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 1,693 records · Page 94Linked to original sources
PubMed1992

Ultrastructural study of the tegument of Cotugnia polyacantha and Killigrewia streptopelia inhabiting the dove Streptopelia senegalensis aegyptiaca.

The ultrastructure of the teguments of the cyclophyllidean cestodes Cotugnia polyacantha and Killigrewia streptopelia naturally infecting the dove Streptopelia senegalensis aegyptiaca, was studied using transmission electron microscopy. The two cestodes inhabit two distinct sites in the small intestine of the same bird. Observations revealed basic similarity between the two cestodes, though, marked differences between the tegument structure details of the two species regarding the structure and dimension of microtriches, types and distribution of vesicles among the regions of the tegumental/perikaryal complex, structure of subtegumental connective tissue and subtegumental muscle layer. The significance of these observations was discussed in possible relation to the different physico-chemical environments known to occur where each cestode resides.

Animals↗
PubMed2004

Transglutaminases, thioredoxins and protein disulphide isomerase: diverse enzymes with a common goal of cross-linking proteins in lower organisms.

Prokaryotes and various eukaryotes have remarkable ability to survive under adverse physiologic conditions and protect themselves from environmental stresses. An important mechanism by which they accomplish this is by synthesizing rigid and biochemically inert structures around them. In general, these structures are highly stable and resistant to mechanical and chemical insults. Biochemically, they are composed of complex carbohydrates, such as chitin and heavily crosslinked scaffold of proteins to form complex structures, such as sheath, cuticle, and epicuticle. Transglutaminases (TGases) are a family of enzymes that share catalytic function with thioredoxin and protein disulphide isomerases (PDI) and catalyze protein crosslink reaction by establishing epsilon-(gamma-glutamyl)lysine isopeptide bonds. The isopeptide bonds thus formed are of great physiologic significance because once formed, they cannot be hydorlysed by any known enzymes of the eukaryote system and exhibit high resistance to reducing agents, detergents, and chaotropic agents. Therefore, it is likely that protective structures viz., sheath, cuticle, epicuticle, and viral core proteins synthesized by microorganisms involve active participation of TGases. In this review, we briefly describe the current knowledge of non-mammalian TGases and their possible role in growth, development, and survival of small organisms. Special reference is made to filarial nematode and bacterial TGases since they are the most well-characterized and studied enzymes among non-mammalian TGases.

Animals↗
PubMed2004

[Molecular mechanisms of neuronal connective tissue genesis during the course of cerebral cortex development].

The cerebral cortex constitutes one of the most complex structures in our brain. In correlation with its elaborate functions, it is characterized by the great complexity of its neuronal connections, but the mechanisms responsible for the generation of these connections remain poorly known. We have recently initiated the characterization of a new multigenic family of axon guidance factors, the ephrin/Eph gene family, during the development of neuronal connections in the mouse cortex. Combining expression studies, in vitro guidance essays, and in vivo analysis of mutant mice, enabled us to demonstrate the critical role of ephrin/Eph genes in the development of cortical networks. Mutant mice for ephrin/Eph genes display a topographic distortion of their cortical somatosensory map, as well as ectopic projections from the motor thalamus to the somatosensory cortex. The identification of factors like ephrins, capable to (re)specify the pattern of neuronal connections, has implications for our understanding of pathological brain development (epilepsy, abnormal movements, psychiatric diseases), and in the perspective of the rational design of cell therapies of neurodegenerative diseases.

Animals↗
PubMed1995

A simple code for protein:RNA interactions.

The Tat and Rev proteins of HIV-1 and the Rex protein of HTLV-I do not interact with their cognate ligands via a particular structural motif but instead specifically recognize RNA molecules by using agglomerations of arginine residues (1). These proteins are members of the so-called arginine-rich motif (ARM) family. There is little data to support (or contradict) the hypothesis that a few simple arginine:RNA interactions govern how ARMs recognize their viral targets. Not only is it unclear how ARM proteins other than Tat interact with their cognate RNA ligands, for the most part it is not even known how structurally complex these RNA ligands are. In order to fully explore the range of RNA sequences and structures that can bind to ARMs we have carried out in vitro genetic selections with two disparate viral proteins: Rev and Rex.

Arginine↗
PubMed1997

Role of aromatic amino acids in carbohydrate binding of plant lectins: laser photo chemically induced dynamic nuclear polarization study of hevein domain-containing lectins.

