Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “complex structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,333 records · Page 74Linked to original sources
PubMed2002

Silica-precipitating peptides isolated from a combinatorial phage display peptide library.

Many biological organisms contain specialized structures composed of inorganic materials. Cellular processes in vivo facilitate the organized assembly of mineral building blocks into complex structures. The structural hierarchy and complexity across a range of length scales are providing new ideas and concepts for materials chemistry. Proteins that direct biomineralization can be used to control the production of nanostructured materials and facilitate the fabrication of new structures. Here, we demonstrate that some of the silica-binding peptides isolated from a combinatorial phage peptide display library can be used in precipitating silica from a solution of silicic acid. The results described in this report demonstrate that peptides displayed by phages act as templates in inorganic material synthesis and provide a means of understanding how some of the biological systems may be carrying out materials chemistry in vivo.

Biomimetic Materials↗
PubMed2001

Characterization of the signal peptide processing and membrane association of human cytomegalovirus glycoprotein O.

Human cytomegalovirus (HCMV) has a structurally complex envelope that contains multiple glycoproteins. These glycoproteins are involved in virus entry, virus maturation, and cell-cell spread of infection. Glycoprotein H (gH), glycoprotein L (gL), and glycoprotein O (gO) associate covalently to form a unique disulfide-bonded tripartite complex. Glycoprotein O was recently discovered, and its basic structure, as well as that of the tripartite complex, remains uncharacterized. Based on hydropathy analysis, we hypothesized that gO could adopt a type II transmembrane orientation. The data presented here, however, reveal that the single hydrophobic domain of gO functions as a cleavable signal peptide that is absent from the mature molecule. Although it lacks a membrane anchor, glycoprotein O is associated with the membranes of HCMV-infected cells. The sophisticated organization of the gH.gL.gO complex reflects the intricate nature of the multicomponent entry and fusion machinery encoded by HCMV.

Amino Acid Sequence↗
PubMed1992

Phosphatic shell plate of the barnacle Ibla (Cirripedia): a bone-like structure.

The carbonate apatite crystals and the segmented structure of the shell plates of the barnacles in the genus Ibla distinguish them from the shell plates of all other barnacles, which are coherent calcitic structures. A detailed study of the hierarchical organization of one of the two shell plate types, the tergum, reveals a remarkably complex structure. Cylinders composed of a chitin-protein complex and nodes of plate-shaped crystals constitute the basic building blocks. The crystals are organized into layered stacks in which the c crystallographic axes are all aligned perpendicular to a 25-nm banded structure. The cylinders are, in turn, ordered in arrays such that parts of each cylinder are aligned in a plane, and parts form arcuate out-of-plane structures. The overall result is a lamellar structure, with a plywood-like motif, that is present throughout an individual segment. A series of segments forms an interlocking mineralized core, which is enclosed within a thick organic envelope. The flexible and complex skeletal structure of the tergum shows some marked similarities to the structure of lamellar bone. Although this is undoubtably a product of convergent evolution, the iblid tergum provides a unique perspective on bone structure, which was heretofore unavailable.

Amino Acids↗
PubMed1983

Epidermal keratinocyte growth: changes in protein composition and synthesis of keratins in differentiating cultures.

