磷酸化对多肽中Xaa-Pro片段肽脯酰胺键顺反异构的影响研究

多肽和蛋白质中Xaa-Pro片段肽脯酰胺键顺反异构对其构象与功能有重要影响.设计合成了一系列模型多肽及其磷酸化多肽,并采用核磁共振实验和分子动力学模拟的方法,研究了所合成多肽中肽脯酰胺键的顺反异构化.结果表明,对脯氨酸之前的Xaa残基进行侧链O-磷酸化会极大地影响该顺反异构化过程,进而调节肽链构象.此外,磷酸化使得多肽顺式构象比例增加,且当磷酸基团不带负电荷时顺式构象所占比例最大.同时,分子动力学模拟所得结果与核磁共振实验相一致,包括最稳定构象和顺反构象统计分布.磷酸基团所带电荷及其空间位阻可能是影响这类磷酸化多肽构象变化的主要因素.     

Kinetic β-deuterium isotope effects suggest a covalent mechanism for the protein folding enzyme peptidylprolyl cis/trans-isomerase

The cis/trans interconversion of Glt-Ala-Ala-Pro-Phe-4-nitroanilide and Glt-Ala-Gly-Pro-Phe-4-nitroanilide was studied both enzymatically and nonenzymatically by measuring kinetic β-deuterium isotope effects. The hydrogen atom at the α-carbon atom of the Xaa residue within the Xaa-Pro moiety was substituted by deuterium. In the nonenzymatic case the transition state of rotation is reflected by k_H/k_D > 1. When catalysed by 17 kDa PPIase the same bond rotation is characterized by k_H/k_D < 1. This suggests a covalent mechanism of catalysis which involves an approximately tetravalent carbon of the prolyl imidic bond for the transition state of reaction.     

The conserved P1' Ser of Bowman-Birk-type proteinase inhibitors is not essential for the integrity of the reactive site loop

The isolated reactive site beta-hairpin loop of Bowman-Birk-type proteinase inhibitors has become a widely studied proteinomimetic because it retains the three-dimensional structure and much of the inhibitory potency of the corresponding region of the complete protein. Here we analyse the role of the P1' Ser residue which is highly conserved and intramolecularly hydrogen bonded in the complete proteins. A combined kinetic and structural analysis of variant proteinomimetic peptides demonstrates that the hydrogen-bond potential of the side-chain oxygen atom of the P1' Ser is not essential for the integrity of the reactive site loop and that it provides only a small contribution to the trypsin affinity and no apparent contribution to the stability against tryptic turnover. We conclude that the potential of the P1' side chain to engineer improved inhibition and selectivity for serine proteinases is best explored further in concert with the side chains of the P2 and P5' residues which may interact or compete for the same space.     

Molecular evolution of the genes encoding receptor tyrosine kinase with immunoglobulinlike domains

Receptor tyrosine kinases (RTK) with five, three, or seven immunoglobulinlike domains in their extracellular regions are classified as subclasses III, IV, and V, respectively. Conservation of the exon/intron structure of the downstream part of the human KIT, FMS, and FLT3 genes that encode RTK of subclass III together with the particular chromosomal localization of these genes suggests that RTKIII genes have evolved from a common ancestor by cis and trans duplications. To strengthen this model of evolution and to determine if it can be extended to RTKIV and V genes, we constructed a phylogenetic tree of RTKIII, IV, and V on the basis of a multiple alignment of their catalytic tyrosine kinase domain sequences and determined the exon/intron structure of PDGFRA (subclass III), FGFR4 (subclass IV), and FLT4 (subclass V) genes in their downstream part. Phylogenetic analyses with amino acid or nucleotide sequences both resulted in one most parsimonious tree. The phylogenetic trees obtained indicate that all three subclasses are well individuated and that RTKIII and RTKV are closer to each other than RTKIV. Furthermore, RTKIII and FLT4 (subclass V) genes possess the same exon/intron structure in their downstream part while the structure of the RTKIV genes is very similar to that of RTKIII and FLT4. Both approaches are in complete agreement and indicate that RTKIII, IV, and V genes most probably evolved from a common ancestor already in pieces by successive duplications involving entire genes.Correspondence to: F. Agnès     

