Application of a directed conformational search for generating 3-D coordinates for protein structures from alpha-carbon coordinates.

A directed conformational search algorithm using the program CONGEN (ref. 3), which samples backbone conformers, is described. The search technique uses information from the partially built structures to direct the search process and is tested on the problem of generating a full set of backbone Cartesian coordinates given only alpha-carbon coordinates. The method has been tested on six proteins of known structure, varying in size and classification, and was able to generate the original backbone coordinates with RMSs ranging from 0.30-0.87A for the alpha-carbons and 0.5-0.99A RMSs for the backbone atoms. Cis peptide linkages were also correctly identified. The procedure was also applied to two proteins available with only alpha-carbon coordinates in the Brookhaven Protein Data Bank; thioredoxin (SRX) and triacylglycerol acylhydrolase (TGL). All-atom models are proposed for the backbone of both these proteins. In addition, the technique was applied to randomized coordinates of flavodoxin to assess the effects of irregularities in the data on the final RMS. This study represents the first time a deterministic conformational search was used on such a large scale.     

Vegetation structure and microclimate of three Dutch Calthion palustris communities under different climatic conditions

Three Dutch Calthion palustris communities, situated in different phytogeographic districts which vary in elimatic conditions, are compared with respect to vegetation structure and microclimate. The three Calthion stands which are similar in soil, management and hydrology, differ slightly in total aboveground biomass in the period just before cutting, but there is a larger difference in the biomass contributed by phanerogams, bryophytes and litter. The structure of the Calthion communities varies in vertical distribution of biomass and leaf area (LAI), and growth form and leaf size composition. These differences are interpreted in terms of elimatic differences such as length of growing season, temperature and wind. Profiles of decreasing light intensity within the vegetation canopy are related to the vertical distribution of biomass, LAI and leaf inclination of the various Calthion communities. Temperature and saturation deficit of the air on the different sites show profiles of a similar shape which suggests that in such ecologically comparable plant communities, vegetation structure differs under influence of the macroclimate in such a way that the resulting vegetation canopies modify the microclimate within the vegetation to become homologous.Nomenclature of species follows Heukels-van Ooststroom (1977). Acknowledgement. This study is part of the pfoject on vegetation structure, financially supported by the Foundation for Fundamental Biological Research (BION), of the Dutch Organization for the Advancement of Pure Research (ZWO). Much of the research was carried out at the Division of Geobotany, University of Nijmegen. The authors kindly acknowledge this hospitality. Also the data contributed by B. Aerssens, J. Cortenraad, and S. Troelstra and the typing help of Mrs R. Jaegermann are gratefully acknowledged.     

Structural implications of primary sequences from a family of Balbiani ring-encoded proteins inChironomus

Summary DNA sequencing has revealed an internal, tandemly repetitive structure in the family of giant polypeptides encoded by three types of Balbiani ring (BR) genes, in three different species ofChironomus. Each major BR repeat can be subdivided into two halves: a region consisting of short subrepeats and a more constant region that lacks obvious subrepeats. Comparative predictions of secondary structure indicate that an -helical segment is consistently present in the amino-terminal half of the constant region in all known BR proteins. Comparative predictions, coupled with consideration of the known phosphorylation of serine and threonine residues in BR proteins, suggest that the -helical structure may also extend into the carboxy-terminal half of the constant region, possibly interrupted by -turn(s). However, it is also possible that the structure is variable, and that a -strand is present in that half in some cases. All of the constant regions conserve one methionine and one phenylalanine residue, as well as all four cysteines; these residues presumably play roles in the packing or cross-linking of aligned constant regions. The structure of the subrepeat region is not clear, but the prevalence of a tripeptide pattern (basic-proline-acidic) suggests some type of structural regularity, possibly an extended helix. The possible significance of these conserved molecular features is discussed in the context of how they may serve the elasticity, insolubility, and hydrophilicity of the fibrils and threads formed by the BR polypeptides.     

The nature of the stable noncovalent dimers of band 3 protein from erythrocyte membranes in solutions of Triton X-100

Stable noncovalent dimers of band 3 protein from human erythrocyte membranes, in which state the protein is thought to exist after solubilization by the nonionic detergent Triton X-100, do not occur when purified batches of the detergent are used. Instead, the protein is in a monomer/dimer/tetramer association equilibrium. The stable dimers do appear, however, when the detergent has been 'aged'. They thus seem to be artifacts.     

