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 1,639 records · Page 91Linked to original sources
PubMed1991

Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes.

The crystal structures of the complexes formed between subtilisin Novo and three inhibitors, eglin c, Arg45-eglin c and Lys53-eglin c have been determined using molecular replacement and difference Fourier techniques and refined at 2.4 A, 2.1 A, and 2.4 A resolution, respectively. The mutants Arg45-eglin c and Lys53-eglin c were constructed by site-directed mutagenesis in order to investigate the inhibitory specificity and stability of eglin c. Arg45-eglin became a potent trypsin inhibitor, in contrast to native eglin, which is an elastase inhibitor. This specificity change was rationalized by comparing the structures of Arg45-eglin and basic pancreatic trypsin inhibitor and their interactions with trypsin. The residue Arg53, which participates in a complex network of hydrogen bonds formed between the core and the binding loop of eglin c, was replaced with the shorter basic amino acid lysine in the mutant Lys53-eglin. Two hydrogen bonds with Thr44, located in the binding loop, can no longer be formed but are partially restored by a water molecule bound in the vicinity of Lys53. Eglin c in complexes with both subtilisin Novo and subtilisin Carlsberg was crystallized in two different space groups. Comparison of the complexes showed a rigid body rotation for the eglin c core of 11.5 degrees with respect to the enzyme, probably caused by different intermolecular contacts in both crystal forms.

Amino Acid Sequence↗
PubMed2004

Heterodimeric GTPase core of the SRP targeting complex.

Two structurally homologous guanosine triphosphatase (GTPase) domains interact directly during signal recognition particle (SRP)-mediated cotranslational targeting of proteins to the membrane. The 2.05 angstrom structure of a complex of the NG GTPase domains of Ffh and FtsY reveals a remarkably symmetric heterodimer sequestering a composite active site that contains two bound nucleotides. The structure explains the coordinate activation of the two GTPases. Conformational changes coupled to formation of their extensive interface may function allosterically to signal formation of the targeting complex to the signal-sequence binding site and the translocon. We propose that the complex represents a molecular "latch" and that its disengagement is regulated by completion of assembly of the GTPase active site.

Amino Acid Motifs↗
PubMed2005

Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 angstroms resolution.

Phospholipase A2 is potentially an important target for structure-based rational drug design. In order to determine the involvement of phospholipase A2 in the action of non-steroidal anti-inflammatory drugs (NSAIDs), the crystal structure of the complex formed between phospholipase A2 and aspirin has been determined at 1.9 angstroms resolution. The structure contains 915 protein atoms, 1 calcium ion, 13 atoms of aspirin and 105 water molecules. The observed electron density of the aspirin molecule in the structure was of very high quality thus allowing the precise determination of its atomic coordinates leading to the clear description of its interactions with the enzyme. The structure of the complex clearly shows that aspirin is literally embedded in the hydrophobic environment of PLA2. It is so placed in the substrate binding channel that it forms several important attractive interactions with calcium ion, His 48 and Asp 49. Thus, the structure of the complex clearly shows that aspirin occupies a favourable place in the specific binding site of PLA2. The binding studies have shown that acetyl salicylate (aspirin) binds to PLA2 enzyme specifically with a dissociation constant of 6.4 x 10(-6) M. The structural details and binding data suggest that the inhibition of PLA2 by aspirin is of pharmacological

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed1997

Electron tomography of large, multicomponent biological structures.

Electron tomography is an extremely useful method for deriving three-dimensional structure from electron microscope images. The application of this technique to the reconstruction of large, complex structures such as mitochondria is described in conjunction with several tools for segmentation, measurement, classification, and visualization. In addition, the use of massively parallel computers to perform the tomographic reconstruction efficiently using R-weighted backprojection or iterative techniques is described.

Algorithms↗
PubMed1992

Performance in an escape task induces fos-like immunoreactivity in a specific area of the motor cortex of the rat.

The expression of the c-fos proto-oncogene was studied in two different areas of the motor cortex and in the hippocampus of the rat after performance in an escape task in a Skinner box. Performance in this task caused an increase in the number of cells showing fos-like immunoreactivity in layers V and VI of the forelimb motor-sensory cortex with respect to yoked animals which had received the same amount, frequency and duration of aversive stimulation and manipulation as the trained animals. Therefore, this increase is the specific effect of performing the behavioral task. In the hindlimb motor-sensory cortex there were no differences between the trained and the yoked animals in any of the cortical layers. No differences were observed in the dentate gyrus of the hippocampus between trained and yoked animals, while the control animals showed a much lower fos-like immunoreactivity. In conclusion, infragranular layers in the forelimb representation of the primary motor cortex become activated with respect to the expression of fos-like immunoreactivity after performance in an escape task in a Skinner box. This result is consistent with the idea that even in complex structures such as the cerebral cortex, specific trace systems become activated for the performance of complex behavioral tasks.

