细胞色素c突变研究进展

在简述细胞色素c的生物功能和结构特征的基础上,综述了细胞色素c突变研究的进展,重点论述了对血红素辅基(heme)的轴向配体Met80、heme所在腔的保守氨基酸残基Tyr67以及蛋白表面的保守氨基酸残基Phe82的突变研究,并对一些突变体蛋白表现出来的特殊性质给予解释。     

鼠脑红蛋白突变体F106L与氰根的结合作用

构建了鼠脑红蛋白(Mouse neuroglobin)的突变体F106L, 以探求近端残基对脑红蛋白血红素口袋结构的贡献. 通过溶液核磁共振方法研究了外来配体氰根离子与NgbF106L蛋白的结合作用, 结果显示, 此结合存在动力学过程, 并且NgbF106LCN 突变蛋白氰根络合物可以可逆地释放氰根离子, 并使原来的第6配体His64(E7)又结合回到血红素铁上. 研究结果揭示, G5(Phe106)残基对脑红蛋白血红素构象而言较为保守; QM/MM结构优化结果表明, 位于G5 和FG5的近端残基对蛋白结构稳定性具有重要作用, 并可调控外来配体与蛋白作用的配位平衡与热动力学性质.     

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。     

紫外吸收光谱法研究Asp44在稳定肌红蛋白结构中的作用

为了了解肌红蛋白Mb表面44位天冬氨酸(Asp)残基对稳定蛋白结构的影响,用聚合酶链式反应(PCR)定点突变的技术将Mb基因上的第44位天冬氨酸的密码子GAT突变成赖氨酸的密码子AAA,获得突变体D44K。突变体蛋白在大肠杆菌BL21-DE3中成功表达并且得到纯化。用紫外-可见光谱研究野生型肌红蛋白及其突变体D44K的耐热、耐酸的变性过程。结果表明,用碱性氨基酸赖氨酸(Lys)取代酸性氨基酸Asp44残基,增强了肌红蛋白耐热、耐酸能力,说明Asp44具有稳定肌红蛋白结构的作用。为进一步研究蛋白表面氨基酸对蛋白质结构、功能的影响提供重要的试验依据。     

神经红蛋白突变体H64V与叠氮离子的作用

将64位组氨酸(His64)突变为缬氨酸(Val),构建了神经红蛋白(Ngb)突变体H64V基因并进行了蛋白的表达纯化,突变使Ngb的血红素Fe由六配位结构变成五配位结构.利用光谱法研究了突变体H64V与叠氮离子(N_3~-)的相互作用.紫外-可见吸收光谱表明,H64V与N_3~-键合后其Soret带吸收峰由406 nm红移至418 nm;荧光光谱表明N_3~-可使H64V的荧光发生静态猝灭.计算得到了H64V与N_3~-键合的平衡解离常数和热力学参数.另外,还研究了不同阴离子对H64V与N_3~-结合的影响,发现阴离子的存在减弱了N_3~-与H64V之间的结合力.     

氨基酸突变对GABAa受体结合能力的影响

采用同源建模技术构建了大鼠γ-氨基丁酸a型受体(GABAaR)模型, 并将氨基酸残基β157Tyr和β205Tyr突变为相应的突变受体模型. 使用分子对接方法计算了γ-氨基丁酸(GABA)与突变前后受体的相互作用. 对接计算结果显示, Tyr突变为Phe后, 两种突变受体的对接能量大幅提高, GABA生物活性降低; 当Phe的对位引入氟原子后, 对接能量与未突变受体相比更低. 另外, 与β205Tyr突变相比, 与配体距离较近的β157Tyr突变, 对受体与配体作用的影响更大.     

