Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog

The crystal structure of the yeast SLN1 response regulator (RR) domain bound to both a phosphoryl analog [beryllium fluoride (BeF₃ ⁻)] and Mg^2 +, in complex with its downstream phosphorelay signaling partner YPD1, has been determined at a resolution of 1.70 Å. Comparisons between the BeF₃ ⁻-activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1·Mg^2 +·BeF₃ ⁻ structure from the complex provides evidence for the first time that the mechanism of phosphorylation-induced activation is highly conserved between bacterial RR domains and this example from a eukaryotic organism. Residues in and around the active site undergo slight rearrangements in order to form bonds with the essential divalent cation and fluorine atoms of BeF₃ ⁻. Two conserved switch-like residues (Thr1173 and Phe1192) occupy distinctly different positions in the apo versus BeF₃ ⁻-bound structures, consistent with the “Y-T” coupling mechanism proposed for the activation of CheY and other bacterial RRs. Several loop regions and the α4-β5-α5 surface of the SLN1-R1 domain undergo subtle conformational changes (∼ 1-3 Å displacements relative to the apo structure) that lead to significant changes in terms of contacts that are formed with YPD1. Detailed structural comparisons of protein-protein interactions in the apo and BeF₃ ⁻-bound complexes suggest at least a two-state equilibrium model for the formation of a transient encounter complex, in which phosphorylation of the RR promotes the formation of a phosphotransfer-competent complex. In the BeF₃ ⁻-activated complex, the position of His64 from YPD1 needs to be within ideal distance of and in near-linear geometry with Asp1144 from the SLN1-R1 domain for phosphotransfer to occur. The ground-state structure presented here suggests that phosphoryl transfer will likely proceed through an associative mechanism involving the formation of a pentacoordinate phosphorus intermediate.     

脆性组氨酸三联体与复制蛋白A相互作用关键氨基酸残基的鉴定

目的：研究脆性组氨酸三联体（Fhit）对ATR/CHK1通路的影响,在确定Fhit与复制蛋白A（RPA）存在相互作用的基础上鉴定Fhit与RPA相互作用的关键氨基酸残基,为进一步研究Fhit特异的信号通路奠定基础。方法：构建一系列Fhit缺失突变体基因Fhit1～Fhit11及6种Fhit点突变体基因,将这些基因插入含GST基因的原核表达载体中,在大肠杆菌中表达并纯化GST-Fhit1～GST-Fhit11融合蛋白、突变体GST-FhitSIYEEL、GST-FhitIY、GST-FhitEL、GST-FhitF、GST-FhitA,以及GST-FhitD融合蛋白,用GST沉降技术研究Fhit与RPA相互作用的关键氨基酸残基。结果：Fhit蛋白第112～117（SIYEEL）残基可能是Fhit与RPA相互作用的关键区域,而第114（Y）残基可能是Fhit与RPA相互作用的关键氨基酸残基。结论：确定了Fhit与RPA相互作用的关键氨基酸残基,为阐明Fhit在维持基因组完整性方面的机理提供了线索。     

Leishmania infantum: prime boost vaccination with C-terminal extension of cysteine proteinase type I displays both type 1 and 2 immune signatures in BALB/c mice

The aims of current study are to describe the immunogenicity and protective efficacy of prime boost vaccine using C-terminal extension (CTE) of cysteine proteinase type I of Leishmania infantum in BALB/c mice. Group I as vaccinated group primed with 100 microg of pcDNA-CTE and 3 weeks later boosted with combination of 30 microg rCTE, 50 microg of CpG and Montanide 720. Groups II and III were served as control groups. Although, this vaccination regimen did not protect mice against the infectious challenge but it was highly immunogenic. IgG2a has been raised strongly against rCTE in contrast to IgG1 and remains high at every time point under study. By analysis of CTE synthetic peptides (CTE100) before challenge, both IgG1 and IgG2a were produced and for all overlapping synthetic peptides (CTE 1-8) IgG1 raised significantly. This statue is changed at 7 weeks after challenge and only CTE2 and CTE3 have shown to induce considerable amount of IgG1. In all groups, the level of IL-5 started to increase with high concentration shortly passing only 3 weeks after infectious challenge. In compare with two control groups, the vaccinated group produced significantly higher level of IL-5 at 7 weeks post-infection. The parasite burden of all groups is similar at 4 weeks post-challenge in both liver and spleen. In contrast, at 8 weeks post challenge, the spleen of the vaccinated group showed significantly higher level of parasite load in compare with two control groups. This study demonstrated that immunization with CTE display both type 1 and 2 immune signatures in experimental murine model of L. infantum infection.     

The importance of conserved amino acid residues in p94 protease sub-domain IIb and the IS2 region for constitutive autolysis

p94/calpain 3, a skeletal muscle-specific member of calpain protease family, is characterized by apparent Ca(2+)-independence during exhaustive autolysis and concomitant proteolysis of non-self substrates. The purpose of our study was to comprehensively profile the structural basis of p94 enabling activation in the cytosol without an extra Ca(2+). Ca(2+)-dependent p94 mutants were screened using "p94-trapping", which is an application of yeast genetic reporter system called "proteinase-trapping". Several amino acids were revealed as critical for apparent Ca(2+)-independent p94 activity. These results highlight the importance of conserved amino acids in domain IIb as well as in the p94-specific IS2 region.     