Effect of the SH Group of Myelopeptide MP-3 on Its Macrophage Stimulating Activity

Peptide Leu-Val-Cys-Tyr-Pro-Gln, identical to the bone marrow peptide MP-3, and its Val³and Ser³analogs, lacking SH group, were synthesized by conventional methods of peptide chemistry in solution and, along with the MP-3 S–S-dimerization product, were studied with respect to their effect on the macrophage phagocytic activity. It was shown that the activity was only enhanced by peptide MP-3, which demonstrated the essential role of the SH group in this function. The dimer analog of MP-3, unlike dimer analogs of other monocycteine-containing peptides, glutathione and HP5b, did not exhibit the inhibitory effect.     

Negative regulation by Ser/Thr phosphorylation of HadAB and HadBC dehydratases from Mycobacterium tuberculosis type II fatty acid synthase system

The type II fatty acid synthase system of mycobacteria is involved in the biosynthesis of major and essential lipids, mycolic acids, key-factors of Mycobacterium tuberculosis pathogenicity. One reason of the remarkable survival ability of M. tuberculosis in infected hosts is partly related to the presence of cell wall-associated mycolic acids. Despite their importance, the mechanisms that modulate synthesis of these lipids in response to environmental changes are unknown. We demonstrate here that HadAB and HadBC dehydratases of this system are phosphorylated by Ser/Thr protein kinases, which negatively affects their enzymatic activity. The phosphorylation of HadAB/BC is growth phase-dependent, suggesting that it represents a mechanism by which mycobacteria might tightly control mycolic acid biosynthesis under non-replicating condition.     

Conformation of the transmembrane domain of the c-erbB-2 oncogene-encoded protein in its monomeric and dimeric states

The human c-erbB-2 oncogene is homologous to the ratneu oncogene, both encoding transmembrane growth factor receptors. Overexpression and point mutations in the transmembrane domain of the encoded proteins in both cases have been implicated in cell transformation and carcinogenesis. In the case of theneu protein, it has been proposed that these effects are mediated by conformational preferences for an-helix in the transmembrane domain, which facilitates receptor dimerization, an important step in the signal transduction process. To examine whether this is the case for c-erbB-2 as well, we have used conformational energy analysis to determine the preferred three-dimensional structures for the transmembrane domain of the c-erbB-2 protein from residues 650 to 668 with Val (nontransforming) and Glu (transforming) at position 659. The global minimum energy conformation for the Val-659 peptide from the normal, nontransforming protein was found to contain several bends, whereas the global minimum energy conformation for Glu-659 peptide from the mutant, transforming protein was found to be-helical. Thus, the difference in conformational preferences for these transmembrane domains may explain the difference in transforming ability of these proteins. The presence of higher-energy-helical conformations for the transmembrane domain from the normal Val-659 protein may provide an explanation for the presence of a transforming effect from overexpression of c-erbB-2. In addition, docking of the oncogenic sequences in their-helical and bend conformations shows that the all--helical dimer is clearly favored energetically over the bend dimer.     

外源水杨酸对盐胁迫下小桐子幼苗脯氨酸代谢的影响

以小桐子幼苗为材料,设置盐胁迫(200mmol·L-1 NaCl)和外源水杨酸处理(0~2.0mmol·L-1 SA)水培试验,通过检测幼苗叶片脯氨酸含量、脯氨酸代谢关键酶活性及相关代谢酶基因的表达水平,研究了外源水杨酸对盐胁迫下小桐子幼苗脯氨酸代谢机理的影响。结果显示:(1)外源0.9mmol·L-1 SA处理可显著提高盐胁迫下小桐子幼苗的脯氨酸含量,上调脯氨酸合成关键酶Δ1-吡咯琳-5-羧酸合成酶(P5CS)和鸟氨酸转氨酶(OAT)活性,以及上调JcP5CS和JcOAT基因的表达水平。(2)SA也显著抑制了脯氨酸降解酶ProDH的活性及JcProDH基因的表达水平。(3)SA处理还显著提高了盐胁迫下小桐子幼苗的组织活力,降低了叶片电解质渗漏率和丙二醛(MDA)含量。研究发现,外源SA可通过活化脯氨酸合成的谷氨酸途径和鸟氨酸途径,以及抑制脯氨酸的降解途径来促进盐胁迫下小桐子幼苗脯氨酸的积累;外源SA处理也可提高小桐子幼苗的耐盐性,且这种提高可能与SA诱导脯氨酸的积累密切相关。     

