点饱和突变技术及其在蛋白质工程中的应用

点饱和突变技术是蛋白质工程中的一门新兴技术,它通过对目的蛋白的编码基因进行改造,短时间内获取靶位点氨基酸分别被其它19种氨基酸替代的突变子。此技术不仅是蛋白质定向改造的强有力工具,而且是蛋白质结构－功能关系研究的重要手段。本文概述了几种常用点饱和突变技术,介绍了其在蛋白质工程中的应用状况,讨论了其在应用中的问题,展望了其应用前景。     

基于物化性质对嗜热蛋白的预测

嗜热蛋白在高温下能保持稳定性和活性,是研究蛋白质热稳定性的理想模型,开发一个蛋白质热稳定性识别的方法将对蛋白质工程和蛋白质的设计很有帮助。目前的研究中,氨基酸的组成及其物化性质一直被认为和蛋白质的热稳定性相关。本研究筛选出可靠的数据集,包括915个嗜热蛋白和793个非嗜热蛋白。利用蛋白质氨基酸的物化性质和氨基酸的组成表征嗜热蛋白,将二肽氨基酸组成整合到9组氨基酸物化性质中使蛋白序列公式化。支持向量机5折叠交叉验证表明:当gap=0时,290个特征产生的精度最高,为92.74%。因此说明对于分析蛋白质的热稳定性,所建立的预测模型将是一个很有效的工具。     

Prediction of thermophilic proteins using feature selection technique

The thermostability of proteins is particularly relevant for enzyme engineering. Developing a computational method to identify mesophilic proteins would be helpful for protein engineering and design. In this work, we developed support vector machine based method to predict thermophilic proteins using the information of amino acid distribution and selected amino acid pairs. A reliable benchmark dataset including 915 thermophilic proteins and 793 non-thermophilic proteins was constructed for training and testing the proposed models. Results showed that 93.8% thermophilic proteins and 92.7% non-thermophilic proteins could be correctly predicted by using jackknife cross-validation. High predictive successful rate exhibits that this model can be applied for designing stable proteins.     

氨基酸组成对蛋白质耐热性的影响

为了研究一级结构对蛋白质耐热性的影响,利用软件DNAMAN对16个家族32种蛋白质序列进行了氨基酸含量分析,并统计分析了氨基酸组成对蛋白质耐热性的影响。通过比较同一家族的高低温蛋白质序列及16个家族中所有高温和低温蛋白质序列中氨基酸含量的变化可以推断(从低温到高温)：Ser、Cys．含量降低显著,Arg、Ile、Pro含量升高显著。由此可知高温蛋白质倾向于含有疏水性氨基酸而避免亲水性氨基酸。     

理性设计提高蛋白质热稳定性的研究进展

通过理性设计提高蛋白质的热稳定性一直是当今计算生物学及蛋白质工程领域中的一个研究热点。与传统的定向进化的方法相比,该方法具有目的性强、效率高的优点,对扩大蛋白质的应用范围与探究蛋白质结构和功能的关系均具有重要意义。本文详细介绍了影响蛋白质热稳定性的因素,以及一些常用的通过理性设计来提高蛋白质的热稳定性的策略。由于影响蛋白质热稳定性的因素众多,并且众多因素之间还具有千丝万缕的联系,到目前为止研究人员还没有提出一个公认的适合于所有蛋白质的理性设计的策略,这也是现代计算生物学家及蛋白质工程学家们努力研究的一个重要方向。     

The consensus concept for thermostability engineering of proteins

Previously, sequence comparisons between a mesophilic enzyme and a more thermostable homologue were shown to be a feasible approach to successfully predict thermostabilizing amino acid substitutions. The 'consensus approach' described in the present paper shows that even a set of amino acid sequences of homologous, mesophilic enzymes contains sufficient information to allow rapid design of a thermostabilized, fully functional variant of this family of enzymes. A sequence alignment of homologous fungal phytases was used to calculate a consensus phytase amino acid sequence. Upon construction of the synthetic gene, recombinant expression and purification, the first phytase obtained, termed consensus phytase-1, displayed an unfolding temperature (T(m)) of 78.0 degrees C which is 15-22 degrees C higher than the T(m) values of all parent phytases used in its design. Refinement of the approach, combined with site-directed mutagenesis experiments, yielded optimized consensus phytases with T(m) values of up to 90.4 degrees C. These increases in T(m) are due to the combination of multiple amino acid exchanges which are distributed over the entire sequence of the protein and mainly affect surface-exposed residues; each individual substitution has a rather small thermostabilizing effect only. Remarkably, in spite of the pronounced increase in thermostability, catalytic activity at 37 degrees C is not compromised. Thus, the design of consensus proteins is a potentially powerful and novel alternative to directed evolution and to a series of rational approaches for thermostability engineering of enzymes and other proteins.     

