Computed three-dimensional structures for theras-binding domain of theraf-p74 protein complexed withras-p21 and with its suppressor protein, rap-1A

The three-dimensional structures of theras-p21 protein and its protein inhibitor, rap-1A, have been computed bound to theras-binding domain, RBD (residues 55–131), of theraf-p74 protein, a critical target protein ofras-p21 in theras-induced mitogenic signal transduction pathway. The coordinates of RBD have been reconstructed from the stereoview of an X-ray crystal structure of this domain bound to rap-1A and have been subjected to energy minimization. The energy-minimized structures of bothras- p21 and rap-1A, obtained in previous studies, have been docked against RBD, using the stereo figure of the RBD-rap-1A complex, based on a six-step procedure. The final energy-minimized structure of rap-1A-RBD is identical to the X-ray crystal structure. Comparison of theras-p21- and rap-1A-RBD complexes reveals differences in the structures of effector domains ofras-p21 and rap-1a, including residues 32–47, a domain that directly interacts with RBD, 60–66, 96–110, involved in the interaction ofras-p21 withjun kinase (JNK) andjun protein, and 115–126, involved in the interaction of p21 with JNK. The structure of the RBD remained the same in both complexes with the exception of small deviations in its-2 binding loop (residues 63–71) and residues 89–91, also involved in binding to rap-1A. The results suggest that the binding of these two proteins to RBD may allow them to interact with other cellular target proteins such as JNK andjun.     

Algorithm independent properties of RNA secondary structure predictions

Algorithms predicting RNA secondary structures based on different folding criteria – minimum free energies (mfe), kinetic folding (kin), maximum matching (mm) – and different parameter sets are studied systematically. Two base pairing alphabets were used: the binary GC and the natural four-letter AUGC alphabet. Computed structures and free energies depend strongly on both the algorithm and the parameter set. Statistical properties, such as mean number of base pairs, mean numbers of stacks, mean loop sizes, etc., are much less sensitive to the choice of parameter set and even of algorithm. Some features of RNA secondary structures, such as structure correlation functions, shape space covering and neutral networks, seem to depend only on the base pairing logic (GC or AUGC alphabet). Received: 16 May 1996 / Accepted: 10 July 1996     

The synthesis and reactions of A-ring aromatic steroid complexes of manganese tricarbonyl

Treatment of the A-ring aromatic steroids estrone 3-methyl ether and β-estradiol 3, 17-dimethyl ether with Mn(CO)₅⁺BF₄⁻ in CH₂Cl₂ yields the corresponding [(steroid)Mn(CO)₃]BF₄ salts 1 and 2 as mixtures of and β isomers. The X-ray structure of [(estrone 3-methyl ether)Mn(CO)₃]BF₄ · CH₂Cl₂ (1) having the Mn(CO)₃ moiety on the side of the steroid is reported: space group P2₁ with a=10.3958(9), b=10.9020(6), c=12.6848(9) Å, β=111.857(6)°, Z=2, V=1334.3(2) ų, _calc=.481 cm⁻³, R=0.0508, and wR=0.0635. The molecule has the traditional ‘piano stool’ structure with a planar arene ring and linear Mn---C---O linkages. The nucleophiles NaBH₄ and LiCH₂C(O)CMe₃ add to [(β-estradiol 3,17-dimethyl ether)Mn(CO)₃]BF₄ (2) in high yield to give the corresponding - and β-cyclohexadienyl manganese tricarbonyl complexes (3). The nucleophiles add meta to the arene -OMe substituent and exo to the metal. The and β isomers of 3 were separated by fractional crystallization and the X-ray structure of the β isomer with an exo-CH₂C(O)CMe₃ substituent is reported (complex 4): space group P2₁2₁2₁ with a=7.5154(8), b=15.160(2), c=25.230(3) Å, Z=4, V=2874.4(5) ų, _calc=1.244 g cm⁻³, R=0.0529 and wR2=0.1176. The molecule 4 has a planar set of dienyl carbon atoms with the saturated C(1) carbon being 0.592 Å out of the plane away from the metal. The results suggest that the manganese-mediated functionalization of aromatic steroids is a viable synthetic procedure with a range of nucleophiles of varying strengths.     

Comparison of the intermediate complexes of human growth hormone bound to the human growth hormone and prolactin receptors.

The crystal structures of complexes of human growth hormone (hGH) with the growth hormone and prolactin receptors (hGHR and hPRLR, respectively), together with the mutational data available for these systems, suggest that an extraordinary combination of conformational adaptability, together with finely tuned specificity, governs the molecular recognition processes operative in these systems. On the one hand, in the active 1:2 ligand-receptor complexes, 2 copies of the same receptor use the identical set of binding determinants to recognize topographically different surfaces on the hormone. On the other hand, comparing the 1:1 hGH-hGHR and hGH-hPRLR complexes, 2 distinct receptors use this same set of binding determinants to interact with the identical binding site on the ligand, even though few residues among the binding determinants are conserved. The structural evidence demonstrates that this versatility is accomplished by local conformational flexibility of the binding loops, allowing adaptation to different binding environments, together with rigid-body movements of the receptor domains, necessary for the creation of specific interactions with the same binding site.     