Theoretical conformational analysis of phospholipids II. Role of hydration in the gel to liquid crystal transition of phospholipids

To obtain a satisfactory agreement between computed transition temperatures and those determined experimentally, we introduce explicitly water molecules which hydrate the polar headgroup of dipalmitoylphosphatidylethanolamine molecules. The calculated free energy curves as a function of the intermolecular interchain distance and the degree of hydration of the polar groups permit the determination of the transition of the phospholipid system from the gel to the liquid crystalline phase. The detailed structure of the hydration shell is defined using the supermolecular approach.     

Germ cell nucleosomes contain remodeled core protein complex

Electrophoretic analysis of the nucleosomal histones from MN1 and MN2 subpopulations of the seminiferous tubules in gels containing either 6.25 or 2.5 M urea revealed the presence of testis specific histone H2S, H1 and protein ‘A’ in addition to the somatic histones in the core protein complex. Size analysis indicated the presence of a 150–160 bp DNA segment in the MNI subpopulation, whereas, an approx 180 bp DNA fragment was present in the MN2 subpopulation of both liver and tubule nucleosomes. These data suggest an extensive remodeling of the nucleosomal core protein complex during mammalian spermatogenesis.     

Der Feinbau der sog. Kugelhaare der Fadenkanker (Opiliones,Nemastomatidae)

Zusammenfassung Der Hohlraum des Kugelhaares von Nemastoma bildet im basalen Teil Ausbuchtungen mit tubulären Strukturen, die mit 40–50 von proximal nach distal ziehenden Kanälen in Verbindung stehen.Nahe der Haarspitze befindet sich ein hohler Schirm mit zahlreichen Chaetoiden. Dicht unter ihm öffnen sich die Kanäle nach außen, und zwar derartig, daß ihr zentrad gelegener Teil der Wand den Schirmstiel bildet, während sich ihr peripherwärts gelegener Wandteil in einzelne Streben aufgliedert. Diese bilden nach Erreichen des Schirmbodens zwischen sich und dem Schirmstiel einen großen Hohlraum, der von einem klebrigen Sekret angefüllt und, zusammen mit dem Schirm, auch umhüllt wird.

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The fine structure of spezialized setae on the pedipalpi of nemastoma (Opiliones, Nemastomatidae)

Summary The cavity of the seta on the pedipalpi of Nemastoma shows protrusions with tubular structures, which are connected with 40–50 channels proceeding from proximal towards distal.Close by the tip of the seta there is a hollow umbrella with numerous secondary chetae. Bight underneath, each channel is widened in a way that the central part of the wall builds the stalk of the umbrella, whereas the more peripheral part of the wall is split in single struts. Both struts fused with the umbrella and its stalk form a large cavity. This cavity is filled with a viscid droplet and enveloped as well together with the umbrella. — The possible meaning of these structures is discussed.

Frl. A. Hennig bin ich für ihre gewissenhafte technische Mitarbeit sehr zu Dank verpflichtet.     

Melanogenesis in amphibians

Summary The pigmented epithelium of Rana pipiens tadpole eyes normally develops at least two types of melanosomes: (1) an elongated melanin granule of relatively homogeneous electron density, and (2) a complex melanosome which has an outer electrondense area and one or more less dense cores. Evidence indicates that complex melanosomes are formed by new melanin enclosing preexisting melanosomes. An organized fibrillar premelanosome is demonstrated with the aid of the antimelanogenic compound phenylthiourea (PTU). These premelanosomes are the developing forms of the elongated melanosomes. There is evidence that the premelanosomes originate in the smooth endoplasmic reticulum. Phenylthiourea blocks melanin synthesis in the premelanosomes; however, removal of the PTU allows pigment deposition. This finding of an organized, fibrillar premelanosome in an amphibian marks the lowest phylogenetic group in which these organelles have been described.An Oak Ridge Graduate Fellow from Catholic University of America, Washington, D.C., under appointment from Oak Ridge Associated Universities.The MAN Program is supported by the National Cancer Institute, the National Institute of General Medical Sciences, the National Institute of Allergy and Infectious Diseases, and the U.S. Atomic Energy Commission.Oak Ridge National Laboratory is operated by Union Carbide Corporation Nuclear Division for the U.S. Atomic Energy Commission.