Structural classification of αββ and ββα supersecondary structure units in proteins

We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded β strands, preceded or followed by an α helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the α helix and β hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the α–β connection are observed. These preferences can be explained by favorable side by side packing of the α helix and the β hairpin, local interactions in the region of the α–β connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database-derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process. Proteins 30:193–212, 1998. © 1998 Wiley-Liss, Inc.     

Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies

The mitochondrial adenosine diphosphate/adenosine triphosphate (ADP/ATP) carrier has been recently crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). In the crystal structure, the six-transmembrane helix bundle that defines the nucleotide translocation pathway is closed on the matrix side due to sharp kinks in the odd-numbered helices. The closed conformation is further sealed by the loops protruding into the matrix that interact through an intricate network of charge-pairs. To gain insight into its structural dynamics we performed molecular dynamics (MD) simulation studies of the ADP/ATP carrier with and without its cocrystallized inhibitor. The two trajectories sampled a conformational space around two different configurations characterized by distinct salt-bridge networks with a significant shift from inter- to intrarepeat bonding on the matrix side in the absence of CATR. Analysis of the geometrical parameters defining the transmembrane helices showed that even-numbered helices can undergo a face rotation, whereas odd-numbered helices can undergo a change in the wobble angle with a conserved proline acting as molecular hinge. Our results provide new information on the dynamical properties of the ADP/ATP carrier and for the first time yield a detailed picture of a stable carrier conformation in absence of the inhibitor.     

Further observations on the ultrastructure of Cystosporogenes operophterae (Canning, 1960) (phylum Microsporidia) parasitic in Operophtera brumata L. (Lepidoptera, Geometridae)

Reinvestigation of Cystosporogenes operophterae [J. Parasitol. 46 (1960) 755] by electron microscopy confirmed that development in host cells takes place in a vacuole with a single membrane at its boundary. Although ribosomes were not clustered on this membrane, it is hypothesised that it originates from host endoplasmic reticulum. The dome-shaped anchoring disc, the morphology of the polaroplast and the separation of the polar tube coils from the ribosome-packed cytoplasm are newly described details of spore structure. The polaroplast consists of an outer region of compact lamellae forming 'arms' surrounding an inner region of widely spaced lamellae. The 'arms' extends back into the region of an elongate nucleus. The genera Cystosporogenes and Endoreticulatus were differentiated by their positions in a previously obtained 16S rDNA phylogeny and on the new ultrastructural data.     

Dictyostelium discoideum as Expression Host: Isotopic Labeling of a Recombinant Glycoprotein for NMR Studies

The advantages of the organism Dictyostelium discoideum as an expression host for recombinant glycoproteins have been exploited for the production of an isotopically labeled cell surface protein for NMR structure studies. Growth medium containing [¹⁵N]NH₄Cl and [¹³C]glycerol was used to generate isotopically labeled Escherichia coli, which was subsequently introduced to D. discoideum cells in simple Mes buffer. A variety of growth conditions were screened to establish minimal amounts of nitrogen and carbon metabolites for a cost-effective protocol. Following single-step purification by anion-exchange chromatography, 8 mg of uniformly ¹³C,¹⁵N-labeled protein secreted by approximately 10¹⁰D. discoideum cells was isolated from 3.3 liters of supernatant. Mass spectrometry showed the recombinant protein of 16 kDa to have incorporated greater than 99.9% isotopic label. The two-dimensional ¹H-¹³C HSQC spectrum confirms ¹³C labeling of both glycan and amino acid residues of the glycoprotein. All heteronuclear NMR spectra showed a good dispersion of cross-peaks essential for high-quality structure determination.     

Influence of Exon Duplication on Intron and Exon Phase Distribution

Nonrandomness in the intron and exon phase distributions in a sample of 305 human genes has been found and analyzed. It was shown that exon duplications had a significant effect on the exon phase nonrandomness. All of the nonrandomness is probably due to both the processes of exon duplication and shuffling. A quantitative estimation of exon duplications in the human genome and their influence on the intron and exon phase distributions has been analyzed. According to our estimation, the proportion of duplicated exons in the human genome constitutes at least 6% of the total. Generalizing the particular case of exon duplication to the more common event of exon shuffling, we modeled and analyzed the influence of exon shuffling on intron phase distribution. Received: 28 March 1997 / Accepted: 9 July 1997     

The structure of (η-C6H5Cl)Cr(CO)2PPh3

In a synthetic route that varies from the standard procedure requiring irradiation, the (η⁶-C₆H₅Cl)Cr(CO)₂PPh₃ complex is obtained upon reacting (η⁶-C₆H₅Cl)Cr(CO)₃ with tetrakis(triphenylphosphine)palladium(0), CuI, and trimethylsilylphenylacetylene in triethylamine. The X-ray crystal structure of the yellow–orange crystals of (η⁶-C₆H₅Cl)Cr(CO)₂PPh₃ allows structural comparisons to related (arene)Cr(CO)₂PR₃ complexes.     