扁圆封印木（相似种）茎干的解剖特征

贵州省水城矿区晚二叠世煤核中扁圆封印木（相似种Ｓｉｇｉｌｌａｒｉａ ｃｆ．ｂｒａｒｄｉｉＢｒｏｎｇｎ．）茎干的主要解剖特征如下：管状中柱,具多边形薄壁细胞组成的髓。初生木质部成环带状,外缘呈规则的齿槽状,向心式发育。次生木质部显束状特征,横切面管胞为方圆至长方形,纵切面为梯状壁增厚,并具流苏纹。射线１—２列细胞宽,数个至十余个细胞高。叶迹起源于初生木质部外缘的槽中,中始式,但以向心发育为主。     

Characterization of the length polymorphism in the A+T-rich region of the Drosophila obscura group species

Summary In the twelve Drosophila obscura group species studied, belonging to the affinis, obscura, and pseudoobscura subgroups, the mitochondrial DNA length ranges from 15.8 to 17.2 kb. This length polymorphism is mainly due to insertions/deletions in the variable region of the A+T-rich region. In addition, one species (D. tristis) possess a tandem duplication of a 470-bp fragment that contains the replication origin.The same duplication has occurred at least twice in the Drosophila evolutionary history due to the fact that the repetition is analogous to repetitions found in the four species of the D. melanogaster complex.By comparing the nucleotide sequence of the conserved region in D. ambigua, D. obscura, D. yakuba, D. teissieri, and D. virilis, we show the presence of a secondary structure, likely implied in the replication origin, which could favor the generation of this kind of duplications.Finally, we propose that the high A and T content in the variable region of the A + T-rich region favors the formation of less-stable secondary structures, which could explain the generation of minor insertion/deletions found in this region.Offprint requests to: A. Latorre     

MORPHOLOGY OF DNA CONTAINING STRUCTURES (NUCLEOIDS) AS A PROSPECTIVE CHARACTER IN CYANOPHYTE TAXONOMY1

DNA containing structures (nucleoids) were visualized by 4′, 6-diamidino-2-phenylindole (DAPI) fluorescent staining in two groups of cyanophytes (59 filamentous oscillatorialean species and 12 coccal Synechococcus-like organisms) to test the possibility of using nucleoid morphology in cyanophyte taxonomy. The morphology of nucleoids (size, shape, and structure) in oscillatorialean species is specific for individual families. The morphology of the nucleoid in Synechococcus-like species agrees from the proposed separation of the genus Cyanothece from Synechococcus. A much different nucleoid morphology in three species of Cyanothece suggests that these species should be separated into a new genus. On the basis of other characters, the species could be returned to the genus Cyanobacterium. My results indicate that the morphology of nucleoids is a valuable character in the classification of the cyanophytes examined; thus, it is a prospective feature that could be used in the taxonomy of other groups of cyanophytes. Additionally, DAPI staining is not a complicated procedure. The new character is easy to see in samples taken from nature, both living and preserved.     

Classification of doubly wound nucleotide binding topologies using automated loop searches

A classification is presented of doubly wound α/β nucleotide binding topologies, whose binding sites are located in the cleft formed by a topological switch point. In particular, the switch point loop nearest the N-terminus is used to identify specific structural classes of binding protein. This yields seven structurally distinct loop conformations, which are subsequently used as motifs for scanning the Protein Data Bank. The searches, which are effective at identifying functional relationships within a large database of structures, reveal a remarkable and previously unnoticed similarity between the coenzyme binding sites of flavodoxin and tryptophan synthetase, even though there is no sequence or topological similarity between them.     

NO2胁迫下三角梅叶片形态解剖结构和最优光响应模型研究

植物的形态结构和光合作用能够反映植物对城市空气污染的响应特性。探究城市道路机动车尾气中的典型污染物NO₂气体,对植物叶片的生理光合响应特性。以二年生三角梅（Bougainvillea spectabilis）幼苗为对象,利用智能化人工熏气室模拟熏气（NO₂体积分数分别为0 μL/L （自然空气）、4 μL/L,8 μL/L,记作CK、T1、T2）,观察NO₂胁迫后三角梅的叶片形态、微观结构和光合特征。结果表明：（1）通过叶片形态观察发现,与CK相比,低浓度T1组叶片变化不明显,随着NO₂气体胁迫浓度的增加,高浓度T2组叶片逐渐出现失水、叶表面有明显的水渍状或烧灼状黄色斑点。（2）通过叶片微观结构解剖发现,高浓度NO₂胁迫后气孔皱缩程度增加,气孔开度减小;叶绿体结构变形,尤其是类囊体结构疏松,膨胀等变化。（3）叶片光合特性分析发现,T1和T2组的NO₂胁迫导致光饱和点（LSP）和最大净光合速率（P_nmax）下降、光补偿点（LCP）增加,表观量子效率（AQE）和暗呼吸速率（Rd）在4种光响应模型中变化规律存在一定的差异性。（4）4种光响应模型中,CK组决定系数（R²）越高,均方根误差（RMSE）越低,精度最高,尤以叶子飘等机理模型为最优,拟合效果最好,其次是直角双曲线模型。研究结果表明三角梅可通过自身的形态变化、调整光合特征参数,较好地适应不同浓度的NO₂,尤其是高浓度急性胁迫下,该研究结果有助于促进不同道路绿地三角梅的推广应用,对探究三角梅的景观效益和生态效益,揭示其对环境异质性的适应机制具有重要意义。     

Three-dimensional structures of the central regulatory proteins of the bacterial phosphotransferase system,HPr and enzyme IIAglc

Enzyme IIA and HPr are central regulatory proteins of the bacterial phosphoenolpyruvate:sugar phosphotransferase (PTS) system. Three-dimensional structures of the glucose enzyme IIA domain (IIA^glc) and HPr of Bacillus subtilis and Escherichia coli have been studied by both X-ray crystallography and Nuclear Magnetic Resonance (NMR) Spectroscopy. Phosphorylation of HPr of B. subtilis and IIA^glc of E. coli have also been characterized by NMR spectroscopy. In addition, the binding interfaces of B. subtilis HPr and IIA^glc have been identified from backbone chemical shift changes. This paper reviews these recent advances in the understanding of the three-dimensional structures of HPr and IIA^glc and their interaction with each other. © 1993 Wiley-Liss, Inc.