The epidermal skin layer undergoes extensive changes in all areas of metabolism as the lowermost basal cell differentiates into a dead structure that forms the upper, protective stratum corneum. Epidermal keratinocyte differentiation was studied in vitro using primary epidermal keratinocyte cultures that grow from a basal cell monolayer to a differentiating and proliferating, multilayered keratinocyte structure. Specific groups of proteins that form complex structures as keratinocyte differentiation occurs were studied. The quantities and synthesis of the proteins forming the tonofilamentous bundles, keratohyaline granules, and cornified cell envelopes in these cultures were determined. The selective solubilities of these proteins in a series of buffers were exploited to separate the proteins into 6 fractions. Protein assays, [3H]-amino acid pulse labeling, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and fluorography were used to quantitate and characterize the proteins extracted from basal monolayers and from stratifying and fully differentiated keratinocyte cultures. The results showed that multilayered, more differentiated cultures accumulated the greatest amount of keratin, keratohyaline granule, and cell envelope proteins, although there was no apparent increase in the synthesis of these proteins in the more differentiated cultures. These cultures showed extensive disulfide cross-linking of the keratins. Covalent keratin bonding occurred at least 6 hr after the synthesis and rapid noncovalent bonding of the polypeptides into keratins; thus various stages of keratin formation were identified. The differentiation of the epidermis appeared to be a complex, orderly, and regulated process that can be studied in vitro using this epidermal cell culture system.

Animals↗
PubMed2003

The "Mozart effect": an electroencephalographic analysis employing the methods of induced event-related desynchronization/synchronization and event-related coherence.

The event-related responses of 18 individuals were recorded while they were listening to 3 music clips of 6 s duration which were repeated 30 times each. The music clips differed in the level of their complex structure, induced mood, musical tempo and prominent frequency. They were taken from Mozart's sonata (K. 448), and Brahms' Hungarian dance (no. 5). The third clip was a simplified version of the theme taken from Haydn's symphony (no. 94) played by a computer synthesizer. Significant differences in induced event-related desynchronization between the 3 music clips were only observed in the lower-1 alpha band which is related to attentional processes. A similar pattern was observed for the coherence measures. While respondents listened to the Mozart clip, coherence in the lower alpha bands increased more, whereas in the gamma band a less pronounced increase was observed as compared with the Brahms and Haydn clips. The clustering of the three clips based on EEG measures distinguished between the Mozart clip on the one hand, and the Haydn and Brahms clips on the other, even though the Haydn and Brahms clips were at the opposite extremes with regard to the mood they induced in listeners, musical tempo, and complexity of structure. This would suggest that Mozart's music--with no regard to the level of induced mood, musical tempo and complexity--influences the level of arousal. It seems that modulations in the frequency domain of Mozart's sonata have the greatest influence on the reported neurophysiological activity.

Acoustic Stimulation↗
PubMed1991

A novel hemidesmosomal plaque component: tissue distribution and incorporation into assembling hemidesmosomes in an in vitro model.

The hemidesmosome and its associated structures, such as anchoring fibrils, form a complex structure, the polypeptide composition of which has only recently begun to be elucidated. We describe the characterization of a monoclonal antibody, mAb6A5, directed against a 200-kDa polypeptide found in the cytoplasmic-most area of the hemidesmosomal plaque. This 200-kDa polypeptide is immunologically distinct from the 180- and 230-kDa hemidesmosomal plaque components recognized by bullous pemphigoid (BP) autoantibodies. mAb6A5 recognizes hemidesmosomes of stratified squamous epithelia in a number of species, including human tissue. mAb6A5 also recognizes pseudo-stratified epithelium, but not simple or transitional epithelia. During de novo hemidesmosome assembly in an in vitro model of epithelial wound healing, the 200-kDa polypeptide is in most instances deposited at the epithelial-stromal interface after plaque components recognized by BP autoantibodies, but before the collagen type VII component of anchoring fibrils. We discuss possible mechanisms of hemidesmosomal plaque assembly.

Animals↗
PubMed2006

Structural basis for the alteration of coenzyme specificity in a malate dehydrogenase mutant.

To elucidate the structural basis for the alteration of coenzyme specificity from NADH toward NADPH in a malate dehydrogenase mutant EX7 from Thermus flavus, we determined the crystal structures at 2.0 A resolution of EX7 complexed with NADPH and NADH, respectively. In the EX7-NADPH complex, Ser42 and Ser45 form hydrogen bonds with the 2'-phosphate group of the adenine ribose of NADPH, although the adenine moiety is not seen in the electron density map. In contrast, although Ser42 and Ser45 occupy a similar position in the EX7-NADH complex structure, both the adenine and adenine ribose moieties of NADH are missing in the map. These results and kinetic analysis of site-directed mutant enzymes indicate (1) that the preference of EX7 for NADPH over NADH is ascribed to the recognition of the 2'-phosphate group by two Ser and Arg44, and (2) that the adenine moiety of NADPH is not recognized in this mutant.

