Structure of a mutant of tyrosyl-tRNA synthetase with enhanced catalytic properties

One surprising outcome of applying the techniques of protein engineering to the enzyme tyrosyl-transfer RNA synthetase was that the enzyme's activity could actually be increased by a specific sequence change. In particular, altering residue threonine 51 to a proline (mutant TP51) increased the enzyme's affinity for tyrosyl adenylate complexes. The non-additive effect of combining the TP51 mutation with a second sequence alteration (histidine 48 to a glycine) suggested that the effect of the TP51 change might be mediated by a structural change involving the peptide backbone. To address the question of the mechanism by which the TP51 change increases the activity of tyrosyl-tRNA synthetase we have determined the structure of the mutant enzyme. We find the change has a purely local effect on the structure of the enzyme, and conclude that the increased activity of the TP51 mutant probably results from the replacement of the polar threonine residue by a non-polar group: in the wild-type enzyme substrate binding is disfavoured by the displacement of solvent from the vicinity of threonine 51. This unfavourable effect is absent in the TP51 mutant.     

北京棒杆菌天冬氨酸激酶突变体P184Q的酶学性质表征

通过分析谷氨酸棒杆菌天冬氨酸激酶(AK)的结构,筛选可能影响别构抑制剂结合的Pro184位点,对其进行饱和定点突变,成功筛选出突变菌株P184Q.酶学性质研究表明:突变体P184Q的V_(max)比野生型(WT)提高了3倍;n=1.39,低于WT的值(2.6),正协同性下降,同时Km值减小,对底物的亲和力增大;P184Q最适pH=6.5,最适反应温度为25℃,半衰期为2.8h;P184Q对金属离子和有机溶剂均表现出良好的抗性,解除抑制剂苏氨酸和甲硫氨酸、赖氨酸和甲硫氨酸、苏氨酸和赖氨酸、赖氨酸对酶活力的抑制作用.     

Crystallographic analysis of mutant human haemoglobins made in Escherichia coli

The expression of beta-globin in Escherichia coli has enabled us to study the functional role of individual amino-acid residues in haemoglobin (Hb) by site-directed mutagenesis. In contrast to mammalian Hbs, some teleost fish haemoglobins show a drastic lowering of oxygen affinity and cooperativity at low pH, a phenomenon known as the Root effect. We have produced the two mutant haemoglobins Hb Nymphéas [Cys(F9)93 beta----Ser] and Hb Daphne [His(H21)143 beta----Arg, Cys(F9)93 beta----Ser] to investigate this allosteric property. Although these substitutions were thought to be responsible for the Root effect, Hb Nymphéas and Hb Daphne show an increased oxygen affinity and a reduced effect of pH on oxygen affinity. Our X-ray crystallographic studies show that the hydroxyl group of Ser 93 beta forms a hydrogen bond with Asp 94 beta which is in equilibrium with the salt bridge between Asp 94 beta and His 146 beta. The oxygen-binding properties of Hbs Nymphéas and Daphne are accounted for by the partial disruption of the salt bridge.     

A model of synthetase/transfer RNA interaction as deduced by protein engineering

The recognition of transfer-RNA by their cognate aminoacyl-tRNA synthetases is the crucial step in the translation of the genetic code. In order to construct a structural model of the complex between the tyrosyl-tRNA synthetase (TyrTS) from Bacillus stearothermophilus and tRNATyr, 40 basic residues at the surface of the TyrTS dimer have been mutated by site-directed mutagenesis and heterodimers created in vitro by recombining subunits derived from different mutants. As reported here a cluster of basic residues (Arg 207-Lys 208) in the N-terminal domain of one TyrTS subunit interacts with the acceptor stem of tRNATyr and two separated clusters of basic residues (Arg 368-Arg 371; Arg 407-Arg 408-Lys 410-Lys 411) in the C-terminal domain of the other subunit interact with the anticodon arm. The TyrTS would thus clamp the tRNA in a fixed orientation. The precise alignment of the flexible... ACCA 3' end of the tRNA for attack on the tyrosyl adenylate is made by contacts closer to the catalytic groups of the enzyme, such as with Lys 151.     