嗜热与嗜常温微生物的蛋白质氨基酸组成比较

嗜热微生物的嗜热特性与其蛋白质的高度热稳定性紧密相关。为了探索嗜热蛋白质的热稳定机制,比较嗜热和嗜常温微生物的蛋白质在氨基酸组成上的差别,收集110对分别来自嗜热和嗜常温微生物的同源蛋白质序列,比较两组蛋白质各种氨基酸含量以及疏水性氨基酸组成、疏水性指数和荷电氨基酸组成的差别,结果两者在多种氨基酸含量上存在微小但统计学上显著的差别,嗜热蛋白质比嗜常温蛋白质具有较高的平均疏水性和荷电氨基酸组成。对两组蛋白质的“脂肪族氨基酸指数”进行分析,证明嗜热蛋白质之所以具有较高的脂肪族氨基酸指数是由于其亮氨酸含量较高,与影响该指数的其它几种氨基酸无关;从而认为该指数的意义值得怀疑。通过对大量同源嗜热蛋白质和嗜常温蛋白质氨基酸组成的比较,能够揭示一些有关蛋白质热稳定性的普遍规律。     

Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution

With the advent of directed evolution techniques, protein engineering has received a fresh impetus. Engineering proteins for thermostability is a particularly exciting and challenging field, as it is crucial for broadening the industrial use of recombinant proteins. In addition to directed evolution, a variety of partially successful rational concepts for engineering thermostability have been developed in the past. Recent results suggest that amino acid sequence comparisons of mesophilic proteins alone can be used efficiently to engineer thermostable proteins. The potential benefits of the underlying, semirational 'consensus concept' are compared with those of rational design and directed evolution approaches.     

Protein design for non-aqueous solvents

Improving protein stability in unnatural and suboptimal environments is a promising application of protein engineering technology. Carefully designed amino acid alterations may lead to dramatic positive effects on the stability of proteins under highly perturbing conditions, such as in non-aqueous solvents. Applications of biocatalysts and proteins with specific binding capabilities in the chemical industry have been severely limited by constraints placed on the solvent environment. With the advent of convenient methods for altering the amino acid composition and even synthesizing entirely new protein molecules, it is worthwhile to consider engineering proteins for stability in non-aqueous solvents. In order to identify the features that a protein would need for stability in organic media, we have been studying the structure and properties of the hydrophobic protein crambin. Crambin is unique in that it is soluble and stable in very high concentrations of polar organic solvents. Crambin and its water-soluble homologs offer a powerful demonstration of protein engineering for non-aqueous solvents. This paper describes the structural features that contribute to crambin's special properties. Based on these observations and consideration of how non-aqueous solvents affect the interactions important in protein folding, a set of rules for designing non-aqueous solvent-stable proteins is proposed.     

一个耐热碱性磷酸酯酶突变型的研究

为了进一步揭示蛋白质的耐热机制,对含有耐热碱性磷酸酯酶（ＦＤ－ＴＡＰ）的表达质粒ｐＴＡＰ５０３Ｆ进行了随机诱变,用菌落原位显色法从约５０００个转化子中筛选到４个耐热性下降的突变型克隆,并对其中１克隆（ＴＡＰＭ３）进行了部分酶学性质、ＤＮＡ和氨基酸序列的研究。酶学性质研究表明,与野生型相比,该突变型酶的耐热性有较大幅度的下降,而热激活性无明显改变。ＤＮＡ序列分析表明在１２３９位ＴＡＰＭ３发生Ｇ→Ａ转     

Protein thermostabilization requires a fine-tuned placement of surface-charged residues