Analysis of Variance↗
PubMed2002

Physicochemical principles of tissue material interactions.

Biocompatibility of a material has to be adapted to the specific properties of the locus of application that are the type of tissue and the composition of extracellular fluid or the blood being in contact with the surface. The biocompatibility is beyond that greatly influenced by the design of the medical device which has to be planned close to the material's properties and the function within the body. Physical chemical reactions at and physical properties of the surface which influence the adsorption behavior for biomacromolecules. Conformational or functional changes of f.i. proteins due to physical forces originating from the surface could be the communication messages to the immunological system. The immersion of a material into an aqueous electrolyte leads generally to a space charge layer on both sides of the interface forming the electrical double layer, physically described by the isoelectric point of the materials surface. A numerical example hints on the importance of the double layer structure for the 'communication' between an implant and the surrounding extracellular fluid including beside ions complex structured proteins as biomacromolecules. Biocompatibility depends on the physical structure of the material and physicochemical properties of the interface to the biosystem. The conductivity of the surface film control reactions across the interface with biomacromolecules of the biological environment. Conformational unchanged macromolecules are the prior condition for biocompatibility and controls the attachment and probably also the degree of attachment via adhesion proteins. Later on, when the cells develop tension through the cytoskeleton on these attachment sites, the strength of the integrin adhesion protein-matrix protein interaction might probably prove decisive in differentiation state of the cell. It has been proved by molecular biological methods that an undestroyed oxide layer of anatase on titanium through passivation leaves for instance albumin conformational unchanged.

Adsorption↗
PubMed1993

Solution multistability in first-order nonlinear differential delay equations.

The dependence of solution behavior to perturbations of the initial function (IF) in a class of nonlinear differential delay equations (DDEs) is investigated. The structure of basins of attraction of multistable limit cycles is investigated. These basins can possess complex structure at all scales measurable numerically although this is not necessarily the case. Sensitive dependence of the asymptotic solution to perturbations in the initial function is also observed experimentally using a task specific electronic analog computer designed to investigate the dynamics of an integrable first-order DDE.

Journal Article↗
PubMed2003

The heparin/heparan sulfate 2-O-sulfatase from Flavobacterium heparinum. Molecular cloning, recombinant expression, and biochemical characterization.

Heparan sulfate glycosaminoglycans are structurally complex polysaccharides critically engaged in a wide range of cell and tissue functions. Any structure-based approach to study their respective biological functions is facilitated by the use of select heparan sulfate glycosaminoglycan-degrading enzymes with unique substrate specificities. We recently reported of one such enzyme, the Delta4,5-glycuronidase cloned from Flavobacterium heparinum and recombinantly expressed in Escherichia coli (Myette, J. R., Shriver, Z., Kiziltepe, T., McLean, M. W., Venkataraman, G., and Sasisekharan, R. (2002) Biochemistry 41, 7424-7434). In this study, we likewise report the molecular cloning of the 2-O-sulfatase from the same bacterium and its recombinant expression as a soluble, highly active enzyme. At the protein level, the flavobacterial 2-O-sulfatase possesses considerable sequence homology to other members of a large sulfatase family, especially within its amino terminus, where the highly conserved sulfatase domain is located. Within this domain, we have identified by sequence homology the critical active site cysteine predicted to be chemically modified as a formylglycine in vivo. We also present a characterization of the biochemical properties of the enzyme as it relates to optimal in vitro reaction conditions and a kinetic description of its substrate specificity. In particular, we demonstrate that in addition to the fact that the enzyme exclusively hydrolyzes the sulfate at the 2-O-position of the uronic acid, it also exhibits a kinetic preference for highly sulfated glucosamines within each disaccharide unit, especially those possessing a 6-O-sulfate. The sulfatase also displays a clear kinetic preference for disaccharides with beta1-->4 linkages but is able, nevertheless, to hydrolyze unsaturated, 2-O-sulfated chondroitin disaccharides. Finally, we describe the substrate-product relationship of the 2-O-sulfatase to the Delta4,5-glycuronidase and the analytical value of using both of these enzymes in tandem for elucidating heparin/heparan sulfate composition.