神经红蛋白突变体(F28Y,F106Y)的构建、 表达与表征

构建了神经红蛋白F28Y, F106Y的两种突变体, 并进行了表达、 纯化和谱学表征. 电喷雾质谱表明突变体蛋白的分子量与理论值一致. 氧化型和还原型F28Y及F106Y的紫外 可见吸收光谱与野生型相似, 仅氧化型F28Y的Soret 带有2 nm的蓝移, 说明这两种突变体蛋白仍保持六配位形式. F28Y的荧光最大发射峰明显红移(340 nm→347 nm), 表明其荧光基团更加暴露于极性环境中. 圆二色光谱表明, 突变体蛋白的α 螺旋含量降低且F28Y产生了β 折叠, 这是由于F28相对于F106则位于疏水腔外部且更加接近于溶剂表面所致. 热稳定性顺序为NGB>F28Y>F106Y, F106Y最不稳定, 是因为其与血红素间存在着较强的疏水作用, 突变使F106与血红素间的作用力减弱, 从而导致血红素在热变性条件下更容易从蛋白中解离出来.     

细胞色素b5 S64X突变体对蛋白结构及稳定性的影响

为了深入了解细胞色素b₅(Cyt b₅)64位氨基酸残基(Ser64)对血红素辅基微环境及蛋白性质的影响,我们分别对Cyt b₅ Ser64进行了保守性突变(S64T)以及非保守性突变(S64K、S64N和S64H),均为亲水性氨基酸残基。对野生型细胞色素b₅及其突变体蛋白S64X(X：T,K,N或H)的热、酸、盐酸胍变性的稳定性研究表明：4个突变体蛋白的稳定性相对于野生型都大大降低了;CD光谱表明,细胞色素b₅ S64X突变体中的α-螺旋明显减少,芳香性氨基酸残基所处的肽链结构受到了影响;盐酸胍变性荧光光谱表明,Trp22周围的蛋白肽链受到了影响,Trp22暴露于水溶液的程度加大。我们认为Ser64不仅对血红素辅基有稳定作用,同时还对维持蛋白Core 1中的第5个α-螺旋结构有重要的作用,在64位引入其他氨基酸残基影响了第5个α-螺旋的结构,并通过蛋白肽链的相互作用,使得Trp22所在的Core 2结构也受到了较为明显的扰动。     

促δ-波睡眠肽的结构与功能的研究

用固相法合成了促δ-波睡眠肽Trp-Ala-Gly-Gly-Asp-Ala-Ser-Glu(DSIP)及其十四种类似物和三个短肽,研究了结构与功能的关系,类似物的设计,主要考虑在分子中引入D-氨基酸以抑制酶的作用和增强稳定性,以及引入疏水侧链氨基酸如Phe和Trp等。位置的修饰主要在1,3,4,5,8和9位,即:D-Trp[1],Tyr[1],Tyr[1]Phe[5],D-Trp[1]Phe[8],Trp[3,4],D-Trp[3,4],D-Trp[1,3,4]Phe[8],D-Glu[9],D-pF-Phe[3,4]Phe[8]D-Glu[9],Phe[5],Glu[5]Asp[9],Tyr[5]Asp[9],Ala[7]和Asp[9]-DSIP以及Trp-Ala-Gly-Gly-Asp,Trp-Ala-Gly-Gly-Glu和Trp-Gly-Glu.合成肽的纯度经氨基酸组成分析、元素分析、薄层层析以及纸电泳鉴定。生物试验表明D-Trp[1],Tyr[1],Tyr[1]Phe[5],Ala[7]-DSIP无促眠活性;而Phe[5]-DSIP的促眠活性与DSIP相接近,其他类似物的生物试验结果将另文发表。     

细胞色素c突变体的共振拉曼光谱研究

采用共振拉曼光谱技术研究了细胞色素c一次突变体（WT）及其突变体Y67F和N52I在低频区的光谱特征。结果表明，以苯丙氨酸替代WT中酪氨酸残基Tyr67并没有明显影响血红素丙氨酸侧基周围多肽氨基酸残基的构象，而异亮氨酸对天冬酰胺残基Asn52的取代则较大程度地改变了蛋白质内部水分子与周围氨基酸残基间的氢键作用和多肽空腔的疏水性，进而使氨基酸残基和血素的构象相应发生调变。两种取代都导致形成血红素周围空腔的多肽氨基酸残基构象的变化。     