江西青岚湖圆顶珠蚌的种群结构与繁殖特征研究

2008年7月至2009年7月研究了江西青岚湖圆顶珠蚌(Unio douglasiae)的种群结构与繁殖特征。从其种群结构的周年变动情况来看,该种群趋于稳定状态,壳长40-65mm的个体占大多数。在采集的标本中,最大个体壳长为83.6mm,最小个体壳长为20.3mm。圆顶珠蚌自然种群性比为1:1.20,性成熟最小雌体壳长为27.6mm,体重为2.62g;最小雄体壳长为27.9mm,体重为2.21g;5至6月间繁殖盛期,检测到最小妊娠个体壳长为29.8mm,体重为2.98g,推断一周年的圆顶珠蚌可能达到性成熟。根据圆顶珠蚌生殖细胞的发育规律和滤泡的变化特点,性腺发育分为生长期和成熟期、排放期、恢复期;属多次产卵类型。育儿囊属外鳃型,胚胎在胶质索中发育,钩介幼虫成熟后,胶质索消失成黏液状,成熟钩介幼虫附在新形成的黏液丝上排出体外。妊娠母蚌在受到刺激后,易发生流产,提前排出胶质索。繁殖期为2至7月,4、5、6月为繁殖高峰期,妊娠率分别为80.43%、84.21%和78.05%。平均繁殖力为(183.72±6.43)千粒/个,最大繁殖力为344.64千粒/个,壳长为54.5mm;最小繁殖力为49.95千粒/个,壳长为29.8mm。繁殖力与壳长和体重显著相关。这些结果不仅可以丰富淡水蚌的生物学内容,也能为淡水蚌保护和湖泊与河流的规范管理提供理论依据。       

A tetrameric allyl complex of sodium, and computational modeling of the Na-allyl chemical shift

Transmetallation of Li[A′] (A′ = [1,3-(SiMe₃)₂C₃H₃]⁻) with sodium tert-butoxide produces the corresponding sodium salt, which crystallizes from THF/toluene in the form of a cyclic tetramer, {Na[A′](thf)}₄. The Na atoms are in a square planar arrangement, bridged with π-bound allyl ligands; the Na-C distances range from 2.591(3)-2.896(3) Å, with an average of 2.70 Å. The geometries of several model organosodium complexes containing cyclopentadienyl and allyl ligands were optimized with density functional theory methods. The optimized structures were used with the gauge-including atomic orbital (GIAO) method to calculate their ²³Na NMR magnetic shielding values. Unlike the case with NaCp, the chemical shift of unsubstituted Na(C₃H₅) is very sensitive to the presence of coordinated THF (causing a 20 ppm upfield shift); silyl substitution has an even larger effect (30 ppm upfield shift). The observed ²³Na shift of δ −3.3 ppm for Na[A′] in THF-d₈, however, cannot be reliably distinguished from that calculated for the [Na(thf)₄]⁺ cation alone.     

Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition

The NLRP3 inflammasome assembles in response to a variety of pathogenic and sterile danger signals, resulting in the production of interleukin-1β and interleukin-18. NLRP3 is a key component of the innate immune system and has been implicated as a driver of a number of acute and chronic diseases. We report the 2.8 Å crystal structure of the NLRP3 NACHT domain in complex with an inhibitor. The structure defines a binding pocket formed by the four subdomains of the NACHT domain, and shows the inhibitor acts as an intramolecular glue, which locks the protein in an inactive conformation. It provides further molecular insight into our understanding of NLRP3 activation, helps to detail the residues involved in subdomain coordination within the NLRP3 NACHT domain, and gives molecular insights into how gain-of-function mutations de-stabilize the inactive conformation of NLRP3. Finally, it suggests stabilizing the auto-inhibited form of the NACHT domain is an effective way to inhibit NLRP3, and will aid the structure-based development of NLRP3 inhibitors for a range of inflammatory diseases.