水环境下氢氧根水分子簇催化缬氨酸旋光异构及羟自由基致其损伤机理

基于MP2/6-311++G(2df,pd)//B3LYP/6-31+G(d,p)双理论水平, 用自洽反应场(SCRF)理论的SMD模型方法, 考察水环境下氢氧根水分子簇催化缬氨酸旋光异构及羟自由基致其损伤机理. 结果表明： 缬氨酸的旋光异构可在2个通道a和b实现, 通道a为氢氧根水分子簇与α-H和氨基通过氢键作用形成底物, 氢氧根抽取α-H后, α-C在另一侧抽取水分子的H; 通道b为氢氧根水分子簇与α-H和羰基通过氢键作用形成底物, 氢氧根抽取α-H后, α-C在另一侧抽取水分子的H, 通道b中的水分子辅助羟自由基抽取α-H可致缬氨酸损伤; 水液相环境下, 构象Val-1（氨基羧基间为单氢键）和构象Val-2（氨基羧基间为双氢键）在通道a旋光异构的决速步骤能垒分别为60.57,65.24 kJ/mol, 在通道b旋光异构的决速步骤能垒分别为56.76,64.11 kJ/mol, 羟自由基水分子簇致缬氨酸在通道b的损伤为温和的放热反应.     

嗜热酯酶EstTs1的远源三维结构模建及分子对接

利用Phyre网络服务器,构建嗜热酯酶EstTs1的三维结构,并通过分子动力学优化构型,得到了可靠的构型.分子对接研究表明,p-硝基苯基丁酸酯是EstTs1的最适底物,其大小正适合EstTs1的活性口袋.Thr111是底物与酶结合的重要残基,与底物形成了氢键; Ser85是重要的催化残基.     

Dimerization inhibits the activity of receptor-like protein-tyrosine phosphatase-alpha.

Protein-tyrosine phosphatases (PTPs) are vital for regulating tryosine phosphorylation in many processes, including growth and differentiation. The regulation of receptor-like PTP (RPTP) activity remains poorly understood, but based on the crystal structure of RPTPalpha domain 1 we have proposed that dimerization can negatively regulate activity, through the interaction of an inhibitory 'wedge' on one monomer with the catalytic cleft of domain 1 in the other monomer. Here we show that dimerization inhibits the activity of a full-length RPTP in vivo. We generated stable disulphide-bonded full-length RPTPalpha homodimers by expressing mutants with single cysteines at different positions in the ectodomain juxtamembrane region. Expression of wild-type RPTPalpha and Phe135Cys and Thr141Cys mutants in RPTPalpha-null mouse embryo cells increased dephosphorylation and activity of Tyr 529 in the protein tyrosine kinase c-Src; in contrast, expression of a Pro137Cys mutant did not. Mutation of Pro 210/211 to leucine in the inhibitory wedge of the Pro137Cys mutant restored its ability to activate c-Src, indicating that dimerization may inhibit full-length RPTPalpha activity in a manner stereochemically consistent with RPTPalpha crystal structures. Our results suggest that RPTPalpha activity can in principle be negatively regulated by dimerization in vivo.     

HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response

Minutes after DNA damage, the variant histone H2AX is phosphorylated by protein kinases of the phosphoinositide kinase family, including ATM, ATR or DNA-PK. Phosphorylated (gamma)-H2AX-which recruits molecules that sense or signal the presence of DNA breaks, activating the response that leads to repair-is the earliest known marker of chromosomal DNA breakage. Here we identify a dynamic change in chromatin that promotes H2AX phosphorylation in mammalian cells. DNA breaks swiftly mobilize heterochromatin protein 1 (HP1)-beta (also called CBX1), a chromatin factor bound to histone H3 methylated on lysine 9 (H3K9me). Local changes in histone-tail modifications are not apparent. Instead, phosphorylation of HP1-beta on amino acid Thr 51 accompanies mobilization, releasing HP1-beta from chromatin by disrupting hydrogen bonds that fold its chromodomain around H3K9me. Inhibition of casein kinase 2 (CK2), an enzyme implicated in DNA damage sensing and repair, suppresses Thr 51 phosphorylation and HP1-beta mobilization in living cells. CK2 inhibition, or a constitutively chromatin-bound HP1-beta mutant, diminishes H2AX phosphorylation. Our findings reveal an unrecognized signalling cascade that helps to initiate the DNA damage response, altering chromatin by modifying a histone-code mediator protein, HP1, but not the code itself.     