Protein plasticity: a single amino acid substitution in the Saccharomyces cerevisiae oxidosqualene-lanosterol cyclase generates protosta-13(17),24-dien-3beta-ol, a rearrangement product

To provide insights into the structure-function relationships of oxidosqualene-lanosterol cyclase (ERG7) from Saccharomyces cerevisiae, the Phe699 was exchanged against hydrophilic polar uncharged residues Ser, Thr, Cys, Gln, and Tyr to characterize its product profile and functional role in ERG7 activity. Among the substitutions, only the ERG7(F699T) mutant produced novel protosta-13(17),24-dien-3beta-ol as the sole truncated rearrangement product. The results suggest that Phe699Thr mutation is likely to affect the C-17 cation stabilization during the rearrangement process.     

Tyrosine 92 of aristolochene synthase directs cyclisation of farnesyl pyrophosphate

A mutant of Aristolochene Synthase (AS), in which Tyr 92 was replaced by Val, produced the alicyclic beta-(E)-farnesene as the major product, indicating that cyclisation of FPP is controlled by Tyr 92 in AS.     

Computer-aided modeling of pentachlorophenol 4-monooxygenase and site-directed mutagenesis of its active site

Homology modeling was used to construct a model of the three-dimensional structure of pentachlorophenol 4-monooxygenase (PcpB). A PSI-BLAST homology search was initially performed to identify the 3D structure of proteins homologous with PcpB. The feasibility of modeled structures of PcpB was evaluated by Verify3D, which calculated structural compatibility scores based on 3D-1D profiles. The predicted structure of PcpB had an acceptable 3D-1D self-compatibility score, beyond the incorrect fold score threshold. A PcpB-pentachlorophenol (PCP) complex was then constructed utilizing the modeled PcpB structure. After energy minimization of the complex, and successive minimizations of the system that consisted of the complex and the water layer surrounding the complex, the molecular dynamics of the system were simulated. The active-site residues of PcpB were identified on the basis of the modeled structure, and PcpB mutants were then designed to change the active site residues, expressed, and purified by affinity chromatography. The mutant activity was compared with that of the wild-type to investigate the validity of the modeled structure. The experimental results suggested that Phe85, Tyr216, and Arg235 were relevant to enzyme activity, and that Tyr397 and Phe87 were important for stabilization of the structure of PcpB.     

Study on a Specific Site Tyr~(444) on a Hyperthermophilic Enzyme APE1547

Hyperthermophilic enzyme APE1547 is an extremely thermostable recombinant protein from thermophilic archaeon Aeropyrum pernix K1. The Tyr444 located in the catalytic domain adjacent to the catalytic amino acid Ser445 and formed hydrogen bond with Ile567. To study the effect of Tyr444 on the activity of APE1547,site-directed mutagenesis was applied. Two mutant enzymes T444S and T444G were created. Comparison of the mutant enzymes with wide enzyme,the thermostability of mutants T444S and T444G decreased by 10...     

