Structural Functional Characteristics Research Articles

Assessment of the present-day state of cooling-basin ecosystem at the Berezovskaya State Regional Power Plant, Krasnoyarsk Territory

The present-day state of the ecosystem of the cooling reservoir of the Berezovskaya State District Power Plant (SDPP) in Krasnoyarsk Territory was assessed in the vegetation period of 2003. The structural-functional characteristics of bacterio-, phyto-, and zooplankton, zoobenthos, and ichthyofauna are considered. Heated waters are supposed to affect the morphology of zooplankters.

Inhibition of Cell Growth in T47D Cancer Cell Line by VACM‐1/cul‐5 is Dependent on its Neddylation and Phosphorylation Status

VACM-1 shares sequence homology with cullins, a family of genes involved in the ubiquitin ligase complex formation and subsequent protein degradation. When expressed in T47D breast cancer cells VACM-1 inhibits growth. The mechanism underlying VACM-1 regulated cell growth involves a decrease in MAPK phosphorylation and in nuclear early growth response element (egr-1) concentration. Little is known about the structure-function characteristics of this protein, however. Since the biological activity of cullins may be regulated by their neddylation status, we next mutated the putative neddylation site in VACM-1 cDNA sequence (K724AVACM-1). In addition, proteins can be regulated by their phosphorylation status. Thus the PKA-dependent phosphorylation site at Ser 730 of VACM-1 sequence was mutated (S730AVACM-1). Finally, a double mutant K724A/S730AVACM-1 cDNA was generated. The expression of all three mutant cDNAs in T47D cells significantly increased cellular proliferation and induced MAPK phosphorylation when compared to the vector or VACM-1 cDNA transfected cells. These data indicate that the regulation of cell growth by VACM-1 is dependent on its phosphorylation and/or neddylation status. Supported by NIH 1R15 CA104014, the Camille and Henry Dreyfus Foundation Grant, and Merck Award to Hope College.

Structural and mutational studies of organophosphorus hydrolase reveal a cryptic and functional allosteric-binding site

Organophosphorus hydrolase detoxifies a broad range of organophosphate pesticides and the chemical warfare agents (CWAs) sarin and VX. Previously, rational genetic engineering produced OPH variants with 30-fold enhancements in the hydrolysis of CWA and their analogs. One interesting variant (H254R) in which the histidine at position 254 was changed to an arginine showed a 4-fold increase in the hydrolysis of demetonS (VX analog), a 14-fold decrease with paraoxon (an insecticide), and a 183-fold decrease with DFP (sarin analog). The three-dimensional structure of this enzyme at 1.9 Å resolution with the inhibitor, diethyl 4-methylbenzylphosphonate (EBP), revealed that the inhibitor did not bind at the active site, but bound exclusively into a well-defined surface pocket 12 A away from the active site. This structural feature was accompanied by non-competitive inhibition of paraoxon hydrolysis by EBP with H254R, in contrast to the native enzyme, which showed competitive inhibition. These parallel structure–function characteristics identify a functional, allosteric site on the surface of this enzyme.

Conservation of the Heterodimeric Glycoprotein Hormone Subunit Family Proteins and the LGR Signaling System from Nematodes to Humans