Amino Acid Sequence↗
PubMed1999

N-glycosylation of the carcinoembryonic antigen related cell adhesion molecule, C-CAM, from rat liver: detection of oversialylated bi- and triantennary structures.

Rat C-CAM is a ubiquitous, transmembrane and carcinoembryonic antigen related cell adhesion molecule. The human counterpart is known as biliary glycoprotein (BGP) or CD66a. It is involved in different cellular functions ranging from intercellular adhesion, microbial receptor activity, signaling and tumor suppression. In the present study N-glycosylation of C-CAM immunopurified from rat liver was analyzed in detail. The primary sequence of rat C-CAM contains 15 potential N-glycosylation sites. The N-glycans were enzymatically released from glycopeptides, fluorescently labeled with 2-aminobenzamide, and separated by two-dimensional HPLC. Oligosaccharide structures were characterized by enzymatic sequencing and MALDI-TOF-MS. Mainly bi- and triantennary complex structures were identified. The presence of type I and type II chains in the antennae of these glycans results in heterogeneous glycosylation of C-CAM. Sialylation of the sugars was found to be unusual; bi- and triantennary glycans contained three and four sialic acid residues, respectively, and this linkage seemed to be restricted to the type I chain in the antennae. Approximately 20% of the detected sugars contain these unusual numbers of sialic acids. C-CAM is the first transmembrane protein found to be oversialylated.

Adenosine Triphosphatases↗
PubMed2001

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.

To assess whether there are universal rules that govern amino acid-base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein-DNA complex structures. DNA-backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base-amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure. Nearly two-thirds of the direct read-out of DNA sequences involves complex networks of hydrogen bonds, which enhance specificity. Two-thirds of all protein-DNA interactions comprise van der Waals contacts, compared to about one-sixth each of hydrogen and water-mediated bonds. This highlights the central importance of these contacts for complex formation, which have previously been relegated to a secondary role. Although common, water-mediated bonds are usually non-specific, acting as space-fillers at the protein-DNA interface. In conclusion, the majority of amino acid-base interactions observed follow general principles that apply across all protein-DNA complexes, although there are individual exceptions. Therefore, we distinguish between interactions whose specificities are 'universal' and 'context-dependent'. An interactive Web-based atlas of side chain-base contacts provides access to the collected data, including analyses and visualisation of the three-dimensional geometry of the interactions.

Base Pairing↗
PubMed2004

Molecular analysis of 10 coding regions from Arabidopsis that are homologous to the MUR3 xyloglucan galactosyltransferase.

Plant cell walls are composed of a large number of complex polysaccharides, which contain at least 13 different monosaccharides in a multitude of linkages. This structural complexity of cell wall components is paralleled by a large number of predicted glycosyltransferases in plant genomes, which can be grouped into several distinct families based on conserved sequence motifs (B. Henrissat, G.J. Davies [2000] Plant Physiol 124: 1515-1519). Despite the wealth of genomic information in Arabidopsis and several crop plants, the biochemical functions of these coding regions have only been established in a few cases. To lay the foundation for the genetic and biochemical characterization of putative glycosyltransferase genes, we conducted a phylogenetic and expression analysis on 10 predicted coding regions (AtGT11-20) that are closely related to the MUR3 xyloglucan galactosyltransferase of Arabidopsis. All of these proteins contain the conserved sequence motif pfam 03016 that is the hallmark of the beta-d-glucuronosyltransferase domain of exostosins, a class of animal enzymes involved in the biosynthesis of the extracellular polysaccharide heparan sulfate. Reverse transcriptase-polymerase chain reaction and promoter:beta-glucuronidase studies indicate that all AtGT genes are transcribed. Although six of the 10 AtGT genes were expressed in all major plant organs, the remaining four genes showed more restricted expression patterns that were either confined to specific organs or to highly specialized cell types such as hydathodes or pollen grains. T-DNA insertion mutants in AtGT13 and AtGT18 displayed reductions in the Gal content of total cell wall material, suggesting that the disrupted genes encode galactosyltransferases in plant cell wall synthesis.

Amino Acid Sequence↗
PubMed1975

Detection of natural complex sounds by cells in the primary auditory cortex of the cat.

