Efficient identification of near‐native conformations in ab initio protein structure prediction using structural profiles

One of the major bottlenecks in many ab initio protein structure prediction methods is currently the selection of a small number of candidate structures for high‐resolution refinement from large sets of low‐resolution decoys. This step often includes a scoring by low‐resolution energy functions and a clustering of conformations by their pairwise root mean square deviations (RMSDs). As an efficient selection is crucial to reduce the overall computational cost of the predictions, any improvement in this direction can increase the overall performance of the predictions and the range of protein structures that can be predicted. We show here that the use of structural profiles, which can be predicted with good accuracy from the amino acid sequences of proteins, provides an efficient means to identify good candidate structures. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Amino acid 95 causes strong alteration of peptide position PΩ in HLA-B*41 variants

There have been several attempts over the years to identify positions in the peptide-binding region (PBR) of human leukocyte antigens (HLA) that influence the specificity of bound amino acids (AAs) at each position in the peptide. Originally, six pockets (A-F) were defined by calculating the surface area of the PBR on the crystal structure of HLA-A2 molecules. More recent crystallographic analyses of a variety of HLA alleles have led to broader pocket definitions. In this study, we examined the peptide-binding specificity of HLA-B*41 alleles and compared our results with the available pocket definitions. By generating recombinant HLA-B molecules and studying the eluted peptides by mass spectrometry and pool sequencing, we detected two different POmega peptide motifs within the B*41 group: Leu vs Val/Pro. Specificity was dependent on the presence of Leu (B*4102, B*4103, and B*4104) vs Trp (B*4101, B*4105, and B*4106) at AA position 95 in the HLA molecule, whose impact on POmega has been a subject of controversy in current pocket definitions. In contrast, the Arg97Ser mutation did not affect pocket F binding specificity in B*41 subtypes although residue 97 was previously identified as a modulator of peptide binding for several HLA class I alleles. According to most pocket definitions, this study shows that the Asn80Lys substitution in B*4105 impels the peptide's POmega anchor toward more promiscuity. Our sequencing results of peptides eluted from HLA-B*41 variants demonstrate the limitations of current pocket definitions and underline the need for an extended peptide motif database for improved understanding of peptide-major histocompatibility complex interactions.     

鸡骨常山属三个种的核形态

研究了鸡骨常山属（Alstonia）3个种的核形态,其中盆架树（A.rostrata）的核型属首次报道,3个种的体细胞染色体数目均为2n=42,且糖胶树（A.scholaris）和鸡骨常山（A.yunnanensis）的染色体数目同前人报道的2n=44不同。盆架树的间期核和有丝分裂前期染色体分别为棒状前染色体型和中间型,核型公式为2n=42=3M＋21m＋18sm,核型不对称性类型为2A型。糖胶树的间期核和有丝分裂前期染色体分别为球状前染色体型和中间型,核型公式为2n=42=14m＋24sm＋4st,核型不对称性类型为3A型。鸡骨常山的间期核和有丝分裂前期染色体分别为复杂染色体中央粒型和中间型,核型公式为2n=42=5m＋37sm,核型不对称性类型为3B型。根据核形态结果,结合形态学特征和已有的细胞学资料,初步讨论了该属几个种的系统位置及演化趋势。     

Phase-dependent nucleotide substitution in protein-coding sequences

It is well known that due to the degeneracy of genetic code, most of the silent substitutions appear in the third codon position, so the mutation frequency of the third codon position is much higher than that of the first two positions. However, it remains unknown whether the directionality of point mutation in three codon positions is similar or not. In this paper, through analyzing 15 sets of orthologous genes, it is revealed that most of the substitution types are significantly different between any two codon positions, especially between the 2nd and the 3rd phases. Furthermore, the average frequencies of each type of substitution calculated from the fifteen sets of orthologous genes are similar to those identified in single nucleotide polymorphisms (SNPs) of human and mouse genome. The present analyses suggest that the nucleotide substitution in protein-coding sequences is not only context-dependent (so called neighboring-nucleotide effects), but also phase-dependent, which is of significance to improving the prevalent nucleotide-evolution models.     

珍稀濒危植物珙桐超氧化物歧化酶活性

采用比色法测定了不同年龄和部位珙桐叶的超氧化物歧化酶(SOD)活性,以探讨不同年龄级珙桐的生理生态适应性。结果表明:不同年龄同一生长期珙桐叶的SOD活性不同,同年龄级同层珙桐叶的SOD活性随叶位增加大致呈先升后降的变化;同叶位不同层及同层不同叶位的珙桐叶的SOD活性不同。珙桐叶SOD活性对生长期敏感,其活性随叶片的生长、衰老呈先升后降变化。即珙桐叶SOD活性受生物和非生物因子共同影响,且不同年龄级、叶位、层次均存在差异。     

Antioxidative defence of old growth beech (Fagus sylvatica) under double ambient O3 concentrations in a free-air exposure system

In this study the influence of chronic free-air ozone exposure and of different meteorological conditions in the very dry year 2003 and the more humid year 2004 on the antioxidative system in sun and shade leaves of adult FAGUS SYLVATICA trees were investigated. Contents of ascorbate, glutathione, and alpha-tocopherol, as well as chloroplast pigments were determined under ambient (1 x O(3)) and double ambient (2 x O(3)) ozone concentrations. Ozone affected the antioxidative system in June and July, causing lower ascorbate contents in the apoplastic space, a more oxidized redox state of ascorbate and glutathione and an increase in pigment contents predominantly in the shade crown. For all measured parameters significant differences between the years were observed. In 2004 the redox state of ascorbate and glutathione was in a more reduced state and leaf contents of alpha-tocopherol, pigments of the xanthophyll cycle, beta-carotene, lutein, neoxanthin, and alpha-carotene were lower compared to 2003. Contents of total glutathione and chlorophyll a + b were increased in the second year. These results indicate a strong influence of the drought conditions in 2003 on the antioxidative system of beech overruling the ozone effects. Shade leaves showed lower contents of ascorbate in both years and the redox states of ascorbate and glutathione were more oxidized compared to sun leaves. Contents of photoprotective and accessory pigments generally were enhanced and the de-epoxidation state of the xanthophyll cycle was lower in the shade compared to the sun crown. Exhibiting less antioxidants shade leaves seem to be more sensitive against ozone than sun leaves.