Essential Role of Gly33 in a Novel Organic Solvent-Tolerant Lipase from Serratia marcescens ECU1010 as Determined by Site-Directed Mutagenesis

A novel lipase lipB from Serratia marcescens ECU1010 is highly stable in the presence of organic solvents. By sequence and structure comparison with homologous lipase lipA, three amino acid residues were found to be different between them. To identify the residues which increase the organic solvent stability of lipB, residues that potentially provide this stability were mutated to the ones of lipA at equivalent positions. The replacement of Gly at position 33 by Asp obviously decreased its stability in organic solvents. Molecular modeling and structural analysis also suggested that the Gly33 residue is important for the organic solvent stability of lipB.     

Site-Directed Mutagenesis Improves the Thermostability and Catalytic Efficiency of Aspergillus niger N25 Phytase Mutated by I44E and T252R

Aspergillus niger phytase (PhyA) has been used as a feed supplement to improve the bioavailability of phytate phosphorus to swine and poultry. However, it is unable to maintain its stability due to high temperature during the feed pelleting process. In this study, we performed site-directed mutagenesis in the Aspergillus niger N25 phyA ^m gene at residue 44I and 252 T, and they were replaced by glutamic acid and arginine. Single-site mutants I44E-PhyA and T252R-PhyA, as well as double-site mutant I44E/T252R-PhyA, were constructed to improve the thermostability of PhyA through hydrogen bondings and ionic interactions. The three mutant enzymes all showed more than 20 % improvement in thermostability compared to the wild-type enzyme after being heated at 80 °C for 10 min. Their melting temperatures (T _m) were increased by 1, 1, and 1.2 °C, respectively. The k _m values of I44E-PhyA, T252R-PhyA, and I44E/T252R-PhyA for sodium phytate were 78, 44, and 79 % lower (P <0.05) than that of the wild-type enzyme. Overall catalytic efficiency (k _cat/k _m) of I44E-PhyA, T252R-PhyA, and I44E/T252R-PhyA was improved by 310, 155, and 84 % (P <0.05) than that of the wild type, respectively. The catalytic efficiency did not seem to be negatively affected by the improvement in thermostability.     

分子动力学模拟残基突变对芳香烃受体配体结合区的影响

芳香烃受体(Aryl hydrocarbon receptor,AhR)属于配体依赖性的转录因子蛋白。本文通过对AhR配体结合区域(Ligand binding domain,LBD)的结构功能及物种特异性分析,发现在其结合腔口有一些关键残基可能起到"门控"作用,进一步将野生型(WT)和3个突变模型(Phe289Ala、Tyr316Ala、Ile319Ala)进行分子动力学模拟,从蛋白稳定性、蛋白结构变化、蛋白结合腔变化及蛋白和配体结合能力4个方面分析3个残基的门控作用。研究发现,Phe289、Tyr316、Ile319氨基酸残基通过形成疏水作用为AhR LBD起到"门控"作用;而将这些氨基酸分别突变后,其蛋白稳定性降低,整体运动性增加,配体亲和力减弱,其中Tyr316、Ile319对腔内体积影响较大,Phe289使腔内环境稳定性降低。本研究可为基于芳香烃受体的药物设计提供相关理论指导。     

Probing the Role of the Conserved Arg174 in Formate Dehydrogenase by Chemical Modification and Site-Directed Mutagenesis

The reactive adenosine derivative, adenosine 5′-O-[S-(4-hydroxy-2,3-dioxobutyl)]-thiophosphate (AMPS-HDB), contains a dicarbonyl group linked to the purine nucleotide at a position equivalent to the pyrophosphate region of NAD⁺. AMPS-HDB was used as a chemical label towards Candida boidinii formate dehydrogenase (CbFDH). AMPS-HDB reacts covalently with CbFDH, leading to complete inactivation of the enzyme activity. The inactivation kinetics of CbFDH fit the Kitz and Wilson model for time-dependent, irreversible inhibition (K_D = 0.66 ± 0.15 mM, first order maximum rate constant k₃ = 0.198 ± 0.06 min⁻¹). NAD⁺ and NADH protects CbFDH from inactivation by AMPS-HDB, showing the specificity of the reaction. Molecular modelling studies revealed Arg174 as a candidate residue able to be modified by the dicarbonyl group of AMPS-HDB. Arg174 is a strictly conserved residue among FDHs and is located at the Rossmann fold, the common mononucleotide-binding motif of dehydrogenases. Arg174 was replaced by Asn, using site-directed mutagenesis. The mutant enzyme CbFDHArg174Asn was showed to be resistant to inactivation by AMPS-HDB, confirming that the guanidinium group of Arg174 is the target for AMPS-HDB. The CbFDHArg174Asn mutant enzyme exhibited substantial reduced affinity for NAD⁺ and lower thermostability. The results of the study underline the pivotal and multifunctional role of Arg174 in catalysis, coenzyme binding and structural stability of CbFDH.     