Coenzyme Q10 as a potent compound that inhibits Cdt1–geminin interaction

A human replication initiation protein Cdt1 is a very central player in the cell cycle regulation of DNA replication, and geminin down-regulates Cdt1 function by directly binding to it. It has been demonstrated that Cdt1 hyperfunction resulting from Cdt1–geminin imbalance, for example by geminin silencing with siRNA, induces DNA re-replication and eventual cell death in some cancer-derived cell lines. In the present study, we first established a high throughput screening system based on modified ELISA (enzyme linked immunosorbent assay) to identify compounds that interfere with human Cdt1–geminin binding. Using this system, we found that coenzyme Q₁₀ (CoQ₁₀) can inhibit Cdt1–geminin interaction in vitro. CoQ compound is an isoprenoid quinine that functions as an electron carrier in the mitochondrial respiratory chain in eukaryotes. CoQ₁₀, having a longer isoprenoid chain, was the strongest inhibitor of Cdt1–geminin binding in the tested CoQs, with 50% inhibition observed at concentrations of 16.2 μM. Surface plasmon resonance analysis demonstrated that CoQ₁₀ bound selectively to Cdt1, but did not interact with geminin. Moreover, CoQ₁₀ had no influence on the interaction between Cdt1 and mini-chromosome maintenance (MCM)4/6/7 complexes. These results suggested that CoQ₁₀ inhibits Cdt1–geminin complex formation by binding to Cdt1 and thereby could liberate Cdt1 from inhibition by geminin. Using three-dimensional computer modeling analysis, CoQ₁₀ was considered to interact with the geminin interaction interface on Cdt1, and was assumed to make hydrogen bonds with the residue of Arg243 of Cdt1. CoQ₁₀ could prevent the growth of human cancer cells, although only at high concentrations, and it remains unclear whether such an inhibitory effect is associated with the interference with Cdt1–geminin binding. The application of inhibitors for the formation of Cdt1–geminin complex is discussed.     

脆性组氨酸三联体基因研究进展

脆性组氯酸三联体（FHIT）基因定位于染色体的3p14．2,经细胞生物学、肿瘤分子生物学研究,及转基因、基因敲除技术等实验证实其为抑癌基因。FHIT主要通过某种信号途径诱导凋亡,从而抑制肿瘤细胞的增殖。研究认为,FHIT通过FHIT-底物复合物产生抑癌作用。越来越多的研究结果表明FHIT在肿瘤的预防和治疗中具有很好的应用前景。     

Minority of mammalian orthologs can be regarded as physiologically closest genes

Orthologs are genes from different genomes that originate from a common ancestor gene by speciation event. They are most similar by the structure of encoded proteins and therefore should have a similar function. Here I apply the principle used for detection of structural orthology for a genome-wide analysis of gene expression. For this purpose, I determine the mutual similarity rank in all-by-all comparison of among-tissues expression patterns. The expression of most part of human–mouse orthologs in homologous tissues is poorly correlated (average mutual coexpression rank is only 4835 out of 18,092). Genes from evolutionarily labile gene families, which experience rapid turnover of family composition, are among those with the strongest expression change. However, the revealed phenomenon is not limited to them. There is no or very weak relationship between protein sequence divergence and mutual coexpression rank. Also, generally there is no relationship between the ratio of nonsynonymous to synonymous nucleotide substitutions and coexpression rank. This relationship is tangible only within evolutionarily labile gene families. These results indicate that despite of a similar biochemical function of orthologs reflected in the conserved protein sequence, the physiological (systemic) context of this function can be changed. Also, these results suggest that gene biochemical function and its physiological role in the organism can evolve independently.     

Properties of N-Acetylhistamine Deacetylase in Mammalian Brain

Properties of N-acetylhistamine deacetylase in rat brain were studied, utilizing a sensitive coupled radioenzymatic assay. The Km for N-acetylhistamine for this deacetylase was 660 microM and its Vmax was 330 pmol/h/mg protein. N-Acetylhistamine deacetylase activity increased 80% in the presence of 1 mM Mn2+. The Km of Mn2+ was 40 microM. The enzyme is primarily a soluble enzyme with a relatively uniform regional distribution, unlike the distribution for histamine and histidine decarboxylase. Neonatal activity of this enzyme in rat brain is higher than in adult brain. alpha-Fluoromethylhistidine does not affect the activity of N-acetylhistamine, indicating that deacetylation probably does not play a regulatory role in the synthesis of brain histamine.     

A biophysical characterization of the iron coordination environment in wheat germ peroxidase

 The heme protein wheat germ peroxidase (isoenzyme C₂) and its cyanide-inhibited form have been investigated by means of electronic, CD and paramagnetic NMR spectroscopy. The data indicate a protein environment of the active site distinct from that of horseradish peroxidase (HRP), with a larger solvent accessibility. The iron is pentacoordinated at neutral and low pH, whereas a hydroxyl anion may be bound at alkaline pH. The fifth axial ligand is a His residue with a partial anionic character, as found in other peroxidases. A spin equilibrium is observed at high enzyme concentrations. Received: 17 September 1996 / Accepted: 10 January 1997     

The Potential Use of Mechanism-Based Enzyme Inactivators in Medicine

Abstract

A new three dimensional representation of enzyme inhibition, applied to Lineweaver-Burk, Hanes and Eadie-Hofstee plots is presented. This type of representation has advantages for enzyme inhibition diagnosis, showing graphic characteristics that pass unnoticed in linear plots.