Dissecting the catalytic triad of a serine protease

Serine proteases are present in virtually all organisms and function both inside and outside the cell; they exist as two families, the 'trypsin-like' and the 'subtilisin-like', that have independently evolved a similar catalytic device characterized by the Ser, His, Asp triad, an oxyanion binding site, and possibly other determinants that stabilize the transition state (Fig. 1). For Bacillus amyloliquefaciens subtilisin, these functional elements impart a total rate enhancement of at least 10(9) to 10(10) times the non-enzymatic hydrolysis of amide bonds. We have examined the catalytic importance and interplay between residues within the catalytic triad by individual or multiple replacement with alanine(s), using site-directed mutagenesis of the cloned B. amyloliquefaciens subtilisin gene. Alanine substitutions were chosen to minimize unfavourable steric contacts and to avoid imposing new charge interactions or hydrogen bonds from the substituted side chains. In contrast to the effect of mutations in residues involved in substrate binding, the mutations in the catalytic triad greatly reduce the turnover number and cause only minor effects on the Michaelis constant. Kinetic analyses of the multiple mutants demonstrate that the residues within the triad interact synergistically to accelerate amide bond hydrolysis by a factor of approximately 2 X 10(6).     

马铃薯贮藏蛋白Patatin及其突变体分子动力学和分子对接的研究

马铃薯贮藏蛋白Patatin具有水解脂肪的能力,且特定位点的突变能够影响Patatin的水解酶活性.Patatin的水解酶活性中心是由Ser77和Asp215组成,首先采用分子动力学方法研究Patatin及其突变体的稳定性和构象变化,通过结构比对没有发现构象规律性的变化,然后采用分子对接方法,发现了两个基团(Patatin及其突变体活性位点Ser77的羟基与底物p-硝基苯基癸酯的酯键)间的距离具有规律性:即H109A和D182A(活性减弱)两个基团之间的距离偏大,而R368A,E140A,H109N(活性增强)两个基团之间的距离偏小,符合之前的生化数据.这说明Ser77的羟基与底物PNPC10的酯键间的距离可能能够影响底物小分子与Patatin蛋白的结合,从而影响Patatin酯酶的活性.同时,根据细胞内溶质磷脂酶A2(cPLA2)反应过程,我们推测了Patatin与底物之间可能的催化机制.     

苏氨酸分子的构象转变及水分子与羟基自由基的催化机理

采用密度泛函理论的B3LYP方法和微扰论的MP2方法, 研究苏氨酸分子构象转变机制以及水分子与羟基自由基对氢迁移反应的催化作用. 结果表明： S-苏氨酸向R 别苏氨酸的构象转变反应有4个通道, R-别苏氨酸向R-苏氨酸与S-苏氨酸向S-别苏氨酸的构象转变反应各有1个通道; S-苏氨酸向R-别苏氨酸构象转变反应的最高能垒为250.2 kJ/mol; R-别苏氨酸向R-苏氨酸构象转变反应的最高能垒为335.0 kJ/mol; S-苏氨酸向S-别苏氨酸构象转变反应的最高能垒为359.6 kJ/mol; 2个水分子构成的链及水分子/羟基自由基构成的链对质子迁移反应有较好的催化作用, 使S-苏氨酸向R-别苏氨酸构象转变反应的高能垒分别降为128.3 kJ/mol和108.6 kJ/mol.     

黄酮类化合物抗氧化活性理论研究

运用密度泛函理论(DFT)B3LYP方法对柯因、高良姜素、山奈酚、桑色素、槲皮素及杨梅酮这6种典型黄酮类化合物进行结构优化及单点能计算,来研究这6种化合物的抗氧化活性.本文从化合物失去最大可能活性位H原子形成半醌式自由基前后的生成热之差(⊿HOF)、失去酚羟基H原子形成的自由基的原子自旋密度、化合物分子中酚羟基数目及形成的半醌式自由基中可形成氢键数目3个方面进行分析.发现这6种黄酮类化合物的抗氧化活性顺序为:杨梅酮>槲皮素>桑色素>山奈酚>高良姜素>柯因.此外,还探讨了化合物的几何构型及最高占据轨道与抗氧化活性间是否存在关联,结果表明它们之间无相关性.     