Glycoprotein hormones, follicle-stimulating hormones (FSHs), luteinizing hormones (LHs), thyroid-stimulating hormones (TSHs), and chorionic gonadotropin (CG) are key endocrine hormones secreted from the pituitary gonadotrophs and thyrotrophs and the placenta in primates. These hormones, consisting of a common alpha subunit and a specific beta subunit, act through the FSH receptor (FSHR), the LH receptor (LHR), and the TSH receptor (TSHR) that are highly specific for their cognate hormones. These glycoprotein hormones are structurally and functionally conserved in various vertebrates and have been identified in most lineages of actinopterygians (bony fish) and sarcopterygians (tetra-pods). Of interest, recent genomic studies showed that vertebrate glycoprotein hormone receptors belong to an ancient subfamily of G protein-coupled receptors (GPCRs) named as leucine-rich repeat-containing GPCRs (LGRs). These findings have prompted the hypothesis that there could be additional glycoprotein hormones in vertebrate genomes. Indeed, searches of vertebrate genomes have led to the identification of two novel glycoprotein hormone subunits, glycoprotein alpha 2 (GPA2) and glycoprotein beta 5 (GPB5), as well as their homologs in invertebrates. Subsequently, it was demonstrated that GPA2 and GPB5 form a heterodimeric hormone, thyrostimulin/OGH, capable of activating TSHR in vivoand the thyroid axis in transgenic mice. However, the exact role of this novel glycoprotein hormone and its homolog in invertebrates is not clear. To gain a better understanding of the physiological role of the novel glycoprotein hormone subunits and their evolution, it is imperative to carry out systematic studies of these genes in representative model species. In the present report, we summarize our findings based on studies of genomes of model organisms from sea anemones to humans. We found that GPA2 and GPB5 represent the ancient forms of glycoprotein hormone alpha and beta subunits, respectively, and that vertebrate and invertebrate glycoprotein hormone subunit proteins shared common ancestors that evolved during early metazoan evolution. It is important to note that glycoprotein hormone alpha and beta subunit proteins from invertebrates formed a heterodimer with structural functional characteristics similar to that of vertebrate glycoprotein hormones. Taken together, both glycoprotein hormone alpha and beta subunits evolved before the evolution of nematodes, arthropods, and vertebrates.

Genome-wide transcriptional profiles are consistent with functional specialization of the extraocular muscle layers.

Compartmentalization of the extraocular muscles into well-defined orbital and global layers is highly conserved. Recently, the active pulley hypothesis correlated the anatomic properties of orbital-global muscle layers with layer-specific division of labor. Microarray technology was used to identify muscle-layer-specific transcriptional profiles and, thereby, extend understanding of the structure-function characteristics of extraocular muscle layers. Laser capture microdissection was used to obtain muscle layer samples from monkey medial rectus muscles. RNA was linearly amplified and hybridized to human U133 series microarrays (Affymetrix, Santa Clara, CA), which have sufficient sequence homology for use in subhuman primates. Data was analyzed using Affymetrix and Robust Multichip Average (RMA) algorithms. Select transcripts were verified by quantitative PCR and in situ hybridization. A broad spectrum of transcriptional differences (> 181 transcripts) was identified between the two extraocular muscle layers. Patterned differences in the sarcomeric contractile machinery and cytoskeleton were suggestive of key layer differences in contraction speed. Differentially expressed transcript identities, however, extended well beyond those traditionally associated with muscle-fiber-group differences. Muscle layer transcriptional profiles correlated with the different loads and usage patterns of extraocular muscle layers, as proposed in the active pulley hypothesis. The magnitude and breadth of orbital-global layer expression differences strongly suggests that oculomotor control systems may drive two distinct motor output pathways, each comprising separate motoneurons and muscle fibers, with one output path adapted to determining pulley position and the other to movement of the eye.

Folding and Stability of Chimeric Immunofusion VL-Barstar

A chimeric protein VL-barstar that comprises the VL domain of anti-human ferritin monoclonal antibody F11 and barstar, the naturally occurring inhibitor of bacterial RNase barnase, has been constructed for study of structure-function characteristics of chimeric immunoglobulin fused proteins. Such chimeric constructs may be potentially employed for development of bivalent/bispecific antibodies on the basis of the high affinity interaction between barstar and barnase (the association constant is about 10(14) M(-1)). We have developed a protocol for VL-barstar expression in E. coli and purification and refolding from inclusion bodies that yields a homogeneous and soluble form of this protein. Differential scanning calorimetry in combination with fluorescence and CD spectroscopy revealed that the VL-barstar formed well-resolved ordered secondary and compact tertiary structures. However, partial loss of tertiary interactions resulted in low stability of the recombinant protein and the lack of functional activity of the two constituent modules. These conformational features suggest that the protein might be referred to the class of native molten globules, which comprises partially unfolded conformations stabilized under physiological conditions. Since individually expressed VL domain and barstar retain completely folded conformation and stable spatial structure, the incomplete folding of the chimeric protein may be attributed to interaction between heterologous domains, which appears at the folding stage preceding formation of a system of tertiary interactions in both structural modules. The results provide evidence for non-native interactions between heterologous modules that may occur in chimeric proteins composed of taxonomically distinct fusion partners.

