Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “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 1,405 records · Page 78Linked to original sources
PubMed2001

The molecular basis of allergenicity: comparative analysis of the three dimensional structures of diverse allergens reveals a common structural motif.

BACKGROUND: Although a large number of allergens have been characterised, the structural, functional, and biochemical features that these molecules have in common, and that could explain their ability to elicit powerful IgE antibody responses, are still uncertain. Recently, there has been considerable interest in the role of the cysteine protease activity of the house dust mite allergen Der p 1 in biasing the immune response in favour of IgE production. AIMS: To search for remote homologues of Der p 1 with sequences similar to the 30 conserved amino acids surrounding the catalytic cysteine residue (Cys34). METHODS: Potential homologues were analysed by examining their three dimensional structures and multiple sequence alignments using the programs PROPSEARCH, ClustalW, GeneDoc, and Swiss Pdb Viewer. RESULTS: Diverse allergens (for example, the plant cysteine protease papain, the transport protein lipocalin Mus m 1, and the ragweed allergen Amb a 5) have a similar structural motif; namely, a groove resembling the substrate binding groove of Der p 1. The groove is located inside an alpha-beta motif, between an alpha helix on one side and an antiparallel beta sheet on the other side. A similar common motif (a cysteine stabilised alpha-beta fold) can also be found in some toxins and defensins. CONCLUSION: Allergens of diverse sources have a common structural motif, namely a groove located inside an alpha-beta motif, which could potentially serve as a ligand binding site.

Allergens↗
PubMed2006

Correlated electronic structure nonlinear response methods for structured environments.

This contribution concerns a brief outline of structural environment models where correlated electronic structure response methods are utilized for the determination of nonlinear optical properties of molecules. The presentation provides theory and applications of a heterogeneous dielectric media model and a quantum mechanical-classical mechanical model at the level of correlated electronic structure response methods. The correlated electronic structure response methods include the multiconfigurational self-consistent field method.

Journal Article↗
PubMed2003

Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site.

BACKGROUND: The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function. RESULTS: The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid. CONCLUSION: The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.

Binding Sites↗
PubMed2002

Structural studies on C-amidated amino acids and peptides: function of amide group in molecular association in crystal structures of Val-Gly-NH2, Ser-Phe-NH2, Gly-Tyr-NH2 and Pro-Tyr-NH2 hydrochloride salts.

As part of a series of elucidation of the structural features of peptides caused by C-terminal alpha-amidation, the crystal structures of H-Val-Gly-NH2, H-Ser-Phe-NH2, H-Gly-Tyr-NH2, and H-Pro-Tyr-NH2 hydrochloride salts were analyzed by the X-ray diffraction method. Although respective molecules take energetically allowable torsion angles concerning the backbone and side chains, their conformations are not necessarily the same as the corresponding unamidated ones. This results from the different molecular packing requirements, rather than from different conformational features inherent in the C-amidated and -unamidated peptides. As for the molecular packing feature, each peptide tended to form a repeated structure through those hydrogen bonds in which both amide NH and O=C groups participate. The chloride ions are located between the neighboring peptides and are hydrogen-bonded to the respective amide NHs, leading to the sheet structure. The hydrogen-bonding feature of the amide group and its function in molecular packing was discussed based on the results analyzed so far.

Amides↗
PubMed1981

[Hemoglobins, XXXVI: The primary structure of a dimeric insect hemoglobin (Erythrocruorin), component IX from Chironomus thummi thummi. Studies on the quarternary structure of the dimeric CTT-hemoglobins (author's transl)].

The primary structure of a dimeric insect hemoglobin (erythrocruorin), component CTT IX (Chironomus thummi thummi) was established by automatic sequence analysis. The alignment of the peptides was facilitated by producing only a few large fragments. The primary structure of CTT IX is compared with the human beta-chains and with CTT III. It is discussed, why for the dimeric CTT-hemoglobins only dimerisation can be observed but no tetramerisation. Experiments were done to locate the binding areas between the subunits in the dimeric molecule. Even after blocking of the alpha-NH2-group by cyanate, the stability of the dimeric molecule is not altered. Therefore the binding regions of the CTT-hemoglobins must be different from those of the tetrameric hemoglobins of vertebrates. Our results lead to a quarternary structure different from that of the hemoglobins of mammalians. This structure explains the possibility of dimerisation, but excludes tetramerisation.