Location of high affinity Ca2+-binding sites within the predicted transmembrane domain of the sarcoplasmic reticulum Ca2+-ATPase

Cation pumps bind and translocate ions with the intermediate formation of a phosphoenzyme. In spite of extensive knowledge of the primary and even secondary structures of several of these cation transport enzymes, however, no high affinity cation binding sites have yet been determined. Here we report the use of oligonucleotide-directed, site-specific mutagenesis to identify the amino acids involved in Ca2+ binding in one of these transport enzymes, the Ca2+-ATPase of sarcoplasmic reticulum. Alteration of Glu 309, Glu 771, Asn 796, Thr 799, Asp 800 or Glu 908, each of which is predicted to lie near the centre of the transmembrane domain in putative transmembrane sequences M4, M5, M6 and M8 resulted in complete loss of Ca2+ transport function and of Ca2+-dependent phosphorylation of the enzyme by ATP. Phosphorylation of each of the mutant enzymes with inorganic phosphate was observed, however, even in the presence of Ca2+, which inhibits phosphorylation in the wild-type enzyme possessing an intact high affinity Ca2+-binding site. These results suggest that at least six polar, oxygen-containing residues lying near the centre of the transmembrane domain provide ligands for one or both of the two high affinity Ca2+ binding sites in the Ca2+-ATPase.     

基于分子对接研究吲哚咔唑类小分子对Tie-2/VEGFR2的双效抑制作用模式*

 运用分子对接技术研究了吲哚咔唑类小分子对人血管内皮生长因子受体2(VEGFR2)和人血管生成素受体Tie-2(ANG-R-Tie-2)的双效抑制作用模式。研究结果表明,吲哚咔唑类小分子的双效抑制作用主要源于两种受体相似的活性口袋,小分子与两者的铰链区均可形成氢键,使其催化活性受到抑制,从而抑制肿瘤细胞的生长。抑制活性的差异主要源于活性口袋的细微差异所导致疏水、静电等相互作用的不同。其中,疏水作用的差异是影响配体选择性的主要原因,静电作用、氢键及空间位阻对结合稳定也有一定影响。该文的研究结果为多靶点酪氨酸激酶小分子抑制剂的设计及提高激酶抑制剂的选择性提供了重要的理论依据。     

Molecular dynamics simulation of the deposition process of hydrogenated diamond-like carbon （DLC） films

The deposition process of hydrogenated diamond-like carbon （DLC） film greatly affects its frictional properties. In this study, CH3 radicals are selected as source species to deposit hydrogenated DLC films for molecular dynamics simulation. The growth and structural properties of hydrogenated DLC films are investigated and elucidated in detail. By comparison and statistical analysis, the authors find that the ratio of carbon to hydrogen in the films generally shows a monotonously increasing trend with the increase of impact energy. Carbon atoms are more reactive during deposition and more liable to bond with substrate atoms than hydrogen atoms. In addition, there exists a peak value of the number of hydrogen atoms deposited in hydrogenated DLC films. The trends of the variation are opposite on the two sides of this peak point, and it becomes stable when impact energy is greater than 80 eV. The average relative density also indicates a rising trend along with the increment of impact energy, while it does not reach the saturation value until impact energy comes to 50 eV. The hydrogen content in source species is a key factor to determine the hydrogen content in hydrogenated DLC films. When the hydrogen content in source species is high, the hydrogen content in hydrogenated DLC films is accordingly high.     

1MAS NMR spectra of kao linite/formamide intercalation compound

The high spinning speed 1H magic angle spinning nuclear magnetic resonance (1H MAS NMR) technique was employed to distinguish the two groups of surface hydroxyls of kaolinite and investigate the intercalation mechanism of kaolinite/formamide compound. The proton chemical shifts of the inner hydroxyl and inner surface hydroxyl of kaolinte are in the range of δ-1.3-0.9 and δ 2.4-3.0 respectively. After formamide intercalation three proton peaks were detected. The proton peak of the inner surface hydroxyls of the intercalation compound shifts to high-field with δ 2.3-2.7, which is assigned to the formation of the hydrogen bond between the inner surface hydroxyl and formamide carbonyl group. Whereas, the proton peak of the inner hydroxyl shifts to δ-0.3 toward low-field, that is attributed to van der Waal's effect between the inner hydroxyl proton and the amino group proton of the formamide which may be keyed into the ditrigonal hole of the kaolinite. The third peak, additional proton peak, is in the range of δ5.4-5.6, that is ascribed to the hydrogen bond formation between the amino group proton of formimide and SiO4 tetrahedral oxygen of the kaolinite.     

