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Actin binding proteins: regulation of cytoskeletal microfilaments.

The actin cytoskeleton is a complex structure that performs a wide range of cellular functions. In 2001, significant advances were made to our understanding of the structure and function of actin monomers. Many of these are likely to help us understand and distinguish between the structural models of actin microfilaments. In particular, 1) the structure of actin was resolved from crystals in the absence of cocrystallized actin binding proteins (ABPs), 2) the prokaryotic ancestral gene of actin was crystallized and its function as a bacterial cytoskeleton was revealed, and 3) the structure of the Arp2/3 complex was described for the first time. In this review we selected several ABPs (ADF/cofilin, profilin, gelsolin, thymosin beta4, DNase I, CapZ, tropomodulin, and Arp2/3) that regulate actin-driven assembly, i.e., movement that is independent of motor proteins. They were chosen because 1) they represent a family of related proteins, 2) they are widely distributed in nature, 3) an atomic structure (or at least a plausible model) is available for each of them, and 4) each is expressed in significant quantities in cells. These ABPs perform the following cellular functions: 1) they maintain the population of unassembled but assembly-ready actin monomers (profilin), 2) they regulate the state of polymerization of filaments (ADF/cofilin, profilin), 3) they bind to and block the growing ends of actin filaments (gelsolin), 4) they nucleate actin assembly (gelsolin, Arp2/3, cofilin), 5) they sever actin filaments (gelsolin, ADF/cofilin), 6) they bind to the sides of actin filaments (gelsolin, Arp2/3), and 7) they cross-link actin filaments (Arp2/3). Some of these ABPs are essential, whereas others may form regulatory ternary complexes. Some play crucial roles in human disorders, and for all of them, there are good reasons why investigations into their structures and functions should continue.

Actins↗

Procyanidins as antioxidants and tumor cell growth modulators.

Five procyanidin fractions with different structural complexities were obtained after fractionation of a grape seed extract. The procyanidin fraction's abilities to inhibit lipid peroxidation induced by 2,2'-azobis-2-methyl-propanimidamide dihydrochloride in a liposomal membrane system were examined. The antioxidant capacities of all fractions were evaluated through monitoring oxygen consumption and by measuring the formation of conjugated dienes. All tested fractions provided protection of membranes against peroxyl radicals by increasing the induction time of oxidation. This effect increased up to fraction II but decreased with the increase of the structural complexity of further procyanidin fractions, possibly due to steric hindrance effects exhibited by the more complex fractions. In addition, the antiradical properties and the reducing power of these fractions were determined by using 2,2-diphenyl-1-picrylhydrazyl and ferric reducing/antioxidant power methods, respectively. Moreover, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium-bromide reduction and DNA synthesis were measured in Michigan Cancer Foundation 7 (MCF-7), a human breast cancer cell line, treated with catechin or procyanidin fractions in order to evaluate the effect of these compounds on cell viability and proliferation. The results obtained showed that at 30 microg/mL, fractions I and II decreased cell viability and proliferation, which was not observed with 60 microg/mL of the same fractions. Catechin was also able to decrease cell viability and proliferation at 30 and 60 microg/mL. It is interesting to notice that the procyanidin fractions that exhibited higher antioxidant activity were the same to affect cell viability and proliferation.

Antineoplastic Agents↗

Current and future considerations for the new classes of biologicals.

PURPOSE: Key structural features of biologicals and their development are explained, and the fundamental distinctions between biological and chemical drugs in terms of their discovery, scale-up from research to commercial quantities, quality control, regulatory requirements, and potential for generic substitution are discussed. SUMMARY: Recent advances in biotechnology have accelerated the introduction of biological protein drugs into the marketplace, offering new treatment options and challenges for pharmacists. Because these drugs are produced in living systems and are structurally complex, they are more difficult to manufacture, purify, and evaluate than are traditional chemical drugs. The production of recombinant-DNA-based protein and monoclonal antibody drugs is explained, and the strengths and limitations in selecting one or another host system (i.e., bacteria, yeast, or mammalian cells) for making a given biological drug are explored. Subtle variations in production methods can lead to significant differences in product volume, potential viral or bacterial contamination, bioactivity, and toxicity. Like manufacturers, federal regulators face difficult new challenges because of the structural complexity and in vivo synthesis of biologicals. Pharmacists and regulators alike must determine when and if therapeutic interchange is relevant to biologicals. Because biologicals are so difficult to manufacture and test, noninnovator biologicals must be subject to more oversight than traditional generic drugs. CONCLUSION: Biologicals are complex agents whose production and properties present many considerations that are not associated with traditional chemical drugs.

