Stable proline box motif at the N-terminal end of alpha-helices.

We describe a novel N-terminal alpha-helix local motif that involves three hydrophobic residues and a Pro residue (Pro-box motif). Database analysis shows that when Pro is the N-cap of an alpha-helix the distribution of amino acids in adjacent positions changes dramatically with respect to the average distribution in an alpha-helix, but not when Pro is at position N1. N-cap Pro residues are usually associated to Ile and Leu, at position N', Val at position N3 and a hydrophobic residue (h) at position N4. The side chain of the N-cap Pro packs against Val, while the hydrophobic residues at positions N' and N4 make favorable interactions. To analyze the role of this putative motif (sequence fingerprint hPXXhh), we have synthesized a series of peptides and analyzed them by circular dichroism (CD) and NMR. We find that this motif is formed in peptides, and that the accompanying hydrophobic interactions contribute up to 1.2 kcal/mol to helix stability. The fact that some of the residues in this fingerprint are not good N-cap and helix formers results in a small overall stabilization of the alpha-helix with respect to other peptides having Gly as the N-cap and Ala at N3 and N4. This suggests that the Pro-box motif will not specially contribute to protein stability but to the specificity of its fold. In fact, 80% of the sequences that contain the fingerprint sequence in the protein database are adopting the described structural motif, and in none of them is the helix extended to place Pro at the more favorable N1 position.     

缬氨酸的模拟移动床分离

首先用动态轴向压缩柱将缬氨酸从丙氨酸、缬氨酸和亮氨酸三种氨基酸的混合物中分离出来,然后又研究了在线性条件下用模拟移动床分离丙氨酸和缬氨酸的工艺,实现了丙氨酸和缬氨酸的良好分离,其中丙氨酸的纯度达到96.15%,缬氨酸的纯度达到了98.79%.     

Response of piglets to the valine content in diet in combination with the supply of other branched-chain amino acids

The branched-chain amino acids (BCAA) valine (Val) and isoleucine (Ile) are considered to be among the next-limiting amino acids for growth in piglets. In earlier studies, we estimated the standardized ileal digestible (SID) Val : Lys (lysine) requirement to be at least 70%, whereas the Ile : Lys requirement may be as low as 50%. Because the BCAA partially share a common route of catabolism, the supply of one BCAA may affect the availability of the other BCAA. Four experiments were conducted to determine the response of 6-week-old piglets to the Val supply in relation to the other BCAA. A deficient supply of Val or Ile typically results in a reduction in average daily feed intake (ADFI). Experiment 1 was designed to determine the effect of a limiting Val supply, independent of the effect on feed intake. In a dose-response study using restrictively fed piglets, nitrogen retention did not increase for an SID Val : Lys supply greater than 64%. In the remaining experiments, piglets were offered feed ad libitum using ADFI, average daily gain (ADG) and gain-to-feed ratio as response criteria. The interaction between the Val and leucine (Leu) was studied in Experiment 2 in a 2 × 2 factorial design (60% and 70% SID Val : Lys, and 111% and 165% SID Leu : Lys). Performance was considerably lower in piglets receiving 60% Val : Lys compared with those receiving 70% Val : Lys and was lowest in piglets receiving the diet with low Val and high Leu content. To further evaluate the interaction between Val and Leu, a dose-response study was carried out in which the response to Val supply was studied in combination with high Leu supply (165% Leu : Lys). Using a curvilinear-plateau model, the average SID Val : Lys requirement was 72%. However, low Val supply (60% SID Val : Lys) reduced performance by 13% to 38%, which was much greater than what we observed in earlier studies. Experiment 4 was carried out to test the hypothesis that the Val requirement is not affected by low Ile supply (50% SID Ile : Lys). Performance was not improved for Val : Lys supplies greater than 65%, which may indicate that Ile (and not Lys) was second-limiting in this study. In conclusion, the first response of piglets to deficient Val supply appears to be a reduction in ADFI, rather than a reduction in ADG or nitrogen retention. A large supply of Leu may not affect the Val requirement per se, but may aggravate the consequences of Val deficiency.     