Carbohydrate recognition by lectins often involves the side chains of tyrosine, tryptophan, and histidine residues. These moieties are able to produce chemically induced dynamic nuclear polarization (CIDNP) signals after laser irradiation in the presence of a suitable radical pair-generating dye. Elicitation of such a response in proteins implies accessibility of the respective groups to the light-absorbing dye. In principle, this technique is suitable to monitor surface properties of a receptor and the effect of ligand binding if CIDNP-reactive amino acids are affected. The application of this method in glycosciences can provide insights into the protein-carbohydrate interaction process, as illustrated in this initial study. It focuses on a series of N-acetylglucosamine-binding plant lectins of increasing structural complexity (hevein, pseudohevein, Urtica dioica agglutinin and wheat germ agglutinin and its domain B), for which structural NMR- or X-ray crystallographic data permit a decision of the validity of the CIDNP method-derived conclusions. On the other hand, the CIDNP data presented in this study can be used for a rating of our molecular models of hevein, pseudohevein, and domain B obtained by various modeling techniques. Experimentally, the shape and intensity of CIDNP signals are determined in the absence and in the presence of specific glycoligands. When the carbohydrate ligand is bound, CIDNP signals of side chain protons of tyrosine, tryptophan, or histidine residues are altered, for example, they are broadened and of reduced intensity or disappear completely. In the case of UDA, the appearance of a new tryptophan signal upon ligand binding was interpreted as an indication for a conformational change of the corresponding indole ring. Therefore, CIDNP represents a suitable tool to study protein-carbohydrate interactions in solution, complementing methods such as X-ray crystallography, high-resolution multidimensional nuclear magnetic resonance, transferred nuclear Overhauser effect experiments, and molecular modeling.

Amino Acids↗
PubMed1976

[Direction of the clinical pathomorphosis of alcoholic delirium].

An examination of 348 patients with alcoholic delirium permitted to detect the main directions in the evolutional variability of the clinical picture. The authors distinguished 3 types in the development of a delirium: short-term with a complete and incomplete (abortive) variant; typical delirium with mono-and polymorphic structure of the syndrome; a protracted development in the form of a severe psychoses of a complex structure and a sluggish protracted variant with an obliviated symptomatology.

Alcohol Withdrawal Delirium↗
PubMed1978

Structural studies of iron and cobalt tetrasulfonated phthalocyanine-globin complexes.

The structure of the complexes of iron and cobalt tetrasulfonated phthalocyanines with globin has been investigated by circular dichroism (CD), electron paramagnetic resonance (EPR) and polyacrylamide gel electrophoresis. Electrophoretic investigations and the molecular weight estimation indicates that the model complexes in the solutions are dimers. It is evident from the results of CD measurements that the incorporation of the iron or cobalt tetrasulfonated phthalocyanine into apohemoglobin significantly increases the helical structure of the protein and causes an appearance of the induced Soret and visible Cotton effects. Unlike methemoglobin, several discrete transition energies in the CD Soret band of Fe(III)L-globin are observed which suggest an inequivalence of the subunits within this complex. This suggestion is supported by EPR studies, which show that the iron atoms in Fe(III)L-globin are in two low electronic states. Electronic structures of the cobalt ions in Co(II)L-globin and oxyCo(II)L-globin are similar to those of coboglobin and oxycoboglobin, respectively, as is proved by EPR results. On this basis we conclude that the oxygen adduct of Co(II)L-globin can be described as a superoxide ion corrdinated to a formally cobaltic phthalocyanine compound.

Chemical Phenomena↗
PubMed2003

Complexation and chiral recognition thermodynamics of gamma-cyclodextrin with N-acetyl- and N-carbobenzyloxy-dipeptides possessing two aromatic rings.

The stability constants (K) and the standard free energy (deltaG degrees ), enthalpy (deltaH degrees ), and entropy changes (deltaS degrees ) for the complexation of gamma-cyclodextrin with 34 enantiomeric and diastereomeric N-acetyl- and N-carbobenzyloxy-d/l-dipeptides with two aromatic moieties were determined in aqueous buffer solution at 298.15 K by titration microcalorimetry. Chiral recognition of the enantiomeric dipeptide pairs by gamma-cyclodextrin was found to be fairly poor, exhibiting only small percentage differences in K, while the diastereomeric dipeptides were discriminated to much greater extent with affinity differences of up to 6-7 times. The complex structures of several selected pairs were elucidated by NMR techniques. Combining the microcalorimetric and NMR data, the complexation and chiral recognition behavior of gamma-cyclodextrin is discussed in particular in terms of the length, bulkiness, and flexibility of the tether connecting the two aromatic moieties in a guest.