环糊精水解酶cds1-3底物通道氨基酸的定点突变研究

本研究对具有大分子水解能力的环糊精水解酶cds1-3的蛋白结构进行分析,选取底物通道相关氨基酸进行定点突变。通过比较突变酶和野生酶的功能差异,定位决定cds1-3特殊功能的氨基酸。采用sybyl 1.2进行蛋白质底物结合分析,选取和多聚体形成、底物结合以及底物通道相关的氨基酸Glu66、Pro48、Phe289为突变位点,反向PCR构建pSE380/E66G、pSE380/P48H、pSE380/F289A表达质粒并进行表达,获得酶活突变体并与原始酶进行底物特异性比较分析。其结果显示,突变酶E66G降解大分子底物木薯淀粉和支链淀粉的相对酶活力分别提高26.96%和23.15%,而对小分子底物普鲁兰糖的水解能力下降13.14%。因此,cds1-3是一个能水解大分子底物的特殊环糊精水解酶,氨基酸Glu66是cds1-3水解大分子支链淀粉的关键氨基酸之一。     

Cis-trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel

5-hydroxytryptamine type 3 (5-HT3) receptors are members of the Cys-loop receptor superfamily. Neurotransmitter binding in these proteins triggers the opening (gating) of an ion channel by means of an as-yet-uncharacterized conformational change. Here we show that a specific proline (Pro 8*), located at the apex of the loop between the second and third transmembrane helices (M2-M3), can link binding to gating through a cis-trans isomerization of the protein backbone. Using unnatural amino acid mutagenesis, a series of proline analogues with varying preference for the cis conformer was incorporated at the 8* position. Proline analogues that strongly favour the trans conformer produced non-functional channels. Among the functional mutants there was a strong correlation between the intrinsic cis-trans energy gap of the proline analogue and the activation of the channel, suggesting that cis-trans isomerization of this single proline provides the switch that interconverts the open and closed states of the channel. Consistent with this proposal, nuclear magnetic resonance studies on an M2-M3 loop peptide reveal two distinct, structured forms. Our results thus confirm the structure of the M2-M3 loop and the critical role of Pro 8* in the 5-HT3 receptor. In addition, they suggest that a molecular rearrangement at Pro 8* is the structural mechanism that opens the receptor pore.     

Capping and alpha-helix stability

The first and last four residues of alpha-helices differ from the rest by not being able to make the intrehelical hydrogen bonds between the backbone greater than C=O groups of one turn and the greater than NH groups of the next. Physico-chemical arguments and statistical analysis suggest that there is a preference for certain residues at the C and N termini (The C- and N-caps) that can fulfil the hydrogen bonding requirements. We have tested this hypothesis by constructing a series of mutations in the two N-caps of barnase (Bacillus amyloliquefaciens ribonuclease, positions Thr 6 and Thr 26) and determining the change in their stability. The N-cap is found to stabilize the protein by up to approximately 2.5 kcal mol(-1). The presence of a negative charge of the N-cap adds some 1.6 kcal mol(-1) of stabilization energy because of the interaction with the macroscopic electrostatic dipole of the helix.     

可卡因与其降解抗体15A10的分子对接及分子动力学研究

可卡因是一种精神依赖性药物．它首先作用于大脑皮层使之兴奋,然后由过度兴奋转为抑制,可卡因最重要的作用是对中枢系统的刺激作用,可卡因中毒后,先是感到欣快,随后会出现情绪不安、恶心、呕吐等症状．严重者出现脉搏增快、血压增高和呼吸加快,可引起高血压及其各种合并症,导致室性纤颤、呼吸和循环系统衰竭而死亡。显然,发展一种合适的抑制剂去治疗可卡因的滥用和上瘾是十分困难的,因为可卡因本身就是一个抑制剂,这意味着要用一个毒性更高的抑制剂去抑制可卡因的作用,既然很难在中枢神经系统中设置一个阻碍可卡因的小分子,我们可以考虑在可卡因到达中枢神经系统之前将之降解,