Biological Products↗

Morpho-functional evaluation of osteomeatal complex in chronic sinusitis by coronal CT.

The objective was to determine whether or not there exists a clinical-radiological correlation in chronic sinusitis of anterior paranasal sinus and to quantitatively evaluate the importance of osteomeatal complex structures and anatomic variants in chronic sinusitis etiopathology. We analyzed 208 nasal fossae with high-resolution and low-irradiation coronal computed tomography. The following inclusion criteria we established: one case control and one control group. We considered any chronic thickness of sinusal mucosal as a radiological indicator of chronic sinusitis. We evaluated the mucosal thickness of internal, external, superior and inferior maxillary walls, the addition of four maxillary walls and the maximal mucosal thickness in frontal sinus and anterior ethmoidal cells. We also obtained 15 parameters of osteomeatal complex structures and anatomical variants in each nasal fossa, and we correlated them statistically with chronic sinusitis radiological indicators. Uncinate process length is the only anatomic element from which we have been able to obtain a statistically significant cut point between case and control groups, but only with a sensitivity of 51.6%, specificity of 71.2%, positive predictive value of 74.2%, and negative predictive value of 47.9%. No association of radiological parameters exists that can explain chronic sinusitis.

Adult↗

A new episcopic method for rapid 3-D reconstruction: applications in anatomy and embryology.

The topographic relations of complex structures and the morphogenesis of organ systems can only be fully understood in their three-dimensional context. Three-dimensional (3-D) reconstruction of physically sectioned specimens has become an indispensable tool in modern anatomical and embryological research. Teaching also makes increasingly use of 3-D representations, in particular in the case of embryonic systems that undergo complicated transformations of form and shape. At present no cheap and simple technique is available that generates accurate 3-D models of sectioned objects. In this study we describe a novel technique that rapidly provides faithful 3-D models of sectioned specimens. The images are captured directly from the cutting surface of the embedding block after each sectioning and "on block" staining step. Automatic image processing generates a stack of binary images of the specimen contour. Binary images of internal structures are obtained both by automatic segmentation and manual tracing. Since these image series are inherently aligned, they can be reconstructed three-dimensionally without time-consuming alignment procedures. The quality and the flexibility of the method are demonstrated by reconstructing three kinds of specimens of different histological composition and staining contrast: a 4 mm mouse embryo together with several of its inner organs, a cavernous sinus region of a human infant, and a segment of a human carotid artery. Very short processing times and the faithful representation of complex structural arrangements recommend this technique for routine use in morphological research and for creating embryologic teaching models or 3-D embryonic staging series.

Anatomy, Cross-Sectional↗

Detection of Escherichia coli O157:H7 using immunomagnetic separation and absorbance measurement.

An assay system for detection of Escherichia coli O157:H7 was developed based on immunomagnetic separation of the target pathogen from samples and absorbance measurement of p-nitrophenol at 400 nm from p-nitrophenyl phosphate hydrolysis by alkaline phosphatase (EC 3.1.3.1) on the "sandwich" structure complexes (antibodies coated onto micromagnetic beads--E. coli O157:H7-antibodies conjugated with the enzyme) formed on the microbead surface. The effects of immunoreaction time, phosphate buffer concentration, pH and temperature on the immunomagnetic separation of E. coli O157:H7 from samples were determined and the conditions used for the separation were 1-h reaction time, 1.0 x 10(-2) M PBS, pH 8.0 and 33 degrees C in this system. The effects of MgCl(2) concentration, Tris buffer concentration, pH and temperature on the activity of alkaline phosphatase conjugated on the immuno-"sandwich" structure complexes were investigated after immunomagnetic separation of the target pathogen and the conditions used for the enzymatic amplification were 1.0 x 10(-4) M MgCl(2), 1.0 M Tris buffer, pH 8.0, 28 degrees C and 30-min reaction time during the assay. The selectivity of the system was examined and no interference from the other pathogens including Salmonella typhimurium, Campylobacter jejuni and Listeria monocytogenes was observed. Its working range was from 3.2 x 10(2) to 3.2 x 10(4) CFU/ml, and the relative standard deviation was 2.5-9.9%. The total detection time was less than 2 h.

