enzyme and the conjugated compounds, enzymes can be modified with both natural and synthetic molecules. This offers access to a myriad of possibilities for tuning the properties of enzymes. At this moment, however, the effects of post-production modification cannot yet be reliably predicted. The increasing number of applications will improve this so that the potential of this technology can be fully exploited. This review will focus on post-production modification of enzymes and its use and opportunities in industry.     

Engineered control of enzyme structural dynamics and function

Enzymes undergo a range of internal motions from local, active site fluctuations to large‐scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post‐translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus‐responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine.     

果胶酶生产及工业应用进展

果胶酶是水解酶家族成员,也是生物技术领域的重要酶,其在全球工业酶市场中所占份额约为25%。果胶酶在工业生产中应用广泛,如植物纤维的脱胶、茶和咖啡的发酵、废水处理、纸浆漂白和动物饲料生产等。在果胶酶的天然来源中,由于微生物具有独特的理化性质,最常被用以生产果胶酶。然而,与许多其他工业酶一样,果胶酶也存在野生菌株产量低、工业生产率低等制约因素,因此,目前果胶酶的研究重点主要集中在如何提高工业规模的生产水平。主要介绍了果胶酶的天然来源,以及在这些来源的基础上通过基因工程改造以获得果胶酶高效表达的最新策略,并概括总结了果胶酶发酵工艺和工业应用,以期为生产具有高活性的果胶酶,提高工业生产的效益奠定理论基础。     

蛋白质酶功能分析和预测方法的进展和前瞻

蛋白质酶是生物体内最重要的生物分子之一。对酶的功能进行系统研究具有重要的科学研究价值和工业应用意义,近年来,以计算机技术为基础的酶功能预测的方法不断发展与完善。基于此背景,本文总结了基于计算方法的酶功能分析与预测的主要方法,包括酶结合位点、分子对接、动力学模拟以及分子设计等内容。同时,本文也对相应的发展趋势进行讨论和展望。     

Manipulation of enzyme properties by noncanonical amino acid incorporation

Since wild-type enzymes do not always have the properties needed for various applications, enzymes are often engineered to obtain desirable properties through protein engineering techniques. In the past decade, complementary to the widely used rational protein design and directed evolution techniques, noncanonical amino acid incorporation (NCAAI) has become a new and effective protein engineering technique. Recently, NCAAI has been used to improve intrinsic functions of proteins, such as enzymes and fluorescent proteins, beyond the capacities obtained with natural amino acids. Herein, recent progress on improving enzyme properties through NCAAI in vivo is reviewed and the challenges of current approaches and future directions are also discussed. To date, both NCAAI methods-residue- and site-specific incorporation-have been primarily used to improve the catalytic turnover number and substrate binding affinity of enzymes. Numerous strategies used to minimize structural perturbation and stability loss of a target enzyme upon NCAAI are also explored. Considering the generality of NCAAI incorporation, we expect its application could be expanded to improve other enzyme properties, such as substrate specificity and solvent resistance in the near future.     

Utilization of enzymes for environmental applications

Enzymes are powerful tools that help sustain a clean environment in several ways. They are utilized for environmental purposes in a number of industries including agro-food, oil, animal feed, detergent, pulp and paper, textile, leather, petroleum, and specialty chemical and biochemical industry. Enzymes also help to maintain an unpolluted environment through their use in waste management. Recombinant DNA technology, protein engineering, and rational enzyme design are the emerging areas of research pertaining to environmental applications of enzymes. The future will also see the employment of various technologies including gene shuffling, high throughput screening, and nanotechnology. This article presents an overview of the enzymatic applications in pollution control and the promising research avenues in this area.     

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。     

高通量筛选系统在定向改造中的新进展

酶和细胞工厂是工业生物技术的核心,在医药、化工、食品、农业、能源等诸多领域发挥重要作用.一般天然酶和细胞均需通过分子改造提高其催化效率、稳定性及立体选择性等.定向改造为快速改善酶和细胞工厂的性能提供了可能性,其中灵敏可靠的高通量筛选方法是决定酶和细胞工厂成功高效定向改造的关键.文中阐述并分析讨论了各种筛选方法的优缺点、...     