Formation and structural organization of the barrier on the outer surface of the brain.

Studies of the structural-functional organization of the boundaries separating different media in the CNS are needed for identification of the barrier mechanisms allowing the creation and maintenance of the constant-composition internal medium. The outer surface of the brain occupies a special position among the anatomical zones of brain barriers. In all areas, this is formed by layer I of the cortex, which serves as the collector of afferent fibers of cortical and extracortical origin and therefore has a key role in forming neocortical cytoarchitectonics at the early stages of ontogenesis [9, 13]. Some authors have suggested that there is a complex structure between the brain and the meningeal vessels, this being typical of the blood-brain barrier (BBB) [12], while other investigators believe that the typical CSFbrain barrier (CBB) occurs at this location, with all the corresponding structural elements [8]. Current data on the existence of a volume transmission effect and the role of barrier structures in forming and regulating the composition of the intercellular medium of the brain [4, 6] indicate that studies of the structural-functional characteristics of cellular and non-cellular elements on the brain surface as a boundary separating media are relevant. This could be significantly facilitated by use of the ontogenetic approach, allowing the development and differentiation of nerve and glial elements to be followed and compared in relation to the type of nutrition of nerve tissue, formation of the vascular bed, and the brain’s acquisition of definitive structural features. Increases in the organizational complexity of the brain in a series of vertebrates are paralleled by specialization and differentiation of its barrier systems [10]. Thus, there is significant interest in studying the organization of the surface barrier system of the human brain, data on the structure and formation of which are incomplete and contradictory. Thus, the aim of the present work was to study barrier structures on the outer surface of the forming human brain during the early prenatal period of development.

Correlated Single Molecule Fluorescence and Scanning Probe Microscopies: Applications to the Study of Soft Materials

ABSTRACTWe recently developed an integrated imaging platform that combines single molecule evanescent wave fluorescence imaging (and spectroscopy) with in situ scanning probe microscopy. The advantages, challenges, and potential represented by this coupled tool will be described in the context of the structure-function characteristics of nanostructured biomaterials and thin lipid films.

Correlated Single Molecule Fluorescence and Scanning Probe Microscopies: Applications to the Study of Soft Materials

AbstractWe recently developed an integrated imaging platform that combines single molecule evanescent wave fluorescence imaging (and spectroscopy) with in situ scanning probe microscopy. The advantages, challenges, and potential represented by this coupled tool will be described in the context of the structure-function characteristics of nanostructured biomaterials and thin lipid films.

Recombinant glutamate carboxypeptidase II (prostate specific membrane antigen--PSMA)--cellular localization and bioactivity analyses.

Glutamate Carboxypeptidase II (also known as Prostate Specific Membrane Antigen-PSMA) is an important marker in the diagnosis of prostate cancer, however, relatively little is known about its biochemical and structure-function characteristics. We have expressed mutant forms of PSMA and have started to address the roles of three putative domains of PSMA in its cellular localization and peptidase activity. Three mutants, a full-length recombinant PSMA (rPSMA-FL), one expressing only the proposed extracellular domain of PSMA (rPSMA-ECD) and one form omitting the proposed transmembrane domain (rPSMA-deltaTMD) have been produced in human cells via a mammalian expression vector system. We show that rPSMA-FL is associated with the cell surface membrane; so too is rPSMA-deltaTMD even though it lacks the proposed transmembrane domain, whereas rPSMA-ECD has a cytosolic localization. Only rPSMA-FL retains functional hydrolytic activity and is similarly glycosylated to PSMA found in the cultured prostate cancer cell line LNCaP.