Study of the Mechanism of Coenzyme Specificity of Phenylacetone Monooxygenase from Thermobifida fusca by Site-Directed Mutagenesis

Moscow University Chemistry Bulletin - Phenylacetone monooxygenase from Thermobifida fusca (EC 1.14.13.92, PAMO) belongs to the Baeyer–Villiger family of monooxygenases and catalyzes the...     

Enhanced Activity and Substrate Specificity by Site-Directed Mutagenesis for the P450 119 Peroxygenase Catalyzed Sulfoxidation of Thioanisole

P450 119 peroxygenase was found to catalyze the sulfoxidation of thioanisole and the sulfonation of sulfoxide in the presence of tert-butyl hydroperoxide (TBHP) for the first time with turnover rates of 1549 min⁻¹ and 196 min⁻¹ respectively. Several mutants were designed to improve the peroxygenation activity and thioanisole specificity by site-directed mutagenesis. The F153G/T213G mutant gave an increase of sulfoxide yield and a decrease of sulfone yield. Moreover the S148P/I161T/K199E/T214V mutant and the K199E mutant with acidic Glu residue contributed to improving the product ratio of sulfoxide to sulfone. Addition of short-alkyl-chain organic acids to the P450 119 peroxygenase-catalyzed sulfur oxidation of thioanisole was investigated. Octanoic acid was found to induce a preferred sulfoxidation of thioanisole catalyzed by the F153G/T213G mutant to give approximately 2.4-fold increase in turnover rate with a k_cat value of 3687 min⁻¹ relative to that of the wild-type, and by the F153G mutant to give the R-sulfoxide up to 30 % ee. The experimental control and the proposed mechanism for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole in the presence of octanoic acid suggested that octanoic acid could partially occupy the substrate pocket; meanwhile the F153G mutation could enhance the substrate specificity, which could lead to efficiently regulate the spatial orientation of thioanisole and facilitate the formation of Compound I. This is the most effective catalytic system for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole.     

基于同源建模和定点突变技术研究嗜热型L-阿拉伯糖异构酶与D-半乳糖的亲和作用

通过同源建模分析选取对Lactobacillus fermentum CGMCC2921来源的L-阿拉伯糖异构酶(简称L-AI酶)催化D-半乳糖生产D-塔格糖起重要作用的氨基酸位点进行突变,发现当Q16,M311,K423和Q438位点的氨基酸突变为丙氨酸时,突变酶Km值降低,其中突变酶M311A降至本体的51.6%,对D-半乳糖的转化率提高了18.7%.当K423位点的氨基酸残基分别突变为丙氨酸、天冬酰胺或精氨酸时,突变酶与底物的亲和力以及D-半乳糖的转化率随着423位点突变氨基酸侧链长度的增加而降低.运用计算机分子模拟技术分析表明,当M311位点氨基酸突变为丙氨酸以后,催化位点氨基酸残基与底物D-半乳糖之间的氢键作用增强,导致与底物亲和力增大,从而提高了酶活力.     