Bacterial Proteins↗
PubMed2004

Inactivated enzymes as probes of the structure of arabinoxylans as observed by atomic force microscopy.

The complex structures of water-soluble wheat arabinoxylans have been mapped along individual molecules, and within populations, using the visualisation of the binding of inactivated enzymes by atomic force microscopy (AFM). It was demonstrated that site-directed mutagenesis (SDM) can be used to produce inactive enzymes as structural probes. For the SDM mutants AFM has been used to compare the binding of different xylanases to arabinoxylans. Xylanase mutant E386A, derived from the Xyn11A enzyme (Neocallimastrix patriciarium), was shown to bind randomly along arabinoxylan molecules. The xylanase binding was also monitored following Aspergillus niger arabinofuranosidase pre-treatment of samples. It was demonstrated that removal of arabinose side chains significantly altered the binding pattern of the inactivated enzyme. Xylanase mutant E246A, derived from the Xyn10A enzyme (Cellvibrio japonicus), was found to show deviations from random binding to the arabinoxylan chains. It is believed that this is due to the effect of a small residual catalytic activity of the enzyme that alters the binding pattern of the probe. Control procedures were developed and assessed to establish that the interactions between the modified xylanases and the arabinoxylans were specific interactions. The experimental data demonstrates the potential for using inactivated enzymes and AFM to probe the structural heterogeneity of individual polysaccharide molecules.

Carbohydrate Sequence↗
PubMed2004

Glycopolymer charge density determines conformation in human ocular mucin gene products: an atomic force microscope study.

Atomic force microscopy (AFM) has been applied to the study of heterogeneity in the structure and function of individual biopolymers with complex structures such as glycoproteins, polysaccharides and nucleic acids. In this work we describe experiments which shed light on the heterogeneity of human ocular mucin gene products. By separating samples of native human ocular mucins on a caesium chloride density gradient, at least three populations consisting predominantly of products of the gene MUC5AC can be identified. Separation on the caesium chloride density gradient is governed by molecular architecture and charge density, and thus provides a route to the discrimination between different glycoforms within a glycoprotein sample. AFM images of these populations show that each is characterised by different conformational properties and polymer diameters, both of which can be attributed to differences in the degree and nature of glycosylation. These differences in glycosylation are likely to be the result of post-translational processing and may also have functional consequences. The AFM's ability to examine the composition of a predominantly single gene product population at the level of the single molecule allows the consequences of post-translational process heterogeneity to be examined at high resolution.

Biopolymers↗
PubMed2001

Assessment and management of the painful shoulder.

The shoulder joint is a complex structure composed of intricate bony architecture and an ornate system of muscles, tendons, and ligaments. What many refer to as the "shoulder joint" is actually a combination of 4 articulations--the glenohumeral joint, acromioclavicular joint, sternoclavicular joint, and the scapulothoracic articulation. These structures work together to provide the shoulder complex with multiple degrees of freedom, which allow the upper extremity to be abducted, adducted, rotated, flexed, and extended. Although this flexibility is vital for positioning the arm in space, it can make the evaluation of pathology difficult. Furthermore, neck pathology can refer pain to the shoulder, which may require a screening evaluation of the neck. This article reviews the relevant anatomy and discusses an approach to the differential diagnosis of shoulder pain.

Algorithms↗
PubMed1993

Peptide mapping and evaluation of glycopeptide microheterogeneity derived from endoproteinase digestion of erythropoietin by affinity high-performance capillary electrophoresis.