Circular Dichroism↗
PubMed1999

Molecular structures of metal complexes with mefenamic acid.

The infrared spectra of Na and Ca complexes of mefenamic acid were investigated in the region between 4000 and 400 cm(-1). These spectra were compared with X-ray powder diffraction patterns of complexes. It is shown that the proposed structure for these complexes obtained from the infrared spectra was supported by X-ray powder diffraction measurements. Bands due to v(as)(COO)- and v(s)(COO)- stretching vibrations appear at about 1580 cm(-1) and in the range 1390-1400 cm(-1) in the infrared spectra of the samples, respectively. The values of NH deformation vibrations do not change in the spectra of mefenamic acid and its metal complexes. On the other hand, molecular mechanic calculations and conformational analysis of three compounds were also established in the present work. As a result of these theoretical studies, the atomic planes and the peak assignments of the powder diffraction patterns were determined. As a result of these experimental and theoretical investigations, it may be concluded that metal atoms are connected to the carboxyl group of the mefenamic acid.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2002

Mechanisms of molecular recognition: crystal structure analysis of human and rat transthyretin inhibitor complexes.

Structure-activity data show that many pharmacological agents are strong competitive inhibitors for thyroxine (T4) binding to transthyretin (TTR) and that this competition can interfere with their normal pharmacological actions. TTR is a tetrameric serum protein responsible for the transport of 20% of the circulating T4 in man, while in lower vertebrates such as rats it is the only carrier. The sequence of rat TTR is 85% homologous to the human protein. Crystallographic analyses of ligand co-crystal complexes of human and rat TTR have been studied to understand the molecular basis for binding selectivity of competitor binding to TTR. Analysis of TTR crystal complexes with several classes of competitors (hormone metabolites, flavonoids, fluorescent probes, analgesics and cardiac agents) revealed multiple modes of binding with both forward and reverse ligand binding orientations. These ligands also have different binding positions along the length of the channel with the smallest ligands located deeper within the hormone domain. Data for the human TTR complex with the bromoflavone EMD21388 incubated at different times revealed variable binding positions and occupancies dependent upon incubation time. Comparison of the structures of T4 thyroacetic acid in complex with both human and rat TTR revealed forward and reverse binding, but also showed different modes of binding in the rat compared to the human complex. These data highlight the importance of hydrogen bonding with Lys-15 and Ser-117 and provide insight into ligand binding affinity and negative cooperativity.

Amino Acid Sequence↗
PubMed1987

Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution.

The molecular structure of the complex between bovine pancreatic alpha-chymotrypsin (EC 3.4.4.5) and the third domain of the Kazal-type ovomucoid from Turkey (OMTKY3) has been determined crystallographically by the molecular replacement method. Restrained-parameter least-squares refinement of the molecular model of the complex has led to a conventional agreement factor R of 0.168 for the 19,466 reflections in the 1.8 A (1 A = 0.1 nm) resolution shell [I greater than or equal to sigma (I)]. The reactive site loop of OMTKY3, from Lys13I to Arg21I (I indicates inhibitor), is highly complementary to the surface of alpha-chymotrypsin in the complex. A total of 13 residues on the inhibitor make 113 contacts of less than 4.0 A with 21 residues of the enzyme. A short contact (2.95 A) from O gamma of Ser195 to the carbonyl-carbon atom of the scissile bond between Leu18I and Glu19I is present; in spite of it, this peptide remains planar and undistorted. Analysis of the interactions of the inhibitor with chymotrypsin explains the enhanced specificity that chymotrypsin has for P'3 arginine residues. There is a water-mediated ion pair between the guanidinium group on this residue and the carboxylate of Asp64. Comparison of the structure of the alpha-chymotrypsin portion of this complex with the several structures of alpha and gamma-chymotrypsin in the uncomplexed form shows a high degree of structural equivalence (root-mean-square deviation of the 234 common alpha-carbon atoms averages 0.38 A). Significant differences occur mainly in two regions Lys36 to Phe39 and Ser75 to Lys79. Among the 21 residues that are in contact with the ovomucoid domain, only Phe39 and Tyr146 change their conformations significantly as a result of forming the complex. Comparison of the structure of the OMTKY3 domain in this complex to that of the same inhibitor bound to a serine proteinase from Streptomyces griseus (SGPB) shows a central core of 44 amino acids (the central alpha-helix and flanking small 3-stranded beta-sheet) that have alpha-carbon atoms fitting to within 1.0 A (root-mean-square deviation of 0.45 A) whereas the residues of the reactive-site loop differ in position by up to 1.9 A (C alpha of Leu18I). The ovomucoid domain has a built-in conformational flexibility that allows it to adapt to the active sites of different enzymes. A comparison of the SGPB and alpha-chymotrypsin molecules is made and the water molecules bound at the inhibitor-enzyme interface in both complexes are analysed for similarities and differences.