The neural mechanisms involved in the detection of natural complex sounds were studied by recording single-neuron responses from 132 cells in the primary auditory cortex of the cat. The cats were paralyzed and under neuroleptanalgesia (NLA). The cells were first stimulated with pure tones; the responses were then compared with those evoked by many different types of complex sounds, most of which were animal vocalizations. Per-stimulus-time (PST) histograms constructed from the responses to repetitive stimuli were compared with the corresponding sound spectrograms formed from the sounds used as stimuli. Of 100 cells 68 per cent gave predictable responses to complex sounds on the basis of their responses to different pure tone frequencies. In 32 per cent of the cells the responses were unpredictable. Half of these cells did not react to pure tones at all but responded to one or more animal vocalizations or generator sounds with different patterns. Some cells reacted to pure tones in quite a different way than to certain complex sounds, e.g. with inhibition instead of excitation. These results indicate that cells in the primary auditory cortex of the cat reacting in an unpredictable way to sounds with a complex structure have a more or less specialized function, in detecting and analyzing natural and other complex sound patterns. Cells reacting phasically to pure tones seem to be involved in the detection of transient sound elements.

Acoustic Stimulation↗
PubMed2005

Proteomic analysis of glycosylation: structural determination of N- and O-linked glycans by mass spectrometry.

This review summarizes the methods, mainly based on mass spectrometry, for the structural determination of N- and O-linked carbohydrates that are post-translationally attached to a large number of proteins and which play a key role in determining the function and biophysical properties of these compounds. Analysis of these carbohydrates has proved difficult in the past due to their structural complexity. However, modern analytical methods such as mass spectrometry have the ability to elucidate most structural details at the concentration levels required for proteomics. This review describes methods for direct examination of glycoproteins by mass spectrometry, the release of N- and O-linked glycans from glycoproteins separated in sodium dodecyl sulfate polyacrylamide electrophoresis gels, and the analysis of these compounds by techniques such as matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry. Matrix-assisted laser desorption/ionization mass spectrometry provides the most rapid method for comparing glycan profiles and is probably most appropriate for clinical studies. One of the most promising techniques for determining the structures of N-glycans in proteomic studies is negative ion fragmentation of electrosprayed ions. This technique combines high throughput with ease of structural interpretation and provides structural details that are difficult to obtain by classical methods.

Automation↗
PubMed2005

Strategies for the design of potent and selective kinase inhibitors.

The characterisation of the human kinome in recent years has resulted in the emergence of numerous kinase drug targets in a variety of therapeutic areas. Through the elucidation of the sequence and structural composition of kinase active sites, coupled with the solution of numerous ATP competitive ligand complex structures, significant advances have been made in developing inhibitors that are highly selective. This has shown to be the case not only for kinases that are divergent in primary structure, but also for isoforms with highly conserved structure and ATP binding sites. Here we review the methods employed in the generation of selective inhibitors and describe several successful examples of the design of highly potent and selective kinase ATP competitive ligands. We also describe examples where an alternate approach to selectivity was used. These include the use of small molecules to sequester kinases in inactive conformations, and to block phospho-transferase activity by preventing substrate docking and recruitment. Substrate recruitment sites are promising from a structure based design perspective as they contain features unique to individual protein kinases.

Adenosine Triphosphate↗
PubMedDate not supplied

Integrated homology modelling and X-ray study of herpes simplex virus I thymidine kinase: a case study.

Knowledge-based homology modelling together with site-directed mutagenesis, epitope and conformational mapping is an approach to predict the structures of proteins and for the rational design of new drugs. In this study we present how this procedure has been applied to model the structure of herpes simplex virus type 1 thymidine kinase (HSV1 TK, HSV1 ATP-thymidine-5'-phosphotransferase, EC 2.7.1.21). We have used, and evaluated, several secondary structure prediction methods, such as the classical one based on Chou and Fastman algorithm, neural networks using the Kabsch and Sander classification, and the PRISM method. We have validated the algorithms by applying them to the porcine adenylate kinase (ADK), whose three-dimensional structure is known and that has been used for the alignment of the TKs as well. The resulting first model of HSV1-TK consisted of the first beta-strand connected to the phosphate binding loop and its subsequent alpha-helix, the fourth beta-strand connected to the conserved FDRH sequence and two alpha-helix with basic amino acids. The 3D structure was built using the X-ray structure of ADK as template and following the general procedure for homology modelling. We extended the model by means of COMPOSER, an automatic process for protein modelling. Site-directed mutagenesis was used to experimentally verify the predicted active-site model of HSV1-TK. The data measured in our lab and by others support the suggestion that the FDRH motif is part of the active site and plays an important role in the phosphorylation of substrates. The structure of HSV1 TK, recently solved in collaboration with Prof. G. Schulz at 2.7 A resolution, includes 284 of 343 residues of the N-terminal truncated TK. The secondary structures could be clearly assigned and fitted to the density. The comparison between crystallographically determined structure and the model shows that nearly 70% of the HSV1 TK structure has been correctly modelled by the described integrated approach to knowledge based ligand protein complex structure prediction. This indicate that computer assisted methods, combined with "manual" correction both for alignment and 3D construction are useful and can be successful.