High-performance capillary electrophoresis (HPCE) has been employed to characterize the peptide map of recombinant human erythropoietin (rHuEPO) expressed from Chinese hamster ovary (CHO) cells. The methodology employs an ion pairing agent, 100 mM heptanesulfonic acid in 40 mM sodium phosphate buffer, pH 2.5, to increase peptide resolution, to decrease analyte wall interactions, and to evaluate glycopeptide microheterogeneity. The total tryptic map is segregated into two regions, nonglycosylated and glycosylated peptides. Reproducibility of the peptide map is excellent; the map results in baseline separation of 16 tryptic peptides and one doublet peak composed of two peptides (resolution 0.22). The map furthermore allows for the evaluation of the microheterogeneity associated with the three rHuEPO glycopeptides. At least 12 glycopeptide forms were separated in the initial peptide map. Peptides were identified by Edman sequencing, and the glycopeptides were further subjected to Dionex anion-exchange chromatography. To simplify the level of complexity associated with the glycopeptides, much of the characterization employed asialoglycopeptides and employed several endoproteolytic diagnosis. The relative percent distribution for each purified asialoglycopeptide was calculated to define the level of complexity and to tentatively assign a known structure to the HPCE peak. The level of structural complexity of the asialoglycopeptides appears to increase from the simplest O-linked form to the more complex N83, N38, and N24 glycosylation positions, respectively. HPCE evaluation of glycopeptide microheterogeneity appears to be simpler, faster, and just as sensitive as other more frequently employed methods for glycopeptide characterizations.

Animals↗
PubMedDate not supplied

Is there a difference between leads and drugs? A historical perspective.

To be considered for further development, lead structures should display the following properties: (1) simple chemical features, amenable for chemistry optimization; (2) membership to an established SAR series; (3) favorable patent situation; and (4) good absorption, distribution, metabolism, and excretion (ADME) properties. There are two distinct categories of leads: those that lack any therapeutic use (i.e., "pure" leads), and those that are marketed drugs themselves but have been altered to yield novel drugs. We have previously analyzed the design of leadlike combinatorial libraries starting from 18 lead and drug pairs of structures (S. J. Teague et al. Angew. Chem., Int. Ed. Engl. 1999, 38, 3743-3748). Here, we report results based on an extended dataset of 96 lead-drug pairs, of which 62 are lead structures that are not marketed as drugs, and 75 are drugs that are not presumably used as leads. We examined the following properties: MW (molecular weight), CMR (the calculated molecular refractivity), RNG (the number of rings), RTB (the number of rotatable bonds), the number of hydrogen bond donors (HDO) and acceptors (HAC), the calculated logarithm of the n-octanol/water partition (CLogP), the calculated logarithm of the distribution coefficient at pH 7.4 (LogD(74)), the Daylight-fingerprint druglike score (DFPS), and the property and pharmacophore features score (PPFS). The following differences were observed between the medians of drugs and leads: DeltaMW = 69; DeltaCMR = 1.8; DeltaRNG = DeltaHAC =1; DeltaRTB = 2; DeltaCLogP = 0.43; DeltaLogD(74) = 0.97; DeltaHDO = 0; DeltaDFPS = 0.15; DeltaPPFS = 0.12. Lead structures exhibit, on the average, less molecular complexity (less MW, less number of rings and rotatable bonds), are less hydrophobic (lower CLogP and LogD(74)), and less druglike (lower druglike scores). These findings indicate that the process of optimizing a lead into a drug results in more complex structures. This information should be used in the design of novel combinatorial libraries that are aimed at lead discovery.

Combinatorial Chemistry Techniques↗
PubMed2005

Development of a biosorbent for arsenite: structural modeling based on X-ray spectroscopy.