Animals↗
PubMed1995

Protein synthesis in eukaryotic organisms: new insights into the function of translation initiation factor eIF-3.

The pathway for initiation of protein synthesis in eukaryotic cells has been defined and refined over the last 25 years using purified components and in vitro reconstituted systems. More recently, powerful genetic analysis in yeast has proved useful in unraveling aspects of translation inherently more difficult to address by strictly biochemical approaches. One area in particular is the functional analysis of multi-subunit protein factors, termed eukaryotic initiation factors (eIFs), that play an essential role in translation initiation. eIF-3, the most structurally complex of the eIFs, has until recently eluded this approach. The identification of the yeast GCD10 gene as the structural gene for the zeta subunit of yeast eIF-3(1) and the analysis of mutant phenotypes has opened the door to the genetic dissection of the eIF-3 protein complex.

Animals↗
PubMed1995

p57KIP2, a structurally distinct member of the p21CIP1 Cdk inhibitor family, is a candidate tumor suppressor gene.

Cyclin-dependent kinases (Cdks) are positive regulators of cell proliferation, whereas Cdk inhibitors (CKIs) inhibit proliferation. We describe a new CKI, p57KIP2, which is related to p21CIP1 and p27KIP1. p57KIP2 is a potent, tight-binding inhibitor of several G1 cyclin/Cdk complexes, and its binding is cyclin dependent. Unlike CIP1, KIP2 is not regulated by p53. Overexpression of p57KIP2 arrests cells in G1. p57KIP2 proteins have a complex structure. Mouse p57KIP2 consists of four structurally distinct domains: an amino-terminal Cdk inhibitory domain, a proline-rich domain, an acidic-repeat region, and a carboxy-terminal domain conserved with p27KIP1. Human p57KIP2 appears to have conserved the amino- and carboxy-terminal domains but has replaced the internal regions with sequences containing proline-alanine repeats. In situ hybridization during mouse embryogenesis revealed that KIP2 mRNA displays a striking pattern of expression during development, showing high level expression in skeletal muscle, brain, heart, lungs, and eye. Most of the KIP2-expressing cells are terminally differentiated, suggesting that p57KIP2 is involved in decisions to exit the cell cycle during development and differentiation. Human KIP2 is located at 11p15.5, a region implicated in both sporadic cancers and Beckwith-Wiedemann syndrome, a familial cancer syndrome, marking it as a candidate tumor suppressor. The discovery of a new member of the p21CIP1 inhibitor family with novel structural features and expression patterns suggests a complex role for these proteins in cell cycle control and development.

Amino Acid Sequence↗
PubMed1995

Crimp as part of a helical structure.

Crimp is generally conceived of as a ribbon, i.e. a planar periodic orientation variation of collagen fibers. This study was carried out to demonstrate that crimps are complex structures with the possibility of being helically arranged. Thick sections, imbibed in glycerol or even in mineral oil and studied under the polarizing microscope with the help of 1st order red and lambda/4 Sénarmont's compensators proved to be adequate to detect details of collagen fiber orientation with respect to crimp structure. It was found that collagen bundles are ordered aggregates forming helical structures, and crimps are part of such a helical arrangement. The major part of the macromolecules in tendons have a helix conformation that probably influences a complex hierarchical construct. It is possible that thermodinamically this ordering is better fitted to respond to the biomechanical requirements of the tendons and to correspond to their rheological properties.

Animals↗
PubMed2006

Electronic structure of bis(imino)pyridine iron dichloride, monochloride, and neutral ligand complexes: a combined structural, spectroscopic, and computational study.