Crystallography, X-Ray↗
PubMed2003

[Microcosmic analysis of amino group implanted titanium].

OBJECTIVE: The purpose of this study was to determine the effects of amino group implantation on the surface structures of titanium. METHODS: The amino groups were implanted into the surfaces of titanium using 100 keV amino group ions at ambient temperature (25 degrees C) with the following three different doses: 5 x 10(17), 1 x 10(17) and 5 x 10(16) ions per cm2. The current density of the ion-beam was (10 microA/cm2. The modified surfaces were characterized using X-ray photoelectron spectroscopy (XPS) to determine the chemical components of the modified surfaces. A scanning electron microscope (SEM) was used to study the physical structure of the surfaces. RESULTS: The wide XPS profiles, the binding energy data and the SEM photos were obtained. The XPS showed that the modified surface contained Ti, O, C and N. The possible chemical states were speculated using Gauss matching analysis. There was no significant difference between the surfaces with and without implanted amino groups. CONCLUSION: The XPS data reveals that the structure of the modified surface layer of aminogroup-implanted titanium is TiN, comprising a complex structure of titanium and amino compound near the surface. The SEM Photos show that this technique has little effect on the surface structures of materials.

Amines↗
PubMed1991

Induction of non-MHC-restricted cytotoxicity in a patient with pure red cell aplasia: functional relevance to antigen-specific cytotoxic T cells.

A functional analysis of an expanded T-cell subpopulation was studied in a patient with pure red cell aplasia who had no evidence of malignancy. In the time of an aggravation of the anemia, an expanded population of large granular lymphocytes (LGL) with T-cell receptor (TCR) alpha beta +CD3+CD8+ phenotype was noted, which reverted to normal with remission. These T cells displayed a polyclonal pattern in DNA analysis. Functionally, the T cells, with suppressor/cytotoxic phenotype exhibited normal capabilities for transducing the signals of the proliferative response, and of interleukin-2R (IL-2R) expression and IL-2 production via the TCR-CD3 complex structure. While they suppressed erythroid colony formation in vitro, neither non-major histocompatibility complex-restricted cytotoxic activity, cytotoxic T-cell activity, nor suppressive activity for immunoglobulin synthesis by B cells was detected. Pretreatment by anti-CD3 or anti-T-cell receptor antibody generated cytotoxicity for FcR+ target cells in the patient cells, but no such augmentation was found with other monoclonal antibodies of FcR- target cells. These findings indicated that the expanded T cells are functionally relevant to antigen-specific cytotoxic T lymphocytes.

Adult↗
PubMed1993

Persistence of a high degree of structural organization of the telencephalon in brain homotransplants in adult Triturus carnifex (Urodele Amphibians).

Brains of adult Urodele Amphibians (Triturus carnifex Laur.) were homoplastically transplanted in conditions of complete morpho-functional isolation and fixed 100 and 365 days after the operation. Results show that in the post-telencephalic regions structural organization disappear in all cases, while, in some cases the telencephalon retain a fairly complex structural organization even after one year. The heterogeneous nature of the histological patterns observed may be attributed to the different size of the matrix areas, besides the different degree of immune response of the host to the graft. In the telencephalic district, where the matrix areas are particularly well developed, undifferentiated elements of these areas would be capable of opposing the degenerative phenomena in the transplants by neoformation of neurons. However, in post-telencephalic districts, where the matrix areas are less developed or absent, it would not be possible to make up for neuronal degeneration and these regions disappear or are formed only by some undifferentiated elements outside the surviving ependyma portions.

Animals↗