Using the information from the genome projects, recent comparative studies of thermostable proteins have revealed a certain trend of amino acid composition in which polar residues are scarce and charged residues are rich on the protein surface. To clarify experimentally the effect of the amino acid composition of surface residues on the thermostability of Escherichia coli Ribonuclease HI (RNase HI), we constructed six variants in which five to eleven polar residues were replaced by charged residues (5C, 7Ca, 7Cb, 9Ca, 9Cb and 11C). The thermal denaturation experiments indicated that all of the variant proteins are 3.2-10.1 degrees C in Tm less stable than the wild proteins. The crystal structures of resultant protein variants 7Ca, 7Cb, 9Ca and 11C closely resemble that of E. coli RNase HI in their global fold, and several different hydrogen bonding and ion-pair interactions are formed by the mutations. Comparison of the crystal structures of these variant proteins with that of E. coli RNase HI reveals that thermal destabilization is apparently related to electrostatic repulsion of the charged residues with neighbours. This result suggests that charged residues of natural thermostable proteins are strictly posted on the surface with optimal interactions and without repulsive interactions.     

Exploring Nonnatural Evolutionary Pathways by Saturation Mutagenesis: Rapid Improvement of Protein Function

Random point mutagenesis does not access a large fraction of protein sequence space corresponding to primarily nonconservative amino acid substitutions. The cost of this limitation during directed evolution is unknown. Random point mutagenesis over the entire gene encoding the psychrophilic protease subtilisin S41 identified a pair of residues (Lys211 and Arg212) where mutations provided significant increases in thermostability. These were subjected to saturation mutagenesis to test whether the amino acids not easily accessible by point mutagenesis provide even better ``solutions' to the thermostabilization challenge. A significant fraction of these variants surpassed the stability of the variants with point mutations. DNA sequencing revealed highly hydrophobic residues in the four most stable variants (Pro/Ala, Pro/Val, Leu/Val, and Trp/Ser). These nonconservative replacements, accessible only by multiple (two to three) base substitutions in a single codon, would be extremely rare in a point mutation library. Such replacements are also extremely rare in natural evolution. Saturation mutagenesis may be used advantageously during directed evolution to explore nonnatural evolution pathways and enable rapid improvement in protein traits. Received: 15 March 1999 / Accepted: 28 June 1999     

Understanding the relationship between the primary structure of proteins and its propensity to be soluble on overexpression in Escherichia coli

Solubility of proteins on overexpression in Escherichia coli is a manifestation of the net effect of several sequence-dependent and sequence-independent factors. This study aims to delineate the relationship between the primary structure and solubility on overexpression. The amino acid sequences of proteins reported to be soluble or to form inclusion bodies on overexpression in E. coli under normal growth conditions were analyzed. The results show a positive correlation between thermostability and solubility of proteins, and an inverse correlation between the in vivo half-life of proteins and solubility. The amino acid (Asn, Thr, Tyr) composition and the tripeptide frequency of the protein were also found to influence its solubility on overexpression. The amino acids that were seen to be present in a comparatively higher frequency in inclusion body-forming proteins have a higher sheet propensity, whereas those that are seen more in soluble proteins have a higher helix propensity; this is indicative of a possible correlation between sheet propensity and inclusion body formation. Thus, the present analysis shows that thermostability, in vivo half-life, Asn, Thr, and Tyr content, and tripeptide composition of a protein are correlated to the propensity of a protein to be soluble on overexpression in E. coli. The precise mechanism by which these properties affect the solubility status of the overexpressed protein remains to be understood.     

Side Chain Dynamics and Alternative Hydrogen Bonding in the Mechanism of Protein Thermostabilization

Abstract

To elucidate the mechanism of protein thermostabilization, the thermodynamic properties of small monomeric proteins from mesophilic and thermophilic organisms have been analyzed. Molecular dynamics simulations were employed in the study of dynamic features of charged and polar side chains of amino acid residues. The basic conclusion has been made: surface charged and polar side chains with high conformational mobility can form alternative hydrogen bonded (H-bonded) donor-acceptor pairs. The correlation between the quantitative content of alternative H-bonds per residue and the temperature of maximal thermostability of proteins has been found. The proposed mechanism of protein thermostabilization suggests continuous disruption of the primary H- bonds and formation of alternative ones, which maintain constant the enthalpy value in the native state and prevent a rapid increase of the conformational entropy with the rising temperature. The analysis of the results show that the more residues located in the N- and C-terminal regions and in the extended loops that are capable of forming alternative longer-range H-bonded pairs, the higher the protein thermostability.     