Some Adaptive Structural-Functional Characteristics of Fish Epidermis and its Derivatives

Some Adaptive Structural-Functional Characteristics of Fish Epidermis and its Derivatives

Effects of Temperature, pH, and Organic Phosphates on Fish Hemoglobins

This review presents data on effects of temperature, pH, and organic phosphates on structural-functional characteristics of fish hemoglobins. Special attention is paid to the structure of pigments insensitive to pH as well as those that have the reverse Bohr effect in alkaline range of pH. The role of surface β-adrenoreceptors and activity of Na+/H+ exchanger in regulation of the acid-base equilibrium of intraerythrocyte medium are considered. There are compared characteristics of participation of nucleotide triphosphates, 2,3-DPG, and other organic phosphates in correction of fish hemoglobin affinity to oxygen. The values of ΔH for fish respiratory pigments are presented, and their dependence on conditions of erythrocyte microsurrounding is discussed.

Solar MHD turbulence in regions with various levels of flare activity

The paper continues investigations of MHD turbulence in active solar regions. The statistical distributions of the increments (structure functions) of the turbulent field are studied analytically in the context of a refined Kolmogorov theory of turbulence. Since photospheric transport of the Bz component of the magnetic field is quite similar to that of a scalar field in a turbulent flow, the theory of transport of a passive scalar can be applied. This approach enables us to show that the structure functions are determined by the competition between the dissipation of the magnetic and kinetic energies and to obtain a number of relations between the structure-function parameters and energy characteristics of the MHD turbulence. Taking into account general conclusions that can be drawn on the basis of the refined Kolmogorov turbulence theory, the structure functions of the Bz field are calculated for eight active regions (from measurements of SOHO/MDI and the Huairou Solar Observing Station, China). These calculations show that the behavior of the structure functions is different for the Bz field of each active region. The energy-dissipation index of the fluctuation spectrum (which is uniquely determined by the structure functions) is closely related to the level of flare activity: the more activity, the less steep the dissipation spectrum for a given active region. This provides a means to test and, consequently, forecast the flare activity of active regions.

Structure function characteristics for 2 metre temperature and relative humidity in different horizontal resolutions

The isotropic correlations of forecast errors in the HIRLAM system are investigated for differenthorizontal grid sizes in order to achieve an improved representation of the structure functionsfor high-resolution surface analysis. The investigation is performed for 2 metre temperature andrelative humidity and makes use of operational forecasts from DMI-HIRLAM at the DanishMeteorological Institute (DMI), which can support the background for a surface analysis inthree different horizontal resolutions. Two different well-known methods for determining isotropicforecast error correlations are applied. The first method compares forecasts to observations(the Observation Method), while the second makes use of two different forecasts validfor the same time (the NMC Method). The latter method is also used to investigate isotropyas well as the influence of land’sea contrast and orography. A comparison of the two mentionedmethods reveals a good correspondence between them, and the investigation of monthly changesshows some seasonal tendencies. The isotropy assumption is shown to be acceptable to a firstapproximation, despite a slight dependency on the predominant flow. The results further suggesta decrease in the background error correlation scales when going to higher horizontal resolutionin the forecast model.

Structure function characteristics for 2 metre temperature and relative humidity in different horizontal resolutions

Structure function characteristics for 2 metre temperature and relative humidity in different horizontal resolutions

The N terminus of the centromere H3-like protein Cse4p performs an essential function distinct from that of the histone fold domain.