Effect of Different Carbon and Nitrogen Sources on Clostridium argentinense Toxigenicity in Coculture withPseudomonas mendocina

The effect of different carbon and nitrogen sources on the production of toxin by Clostridium argentinense was examined. The toxin production by C. argentinense in coculture with Pseudomonas mendocina increased in all the cases in relation to that produced by monocultures independent of the nature of the source. Using dextrin as carbon source C. argentinense produced the highest levels of toxin both in monocultures (300 LD₅₀/mL) and in cocultures with P. mendocina (5000 LD₅₀/mL). Experiments run in a microfermenter showed that the slow growth of cocultures associated with the assimilation of dextrin and the pH and Eh profiles favoured the production of toxin. Of the nitrogen sources assayed, corn steep liquor sustained the highest levels of toxin in both monocultures and cocultures with 3 and 2.8 fold increases with respect to that obtained using proteose peptone. The toxin production by C. argentinense cultures and C. argentinense–P. mendocina cocultures was highly dependent on the nature of the carbon and nitrogen sources used in the culture media. Growth of C. argentinense on substrates slowly assimilated stimulated the production of toxin.     

Effect of supplementation with exogenous fatty acid on the biological properties of a fatty acid requiring auxotroph ofSalmonella typhimurium

The effects of changes in fatty acid composition of the cell membrane on different biological functions ofSalmonella typhimurium have been studied with the help of a temperature sensitive fatty acid auxotroph which cannot synthesise unsaturated fatty acids at high temperature. On being shifted to nonpermissive temperature the cells continue growing for another one and half to two generations. The rates of protein and DNA syntheses run parallel to the growth rate but the rate of RNA synthesis is reduced. Further, there is a gradual reduction in the rate of transport of exogenous uridine and thymidine into the soluble pool. The transport process can be restored by supplementing the growth medium with cis-unsaturated fatty acids but not trans-unsaturated ones although the growth of the cells is resumed by supplementation with eithercis or trans-unsaturated fatty acids. However, supplementation withtrans, trans-unsaturated fatty acids leads to only partial recovery of the transport process. The rate of oxygen uptake is also affected in cells grown in the presence of thetrans-unsaturated fatty acids, elaidic acid and palmitelaidic acid. Analysis of cells grown under different fatty acid supplementation indicate that fatty acid composition of the cell membrane, especially the ratio of unsaturated to saturated fatty acids varies with temperature shift and supplementation of the growth media with fatty acids.     

Cis-trans isomerization of the Epstein-Barr virus determinant peptide EENLLDFVRF after the DM1 TCR recognition of the HLA-B*4405/peptide complex

The Epstein–Barr virus determinant peptide EENLLDFVRF shows high immunogenicity when presented by HLA-B*4405 allotype. This fact is accompanied by a cis–trans isomerization of the Leu5-Asp6 peptide bond upon TCR binding of the pMHC complex. Molecular dynamics simulations of pMHC/TCR structures, with the EENLLDFVRF peptide in cis and trans conformations have been employed in order to examine the structure and dynamics of the pMHC complex with such an unusual conformation. The results, based on MM-PBSA free energy computations as well as buried surface area analysis and interactions at the pMHC/TCR interface, indicate that the TCR binds preferably the pMHC complex with the Leu5-Asp6 peptide bond in cis conformation. It is the first time that this notable conformational feature of T-cell epitope is investigated.     