This work describes a biological route for direct sorption of aqueous As(III) species, which are the most toxic and mobile arsenic species found in soils. Based upon the biochemical mechanisms that explain arsenic toxicity, we propose that a waste biomass with a high fibrous protein content obtained from chicken feathers can be used for selective As(III) adsorption. Prior to adsorption, the disulfide bridges present in the biomass are reduced by thioglycolate. Our investigations demonstrated that As(III) is specifically adsorbed on the biomass and, contrary to the behavior observed with inorganic sorbents, the lower is the pH the more effective is the removal. Arsenic uptake reaches values of up to 270 micromol As(III)/g of biomass. Analyses by synchrotron light techniques, such as XANES, demonstrated that arsenic is adsorbed in its trivalent state, an advantage over conventional techniques for As uptake, which usually require a previous oxidation stage. EXAFS analyses showed that each As atom is directly bound to three S atoms with an estimated distance of 2.26 A. The uptake mechanism is explained in terms of the structural similarities between the As(III)-biomass complex structure and that of arsenite ions and Ars-Operon system encoded proteins and phytochelatins. The biological route presented here offers the perspective of a direct removal of arsenic in its reduced form.

Adsorption↗
PubMed2002

Diastereoselective formation of glycoluril dimers: isomerization mechanism and implications for cucurbit[n]uril synthesis.

Cucurbit[6]uril (CB[6]) is a macrocyclic compound, prepared in one pot from glycoluril and formaldehyde, whose molecular recognition properties have made it the object of intense study. Studies of the mechanism of CB[n] formation, which might provide insights that allow the tailor-made synthesis of CB[n] homologues and derivatives, have been hampered by the complex structure of CB[n]. By reducing the complexity of the reaction to the formation of S-shaped (12S-18S) and C-shaped (12C-18C) methylene bridged glycoluril dimers, we have been able to probe the fundamental steps of the mechanism of CB[n] synthesis to a level that has not been possible previously. For example, we present strong evidence that the mechanism of CB[n] synthesis proceeds via the intermediacy of both S-shaped and C-shaped dimers. The first experimental determination of the relative free energies of the S-shaped and C-shaped dimers indicates a thermodynamic preference (1.55-3.25 kcal mol(-)(1)) for the C-shaped diastereomer. This thermodynamic preference is not because of self-association, solvation, or template effects. Furthermore, labeling experiments have allowed us to elucidate the mechanism of this acid-catalyzed equilibrium between the S-shaped and C-shaped diastereomers. The equilibration is an intramolecular process that proceeds with high diastereoselectivity and retention of configuration. On the basis of the broad implications of these results for CB[n] synthesis, we suggest new synthetic strategies that may allow for the improved preparation of CB[n] (n > 8) and CB[n] derivatives from functionalized glycolurils.

Alkynes↗
PubMed2006

The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution.

Beta-lactamases confer bacterial resistance to beta-lactam antibiotics, such as penicillins. The characteristic class C beta-lactamase AmpC catalyzes the reaction with several key residues including Ser64, Tyr150, and Lys67. Here, we describe a 1.07 A X-ray crystallographic structure of AmpC beta-lactamase in complex with a boronic acid deacylation transition-state analogue. The high quality of the electron density map allows the determination of many proton positions. The proton on the Tyr150 hydroxyl group is clearly visible and is donated to the boronic oxygen mimicking the deacylation water. Meanwhile, Lys67 hydrogen bonds with Ser64Ogamma, Asn152Odelta1, and the backbone oxygen of Ala220. This suggests that this residue is positively charged and has relinquished the hydrogen bond with Tyr150 observed in acyl-enzyme complex structures. Together with previous biochemical and NMR studies, these observations indicate that Tyr150 is protonated throughout the reaction coordinate, disfavoring mechanisms that involve a stable tyrosinate as the general base for deacylation. Rather, the hydroxyl of Tyr150 appears to be well positioned to electrostatically stabilize the negative charge buildup in the tetrahedral high-energy intermediate. This structure, in itself, appears consistent with a mechanism involving either Tyr150 acting as a transient catalytic base in conjunction with a neutral Lys67 or the lactam nitrogen as the general base. Whereas mutagenesis studies suggest that Lys67 may be replaced by an arginine, disfavoring the conjugate base mechanism, distinguishing between these two hypotheses may ultimately depend on direct determination of the pK(a) of Lys67 along the reaction coordinate.