Alkaline Phosphatase↗

Direct imaging of interactions between an icosahedral virus and conjugate F(ab) fragments by cryoelectron microscopy and X-ray crystallography.

The binding properties of seven mouse monoclonal antibodies (McAbs) raised against cowpea mosaic virus (CPMV) were characterized by conventional and inhibition enzyme-linked immunosorbent assay (ELISA) technique. McAb binding to CPMV on electron microscope (EM) grids was also assayed with gold-labeled anti-mouse antibodies. Two of the seven McAbs (5B2 and 10B7) were found to bind tighter to CPMV than the others in the inhibition ELISA and the EM assay. F(ab) fragments from both of these McAbs were prepared and complexed with CPMV in solution. Electron micrographs of flash frozen (vitrified) samples of native CPMV and CPMV complexed with F(ab) fragments from McAbs 5B2 and 10B7 as well as IgGs from 5B2 were recorded and reconstructions were computed at 23 A resolution for the CPMV/F(ab) complexes and 30 A resolution for the CPMV/IgG complex. Structures of all three complexes clearly displayed the F(ab) fragments distributed with icosahedral symmetry on the surface of CPMV. The IgG bound in a monodentate fashion with only one F(ab) attached to the virus surface. F(ab) fragments from 5B2 and 10B7 bound to nearly identical positions. The refined 2.8 A X-ray structure of CPMV was used to identify the roughly 30 amino acids covered by the F(ab) fragments. The "footprint" spans a subunit interface and appears spatially similar to antigenic site 3B on poliovirus. In a previous, preliminary report of the CPMV/F(ab) 5B2 complex (Wang et al., 1992, Nature 355, 275-278) the wrong enantiomorph of the reconstruction was chosen. This was corrected and, since the F(ab) binds close to a mirror plane, the change in the footprint was minor.

Animals↗

An ambiguous structure of a DNA 15-mer thrombin complex.

The structure of a complex between thrombin and a GGTTGGTGTGGTTGG DNA 15-mer has been analyzed crystallographically. The solution NMR structure of the 15-mer has two stacked G-quartets similar to that found in the previous X-ray structure determination of the 15-mer-thrombin complex [Padmanabhan, Padmanabhan, Ferrara, Sadler & Tulinsky (1993). J. Biol. Chem. 268, 17651-17654]; the strand polarity, however, is reversed from that of the crystallographic structure. The structure of the complex here has been redetermined with better diffraction data confirming the previous crystallographic structure but also indicating that the NMR solution structure fits equally well. Both 15-mer complex structures refined to an R value of about 0.16 presenting a disconcerting ambiguity. Since the two 15-mer structures associate with thrombin in different ways (through the TGT loop in the X-ray and TT loop in the NMR model), other independent lines of physical or chemical evidence are required to resolve the ambiguity.

Journal Article↗

Scale-free and stable structures in complex ad hoc networks.

Unlike the well-studied models of growing networks, where the dominant dynamics consist of insertions of new nodes and connections and rewiring of existing links, we study ad hoc networks, where one also has to contend with rapid and random deletions of existing nodes (and, hence, the associated links). We first show that dynamics based only on the well-known preferential attachments of new nodes do not lead to a sufficiently heavy-tailed degree distribution in ad hoc networks. In particular, the magnitude of the power-law exponent increases rapidly (from 3) with the deletion rate, becoming infinity in the limit of equal insertion and deletion rates. We then introduce a local and universal compensatory rewiring dynamic, and show that even in the limit of equal insertion and deletion rates true scale-free structures emerge, where the degree distributions obey a power law with a tunable exponent, which can be made arbitrarily close to 2. The dynamics reported in this paper can be used to craft protocols for designing highly dynamic peer-to-peer networks and also to account for the power-law exponents observed in existing popular services.

Journal Article↗

Critical assessment of electron spin resonance studies on Cu(I)-NO complexes in Cu-ZSM-5 zeolites prepared by solid- and liquid-state ion exchange.

