酶体外定向进化(Ⅲ)展示技术及其应用

利用展示技术构建的蛋白质／多肽的突变体库，可以通过高通量进行高效地分析和筛选，因此特别适用于改造蛋白质．文中综述噬菌体、细胞表面、核糖体、mRNA等展示技术的原理和方法，以及其在酶定向进化中的应用．     

酶改性技术研究

酶具有催化效率高、催化专一性强等显著特点,然而,酶的活力和稳定性往往不能满足应用的要求.为了改进酶的催化特性,笔者及其所在课题组20多年来长期进行酶分子修饰、酶固定化、酶非水相催化、酶定向进化等酶改性技术的研究,发现通过酶的改性,可以显著改进酶活力和稳定性.文中对笔者及其所在课题组在酶改性技术方面的研究成果和进展作了介绍.     

海洋极端微生物和极端酶分子生物学研究

分离自海洋极端微生物的极端酶具有超常的生物学稳定性，能够在极端温度、pH值、压力和离子强度下表现出生物学活性，因此海洋极端酶为生物催化和生物转化提供了良机。新的极端物种的发现、基因组序列的确定及基因工程技术的应用，加快了发现和制各新酶的进程。蛋白质工程和定向进化技术进一步改善酶的活性和特异性，促进了海洋极端酶的工业应用。对极端酶的分子生物学研究加深了人们对酶稳定性机制的理解，丰富了分子进化理论。     

计算机辅助蛋白结构预测及酶的计算设计研究进展

随着不可再生资源的日益减少以及化学催化所带来的环境污染问题的日益严重,应用低污染的生物催化技术改造或取代传统化工工艺已经成为可持续发展的研究热点。酶作为一种重要的生物催化剂,具有高效无污染、专一性较强等优点,在化工、医药等领域具有巨大的应用潜力和良好的发展前景。但由于新功能酶的开发速度较慢,使其应用受到严重限制。酶的理性设计是新酶发现的一个重要来源,随着计算机技术的发展,蛋白质结构预测方法和新功能酶计算设计策略得到迅猛的发展,已成为酶功能改造的有力工具和新的研究前沿。本文就蛋白质结构预测方法、新功能酶计算设计方法和策略以及未来发展趋势进行简要介绍和讨论。     

酶体外定向进化(Ⅱ)文库筛选的方法及其应用

定向进化是改造蛋白质分子的一种有效的新策略,但其构建的文库非常大,待筛选的克隆常常多达10^5～10^10．同时在目的酶筛选中,至关重要的是找到高灵敏度、高选择性和高通量的筛选方法．居于此,文中综合评述在突变株分离、酶检测和信号探测等方面,目前的一些常用技术及其最新进展．     

酶定向进化技术研究进展

酶定向进化是模拟自然进化过程、用于改造酶性质的一种新策略．在以易错PCR为代表的无性进化技术基础之上,有性进化技术的发展使酶定向进化更接近于自然进化过程．与此同时为解决巨大容量的突变文库与有限的筛选技术之间的矛盾,许多新的高通量筛选方法不断涌现,大大加快了酶定向进化技术的发展．文章从构建高质量的突变基因文库和选择有效的高通量筛选方法两方面,详细总结了近几年出现的新技术并对其应用情况进行介绍．     

用蛋白质工程方法设计和改造工业用酶

本文从改良热稳定性，最适ＰＨ，催化效率和底物专一性等方面介绍了用蛋白质工程方法设计和改造工业酶的研究及其进展，讨论了蛋白质的结构与功能关系和蛋白质工程研究的前景。     

催化光度法研究血红素受体类过氧化物酶活性

介绍含血红素的过氧化物酶作为超分子受体在信生催化体系中的应用研究。以动态分光光度分析法研究血红素蛋白质作为过氧化物酶的催化作用和其在胶束中的类酶活性。通过对催化过程及反应活性中间体的分子吸收光谱研究，发现血红蛋白催化活性怀氢供体底物邻苯二胺浓度之间遵从米氏方程，并获得牛血红蛋白、血红素及其血红素的环糊精衍生物作为生物催化试剂所具有的类酶特征常数。     

酶体外定向进化(Ⅰ)突变基因文库构建技术及其新进展

介绍在酶体外定向进化研究中，几种常用基因文库构建技术及其应用方面的最新进展．同时介绍近年来．一些新开发的基因文库的构建技术及其应用情况．对目前几种主要方法的特色和缺陷进行讨论．     

抗体酶的研究与展望

抗体酶自１９８６年问世以来，一直是科学界的“宠儿”，短短的１０多年，研究的范围不断拓宽，研究的成果层出不穷，采用的技术日益先进。它集生物学、免疫学、化学于一身，采用单克隆、多克隆、基因工程、蛋白质工程等高新技术，开创了催化剂研究和生产的崭新领域，使模拟酶的研究水平发生了质的飞跃，预示着在催化化学、化学动力学、医学、制药学等诸多领域广阔的应用前景。一、抗体酶的诞生抗体与酶都是高分子物质，在进化过程中形成各自不同的使命。它们的结构虽然不同，但却具有两大共性：都是蛋白质；都能高选择性高紧密性地与靶分子…     

Selection and evolution of enzymes from a partially randomized non-catalytic scaffold