鼠伤寒沙门氏菌Ⅵ型分泌系统相关基因敲除及其功能特性

Ⅵ型分泌系统(T6SS)是大多数革兰氏阴性细菌中都存在的一种重要的分泌系统,能介导细菌与细菌之间以及细菌和宿主细胞之间的相互作用,溶血素共调节蛋白(Hcp)和缬氨酸甘氨酸重复蛋白G(VgrG)是组成T6SS穿刺装置的重要组分。但鼠伤寒沙门氏菌Ⅵ型分泌系统的Hcp与VgrG在该菌入侵宿主细胞及抗吞噬过程中发挥的作用尚不十分清楚。【目的】本研究旨在利用基因敲除技术构建的鼠伤寒沙门氏菌hcp及vgrg基因缺失株体外接种真核上皮细胞和巨噬细胞,并以其亲本株作为对照,以研究Hcp及VgrG在该菌粘附、侵入上皮细胞及抗吞噬过程中所发挥的作用。【方法】通过优化Red同源重组系统操作过程中各个条件,建立一套快速敲除鼠伤寒沙门氏菌Ⅵ型分泌系统相关基因的操作系统,成功构建鼠伤寒沙门氏菌CVCC541的hcp及vgrg单基因缺失株、双基因缺失株及三基因缺失株,并用Hela细胞接种试验和菌落计数试验,评估不同菌株的粘附和侵袭能力;用小鼠巨噬细胞RAW 264.7接种试验,评估不同菌株的抗吞噬能力。【结果】与亲本株CVCC541粘附侵袭Hela细胞相比,基因缺失株CVCC541Δvgrg、CVCC541Δhcp2Δvgrg和CVCC541Δhcp1Δhcp2Δhcp3的粘附率分别为17.17%±2.1%、14.73%±2.5%和82%±3.7%;CVCC541Δvgrg、CVCC541Δhcp2Δvgrg和CVCC541Δhcp1Δhcp2Δhcp3的侵袭率分别为7.05%±1.05%、6.21%±1.35%和87%±3.25%;与亲本株CVCC541在小鼠巨噬细胞RAW 264.7中的存活相比,基因缺失株CVCC541Δvgrg、CVCC541Δhcp2Δvgrg和CVCC541Δhcp1Δhcp2Δhcp3的存活率分别为15.67%±2.9%、14.47%±1.87%和56.12%±3.48%。【结论】鼠伤寒沙门氏菌Ⅵ型分泌系统VgrG和Hcp对该菌入侵细胞和抗吞噬方面具有重要作用,该研究为鼠伤寒沙门氏菌通过六型分泌系统与宿主细胞相互作用的机制研究奠定了基础。     

Molecular characterization of tissue-nonspecific alkaline phosphatase with an Ala to Thr substitution at position 116 associated with dominantly inherited hypophosphatasia

Mutations in the tissue-nonspecific alkaline phosphatase (TNSALP) gene are responsible for hypophosphatasia, an inborn error of bone and teeth metabolism associated with reduced levels of serum alkaline phosphatase activity. A missense mutation (c.346G>A) of TNSALP gene, which converts Ala to Thr at position 116 (according to standardized nomenclature), was reported in dominantly transmitted hypophosphatasia patients (A.S. Lia-Baldini et al. Hum Genet. 109 (2001) 99-108). To investigate molecular phenotype of TNSALP (A116T), we expressed it in the COS-1 cells or Tet-On CHO K1 cells. TNSALP (A116T) displayed not only negligible alkaline phosphatase activity, but also a weak dominant negative effect when co-expressed with the wild-type enzyme. In contrast to TNSALP (W, wild-type), which was present mostly as a non-covalently assembled homodimeric form, TNSALP (A116T) was found to exist as a monomer and heterogeneously associated aggregates covalently linked via disulfide bonds. Interestingly, both the monomer and aggregate forms of TNSALP (A116T) gained access to the cell surface and were anchored to the cell membrane via glycosylphosphatidylinositol (GPI). Co-expression of secretory forms of TNSALP (W) and TNSALP (A116T), which are engineered to replace the C-terminal GPI anchor with a tag sequence (his-tag or flag-tag), resulted in the release of heteromeric complexes consisting of TNSALP (W)-his and TNSALP (A116T)-flag. Taken together, these findings strongly suggest that TNSALP (A116T) fails to fold properly and forms disulfide-bonded aggregates, though it is indeed capable of interacting with the wild-type and reaching the cell surface, therefore explaining its dominant transmission.     

