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PubMed1996

On the origin of respiration: electron transport proteins from archaea to man.

All aerobic organisms use the exergonic reduction of molecular oxygen to water as primary source of metabolic energy. This reaction is catalyzed by membrane residing terminal heme/Cu-oxidases which belong to a superfamily of widely varying structural complexity between mitochondrial and bacterial members of this family. Over the last few years, considerable information from this and other laboratories accumulated also on archaeal respiratory chains and their terminal oxidases. In the following, the molecular and catalytic properties of the latter are discussed and compared to those from bacteria and eucarya under the aspect of their energy conserving capabilities and their phylogenetic relations. The Rieske iron-sulfur proteins being important functional constituents of energy transducing respiratory complexes are included in this study. A number of essential conclusions can be drawn. (1) Like bacteria, archaea can also contain split respiratory chains with parallel expression of separate terminal oxidases. (2) The functional core of all oxidases is the highly conserved topological motif of subunit I consisting of at least 12 membrane spanning helices with the 6 histidine residues of the heme/Cu-binding centers in identical locations. (3) Some archaeal oxidases are organized in unusual supercomplexes with other cytochromes and Rieske [2Fe2S] proteins. These complexes are likely to function as proton pumps, whereas on a structural basis several subunit I equivalents alone are postulated to be unable to pump protons. (4) The genes of two archaeal Rieske proteins have been cloned from Sulfolobus; phylogenetically they are forming a separate archaeal branch and suggest the existence of an evolutionary ancestor preceding the split into the three urkingdoms. (5) Archaeal oxidase complexes may combine features of electron transport systems occurring exclusively as separate respiratory complexes in bacteria and eucarya. (6) As far back as the deepest branches of the phylogentic tree, terminal oxidases reveal a degree of complexity comparable to that found in higher organisms. (7) Sequence analysis suggests a monophyletic origin of terminal oxidases with an early split into two types found in archaea as well as bacteria. This view implies an origin of terminal oxidases prior to oxygenic photosynthesis in contrast to the widely accepted inverse hypothesis.

Amino Acid Sequence↗
PubMed2002

Thermal barrier coatings for gas-turbine engine applications.

Hundreds of different types of coatings are used to protect a variety of structural engineering materials from corrosion, wear, and erosion, and to provide lubrication and thermal insulation. Of all these, thermal barrier coatings (TBCs) have the most complex structure and must operate in the most demanding high-temperature environment of aircraft and industrial gas-turbine engines. TBCs, which comprise metal and ceramic multilayers, insulate turbine and combustor engine components from the hot gas stream, and improve the durability and energy efficiency of these engines. Improvements in TBCs will require a better understanding of the complex changes in their structure and properties that occur under operating conditions that lead to their failure. The structure, properties, and failure mechanisms of TBCs are herein reviewed, together with a discussion of current limitations and future opportunities.

Journal Article↗
PubMedDate not supplied

[Features of the structure and evolution of complex, tandemly organized Bsp-repeats in the fox genome. I. Structure and internal organization of the BamHI-dimer].

A 1468 b.p. DNA BamHI-fragment homologous to the Bsp-repeat was isolated from the fox genome and sequenced. This fragment is an hierarchically arranged dimer. Its 734 b.p.-monomers consist of three subrepeats (SR), each 245 b.p. long, abundant with overlapping imperfect tandem repeats which in turn are rich in short direct related repeats (each 4-7 b.p. in size). The latters are mainly composed of AG, TG dinucleotides and their complements CT, CA. All subrepeats in the BamHI-dimer are flanked by motifs homologous to Jeffreys' sites. At certain points the sites are doubled. The above data allow to assume that the Bsp-repeat complex structure is likely to have developed throughout long multi-step evolution of relatively simple DNA sequences which had emerged de novo. Single substitutions, small inserts and deletions, multiple duplication and recombination events seem to have most contributed to the evolution of the Bsp-repeats. Single substitutions in SRs with respect to the consensus are not equally distributed along their length. A wave-like pattern of this distribution is the evidence for non-random character of mutations accumulation. A correspondence was noted between conservative regions in SR and the presence therein of functional motifs homologous to the binding sites of already known regulatory proteins.

Animals↗
PubMed2002

High resolution structural studies of complex icosahedral viruses: a brief overview.