Cse4p is an evolutionarily conserved histone H3-like protein that is thought to replace H3 in a specialized nucleosome at the yeast (Saccharomyces cerevisiae) centromere. All known yeast, worm, fly, and human centromere H3-like proteins have highly conserved C-terminal histone fold domains (HFD) but very different N termini. We have carried out a comprehensive and systematic mutagenesis of the Cse4p N terminus to analyze its function. Surprisingly, only a 33-amino-acid domain within the 130-amino-acid-long N terminus is required for Cse4p N-terminal function. The spacing of the essential N-terminal domain (END) relative to the HFD can be changed significantly without an apparent effect on Cse4p function. The END appears to be important for interactions between Cse4p and known kinetochore components, including the Ctf19p/Mcm21p/Okp1p complex. Genetic and biochemical evidence shows that Cse4p proteins interact with each other in vivo and that nonfunctional cse4 END and HFD mutant proteins can form functional mixed complexes. These results support different roles for the Cse4p N terminus and the HFD in centromere function and are consistent with the proposed Cse4p nucleosome model. The structure-function characteristics of the Cse4p N terminus are relevant to understanding how other H3-like proteins, such as the human homolog CENP-A, function in kinetochore assembly and chromosome segregation.

Investigations into the cross-reactivity of rabbit antibodies raised against nonhomologous pairs of synthetic peptides derived from HIV-1 gp120 proteins.

The immunological cross-reactivity of several peptides with specific pattern-property characteristics related to the epitopes of human immunodeficiency virus type 1 (HIV-1) gp160/ 120 envelope proteins has been investigated. Proteins with similar primary structures can be expected to show functional or topographic similarities, such as specific epitopes which may cross-react with antibodies derived from the immunisation of animals with other members of the same protein family. These structure-function characteristics may be revealed as periodicities derived from presentations based on the discrete Fourier transformation of the distributions of various physico-chemical amino acid descriptors, constituting the polypeptide backbone and amino acid side-chains of the protein molecule. Such approaches, for example, have permitted prediction of periodicities corresponding to secondary structural motifs, including amphipathic alpha-helices and beta-sheets, within protein sequences, and have helped to clarify potential binding sites for ligands, substrates or cofactors with interacting macromolecules. Based on this approach, characteristic periodicities have been identified which represent common Fourier transform spectral properties of the envelope (ENV) gp160/120 glycoproteins from a range of HIV-1 isolates. In addition, similar periodicities have been detected as components of the discrete Fourier transform representation of the corresponding amino acid descriptors of the CD4 binding domain of gp120. Accordingly, we have synthesised several peptides having periodic characteristics in their discrete Fourier transform representations similar to these HIV-1 proteins. These nonhomologous synthetic peptides induced cross-reactive antibodies in New Zealand White rabbits. Polyclonal antibodies raised to one of these peptides reacted with HIV-1 ENV gp120-related proteins, as determined by enzyme-linked immunosorbent assay and Western blotting techniques. These findings provide further evidence for a role of immunological cross-reactivity and molecular biomimicry in the development of peptide-based vaccines directed against viral or bacterial pathogens.

Structural-functional characteristics of toxins from spiders of the araneidae family

With the aid of a series of chromatographic operations we have isolated 14 individual tow-molecular-mass compounds (MT — 624-744 Da) blocking postsynaptic glutamate and acetylcholine receptors from the venoms of species of spiders of the family Araneidae. It has been shown that from their structural characteristics and the nature of their action they can be divided into two families differing by their chromophoric groups and the degree of reversibility of their interaction with various receptors.

Structural-functional characteristics of some protein-peptide regulators of the transmissions of a hormonal signal in the cotton plant

Water-soluble cytokinin- and ethylene-binding proteins have been isolated from cotton plant shoots, and some of their physicochemical characteristics have been studied. It has been shown that, by a number of criteria, the proteins isolated must be assigned to the phytohormone receptors.

Heparin cofactor II and thrombin: Heparin-binding proteins linking hemostasis and inflammation

α-Thrombin is a trypsinlike serine proteinase involved in blood coagulation and wound-healing processes, which interacts with many different macromolecular substances. Heparin cofactor II is a serpin (serine proteinase inhibitor) superfamily member that specifically inhibits thrombin but no other proteinase in blood coagulation. Both heparin cofactor II and thrombin interact with highly negatively charged glycosaminoglycans like heparin and dermatan sulfate, and they both are leukocyte chemoattractants. The focus of this brief review is structure-function characteristics of heparin cofactor II and thrombin and their physiologic participation in uniting hemostatic and inflammatory processes.