The contribution of proline residues to protein stability is associated with isomerization equilibrium in both unfolded and folded states

It has long been understood that the proline residue has lower configurational entropy than any other amino acid residue due to pyrrolidine ring hindrance. The peptide bond between proline and its preceding amino acid (Xaa-Pro) typically exists as a mixture of cis- and trans-isomers in the unfolded protein. Cis–trans isomerization of Xaa-Pro peptide bonds are infrequent, but still occur in folded proteins. Therefore, the effects of the cis–trans isomerization equilibrium in both unfolded and folded states should be taken into account when estimating the stability contribution of a specific proline residue. In order to study the stability contribution of the four proline residues to the hyperthermophilic protein Ssh10b, in this work, we expressed and purified a series of Pro→Ala mutants of Ssh10b, and performed correlative unfolding experiments in detail. We proposed a new unfolding model including proline isomerization. The model predicts that the contribution of a proline residue to protein stability is associated with the thermodynamic equilibrium between cis- and trans-isomers both in the unfolded and folded states, agreeing well with the experimental results.     

不同光质对红花檵木愈伤组织生长及黄酮类物质含量的影响

该试验以红花檵木叶片诱导的愈伤组织为试验材料,以黑暗(CK)为对照,分别进行白光(W)、红光(R)、蓝光(B)、蓝紫光(BP)、蓝光+UV-A(B+UV A)和UV-A处理15d和30 d,通过对愈伤组织的生长、生理指标、花色素苷和总黄酮含量的比较分析,探讨光质对红花檵木愈伤组织生长和黄酮类物质含量的影响.结果 显示:...     

The Effect of Ser 128 Substitution on the Structure and Stability of cAMP Receptor Protein from Escherichia coli

Kinetic measurements of denaturation and renaturation of two mutants of cAMP receptor protein (CRP) at position 128, namely SerAla and SerPro, were performed in order to assess changes introduced by the mutation in the quaternary structure and protein stability. No significant changes were found in the unfolding/refolding reactions. However, small perturbations in the dissociation of CRP dimer can be seen, which indicate that subunit interactions are influenced by the mutation. Studies of intrinsic fluorescence quenching of these two mutants are also reported, showing changes compared with wild-type protein. Near-UV circular dichroism measurements indicate, however, that Trp residues remain in the same environment as in the wild-type CRP. It is proposed that Ser at position 128 is involved in maintaining the proper domain alignment within CRP subunits.     

基于LC-MS/MS分析马缨杜鹃花代谢物的变化

为分析马缨杜鹃(Rhododendron delavayi)花开花至凋谢过程中的代谢产物差异及其通路,该文采用LC-MS/MS技术对其花苞期、开裂期、传粉期、盛开期、衰老期和凋谢期的化学成分进行非靶向代谢组学分析。结果表明:(1)共鉴定到973种代谢物,主要包含黄酮类、有机酸、酚酸类、氨基酸及其衍生物、脂类、生物碱等。(2)主成分分析(PCA)表明样本间代谢物存在差异,结合正交偏最小二乘判别分析(OPLS-DA)、t检验的P值和单变量分析的差异倍数(fold-change)筛选差异代谢物(VIP>1,P<0.05,Fc>2或Fc<0.5),涉及591种,在马缨杜鹃花期进入衰老期和凋谢期后差异代谢物数量和表达量显著上升,其中花苞期至开裂期差异代谢物的表达主要呈现下调,而进入衰老期和凋谢期后差异代谢物的表达主要呈现上调。(3)KEGG注释到68条代谢通路,其中差异代谢物极显著富集(P < 0.01)通路3条,包括苯丙素类生物合成、植物激素的生物合成和类黄酮生物合成。(4)结合苯丙素类、黄酮类等有效成分生物合成通路共筛选到10种代谢物包括苯丙氨酸(L-phenylalanine)、反式肉桂酸(trans-cinnamic acid)、查耳酮(chalcone)、柚皮素(naringenin)、对香豆酰基莽草酸(p-coumaroyl shikimic acid)、阿魏酸(ferulic acid)、松柏醇(coniferyl alcohol)、芥子酸(sinapic acid)、紫丁香苷(syringin)、槲皮素(quercetin)。此外,有效成分的差异代谢物表明苯丙素类生物合成代谢活动随马缨杜鹃花的发育逐渐增强,而黄酮类化合物生物合成逐渐减弱,这些关键差异代谢物可能对马缨杜鹃花的发育有重要的调控作用。该研究为马缨杜鹃花开花至凋谢进程中的有效成分代谢途径活性物质的研究提供了代谢组学基础,为进一步研究马缨杜鹃花花期调控的分子机理提供参考。     

