Identification of the core structure of lysozyme amyloid fibrils by proteolysis

Human lysozyme variants form amyloid fibrils in individuals suffering from a familial non-neuropathic systemic amyloidosis. In vitro, wild-type human and hen lysozyme, and the amyloidogenic mutants can be induced to form amyloid fibrils when incubated under appropriate conditions. In this study, fibrils of wild-type human lysozyme formed at low pH have been analyzed by a combination of limited proteolysis and Fourier-transform infrared (FTIR) spectroscopy, in order to map conformational features of the 130 residue chain of lysozyme when embedded in the amyloid aggregates. After digestion with pepsin at low pH, the lysozyme fibrils were found to be composed primarily of N and C-terminally truncated protein species encompassing residues 26-123 and 32-108, although a significant minority of molecules was found to be completely resistant to proteolysis under these conditions. FTIR spectra provide evidence that lysozyme fibrils contain extensive beta-sheet structure and a substantial element of non beta-sheet or random structure that is reduced significantly in the fibrils after digestion. The sequence 32-108 includes the beta-sheet and helix C of the native protein, previously found to be prone to unfold locally in human lysozyme and its pathogenic variants. Moreover, this core structure of the lysozyme fibrils encompasses the highly aggregation-prone region of the sequence recently identified in hen lysozyme. The present proteolytic data indicate that the region of the lysozyme molecule that unfolds and aggregates most readily corresponds to the most highly protease-resistant and thus highly structured region of the majority of mature amyloid fibrils. Overall, the data show that amyloid formation does not require the participation of the entire lysozyme chain. The majority of amyloid fibrils formed from lysozyme under the conditions used here contain a core structure involving some 50% of the polypeptide chain that is flanked by proteolytically accessible N and C-terminal regions.     

Studies on the regioselectivity and kinetics of the action of trypsin on proinsulin and its derivatives using mass spectrometry

Human M-proinsulin was cleaved by trypsin at the R³¹R³²–E³³ and K⁶⁴R⁶⁵–G⁶⁶ bonds (B/C and C/A junctions), showing the same cleavage specificity as exhibited by prohormone convertases 1 and 2 respectively. Buffalo/bovine M-proinsulin was also cleaved by trypsin at the K⁵⁹R⁶⁰–G⁶¹ bond but at the B/C junction cleavage occurred at the R³¹R³²–E³³ as well as the R³¹–R³²E³³ bond. Thus, the human isoform in the native state, with a 31 residue connecting C-peptide, seems to have a unique structure around the B/C and C/A junctions and cleavage at these sites is predominantly governed by the structure of the proinsulin itself. In the case of both the proinsulin species the cleavage at the B/C junction was preferred (65%) over that at the C/A junction (35%) supporting the earlier suggestion of the presence of some form of secondary structure at the C/A junction. Proinsulin and its derivatives, as natural substrates for trypsin, were used and mass spectrometric analysis showed that the k_cat./K_m values for the cleavage were most favourable for the scission of the bonds at the two junctions (1.02 ± 0.08 × 10⁵ s^− 1 M^− 1) and the cleavage of the K²⁹–T³⁰ bond of M-insulin-RR (1.3 ± 0.07 × 10⁵ s^− 1 M^− 1). However, the K²⁹–T³⁰ bond in M-insulin, insulin as well as M-proinsulin was shielded from attack by trypsin (k_cat./K_m values around 1000 s^− 1 M^− 1). Hence, as the biosynthetic path follows the sequence; proinsulin → insulin-RR → insulin, the K²⁹–T³⁰ bond becomes shielded, exposed then shielded again respectively.     

An empirical energy function for threading protein sequence through the folding motif

In this paper we present a new residue contact potantial derived by statistical analysis of protein crystal structures. This gives mean hydrophobic and pairwise contact energies as a function of residue type and distance interval. To test the accuracy of this potential we generate model structures by “threading” different sequences through backbone folding motifs found in the structural data base. We find that conformational energies calculated by summing contact potentials show perfect specificity in matching the correct sequences with each globular folding motif in a 161-protcin data set. They also identify correct models with the core folding motifs of heme-rythrin and immunoglobulin McPC603 V₁-do- main, among millions of alternatives possible when we align subsequences with α-helices and β-strands, and allow for variation in the lengths of intervening loops. We suggest that contact potentials reflect important constraints on nonbonded interaction in native proteins, and that “threading” may be useful for structure prediction by recognition of folding motif. © 1993 Wiley-Liss, Inc.     

农田生态条件下玉米秸杆腐解过程腐解物的热解变化特征

用热分析法研究了农田生态条件下玉米秸杆腐解过程腐解物的热解变化特征 ,并探讨了腐解物中不同组分对腐解物热解特征的影响。结果表明 ,腐解物 DTA曲线的 2 80℃、3 3 0℃、4 50℃放热峰 ,DTG曲线的第二失重峰和 h330℃ /h4 50℃ 值可作为表征腐解进程的特征峰和特征值。由腐解物 DTA、DTG所得能量各参数 ( ΔH,E)与文献 [3 ]所述腐解物能态 ( Qv)呈现波动起伏 ,趋于稳定 2个阶段相符 ,二者相互印证 ,显示热分析方法用于植物残体腐解进程研究的可行性。 DTA的2 80℃放热峰主要由苯 -醇溶性物、水溶性物引起。苯 -醇溶性物、水溶性物和纤维素、半纤维素是影响腐解物热解及其能态变化特征的主要物质组分。木质素组分对腐解后期腐解物的热解及其能态特征趋于稳定具有重要作用     

Nitrogen mineralization and denitrification as influenced by crop residue particle size