A general approach for the generation of orthogonal tRNAs

BACKGROUND: The addition of new amino acids to the genetic code of Escherichia coli requires an orthogonal suppressor tRNA that is uniquely acylated with a desired unnatural amino acid by an orthogonal aminoacyl-tRNA synthetase. A tRNA(Tyr)(CUA)-tyrosyl-tRNA synthetase pair imported from Methanococcus jannaschii can be used to generate such a pair. In vivo selections have been developed for selecting mutant suppressor tRNAs with enhanced orthogonality, which can be used to site-specifically incorporate unnatural amino acids into proteins in E. coli. RESULTS: A library of amber suppressor tRNAs derived from M. jannaschii tRNA(Tyr) was generated. tRNA(Tyr)(CUA)s that are substrates for endogenous E. coli aminoacyl-tRNA synthetases were deleted from the pool by a negative selection based on suppression of amber nonsense mutations in the barnase gene. The remaining tRNA(Tyr)(CUA)s were then selected for their ability to suppress amber nonsense codons in the beta-lactamase gene in the presence of the cognate M. jannaschii tyrosyl-tRNA synthetase (TyrRS). Four mutant suppressor tRNAs were selected that are poorer substrates for E. coli synthetases than M. jannaschii tRNA(Tyr)(CUA), but still can be charged efficiently by M. jannaschii TyrRS. CONCLUSIONS: The mutant suppressor tRNA(Tyr)(CUA) together with the M. jannaschii TyrRS is an excellent orthogonal tRNA-synthetase pair for the in vivo incorporation of unnatural amino acids into proteins. This general approach may be expanded to generate additional orthogonal tRNA-synthetase pairs as well as probe the interactions between tRNAs and their cognate synthetases.     

Posttranslational hydroxylation of human phenylalanine hydroxylase is a novel example of enzyme self-repair within the second coordination sphere of catalytic iron

Phenylalanine hydroxylase, a mononuclear non-heme iron enzyme, catalyzes the hydroxylation of phenylalanine to tyrosine in the presence of oxygen and reduced pterin cofactor. X-ray structural studies have established the coordination around the iron metal center and point to significant interactions within the second coordination sphere. One such interaction involves Tyr325 in human phenylalanine hydroxylase (hPAH), which forms a hydrogen-bonding network with an aqua ligand on iron and the pterin cofactor. The full-length tetramer (1-452) and truncated dimer (117-424) Tyr325Phe hPAH mutant enzymes showed similar kinetics, thermal stabilities, and oligomerization profiles as their corresponding wild-type proteins. The possibility of in vivo posttranslational hydroxylation that would restore the activity of hPAH was examined by mass spectrometry on the trypsin digested full-length (1-452) hPAH Tyr325Phe point mutant. The amino acid tags obtained by ESI-MS/MS confirmed the presence of a Phe325 in the peptide corresponding to the doubly charged precursor ion at m/z 916.4 (L A T I F W F T V E F G L C K), and its hydroxylated counterpart in the peptide corresponding to the m/z 924.4 (L A T I F-OH W F T V E F G L C K) byproduct ion series comprising the fragments y(5)-y(12). Furthermore, the point mutation Tyr325Ala resulted in an enzyme that was totally inactive and did not display any evidence of hydroxylation. These results demonstrate the importance of Tyr325 for proper conformation of the active site, substrate binding, and catalysis. The rescue of the Tyr325Phe mutant in hPAH via self-hydroxylation presents a novel example of oxidative repair on the molecular level.     

蓖麻毒素A链(RTA)功能域突变体构效关系的量子化学研究

结合对蓖麻毒素A链(RTA)功能域氨基酸(Tyr80,Trr123,Gln177,Arg180)点突变后对其生物活性影响的实验研究,利用半经验量子化学AMI方法对RTA功能域及其点突变进行了理论计算.通过分析前线分子轨道性质和能级,从理论上探讨了其功能域点突变对其生物活性的影响,并预测了突变体(Tyr123→TrP)比RTA生物活性高.     

Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis

We report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. The assigned role of Tyr728 differs from previous suggestions but is consistent with the established mechanism of other zinc proteases.     

Protein:Ligand binding free energies: A stringent test for computational protein design

A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl‐tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l ‐tyrosine (l ‐Tyr), compared to the analogs d ‐Tyr, p‐acetyl‐, and p‐azido‐phenylalanine (ac‐Phe, az‐Phe). We simulate l ‐ and d ‐Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous “MD/GBSA” procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l ‐Tyr, ac‐ and az‐Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l ‐Tyr or d ‐Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l ‐Tyr is the ligand and a d ‐Tyr specific mutant when d ‐Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln. © 2015 Wiley Periodicals, Inc.