Prediction of thermostability from amino acid attributes by combination of clustering with attribute weighting: a new vista in engineering enzymes

The engineering of thermostable enzymes is receiving increased attention. The paper, detergent, and biofuel industries, in particular, seek to use environmentally friendly enzymes instead of toxic chlorine chemicals. Enzymes typically function at temperatures below 60°C and denature if exposed to higher temperatures. In contrast, a small portion of enzymes can withstand higher temperatures as a result of various structural adaptations. Understanding the protein attributes that are involved in this adaptation is the first step toward engineering thermostable enzymes. We employed various supervised and unsupervised machine learning algorithms as well as attribute weighting approaches to find amino acid composition attributes that contribute to enzyme thermostability. Specifically, we compared two groups of enzymes: mesostable and thermostable enzymes. Furthermore, a combination of attribute weighting with supervised and unsupervised clustering algorithms was used for prediction and modelling of protein thermostability from amino acid composition properties. Mining a large number of protein sequences (2090) through a variety of machine learning algorithms, which were based on the analysis of more than 800 amino acid attributes, increased the accuracy of this study. Moreover, these models were successful in predicting thermostability from the primary structure of proteins. The results showed that expectation maximization clustering in combination with uncertainly and correlation attribute weighting algorithms can effectively (100%) classify thermostable and mesostable proteins. Seventy per cent of the weighting methods selected Gln content and frequency of hydrophilic residues as the most important protein attributes. On the dipeptide level, the frequency of Asn-Glu was the key factor in distinguishing mesostable from thermostable enzymes. This study demonstrates the feasibility of predicting thermostability irrespective of sequence similarity and will serve as a basis for engineering thermostable enzymes in the laboratory.     

Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

Protein thermostability is a crucial factor for biotechnological enzyme applications. Protein engineering studies aimed at improving thermostability have successfully applied both directed evolution and rational design. However, for rational approaches, the major challenge remains the prediction of mutation sites and optimal amino acid substitutions. Recently, we showed that such mutation sites can be identified as structural weak spots by rigidity theory-based thermal unfolding simulations of proteins. Here, we describe and validate a unique, ensemble-based, yet highly efficient strategy to predict optimal amino acid substitutions at structural weak spots for improving a protein’s thermostability. For this, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state has been found as the cause for thermostability. When applied prospectively to lipase A from Bacillus subtilis, we achieved both a high success rate (25% over all experimentally tested mutations, which raises to 60% if small-to-large residue mutations and mutations in the active site are excluded) in predicting significantly thermostabilized lipase variants and a remarkably large increase in those variants’ thermostability (up to 6.6°C) based on single amino acid mutations. When considering negative controls in addition and evaluating the performance of our approach as a binary classifier, the accuracy is 63% and increases to 83% if small-to-large residue mutations and mutations in the active site are excluded. The gain in precision (predictive value for increased thermostability) over random classification is 1.6-fold (2.4-fold). Furthermore, an increase in thermostability predicted by our approach significantly points to increased experimental thermostability (p < 0.05). These results suggest that our strategy is a valuable complement to existing methods for rational protein design aimed at improving thermostability.     

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。     

Bt杀虫基因与Bt转基因抗虫植物研究进展

苏云金杆菌是一类非常重要的昆虫病原体,它能产生特异性的杀虫结晶蛋白,对农业上和生物医学上的许多有害的昆虫有毒杀作用,这些害虫包括鳞翅目、双翅目、鞘翅目、膜翅目、螨类和线虫。近三十年来,以苏云金杆菌为基础的生物杀虫剂已在世界范围内商业化用于防治重要经济作物的害虫。近年来有关Bt基因的遗传、分子生物学和基因工程已取得显著进展。本文对苏云金杆菌杀虫晶体蛋白基因的分类和杀虫机理及用该类基因构建的工程转基因植物研究状况作一简要综述,同时对Bt基因工程存在的潜在问题和解决途径作了简单的探讨。