Managing the crop residue particle size has the potential to affect N conservation in agricultural systems. We investigated the influence of barley (Hordeum vulgare) and pea (Pisum sativum) crop residue particle size on N mineralization and denitrification in two laboratory experiments. Experiment 1: ¹⁵N-labelled ground (3 mm) and cut (25 mm) barley residue, and microcrystalline cellulose+glucose were mixed into a sandy loam soil with additional inorganic N. Experiment 2: inorganic¹⁵ N and C₂H₂ were added to soils with barley and pea material after 3, 26, and 109 days for measuring gross N mineralization and denitrification.Net N immobilization over 60 days in Experiment 1 cumulated to 63 mg N kg^-1 soil (ground barley), 42 (cut barley), and 122 (cellulose+glucose). More N was seemingly net mineralized from ground barley (3.3 mg N kg^-1 soil) than from cut barley (2.7 mg N kg^-1 soil). Microbial biomass peaked at day 4 with the barley treatments and at day 14 with the cellulose+glucose whereafter the biomass leveled out at values 79 mg C kg^-1 (ground), 104 (cut), and 242 (cellulose+glucose) higher than for the control soil. Microbial growth yields were similar for the two barley treatments, ca. 60 mg C g^-1 substrate C added, which was lower than the 142 mg C g^-1 C added with cellulose+glucose. This suggests that the 75% (w/w) holocelluloses and sugars contained with the barley material remained physically protected despite grinding. In Experiment 2 gross mineralization on day 3 was 4.8 mg N kg^-1 d^-1 with ground pea, twice as much as for all other treatments. On day 26 the treatment with ground barley had the greatest gross N mineralization. In static cores ground barley denitrified 11-fold more than did cut barley, whereas denitrification was similar for the two pea treatments. In suspensions denitrification was similar for the two treatments both with barley and pea residue.We conclude that the higher microbial activity associated with the initial decomposition of ground plant material is due to a more intimate plant residue-soil contact. On the long term, grinding the plant residues has no significant effect on N dynamics.     

Fungal response from oat (Avena sativa) plants and surface residue in relation to soil aggregation and organic carbon

Abstract

The influence of soil fungi on soil organic carbon (OC) from surface residue was tested in outdoor plots in southern Ontario, Canada, 2004. Fungal hyphal length, soil aggregation, OC and light and heavy fractions of organic matter were compared with factors of plant growth (with or without oat [Avena sativa]) and surface residue (no residue, oat straw (low C:N) or corn (Zea mays) stalks (high C:N)) in a factorial arrangement. Significant increases were observed in soil OC from the oat plants, and from corn stalks compared to straw residue, in the growing season with very moist, high OC, sandy soil. In treatments with corn stalk residue, fungal hyphal length was increased with interaction from the oat plants and residue and was positively correlated with the heavy fraction organic matter along with soil OC. Fungal hyphae, plant roots and high C:N residue were all factors in soil OC increases.     

OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries

In this article, we present a de novo method for predicting protein domain boundaries, called OPUS-Dom. The core of the method is a novel coarse-grained folding method, VECFOLD, which constructs low-resolution structural models from a target sequence by folding a chain of vectors representing the predicted secondary-structure elements. OPUS-Dom generates a large ensemble of folded structure decoys by VECFOLD and labels the domain boundaries of each decoy by a domain parsing algorithm. Consensus domain boundaries are then derived from the statistical distribution of the putative boundaries and three empirical sequence-based domain profiles. OPUS-Dom generally outperformed several state-of-the-art domain prediction algorithms over various benchmark protein sets. Even though each VECFOLD-generated structure contains large errors, collectively these structures provide a more robust delineation of domain boundaries. The success of OPUS-Dom suggests that the arrangement of protein domains is more a consequence of limited coordination patterns per domain arising from tertiary packing of secondary-structure segments, rather than sequence-specific constraints.     

茉莉花蕾螟的田间综合防治技术

在广西横县进行了人工释放赤眼蜂、喷施无公害生物农药、黑光灯诱杀成虫等技术协调组合防治茉莉花蕾螟的田间示范试验。试验结果表明 :处理区茉莉花农药残留降低 90 %以上 ,农药残留指标达到中华人民共和国农业行业标准NY5 0 1 7 2 0 0 1的要求 ;防治效果显著提高 ,防治成本降低 3 9.2 % ,为农户增收节支约 280 5 .0元 /hm2 。     

残留地膜对番茄幼苗形态和生理特性的影响

采用盆栽试验的方法,研究了土壤中残留地膜对番茄(Lycopersicon esculentum L.)幼苗形态及生理特性的影响.结果表明,残留地膜使番茄幼苗的株高、茎粗、地上部和根系鲜重、根系活力及叶片氮代谢水平等降低;而且根系的IBA含量降低和ABA含量增加,抑制了根系的生长.同时地膜残留量越大,抑制的效果越显著.这...     

川西北泡沙参种群根系生长动态及其与环境因素关系研究

对川西北地区泡沙参种群根系生物量累积和形态发育过程及其与环境因素的关系进行了研究.结果表明,泡沙参种群根系生物量累积一般规律符合Logistic增长过程.较高的泡沙参根系生物量累积和形态发育时期可以持续到15～17年生以后,根系采收直径应在1.7cm以上.动物啃食、人为采挖、土壤、气候等环境条件与不同海拔各种群的根系生物量累积等有着密切联系,中海拔地区(2800～3300m)人为干扰少,土壤和水热条件适宜,根系生物量和形态发育达到较高水平,适合高产栽培.而低海拔和高海拔地区的不利环境条件限制了泡沙参根系生长.在进行野生资源保护利用以及人工栽培泡沙参时应充分考虑环境因素,努力减少放牧、采挖等人为破坏,有条件的地区应实行分区禁牧、禁采挖,为泡沙参种群恢复和药材品质提高创造条件.