Cu(I)-NO adsorption complexes were formed over Cu-ZSM-5 zeolites prepared by (i) solid-state ion exchange of NH(4)-ZSM-5 with CuCl and (ii) liquid-state ion exchange of ZSM-5 with Cu(CH(3)COO)(2). Electron spin resonance spectroscopy revealed the formation of two different Cu(I)-NO species A and B in both systems, whose spin Hamiltonian parameters are comparable with those already reported for the Cu(I)-NO species formed over 66% Cu(II) liquid-state ion-exchanged Cu-ZSM-5 materials. The population of the species A and B differs for the two systems studied. Formation of species B is more favored in the solid-state ion-exchanged Cu-ZSM-5 when compared to the liquid-state exchanged zeolite. The X-, Q- and W-band electron spin resonance spectra recorded at 6 and 77 K reveal the presence of a rigid geometry of the adsorption complexes at 6 K and a dynamic complex structure at higher temperatures such as 77 K. This is indicated by the change in the spin Hamiltonian parameters of the formed Cu(I)-NO species in both the liquid- and solid-state ion-exchanged Cu-ZSM-5 zeolites from 6 to 77 K. Possible models for the motional effects found at elevated temperatures are discussed. The temperature dependence of the electron spin phase memory time measured by two-pulse electron spin-echo experiments indicates, likewise, the onset of a motional process of the adsorbed NO molecules at temperatures above 10 K. The studies support previous assignments where the NO complexes are formed at two different Cu(I) cationic sites in the ZSM-5 framework and highlight that multifrequency electron spin resonance experiments at low temperatures are essential for reliable determination of the spin Hamiltonian parameters of the formed adsorption complexes for further comparison with Cu(I)-NO complex structures predicted by quantum chemical calculations.

Journal Article↗

Low-resolution docking: prediction of complexes for underdetermined structures.

One of the most fundamental questions concerning ligand-receptor interaction is whether such a process of intermolecular association is generally determined by local structural elements of the participating molecules, or whether there are also large-scale motifs in molecule structures that facilitate complex formation. From the point of view of practical docking computations, the elaborate character of local structural details in ligand-receptor interaction creates a large number of false-positive matches, which interfere with determination of the best fit. Another significant obstacle in protein docking is the problem of structural data inaccuracy (poor structure resolution, conformational changes upon complex formation, etc.). Our study [Vakser (1995) Protein Eng., 8, 371-377], based on ultralow (approximately 7 A resolution) representation of molecular structures, allowes to average all high-resolution structural details, and still predict most of the structural features of the ligand-receptor complex. The approach dramatically improves the signal-to-noise ratio in determination of the best fit, and moves the structure inaccuracy tolerance to the range of the macrostructure. In the present paper, we describe a further validation of the main principles of this approach and a detailed analysis of the low-resolution docking results. This includes clustering of ligand positions around the receptor molecule and cross-validation of ligands and receptors from different complexes. We also discuss the important implications of the approach to the multiple-minima problem and a possible role of different structural elements in the recognition mechanism.

Animals↗

Preparation of bionanoreactor based on core-shell structured polyion complex micelles entrapping trypsin in the core cross-linked with glutaraldehyde.

Recently, the polyion complex (PIC) micelle has been suggested as a promising carrier system for peptide and proteins. However, its utilities are limited by its sensitivity to the environment such as dilution and ionic strength of the solution. In this study, to overcome these obstructions, PIC micelles prepared from an anionic block copolymer, poly(ethylene glycol)-poly(alpha,beta-aspartic acid), and a cationic protein, trypsin, were cross-linked with glutaraldehyde through the Schiff base formation. On the basis of a light scattering technique, the results revealed an efficient resistance of the cross-linked PIC micelle to a high salt concentration, which was a key parameter controlling the structure of the PIC micelles. Moreover, the stability of trypsin after cross-linking was remarkably improved. Evidently, as a bionanoreactor and/or bionanoreservoir, the PIC micelles entrapping protein molecules in the cross-linked core reveal an improved stability, allowing their wide application in the fields of biotechnology and pharmaceutical sciences.

Cross-Linking Reagents↗

Overexpression and mechanistic characterization of blastula protease 10, a metalloprotease involved in sea urchin embryogenesis and development.