Tuning the Product Spectrum of a Glycoside Hydrolase Enzyme by a Combination of Site-Directed Mutagenesis and Tyrosine-Specific Chemical Modification

Selective chemical modification of proteins plays a pivotal role for the rational design of enzymes with novel and specific functionalities. In this study, a strategic combination of genetic and chemical engineering paves the way for systematic construction of biocatalysts by tuning the product spectrum of a levansucrase from Bacillus megaterium (Bm-LS), which typically produces small levan-like oligosaccharides. The implementation of site-directed mutagenesis followed by a tyrosine-specific modification enabled control of the product synthesis: depending on the position, the modification provoked either enrichment of short oligosaccharides (up to 800 % in some cases) or triggered the formation of high molecular weight polymer. The chemical modification can recover polymerization ability in variants with defective oligosaccharide binding motifs. Molecular dynamic (MD) simulations provided insights into the effect of modifying non-native tyrosine residues on product specificity.     

Kinetics of Enzymatic Synthesis of Cinnamyl Butyrate by Immobilized Lipase

This work illustrates the enzymatic synthesis of cinnamyl butyrate by esterification of butyric acid and cinnamyl alcohol. Experiments were performed to study the various operating parameters such as molar ratio, enzyme concentration, temperature, and speed of agitation. Also, the suitable kinetic model for esterification reaction was predicted and the various kinetic parameters were determined. It has been observed that the experimental results agree well with the simulated results obtained by following the ping-pong bi-bi mechanism with dead-end inhibition by both the substrate acid and alcohol. The highest 90% conversion of butyric acid was observed after 12 h at the following reaction conditions: substrate molar ratio 1:2 (butyric acid/cinnamyl alcohol), temperature 50 °C, enzyme loading 2% (with respect to the weight of the substrates), and agitation speed 250 rpm. Diffusional mass transfer limitations between substrate and enzyme surface do not show significant effect on reaction kinetics. Enzyme reusability study reveals that it retains 85% of its catalytic activity after five consecutive cycles.     

脂肪酶Novozym 435催化合成单月桂酸甘油酯

生物酶催化的有机化学反应具有选择性高、反应条件温和、环境友好等优点,本项目通过对酶催化合成单月桂酸甘油酯的反应条件和产物分离条件进行详细研究,将酶催化反应引入本科实验教学,使学生学习先进的知识技术。本项目的合成部分采用月桂酸:甘油=1:3.5 (摩尔比)的投料比、5%酶用量,在52℃反应80 min;回收脂肪酶后,洗涤除去甘油,蒸馏除去叔丁醇,最后用石油醚重结晶可得到纯度90%以上的高含量产品,分离产率47%–53%,实验的稳定性和重现性好,很适合作为一个大学本科有机实验项目。     

W544F定点突变提高苏云金杆菌Cry1Ac蛋白的稳定性

W544是Cry1Ac蛋白上独特于其它Cry类蛋白的一个氨基酸, 它与F578和F604一起组成一个“螺旋桨状”的疏水簇, 通过疏水相互作用维持蛋白的三维结构稳定. 本研究通过定点突变将W544保守地替换为苯丙氨酸, SDS-PAGE分析结果表明其纯化的原毒素对紫外照射、胰蛋白酶处理和室温存贮的稳定性相对于野生Cry1Ac都有一定程度的提高; 经原子力显微镜观察, 发现W544F产生的晶体两个顶点间的垂直距离比野生型Cry1Ac约长0.6 μm, 且晶体表面不及野生型光滑; 此外, W544F与野生Cry1Ac的杀虫活性相似, 但经过紫外光照射9 h后, 其保留的杀虫活性比野生型高4倍以上. W544F突变较好地解决了Cry1Ac毒素蛋白田间应用不持久的问题, 具有重要的应用价值.     

Enzymatic Ring-Opening Polymerization of Lactones by Lipase Catalyst: Mechanistic Aspects

Mechanistic aspects of lipase-catalyzed ring-opening polymerization (ROP) of lactones to give polyesters are discussed from accumulated experimental data and new insight. Comparison of the ROP reactivity by lipase catalyst with the anionic ROP reactivity by a metal-catalyst clearly demonstrates the characteristics of lipase catalysis; the larger ring-sized monomers with lower ring strain showed higher polymerizability than medium ring-sized ones, in contrast to the anionic ROP showing the reverse direction where the ring strain of monomer is operative. The enzyme-catalysis involves an acyl-enzyme intermediate formation as a key-step. From the copolymerization results a new mechanism is proposed, that involves the formation of the acyl-enzyme intermediate (acylation step) and/or the nucleophilic attack of the propagationg alcohol end to the carbonyl carbon of the intermediate to open the monomer ring (deacylation step) as the rate-determining step. The structure of the propagating alcohol end (primary or secondary) affects much on which step is more operative.     