Acylation↗
PubMed1988

Structure of native porcine pancreatic elastase at 1.65 A resolutions.

The structure of native porcine pancreatic elastase in 70% methanol has been refined using film data to 1.65 A resolution, R = 0.169. A total of 134 molecules of water (but no methanol) has been refined. This structure, because of its native state and modestly high resolution, serves as the basis for comparison with other elastase structures complexed with natural or synthetic ligands. Internal structured water occupies distinct regions. Two regions (IW1 and IW7) suggest a mechanism for equalizing 'hydrostatic pressure' related to ligand binding and release. A third region (IW4) forms part of a hydrogen-bonding network linking the catalytic Ser 195 O gamma with a remote (13.4 A) surface of the enzyme. A comparison with the structures of all known serine proteases reveals that a linkage of Ser O gamma to remote surface is conserved in all cases, suggesting that the accepted catalytic mechanism of serine proteases needs to be re-evaluated. One possible mechanism for base catalysis of Ser O gamma H proton extraction is presented.

Animals↗
PubMed1974

Intracytoplasmic junctions in cardiac muscle cells.

JUNCTIONAL STRUCTURES FORMED BY TWO PARTS OF THE PLASMA MEMBRANE OF THE SAME CARDIAC MUSCLE CELL WERE OBSERVED IN VENTRICULAR MYOCARDIUM OF: a) patients with neoplasms, aortic valvular disease or idiopathic hypertrophic subaortic stenosis and b) dogs subjected to prolonged normothermic anoxic cardiac arrest. Most of these structures had features of desmosomes; other, more complex structures had components with features of desmosomes, fasciae adherentes and nexuses, and, therefore, resembled intercalated discs. These intracytoplasmic junctions were localized to: a) the peripheral cytoplasm at the sides or ends of cells, b) narrow invaginations of plasma membranes, c) narrow zones of deep, broad plasmalemmal invaginations and d) narrow branches of T tubules. In patients with idiopathic hypertrophic subaortic stenosis or aortic valvular disease and in the dogs subjected to anoxic cardiac arrest, intracytoplasmic junctions were observed in hypertrophied or degenerated muscle cells which were located in areas of fibrosis and which showed loss of contact with adjacent cells. In patients with neoplasms, intracyto-plasmic junctions were found in degenerated cells which were located in areas of interstitial edema and which also showed loss of contact with adjacent cells. Our observations suggest that remodeling of cell surfaces following loss of intercellular contact is the most likely mechanism of formation of intracytoplasmic junctions.

Animals↗
PubMed1995

A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies.

A phosphonate analog of N-acetyl neuraminic acid (PANA) has been designed as a potential neuraminidase (NA) inhibitor and synthesized as both the alpha (ePANA) and beta (aPANA) anomers. Inhibition of type A (N2) and type B NA activity by ePANA was approximately a 100-fold better than by sialic acid, but inhibition of type A (N9) NA was only ten-fold better than by sialic acid. The aPANA compound was not a strong inhibitor for any of the NA strains tested. The crystal structures at 2.4 A resolution of ePANA complexed to type A (N2) NA, type A (N9) NA and type B NA and aPANA complexed to type A (N2) NA showed that neither of the PANA compounds distorted the NA active site upon binding. No significant differences in the NA-ePANA complex structures were found to explain the anomalous inhibition of N9 neuraminidase by ePANA. We put forward the hypothesis that an increase in the ePANA inhibition compared to that caused by sialic acid is due to (1) a stronger electrostatic interaction between the inhibitor phosphonyl group and the active site arginine pocket and (2) a lower distortion energy requirement for binding of ePANA.

Binding Sites↗