Blastula protease 10 (BP10) is a metalloenzyme involved in sea urchin embryogenesis, which has been assigned to the astacin family of zinc-dependent endopeptidases. It shows greatest homology with the mammalian tolloid-like genes and contains conserved structural motifs consistent with astacin, tolloid, and bone morphogenetic protein 1. Astacin, a crustacean digestive enzyme, has been proposed to carry out hydrolysis via a metal-centered mechanism that involves a metal-coordinated "tyrosine switch." It has not been determined if the more structurally complex members of this family involved in eukaryotic development share this mechanism. The recombinant BP10 has been overexpressed in Escherichia coli, its metalloenzyme nature has been confirmed, and its catalytic properties have been characterized through kinetic studies. BP10 shows significant hydrolysis toward gelatin both in its native zinc-containing form and copper derivative. The copper derivative of BP10 shows a remarkable 960% rate acceleration toward the hydrolysis of the synthetic substrate N-benzoyl-arginine-p-nitroanilide when compared with the zinc form. The enzyme also shows calcium-dependent activation. These are the first thorough mechanistic studies reported on BP10 as a representative of the more structurally complex members of astacin-type enzymes in deuterostomes, which can add supporting data to corroborate the metal-centered mechanism proposed for astacin and the role of the coordinated Tyr. We have demonstrated the first mechanistic study of a tolloid-related metalloenzyme involved in sea urchin embryogenesis.

Animals↗

Analysis of splicing patterns of human spumaretrovirus by polymerase chain reaction reveals complex RNA structures.

Mapping of transcripts of the human foamy virus genome was carried out in permissive human embryonic fibroblast cells by Northern blot hybridization and S1 nuclease analysis. Since several splice sites that are localized within a relatively narrow genomic region were detected, the polymerase chain reaction (PCR) was employed, and cloning and sequencing of the splice site junctions of the corresponding viral cDNAs were subsequently performed. All spumavirus transcripts have a common but relatively short leader RNA. Genomic, singly spliced env mRNAs and several singly and multiply spliced subgenomic transcripts were identified. The multiply spliced viral mRNAs consist of various exons located in the central or 3' part of the viral genome. At least four novel gene products, termed Bet, Bes, Beo, and Bel3, are predicted to exist. The poly(A) addition site that defines the boundary of the R and U5 region in the 3' long terminal repeat was determined. The pattern of spumavirus splicing is more complex than that of oncoviruses and more similar to that of lentiviruses. One of the characteristic features of spumavirus transcription is the existence of singly spliced bel1 and bel2 mRNAs that alternatively are multiply spliced, thereby generating a complexity comparable to, but different from, that of lentiviruses and from that of other known retroviruses. The complex spumavirus transcriptional pattern of human spumavirus and the coding potential of the 10 exons identified are discussed.

Amino Acid Sequence↗

Escherichia coli cAMP receptor protein-DNA complexes. 2. Structural asymmetry of DNA bending.

The effect of DNA sequence variability and the degree of cyclic AMP receptor protein (CRP)-induced bending of the flanking ends of fluorescently labeled DNA were investigated by steady-state fluorescence and differential phase polarization studies in the presence and absence of CRP. Six sequences, including the primary CRP binding sites of lac P1 (class I) and gal P1 (class II), were studied. Excitation and emission spectra of CPM-DNA upon binding CRP were observed to be qualitatively similar to one another, regardless of the CRP binding site sequence examined or the location of the probe. This result implies that the probe is not interacting with the protein. However, the magnitude of the changes in the fluorescence intensities of sensitized emission spectra of CPM-DNA is apparently dependent on the DNA sequence, indicating that the environments of the flanking ends of DNA may be different from one another in the protein-DNA complex. Differential phase polarization results were qualitatively consistent with the fluorescence energy transfer measurements. The implication of this study supports the idea that the DNA is bent symmetrically in the lac-CRP complex but is asymmetrically bent in the gal-CRP complex. The sequence in the half-site in conjunction with the flanking sequence defines the geometry of the bent DNA. It appears that the CRP-induced bend in the DNA may also be class dependent. This may be an important feature used by the system to regulate transcription at different promoter sites.

Bacterial Proteins↗

Combining structure-based drug design and pharmacophores.