Structural descriptions of viral particles are key to our understanding of their assembly mechanisms and properties. We will describe the application of X-ray crystallography and electron cryomicroscopy to the structural determination of the bluetongue virus core and the herpesvirus capsid. These represent the highest resolution structural studies carried out by these techniques on such complex and large icosahedral virus particles. The bluetongue virus core consists of two layers of distinct proteins with different protein packing symmetries, while the herpes virus capsid is made up of four types of proteins with 3.3 MDa per asymmetric unit. The structural results reveal that each of these proteins has distinct folds and they are packed uniquely to form stable particles.

Animals↗
PubMed2005

Multiple power-law structures in heterogeneous complex networks.

This paper develops a framework for analyzing and designing dynamic networks comprising different classes of nodes that coexist and interact in one shared environment. We consider ad hoc (i.e., nodes can leave the network unannounced, and no node has any global knowledge about the class identities of other nodes) preferentially grown networks, where different classes of nodes are characterized by different sets of local parameters used in the stochastic dynamics that all nodes in the network execute. We show that multiple scale-free structures, one within each class of nodes, and with tunable power-law exponents (as determined by the sets of parameters characterizing each class), emerge naturally in our model. Moreover, the coexistence of the scale-free structures of the different classes of nodes can be captured by succinct phase diagrams, which show a rich set of structures, including stable regions where different classes coexist in heavy-tailed (i.e., the exponent is between 2 and 3) and light-tailed (i.e., the exponent is greater than 3) states, and sharp phase transitions. The topology of the emergent networks is also shown to display a complex structure, akin to the distribution of different components of an alloyed material; e.g., nodes with a light-tailed scale-free structure get embedded to the outside of the network, and have most of their edges connected to nodes belonging to the class with a heavy-tailed distribution. Finally, we show how the dynamics formulated in this paper will serve as an essential part of ad hoc networking protocols, which can lead to the formation of robust and efficiently searchable networks [including, the well-known peer-to-peer networks] even under very dynamic conditions.

Journal Article↗
PubMed2006

Carbohydrate binding properties and carbohydrate induced conformational switch in sheep secretory glycoprotein (SPS-40): crystal structures of four complexes of SPS-40 with chitin-like oligosaccharides.

Crystal structures of four complexes of sheep secretory glycoprotein (SPS-40) with N-acetylglucosamine oligosaccharides (GlcNAc(n), (n=3-6)) have been determined at moderate resolutions. The binding studies of SPS-40 have been carried out using fluorescence spectroscopy and Surface Plasmon Resonance (SPR). Structure determinations of four complexes have shown a novel binding pattern of GlcNAc(n) molecules to SPS-40. The results indicate that the most preferred recognition region in the carbohydrate binding groove in SPS-40 is at subsites -4 to -2 among which subsite -2 provides the maximum interactions with carbohydrate residues. These structures have also shown that the interactions of GlcNAc3 and GlcNAc4 do not perturb the protein structure and those of GlcNAc5 induce partial conformational changes while in the case of GlcNAc6 the partially closed binding groove opened up completely. As in other SPX-40 structures, SPS-40 structure contains three overlapping flexible surface segments, His188-His197, Phe202-Arg212 and Phe244-Pro260 with several charged residues protruding outwardly. It creates a cluster of positive charges with a flexible base thus indicating a good scope of promoting the intermolecular interactions. This protein is glycosylated at Asn39 and may recognize other receptors having sugar binding sites. It appears that SPS-40 may involve both carbohydrate and protein bindings. The systematic carbohydrate-binding studies and the detailed structural results of four protein-carbohydrate complexes provide an excellent insight into the mechanism of carbohydrate binding. These are the first studies of this kind on secretory glycoproteins and their interactions with carbohydrates.

Acetylgalactosamine↗
PubMed1998

Ligand substitution of receptor targeted DNA complexes affects gene transfer into hepatoma cells.