功能化磁性纳米粒子在固定化酶研究中的应用

酶是高效的生物催化剂,在生物技术领域有广泛的应用。然而,不可再生催化的高成本和酶的有效成分分离回收,是实现大规模工业化应用需要解决的关键问题。磁性纳米粒子(magnetic nanoparticles,MNPs)具有优异的磁回收性质。通过设计和制备功能化MNPs作为固定化酶的多功能载体,是解决这一问题的有效途径之一,可为酶的工业化大规模应用提供条件。近年来,功能化磁性纳米粒子在酶的固定化领域基于载体性质、固定化方法和应用有广泛研究。文中重点介绍了近年来各种功能化磁性纳米载体,特别是Fe3O4纳米粒子,在固定化酶中的应用。根据功能化试剂的差异分类,实例讨论了不同功能化修饰的磁性纳米载体对酶的固定化,包括硅烷修饰的磁性纳米载体、有机聚合物修饰的磁性纳米载体、介孔材料修饰的磁性纳米载体以及金属-有机骨架材料(metal-organic framework,MOF)修饰的磁性纳米载体。同时,结合可持续工业催化的发展要求,对磁性复合载体固定化酶的发展前景进行了展望。     

Utilization of Enzymes for Environmental Applications

ABSTRACT

Enzymes are powerful tools that help sustain a clean environment in several ways. They are utilized for environmental purposes in a number of industries including agro-food, oil, animal feed, detergent, pulp and paper, textile, leather, petroleum, and specialty chemical and biochemical industry. Enzymes also help to maintain an unpolluted environment through their use in waste management. Recombinant DNA technology, protein engineering, and rational enzyme design are the emerging areas of research pertaining to environmental applications of enzymes. The future will also see the employment of various technologies including gene shuffling, high throughput screening, and nanotechnology. This article presents an overview of the enzymatic applications in pollution control and the promising research avenues in this area.     

The industrial production of enzymes

The production of enzymes is a pursuit central to the modern biotechnology industry. Markets for traditional industrial enzymes continue to grow while the continued emphasis on biotechnological endeavours has generated demand for an ever increasing number of additional biocatalysts. The advent of genetic engineering has now facilitated the large-scale production of enzymes and other proteins which are produced naturally only in minute quantities. This development is particularly significant with regard to the production of enzymes and other proteins of therapeutic significance, which are now available in clinically useful quantities.

The level of downstream processing to which any enzyme is subjected is dependent upon its intended application. Industrial enzymes produced in bulk generally require little downstream processing, and hence are relatively crude preparations. Enzymes destined for therapeutic applications are subject to a far higher degree of downstream processing, often incorporating 3–4 chromatographic steps.

While enzymology is one of the longest established branches of the biochemical sciences, it continues to be an area of ongoing, active research. The continual discovery of new enzymes and a greater understanding of previously discovered enzymes and their functional significance suggests many novel applications for these catalytic activities. The intestinal production and utilization of enzymes will continue to be of central importance in the biotechnology industry.     

Multifunctional enzymes in archaea: promiscuity and moonlight

Enzymes from many archaea colonizing extreme environments are of great interest because of their potential for various biotechnological processes and scientific value of evolution. Many enzymes from archaea have been reported to catalyze promiscuous reactions or moonlight in different functions. Here, we summarize known archaeal enzymes of both groups that include different kinds of proteins. Knowledge of their biochemical properties and three-dimensional structures has proved invaluable in understanding mechanism, application, and evolutionary implications of this manifestation. In addition, the review also summarizes the methods to unravel the extra function which almost was discovered serendipitously. The study of these amazing enzymes will provide clues to optimize protein engineering applications and how enzymes might have evolved on Earth.