施氮及不同根系分隔模式对尾叶桉和降香黄檀幼苗生长及叶片生理特性的影响

豆科与非豆科树种混交作为一种人工林培育可持续发展模式,在保证木材产量和维持氮素平衡中发挥了重要作用。该研究通过大棚盆栽试验,设计3个施氮水平(0、3、6g·株-1)及3种根系分隔方式(不隔、网隔、膜隔),分析了不同氮素水平及根系分隔模式对尾叶桉(Eucalyptus urophylla)与降香黄檀(Dalbergia odorifera)植株幼苗生长、叶片生理特性、根系形态及生物量的影响。结果表明:(1)随施氮量的增加,尾叶桉与降香黄檀的苗高、地径均呈递增趋势;不同根系分隔模式下,尾叶桉苗高、地径均在不隔模式下生长最好,降香黄檀则在膜隔模式下生长最好。(2)与不施氮处理相比,施氮3、6g·株-1水平下尾叶桉与降香黄檀叶片的超氧化物歧化酶(SOD)活性、过氧化物酶(POD)活性及可溶性蛋白含量均显著升高,而丙二醛(MDA)含量则呈降低趋势。(3)尾叶桉与降香黄檀根系的总长度、总表面积、总体积、平均直径、根尖数和比根长均随氮素水平的增加而增加,且各氮素水平间的差异显著;同一氮素水平下,尾叶桉的根系生长总体表现为不隔网隔膜隔,而降香黄檀根系生长则表现为膜隔不隔网隔,且两树种不同分隔模式间差异显著。(4)尾叶桉与降香黄檀各器官生物量及总生物量均随施氮量的增加而增加,并在6g·株-1施氮水平下生物量最大;各器官生物量分配中,尾叶桉各器官生物量所占比例大小依次为:茎(40.59%)叶(32.37%)根(27.04%),降香黄檀各器官生物量所占比例大小依次为:根(47.67%)茎(40.08%)叶(12.25%)。研究表明,尾叶桉与降香黄檀混交一定程度上扩展了根系横向和纵向水平的养分生态位,扩大了根系吸收土壤养分的空间,同时根系互作提高了降香黄檀的固氮能力,对土壤有效氮的产生有较大影响。     

Effect of Didymella applanata (Niessl/Sacc.) on proline and hydroxyproline containing cell wall proteins of red raspberry

Structural cell wall proteins and their immobilisation through formation of covalent cross-links belong to important defense response mechanisms. In this work, the D. applanata — induced increase of wall-bound proline and hydroxyproline contents were associated with red raspberry resistance. The effect did not depend on the developmental stage and lignification degree of infected primocanes. Pathogen-induced accumulation of hydroxyproline noted in susceptible plants suggested the post-translational hydroxylation of proline-rich proteins and/or may be of other wall proteins. Moreover, the developmentally related increase of hydroxyproline content was associated with the resistance acquirement noted at the end of the summer period. The increase of cell wall structural protein levels was accompanied by free proline accumulation in the cytosol fraction.     

Effect of DNA Local Conformation on the Affinity and Binding Specificity of bis-Netropsins to DNA

The interaction of short nucleotide duplexes with bis-netropsins, in which netropsin fragments are linked tail-to-tail via cis-diammineplatinum group (Nt–Pt(NH ₃ )–Nt) or aliphatic pentamethylene chain (Nt–(CH ₂ ) ₅ –Nt), has been studied. Both bis-netropsins have been shown to bind to DNA oligomer 5"-CCTATATCC-3" (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5"-CCXCC-3" [where X = TTATT (II), TTAT (III), TTTTT (IV), and AATTT (V)] along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of Nt–(CH ₂ ) ₅ –Nt with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin ( ₂) to monodentate binding constant ( ₁) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for Nt–Pt(NH ₃ )–Nt and Nt–(CH ₂ ) ₅ –Nt binding as a hairpin has been found to be DNA duplex 5"-CGTATACG-3".