We have targeted the serpin enzyme complex receptor for gene transfer in human hepatoma cell lines using peptides < 30 amino acids in length which contain the five amino acid recognition sequence for this receptor, coupled to poly K of average chain length 100 K, using the heterobifunctional coupling reagent sulfo-LC SPDP. The number of sulfo-LC SPDP modified poly-L-lysine residues, as well as the degree of peptide substitution was assessed by nuclear magnetic resonance spectroscopy. Conjugates were prepared in which 3.5%, 7.8% or 26% of the lysine residues contained the sulfo-LC SPDP moiety. Each of these conjugates was then coupled with ligand peptides so that one in 370, one in 1039, or one in 5882 lysines were substituted with receptor ligand. Electron microscopy and atomic force microscopy were used to assess complex structure and size. HuH7 human hepatoma cells were transfected with complexes of these conjugates with the plasmid pGL3 and luciferase expression measured 2 to 16 days after treatment. All the protein conjugates in which 26% of the K residues were modified with sulfo-LC SPDP were poor gene transfer reagents. Complexes containing less substituted poly K, averaged 17 +/- 0.5 nm in diameter and gave peak transgene expression of 3-4 x 10(6) ILU/mg which persisted (> 7 x 10(5) ILU) at 16 days. Of these, more substituted polymers condensed DNA into complexes averaging 20 +/- 0.7 nm in diameter and gave five-fold less luciferase than complexes containing less substituted conjugates. As few as eight to 11 ligands per complex are optimal for DNA delivery via the SEC receptor. The extent of substitution of receptor-mediated gene transfer complexes affects the size of the complexes, as well as the intensity and duration of transgene expression. These observations may permit tailoring of complex construction for the usage required.

Animals↗
PubMed2002

Bone modeling and structural measures of complexity.

We test sensitivity and powerfulness of recently suggested Structure Measures of Complexity (SMC) with simulated test objects, represented by simple structures or modelled on the basis of a real bone image. We check how these SMC reflect the local and global disordering processes, as well as a deterioration of the bone structure. We show that applications of SMC provide additional information about any changes of the bone structure in comparison to bone mineral density (BMD), and that they can be potentially helpful in the diagnosis of osteoporosis.

Journal Article↗
PubMed1987

Lectin affinity fractionation of asparagine-linked oligosaccharides from normal human and chronic leukemic leukocytes.

Asparagine-linked oligosaccharides were isolated from normal and chronic leukemic leukocytes (normal neutrophils, normal lymphocytes, chronic myeloid, chronic lymphoid and hairy cell leukemic leukocytes) and analyzed by sequential lectin affinity column chromatography. The neutral and sialylated glycopeptides ranged in size from 1,800 to 4,000 da. on gel filtration. Sequential lectin affinity analysis was then used to fractionate the Asn-oligosaccharides into major structural classes of high mannose, hybrid, and bi-, tri- and tetraantennary complex structures. Using lectins of well defined specificity, the sequential chromatography provided a satisfactory means of assessing the overall glycopeptide profiles of the different leukocyte types. Results from 10 patient samples show that alterations in leukocyte Asn-oligosaccharides occur during leukemogenesis. Most notable was an average twofold increase in the relative amount of high mannose glycopeptides compared to complex glycopeptides for the leukemic cells. High mannose glycopeptides comprised 8.6 percent of the total lectin-adherent glycopeptides from leukemics, and 4.2 percent in the normals. In addition, carbohydrate analysis has revealed that the total amount of neutral hexose was markedly decreased in all leukemic samples. Leukemics ranged from 10.5 to 18.8, while normals ranged from 24.2 to 49.2 nanomole of hexose per 100 micrograms protein. The sialic acid content of the leukemic glycopeptides was relatively unchanged from that of normals, resulting in an apparent increase in the sialic acid: hexose ratio for all leukemic glycopeptides. The results suggest that in the leukemic cells, high mannose structures constitute a larger proportion of the total Asn-linked oligosaccharides, while the overall level of protein glycosylation is decreased. Complex multiantennary glycopeptides, when synthesized, tended to be more fully sialylated than their normal counterparts.

Asparagine↗
PubMed2004

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.

Emerging high-throughput techniques for the characterization of protein and protein-complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. One such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing the consistency between cross-linking data and model geometry. This paper develops a probabilistic framework for analyzing the information content in cross-linking experiments, accounting for anticipated experimental error. This framework supports a mechanism for planning experiments to optimize the information gained. We evaluate potential experiment plans using explicit trade-offs among key properties of practical importance: discriminability, coverage, balance, ambiguity, and cost. We devise a greedy algorithm that considers those properties and, from a large number of combinatorial possibilities, rapidly selects sets of experiments expected to discriminate pairs of models efficiently. In an application to residue-specific chemical cross-linking, we demonstrate the ability of our approach to plan experiments effectively involving combinations of cross-linkers and introduced mutations. We also describe an experiment plan for the bacteriophage lambda Tfa chaperone protein in which we plan dicysteine mutants for discriminating threading models by disulfide formation. Preliminary results from a subset of the planned experiments are consistent and demonstrate the practicality of planning. Our methods provide the experimenter with a valuable tool (available from the authors) for understanding and optimizing cross-linking experiments.