The electronic structure of a family of bis(imino)pyridine iron dihalide, monohalide, and neutral ligand compounds has been investigated by spectroscopic and computational methods. The metrical parameters combined with Mössbauer spectroscopic and magnetic data for ((i)PrPDI)FeCl(2) ((i)PrPDI = 2,6-(2,6-(i)Pr(2)C(6)H(3)N=CMe)(2)C(5)H(3)N) established a high-spin ferrous center ligated by a neutral bis(imino)pyridine ligand. Comparing these data to those for the single electron reduction product, ((i)PrPDI)FeCl, again demonstrated a high-spin ferrous ion, but in this case the S(Fe) = 2 metal center is antiferromagnetically coupled to a ligand-centered radical (S(L) = (1)/(2)), accounting for the experimentally observed S = (3)/(2) ground state. Continued reduction to ((i)PrPDI)FeL(n) (L = N(2), n = 1,2; CO, n = 2; 4-(N,N-dimethylamino)pyridine, n = 1) resulted in a doubly reduced bis(imino)pyridine diradical, preserving the ferrous ion. Both the computational and the experimental data for the N,N-(dimethylamino)pyridine compound demonstrate nearly isoenergetic singlet (S(L) = 0) and triplet (S(L) = 1) forms of the bis(imino)pyridine dianion. In both spin states, the iron is intermediate spin (S(Fe) = 1) ferrous. Experimentally, the compound has a spin singlet ground state (S = 0) due to antiferromagnetic coupling of iron and the ligand triplet state. Mixing of the singlet diradical excited state with the triplet ground state of the ligand via spin-orbit coupling results in temperature-independent paramagnetism and accounts for the large dispersion in (1)H NMR chemical shifts observed for the in-plane protons on the chelate. Overall, these studies establish that reduction of ((i)PrPDI)FeCl(2) with alkali metal or borohydride reagents results in sequential electron transfers to the conjugated pi-system of the ligand rather than to the metal center.

Algorithms↗
PubMed2003

A computational study of regioselectivity in a cyclodextrin-mediated Diels-Alder reaction: revelation of site selectivity and the importance of shallow binding and multiple binding modes.

The use of a cyclodextrin.Diels-Alder transition structure complex (CD.TS) as a model in molecular dynamics simulations has enabled us to gain insight into the controlling factors in the cyclodextrin-mediated Diels-Alder reaction of methyl-p-benzoquinone with isoprene. MD simulations were carried out with multiple binding configurations of the CD.TS (TS=meta-TS, para-TS) complexes at the top and bottom rims of beta-CD. We discovered that i) only shallow binding with the CD is necessary for the regioselectivity, and multiple binding geometries are possible; ii) the narrow bottom rim, with the primary hydroxyl groups, of the CD binds both regio-TSs better than at the wider top rim (secondary hydroxyl groups), which was unexpected from the perspective of shape complementarity that governs the stability of most CD.guest complexes. Overall, the bottom rim of the CD exhibits higher regioisomer discrimination for the meta-TS; iii) structural clustering analyses of the CD.TS configurations (sampled during MD simulations) have enabled us to evaluate the binding energies of the different binding configurations. The result indicates that there is a direct correlation between meta-product selectivity and a higher number of binding configurations favoring the formation of the CD.meta-TS complex. The main forces of stabilization in the CD.TS complexes are the van der Waals interactions when the TS is bound at the top rim. At the bottom rim, closer contacts between polar functional groups of the TS and CD have increased the importance of electrostatic interactions. We found that van der Waals, solvation, and torsional forces are less favorable for complexation at the bottom rim; however, this is compensated by large favorable electrostatic interactions. With insights obtained from the study of CD.TS complexes and MD simulations of the modified heptakis-[6-O-(2-hydroxy)propyl]-beta-CD, we were able to explain why a low selectivity was observed when the Diels-Alder reaction was carried out in this modified CD. Two types of search method [Monte Carlo and multiple minimum (MCMM) and molecular dynamics (MD)] to explore and evaluate the different possible binding geometries of the TS within beta-CD, were discussed.

Chemical Phenomena↗
PubMed2003

Abnormal sinus node function in clinical arrhythmias.

To understand abnormal sinus node function in clinical atrial arrhythmias, it is essential to understand the normal function of the sinus node. Much of our understanding of the sinus node comes from work done in rabbits. In small animals, the node is a thin structure and can be modeled in two dimensions. However, in canines and humans, the node is a more complex structure completely surrounded by myocytes. Recent data suggest that the node may be insulated from the surrounding atrial myocytes, except at a limited number of exit sites. A model of the node with discrete exit sites explains how atrial activation can be initiated from multiple sites simultaneously. Within the node there may exist specialized pathways that explain the complex conduction within the node. Multiple cell types, with different intrinsic rates, combined with the nonuniform distribution of autonomic receptors, provide a basis for understanding the dynamics of heart rate control and the initiation of atrial activation. In addition, this model of the sinus node provides a framework to propose novel mechanisms underlying various atrial arrhythmias, such as atrial premature depolarizations or sinus node reentry.

Action Potentials↗