紫外圆二色光谱预测蛋白质结构的研究方法

介绍了蛋白质紫外圆二色性(CD)产生的原理及其与蛋白质结构的关系。评述了用远紫外CD预测蛋白质二级结构的方法原理、参考蛋白、拟合算法和拟合程序,以及方法存在的问题。近紫外CD与蛋白质的三级结构密切相关,近紫外蛋白质CD反映芳香氨基酸残基、二硫键等微环境的变化,表征着丰富的蛋白质三级结构的信息。     

Computational Model of the Complex between GR113808 and the 5-HT4 Receptor Guided by Site-Directed Mutagenesis and the Crystal Structure of Rhodopsin

A computational model of the transmembrane domain of the human 5-HT₄ receptor complexed with the GR113808 antagonist was constructed from the crystal structure of rhodopsin and the putative residues of the ligand-binding site, experimentally determined by site-directed mutagenesis. The recognition mode of GR113808 consist of: (i) the ionic interaction between the protonated amine and Asp^3.32; (ii) the hydrogen bond between the carbonylic oxygen and Ser^5.43; (iii) the hydrogen bond between the ether oxygen and Asn^6.55; (iv) the hydrogen bond between the C-H groups adjacent to the protonated piperidine nitrogen and the electrons of Phe^6.51; and (v) the - aromatic-aromatic interaction between the indole ring and Phe^6.52.This computational model offers structural indications about the role of Asp^3.32, Ser^5.43, Phe^6.51, Phe^6.52, and Asn^6.55 in the experimental binding affinities. Asp^3.32Asn mutation does not affect the binding of GR113808 because the loss of binding affinity from an ion pair to a charged hydrogen bond is compensated by the larger energetical penalty of Asp to disrupt its side chain environment in the ligand-free form, and the larger interaction between Phe^6.51 and the piperidine ring of the ligand in the mutant receptor. In the Phe^6.52Val mutant the indole ring of the ligand replaces the interaction with Phe^6.52 by a similarly intense interaction with Tyr^5.38, with no significant effect in the binding of GR113808. The mutation of Asn^6.55 to Leu replaces the hydrogen bond of the ether oxygen of the ligand from Asn^6.55 to Cys^5.42, with a decrease of binding affinity that approximately equals the free energy difference between the SHO and NHO hydrogen bonds.Because these residues are also present in the other members of the neurotransmitter family of G protein-coupled receptors, these findings will also serve for our understanding of the binding of related ligands to their cognate receptors.     

Influence of Enzymatic Hydrolysis and Molecular Weight Fractionation on the Antioxidant and Lipase / α-Amylase Inhibitory Activities In Vitro of Watermelon Seed Protein Hydrolysates

This study aims to evaluate the potential in vitro antioxidant and anti-obesity activities of watermelon seed protein hydrolysates (WSPH) obtained using different combinations of enzymes alcalase–proteinase K (ALC-PK) and alcalase–actinidin (ALC-ACT). There was a direct relationship between the degree of hydrolysis (DH) and the biological activities of the WSPH, with the highest DPPH (approximately 85%) and lipase inhibitory activities (≈59%) appreciated at DH of 36–37% and 33–35% when using ALC-PK and ALC-ACT, respectively. Following molecular weight fractionation, the ALC-PK WSPH < 3 kDa (F1) assayed at 1 mg.mL⁻¹ had the highest DPPH-radical scavenging (89.22%), ferrous chelating (FC) (79.83%), reducing power (RP) (A 0.51), lipase inhibitory (71.36%), and α-amylase inhibitory (62.08%) activities. The amino acid analysis of ALC-PK WSPH and its fractions revealed a relationship between the biological activity of the extracts and their composition. High contents of hydrophobic amino acids, arginine, and aromatic amino acids were related to high antioxidant, lipase inhibitory, and α-amylase inhibitory activities in the extracts, respectively. Overall, this study revealed that underutilized protein sources such as WSPH, using the appropriate combination of enzymes, could result in the generation of new ingredients and compounds with powerful antioxidant and anti-obesity activities with promising applications as nutraceuticals or functional foods.     