Algorithms↗
PubMed2006

Binding of oxovanadium ions to the major and minor grooves of DNA duplex: stability and structural models.

Vanadate induces DNA strand breaks in cultured human fibroblasts at doses that are relative to the occupational exposure. Oxovanadium compounds also exert preventive effects against chemical carcinogenesis in animals and form complexes with DNA in vivo. This study was designed to examine the interaction of calf-thymus DNA with VO2+ and VO3 ions in aqueous solution at physiological pH, with a constant DNA concentration of 12.5 mmol/L and vanadium-DNA (phosphate) molar ratios (r) of 1:160 to 1:2. Capillary electrophoresis and Fourier transform infrared difference spectroscopy were used to determine the cation binding site, the binding constant, the helix stability, and DNA conformation in the oxovanadium-DNA complexes. Structural analysis showed that VO2+ binds DNA through guanine and adenine N-7 atoms and the backbone PO2 group with apparent binding constants of KG = 8.8 x 10(5) (mol/L)-1 and KA = 3.4 x 10(5) (mol/L)-1. The VO3 shows weaker binding through thymine, adenine, and guanine bases, with K = 1.9 x 10(4) (mol/L)-1 and no interaction with the backbone phosphate group. A partial B-to-A DNA transition occurred upon VO-DNA complexation, while DNA remains in the B-family structure in the VO3 complexes.

Animals↗
PubMed2005

[The biology of hair follicle].

The human hair follicle is a unique appendage which results from epithelio-mesenchymal interactions initiated around the 3rd month of development. This appendage has a very complex structure, with more than 20 different cell types distributed into 6 main compartments, namely the connective tissue sheath, the dermal papilla, the outer root sheath, the inner root sheath, the shaft and the sebaceous gland. The pigmentation unit, responsible for hair color, is made of fully active melanocytes located on top of the dermal papilla. This complex appendage has a unique behavior in mammals since, after a hair production phase, it involutes in situ before entering a resting phase after which it renews in a cyclical but stochastic fashion, out of a double reservoir of pluripotent stem cells also to able regenerate epidermis. The pigmentation unit also renews in a cyclical fashion, out of a melanocyte progenitor reservoir which progressively declines with time, provoking the hair whitening process. Finally, the shape of the hair shaft is programmed from the bulb. The hair follicle thus behaves as a fully autonomous skin appendage with its own hormonal control, its own autocrine and paracrine network, its own cycle, appearing as an incredibly complex and stable structure which summarizes the main rules of tissue homeostasis.

Aging↗
PubMed2003

Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands.

Engagement of diverse protein ligands (MIC-A/B, ULBP, Rae-1, or H60) by NKG2D immunoreceptors mediates elimination of tumorigenic or virally infected cells by natural killer and T cells. Three previous NKG2D-ligand complex structures show the homodimeric receptor interacting with the monomeric ligands in similar 2:1 complexes, with an equivalent surface on each NKG2D monomer binding intimately to a total of six distinct ligand surfaces. Here, the crystal structure of free human NKG2D and in silico and in vitro alanine-scanning mutagenesis analyses of the complex interfaces indicate that NKG2D recognition degeneracy is not explained by a classical induced-fit mechanism. Rather, the divergent ligands appear to utilize different strategies to interact with structurally conserved elements of the consensus NKG2D binding site.

Amino Acids↗
PubMed1988

Analysis of conformational parameters in nucleic acid fragments. IV. Intercalating drug complexes of very short chain oligonucleotides.

Studies have been made of base-pairing conformational parameters in single crystal structures of very short chain oligonucleotide structures complexed with drug molecules, using data extracted from the Cambridge structural database. The planar portion of the drug has a tendency to intercalate between two bases, utilising strong stacking interactions to stabilise the configuration. The effect of the existence of a formative backbone is seen in the high occurrence of standard base-pairing schemes and a consistent C1'-C1' separation, although the choice of compounds studied does tend to emphasise complementary pairing. In addition to the modulation of the general magnitude which is reduced from that in uncomplexed oligonucleotides, there appears to be some correlation of propeller twist value with the presence of planar groups sandwiching a base-pair. The average twist in such sandwiched pairs is lower than in any other group studied to date.