Enzymes are exceptional catalysts that facilitate a wide variety of reactions under mild conditions, achieving high rate-enhancements with excellent chemo-, regio- and stereoselectivities. There is considerable interest in developing new enzymes for the synthesis of chemicals and pharmaceuticals and as tools for molecular biology. Methods have been developed for modifying and improving existing enzymes through screening, selection and directed evolution. However, the design and evolution of truly novel enzymes has relied on extensive knowledge of the mechanism of the reaction. Here we show that genuinely new enzymatic activities can be created de novo without the need for prior mechanistic information by selection from a naive protein library of very high diversity, with product formation as the sole selection criterion. We used messenger RNA display, in which proteins are covalently linked to their encoding mRNA, to select for functional proteins from an in vitro translated protein library of >10(12 )independent sequences without the constraints imposed by any in vivo step. This technique has been used to evolve new peptides and proteins that can bind a specific ligand, from both random-sequence libraries and libraries based on a known protein fold. We now describe the isolation of novel RNA ligases from a library that is based on a zinc finger scaffold, followed by in vitro directed evolution to further optimize these enzymes. The resulting ligases exhibit multiple turnover with rate enhancements of more than two-million-fold.     

体外定向分子进化的新策略及新应用

体外定向分子进化是发现和改造生物活性分子的重要方法,提供了一种高效的获得多样性的方法。DNA改组(DNA shuffling)是重要的体外分子进化技术,结合高通量筛选能够改造许多重要的医药、工业、环境保护等方面的商业酶。近年来,许多体外分子进化的新策略和新方法层出不穷,得到了良好的发展和应用,其中有代表性的11种是DNA家族改组(DNA family shuffling),部分基因片段改组、单链DNA家族改组(SSDNAs)、简并引物基因改组(DOGS)、基因组改组(Genome Shuffling)、瞬时模板的随机嵌合(RACHITT)、单向引物的随机重组(MURA)、自我复制(CSR)改组、易错环行扩增(error-prone RCA)、基于遗传密码随机切除(COBARDE)、核酸内切酶V(endonuclease V)替代核酸内切酶DNaseI等。     

Kemp elimination catalysts by computational enzyme design

The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a >200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of >10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.     

多肽的表面展示与结构库

表面展示是一种新的基因操作技术,它使表达的多肽以融合蛋白形式展现在噬菌体或细胞表面,保持相对独立的空间结构和生物活性。该技术可用于研究多肽(蛋白质)的性质、相互识别和作用,并据此从巨大展示库中选择特定靶功能的多肽结构。常用丝状噬菌体、T₄噬菌体、λ噬菌体以及细胞构建表面展示系统。表面展示库包括重组噬菌体抗体库、随机短肽库、多肽构象库、cDNA展示库和基因突变体展示库。表面展示技术可用于人工抗体和疫苗的制备、抗原决定簇的定位、蛋白质相互作用位点的确定、特异调节分子的分离、细胞表面工程的研究、多肽药物的研制,以及生物分子实验定向进化等研究。     

New strategies of protein engineering——directed evolution of enzyme in vitro

New and highly effective strategies for directed enzyme evolution in vitro have been developed in the protein engineering field. They allow engineering all kinds of enzymes in vitro so that new ones with novel functions and features can be obtained by the methods of error-prone PCR, DNA shuffling (exon shuffling), hybrid enzyme, random-priming in vitro recombination (RPR), stagger extension process (StEP), random-directed mutagenesis in vitro, etc., even with little knowlodge of spatial structure and catalytic mechanism of enzymes in advance. The process that would take millions of years in nature can in principle be accomplished in the test within several years.     

Enabling the chemistry of life

Enzymes are the subset of proteins that catalyse the chemistry of life, transforming both macromolecular substrates and small molecules. The precise three-dimensional architecture of enzymes permits almost unerring selectivity in physical and chemical steps to impose remarkable rate accelerations and specificity in product-determining reactions. Many enzymes are members of families that carry out related chemical transformations and offer opportunities for directed in vitro evolution, to tailor catalytic properties to particular functions.     

Computational design of receptor and sensor proteins with novel functions

The formation of complexes between proteins and ligands is fundamental to biological processes at the molecular level. Manipulation of molecular recognition between ligands and proteins is therefore important for basic biological studies and has many biotechnological applications, including the construction of enzymes, biosensors, genetic circuits, signal transduction pathways and chiral separations. The systematic manipulation of binding sites remains a major challenge. Computational design offers enormous generality for engineering protein structure and function. Here we present a structure-based computational method that can drastically redesign protein ligand-binding specificities. This method was used to construct soluble receptors that bind trinitrotoluene, l-lactate or serotonin with high selectivity and affinity. These engineered receptors can function as biosensors for their new ligands; we also incorporated them into synthetic bacterial signal transduction pathways, regulating gene expression in response to extracellular trinitrotoluene or l-lactate. The use of various ligands and proteins shows that a high degree of control over biomolecular recognition has been established computationally. The biological and biosensing activities of the designed receptors illustrate potential applications of computational design.     

A new method of research on molecular evolution of proteinase superfamily

The molecular evolutionary tree, also known as a phylogenetic tree, of the serine proteinase superfamily was constructed by means of structural alignment. Three-dimensional structures of proteins were aligned by the SSAP program of Orengo and Taylor to obtain evolutionary distances. The resulting evolutionary tree provides a topology graph that can reflect the evolution of structure and function of homology proteinase. Moreover, study on evolution of the serine proteinase superfamily can lead to better understanding of the relationship and evolutionary difference among proteins of the superfamily, and is of significance to protein engineering, molecular design and protein structure prediction. Structure alignment is one of the useful methods of research on molecular evolution of protein.