Conformation and Atropisomeric Properties of Indometacin Derivatives

The stereochemistry around the N‐benzoylated indole moiety of indometacin was studied by restricting the rotation about the N? C7′ and/or C7′? C1′ bond. In the 2′,6′‐disubstituted ones, an atropisomeric property was found and the atropoisomers were separated and isolated as stable forms. Their biological abilities to inhibit cyclooxygenase‐1 (COX‐1) and cyclooxygenase‐2 (COX‐2) were examined. Only the aR‐isomer showed specific inhibition of COX‐1, and COX‐2 was not inhibited by either atropisomer. Conformational analysis in NMR studies and X‐ray crystallography, and CD spectra in combination with calculations were utilized to elucidate the bioactive conformations.     

Heme Pocket Architecture in Human Serum Albumin: Regulation of O2 Binding Affinity of a Prosthetic Heme Group by Site-Directed Mutagenesis

Summary : We present the O₂ binding properties of recombinant human serum albumin (rHSA) mutants complexed with an iron(II) protoporphyrin IX as a prosthetic heme group. Iron(III) protoporphyrin IX (hemin) is bound within subdomain IB of HSA with weak axial coordination by Tyr-161. In order to confer O₂ binding capability to this naturally occurring hemoprotein: (i) a proximal histidine was introduced into position Ile-142; and (ii) the coordinated Tyr-161 was replaced with hydrophobic Leu using site-directed mutagenesis. It provided a recombinant HSA double-mutant [rHSA(I142H/Y161L) = rHSA(HL)]. The rHSA(HL)–heme formed a ferrous five-coordinate high-spin complex with axial ligation of His-142 under an Ar atmosphere. This artificial hemoprotein binds O₂ at room temperature. Laser flash photolysis experiments demonstrated that O₂ rebinidng to rHSA(HL)–heme displays monophasic kinetics, whereas the CO recombination process obeyed a double-exponential pattern. This might be attributable to the two different geometries of the axial imidazole coordination arising from the two orientations of the porphyrin plane in the heme pocket. The O₂ binding affinity of rHSA(HL)–heme was considerably lower than those of R-state hemoglobin (Hb) and myoglobin (Mb), principally because of the high O₂ dissociation rate constant. The third mutations have been introduced into the distal side of the heme (at position Leu-185 or Arg-186) to increase the O₂ binidng affinity. The rHSA(HL/L185N)–heme showed high O₂ binding affinity ( : 1 Torr), which is 18-fold greater than that of the original double mutant rHSA(HL)–heme and which is rather close to those of Hb (R-state) and Mb. Furthermore, replacement of polar Arg-186 with Leu or Phe adjusted the O₂ binding affinity ( ) to 10 Torr, which is almost equivalent to value for human red blood cells.     

Influence of the Degree of Hydrolysis on Functional Properties and Antioxidant Activity of Enzymatic Soybean Protein Hydrolysates

Soybean protein hydrolysates were prepared using two proteolytic enzymes (Alcalase and Protamex) and the degree of hydrolysis (DH) and their functional and antioxidant properties were evaluated. The highest DH value was 20%, with a yield of 19.77% and protein content of 51.64%. The total amino acid content was more than 41% for all protein hydrolysates. The protein hydrolysates from Protamex at pH 2.0 had excellent solubility, emulsifying activity, and foaming capacity, at 83.83%, 95.03 m²/g, and 93.84%, respectively. The water-holding capacity was 4.52 g/g for Alcalase, and the oil-holding capacity was 4.91 g/g for Protamex. The antioxidant activity (62.07%), as measured by the samples’ reaction with DPPH (2,2-diphenyl-1-picrylhydrazyl) and the reducing power (0.27) were the strongest for Protamex. An ABTS activity rate of 70.21% was recorded for Alcalase. These findings indicated a strong potential for the utilization of soybean protein hydrolysates to improve the functional properties and antioxidant activity of soybeans as well as their nutritional values.