Base Composition↗
PubMed1988

Collisional spectroscopy in structural characterization of melanins. 2--Laser desorption experiments on bio- and synthetic tryptophan melanins.

Melanins are naturally occurring macromolecules whose structural complexity appeared evident from the first researches of Quilico. Their structural characterization remains a difficult problem, mainly due to the physico-chemical properties of such compounds. Melanins are insoluble in organic solvents as well as aqueous solutions and are infusible. Consequently the traditional chemical degradation and physicochemical methods such as ultraviolet, infrared, 1H and 13C nuclear magnetic resonance, ESR (electron spin resonance), XPS (X-rays photoelectron spectroscopy) and X-ray diffraction have led, until now, to limited information on melanin chemical structure.

Chemical Phenomena↗
PubMed1991

Site-specific integration of genes into hot spots for recombination flanking aadA in Tn21 transposons.

Tn21-related transposons are widespread among bacteria and carry various resistance determinants at preferential sites, hs1 and hs2. In an in vivo integrative recombination assay it was demonstrated that these hot spots direct the integration of aminoglycoside resistance genes like aadB from Klebsiella pneumoniae and aacAI from Serratia marcescens, in a recA- background. The maximum required recognition sequence which must be present in both the donor and recipient plasmids is 5' CTAAAACAAAGTTA 3' (hs2). The double-site-specific recombination occurred with a frequency of 10(-5)-10(-6). The resulting structures include not only replicon fusion products but also more complex structures carrying two copies of the donor plasmid or simply the donor gene flanked by hs elements. hs1 and hs2 are thought to act as recognition sites for a transacting site-specific recombinase. By the use of Tn21 deletion derivatives, it has been shown that the recombinase is not encoded by Tn21. This new integrative recombination system is involved in the acquisition of new genes by Tn21-related transposons and their spread among bacterial populations.

Base Sequence↗
PubMed2004

Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair.

Flap EndoNuclease-1 (FEN-1) and the processivity factor proliferating cell nuclear antigen (PCNA) are central to DNA replication and repair. To clarify the molecular basis of FEN-1 specificity and PCNA activation, we report here structures of FEN-1:DNA and PCNA:FEN-1-peptide complexes, along with fluorescence resonance energy transfer (FRET) and mutational results. FEN-1 binds the unpaired 3' DNA end (3' flap), opens and kinks the DNA, and promotes conformational closing of a flexible helical clamp to facilitate 5' cleavage specificity. Ordering of unstructured C-terminal regions in FEN-1 and PCNA creates an intermolecular beta sheet interface that directly links adjacent PCNA and DNA binding regions of FEN-1 and suggests how PCNA stimulates FEN-1 activity. The DNA and protein conformational changes, composite complex structures, FRET, and mutational results support enzyme-PCNA alignments and a kinked DNA pivot point that appear suitable to coordinate rotary handoffs of kinked DNA intermediates among enzymes localized by the three PCNA binding sites.

Archaeoglobus↗
PubMed2003

Are gap junction membrane plaques implicated in intercellular vesicle transfer?

Gap junction channels are concentrated in specialised plaques of plasma membrane where cells are in close apposition. In this communication evidence is provided showing that these specialised regions of membrane also provide a site for vesicular transfer between cells. Vesicle distribution in eye lenses was found to generally reflect the reported distribution of gap junction membrane plaques. In certain areas of the lens gap junction membrane plaques and vesicles could be seen to form combined, complex structures. Ultrastructure of the vesicle and gap junction membrane plaque complexes was consistent with the vesicles moving through membrane plaques from one lens fibre cell to the next. To investigate whether transport of substances was consistent with intercellular vesicle transfer, transport of various markers was investigated. Time course experiments showing the rate of uptake of various markers into the lens did not show dramatic differences for molecules smaller or larger then gap junction pores formed by connexons. While considered as a primary intercellular transport mechanism in the lens, connexon pores were not the sole agent mediating the observed transport. Other reported mechanisms of intercellular transport in the lens can only account for the movement of relatively small molecules. Vesicular transport may therefore be a major form of transport into the outer lens layers for larger molecules. Implicit in these observations is a new hypothesis for intercellular vesicle movement via gap junction membrane plaques. Intercellular vesicle movement could possibly provide a path for large molecules associated with intact vesicles to be transported into the eye lens tissue.

Animals↗