基于蛋白质骨架的人工水解酶的理性设计

蛋白质是生命体的重要组成部分,其中生物酶在生命体系中发挥至关重要的作用。蛋白质分子设计是研究生物酶结构与功能关系的重要手段。本文综述了基于蛋白质骨架的人工水解酶的理性设计与功能研究进展,包括对天然蛋白的重新利用和重新改造,基于3-股螺旋、4-股螺旋或锌指蛋白的分子设计,以及血红蛋白(如细胞色素b₅和肌红蛋白突变体)水解酶催化活性的调控等,阐明了人工水解酶分子设计的基本思路与研究方法,为合理构建人工水解酶或其他生物酶提供了重要的信息。人工水解酶的理性设计进展,不但深化我们对天然酶结构-性质-反应-功能关系的认识,而且还提升我们创造具有优越功能的人工生物酶的能力。     

Using theozymes for designing transition‐state analogs for the intramolecular aldol reaction of δ‐diketones

Two theozymes for the intramolecular aldol reaction of δ‐diketones have been studied using ab initio methods. The presence of both acid/base residues favors several steps of the aldol reaction. The appropriate positioning of these residues can accelerate one of two diastereromeric reaction pathways, the catalyzed aldol reaction being highly stereoselective. Analysis of the geometrical parameters, charge distribution, and the shape of molecular electrostatic potential for the corresponding acid/base catalyzed transition structure allows us to design adequate transition‐state analogs to favor a reactive channel of this intramolecular aldol reaction. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 338–347, 2001     

Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases

Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6–12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d /l -, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Locked by Design: A Conformationally Constrained Transglutaminase Tag Enables Efficient Site‐Specific Conjugation

Based on the crystal structure of a natural protein substrate for microbial transglutaminase, an enzyme that catalyzes protein crosslinking, a recognition motif for site‐specific conjugation was rationally designed. Conformationally locked by an intramolecular disulfide bond, this structural mimic of a native conjugation site ensured efficient conjugation of a reporter cargo to the therapeutic monoclonal antibody cetuximab without erosion of its binding properties.     

Mechanistic Studies of the Radical S‐Adenosylmethionine Enzyme DesII with TDP‐D‐Fucose

DesII is a radical S‐adenosylmethionine (SAM) enzyme that catalyzes the C4‐deamination of TDP‐4‐amino‐4,6‐dideoxyglucose through a C3 radical intermediate. However, if the C4 amino group is replaced with a hydroxy group (to give TDP‐quinovose), the hydroxy group at C3 is oxidized to a ketone with no C4‐dehydration. It is hypothesized that hyperconjugation between the C4 C? N/O bond and the partially filled p orbital at C3 of the radical intermediate modulates the degree to which elimination competes with dehydrogenation. To investigate this hypothesis, the reaction of DesII with the C4‐epimer of TDP‐quinovose (TDP‐fucose) was examined. The reaction primarily results in the formation of TDP‐6‐deoxygulose and likely regeneration of TDP‐fucose. The remainder of the substrate radical partitions roughly equally between C3‐dehydrogenation and C4‐dehydration. Thus, changing the stereochemistry at C4 permits a more balanced competition between elimination and dehydrogenation.