Development of fructosyl valine binding polymers by covalent imprinting

Molecularly imprinted polymers (MIPs) against fructosyl valine (Fru-Val), the N-terminal constituent of hemoglobin A1c β-chains, were prepared by cross-linking of β-d-Fru-Val-O-bis(4-vinylphenylboronate) with an excess of ethylene glycol dimethacrylate (EDMA) or trimethylolpropane trimethacrylate (TRIM). Control MIPs were prepared in analogy by cross-linking the corresponding vinylphenylboronate esters of fructose and pinacol. After template extraction batch rebinding studies were performed using different pH values and buffer compositions. The Fru-Val imprinted TRIM cross-linked polymer binds about 1.4 times more Fru-Val than the fructose imprinted polymer and 2.7 times more Fru-Val than pinacol imprinted polymer. The highest imprinting effect was obtained in 100 mM sodium carbonate/10% methanol (pH 11.4). The TRIM cross-linked Fru-Val imprinted polymer showed a better specificity than the EDMA cross-linked polymer. The binding of valine was very low. Thermo gravimetric analysis indicated that the generated Fru-Val imprinted polymer has high thermo stability. No change in binding was observed after incubation of the polymers in buffer at 80 °C for 36 h. Since the functional group of the polymers (phenyl boronic acid) targets the sugar part of Fru-Val the imprint technique used should also be applicable for the development of MIPs against other glycated amino acids and peptides.     

Mutation of a conserved glycine in the SH1-SH2 helix affects the load-dependent kinetics of myosin

The ATP hydrolysis rate and shortening velocity of muscle are load-dependent. At the molecular level, myosin generates force and motion by coupling ATP hydrolysis to lever arm rotation. When a laser trap was used to apply load to single heads of expressed smooth muscle myosin (S1), the ADP release kinetics accelerated with an assistive load and slowed with a resistive load; however, ATP binding was mostly unaffected. To investigate how load is communicated within the motor, a glycine located at the putative fulcrum of the lever arm was mutated to valine (G709V). In the absence of load, stopped-flow and laser trap studies showed that the mutation significantly slowed the rates of ADP release and ATP binding, accounting for the ~270-fold decrease in actin sliding velocity. The load dependence of the mutant's ADP release rate was the same as that of wild-type S1 (WT) despite the slower rate. In contrast, load accelerated ATP binding by ~20-fold, irrespective of loading direction. Imparting mechanical energy to the mutant motor partially reversed the slowed ATP binding by overcoming the elevated activation energy barrier. These results imply that conformational changes near the conserved G709 are critical for the transmission of mechanochemical information between myosin's active site and lever arm.     

Codon substitution models based on residue similarity and their applications

Codon models are now widely used to draw evolutionary inferences from alignments of homologous sequence data. Incorporating physicochemical properties of amino acids into codon models, two novel codon substitution models describing the evolution of protein-coding DNA sequences are presented based on the similarity scores of amino acids. To describe substitutions between codons a continue-time Markov process is used. Transition/transversion rate bias and nonsynonymous codon usage bias are allowed in the models. In our implementation, the parameters are estimated by maximum-likelihood (ML) method as in previous studies. Furthermore, instantaneous mutations involving more than one nucleotide position of a codon are considered in the second model. Then the two suggested models are applied to five real data sets. The analytic results indicate that the new codon models considering physicochemical properties of amino acids can provide a better fit to the data comparing with existing codon models, and then produce more reliable estimates of certain biologically important measures than existing methods.