Development towards integrated computer-aided drug design methodologies is presented by utilising crystal structure complexes to produce structure-based pharmacophores. These novel pharmacophores represent the ligand features that are involved in interactions with the target protein, as well as the space around the ligand occupied by the protein. The protein-ligand complexes can also yield information about all interactions that ligands could potentially form with the binding site, as well as about the size of the binding cavity. Together, these describe a 'superligand', which can also be viewed as a pharmacophore. Various types of novel pharmacophores are discussed and compared, using HIV-1 reverse transcriptase (RT) as the target protein, and their application in database searching is presented.

Binding Sites↗

Progress in plasmodial differentiation improves regularity of oscillating contractions in Physarum polycephalum.

Based on the knowledge about subcellular morphogenetic processes in the acellular slime mold Physarum polycephalum, we hypothesized that during differentiation of undifferentiated endoplasm to the highly differentiated complex structure of the contractile apparatus of this organism, the regularity of oscillating contractions must improve. We measured the endogenous contraction automaticity starting from the de novo generation within minutes after sampling small portions of undifferentiated endoplasm. The standard deviation of the normalized period duration of these samples was compared to the respective values of radial contractions of differentiated protoplasmic plasmodial strands. The mean normalized standard deviation in endoplasmic drops was 28.3+/-12.2%. Respective values in protoplasmic strands were 10.0+/-3.7%. The difference between the experimental groups was highly significant (p<<0.0001). We interpret the verification of our hypothesis as an indication that the very regular oscillating contractions in fully differentiated stages of Physarum require the complex structure of the sophisticated contractile apparatus, represented by the circular plasmalemma invagination system of protoplasmic strands, while the regularity is lower in stages, where the differentiation is still in progress. We believe that this is due to deficits in coordination capabilities, which need a directional and spatially oriented protoplasmic streaming as a precondition.

Animals↗

Heparan sulfate fibroblast growth factor receptor complex: structure-function relationships.

Splice variations in genes coding for the transmembrane FGF receptor (FGFR) result in isoforms that vary in the ectodomain, intracellular juxtamembrane domain, and the intracellular kinase domain. An analysis of biochemical functions of distinct recombinant isoforms expressed in baculoviral-infected insect cells allowed generation of models for function of splice variants in both the ecto- and intracellular domains. A structural model for the ectodomain of the FGFR is proposed as follows. Alternately-spliced immunoglobulin-like disulfide Loop I, which is not required for ligand-binding, is sufficiently interactive with the base FGF binding site formed by Loops II and III to modify ligand affinity and affect interaction of the receptor with heparan sulfate cofactor. The NH2-terminal domain of Loop II, which is highly conserved across all isoforms, exhibits a 19-residue heparin-binding domain which is obligatory for FGF binding. Heparin protects a 30-kDa ligand-binding fragment from proteolysis that is composed of Loop II, the inter-Loop II/III sequence, and the NH2-terminus of Loop III. This suggests that the high-affinity FGF receptor complex is an intimate ternary complex of transmembrane tyrosine kinase, heparan sulfate glycosaminoglycan, and FGF, each of which have interactive binding domains for the other and may contribute to specificity of the FGFR complex. Although Ig Loop II, the inter-Loop II/III sequence, and the NH2-terminus of Loop III with heparan sulfate form the base FGF binding site, mutually exclusive alternate splicing of two exons coding for the COOH-terminal half of Loop III determines which specific members of the FGF ligand family bind with high affinity to the base site. A kinase- and tyrosine phosphorylation site-defective splice variant, FGFR type 2, acts as a dominant-negative suppressor of phosphorylation of specifically tyr-653 in the catalytic domain of the kinase, with less effect on phosphorylation of tyr-766 in the COOH-terminal tail. We propose that phosphorylation of tyr-766, which is required for interaction of phospholipase C gamma 1 (PLC gamma 1) with the receptor, may occur by a cis-intramolecular mechanism within FGFR monomers, while phosphorylation of tyr-653, which is required for phosphorylation of PLC gamma 1, may occur by a trans-intermolecular mechanism between monomers within kinase homodimers. From the combined results, we propose a model whereby increasing concentrations of FGF may control FGF-mediated signal transduction by heterodimerization of different FGFR monomers. Different monomers arise by regulated combinatorial alternate splicing that alters both the extracellular and intracellular domains.

Amino Acid Sequence↗