Amino Acid Sequence↗
PubMedDate not supplied

Antibodies against non-structural c100/3 and structural core antigen of hepatitis C virus (HCV) in hemodialysis patients.

Two groups of patients undergoing hemodialysis (HD) maintenance were evaluated for their antibody response to non-structural c100/3 protein and structural core protein of hepatitis C virus (HCV). Forty-six patients (Group 1) never presented liver abnormalities during HD treatment, while 52 patients (Group 2) had either current or prior liver enzyme elevations. Prevalence rates of 32.6% and 41.3% were found for anti-c100/3 and anti-HCV core antibodies, respectively, in patients with silent infections (Group 1). The rate of anti-c100/3 in patients of Group 2 was 71.15% and reached 86.5% for anti-HCV core antibodies. The recognition of anti-c100/3 and anti-core antibodies was significantly higher in Group 2 than in Group 1. A line immunoassay composed of structural and non-structural peptides was used as a confirmation assay. HBV infection, measured by the presence of anti-HBc antibodies, was observed in 39.8% of the patients. Six were HBsAg chronic carriers and 13 had naturally acquired anti-HBs antibodies. The duration of HD treatment was correlated with anti-HCV positivity. A high prevalence of 96.7% (Group 2) was found in patients who underwent more than 5 years of treatment. Our results suggest that anti-HCV core ELISA is more accurate for detecting HCV infection than anti-c100/3. Although the risk associated with the duration of HD treatment and blood transfusion was high, additional factors such as a significant non-transfusional spread of HCV seems to play a role as well. The identification of infective patients by more sensitive methods for HCV genome detection should help to control the transmission of HCV in the unit under study.

Adult↗
PubMed2005

Pre-edge features of Ti K-edge X-ray absorption near-edge structure for the local structure of sol-gel titanium oxides.

Titanium K-edge X-ray absorption near-edge structure (XANES) spectroscopy is used to examine the local Ti environments in the sol, gel, and xerogels of titanium oxide prepared by a sol-gel method. The xerogels were prepared by heat treatment at 200, 300, 400, 500, and 600 degrees C (denoted xero-200, xero-300, xero-400, xero-500, and xero-600), and the xerogels were doped with Fe(II), Ni(II), and Cu(II) ions (xero-Fe, xero-Ni, and xero-Cu). The local structures of the samples are compared using the pre- and post-edge features of the XANES spectra. Further analysis of the pre-edge features using Gaussian functions provides the energy and height of each peak, and the intensity ratios between peaks. Based on the resulting data, the samples can be classified into three groups: a weak Ti-Ti interaction group, an anatase-like structure group, and an anatase group. The sol, gel, xerogel, and xero-Ni are in the weak Ti-Ti interaction group, and the xero-200, xero-Fe, and xero-Cu are in the anatase-like structure group. The remaining samples are in the anatase group.

Journal Article↗
PubMed2000

Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis-intercalated DNA complex solved by MAD phasing.

We characterize intercalative complexes as either "high charge" and "low charge". In low charge complexes, stacking interactions appear to dominate stability and structure. The dominance of stacking is evident in structures of daunomycin, nogalamycin, ethidium, and triostin A/echinomycin. By contrast in a DNA complex with the tetracationic metalloporphyrin CuTMPyP4 [copper (II) meso-tetra(N-methyl-4-pyridyl)porphyrin], electrostatic interactions appear to draw the porphyrin into the duplex interior, extending the DNA along its axis, and unstacking the DNA. Similarly, DNA complexes of tetracationic ditercalinium and tetracationic flexi-di show significant unstacking. Here we report x-ray structures of complexes of the tetracationic bis-intercalator D232 bound to DNA fragments d(CGTACG) and d(BrCGTABrCG). D232 is analogous to ditercalinium but with three methylene groups inserted between the piperidinium groups. The extension of the D232 linker allows it to sandwich four base pairs rather than two. In comparison to CuTMPyP4, flexi-di and ditercalinium, stacking interactions of D232 are significantly improved. We conclude that it is not sufficient to characterize intercalators simply by net charge. One anticipates strong electrostatic forces when cationic charge is focused to a small volume or region near DNA and so must consider the extent to which cationic charge is focused or distributed. In sum, ditercalinium, with a relatively short linker, focuses cationic charge more narrowly than does D232. So even though the net charges are equivalent, electrostatic charges are expected to be of greater structural significance in the ditercalinium complex than in the D232 complex.

Cations↗
PubMed1982

The structure of melittin. I. Structure determination and partial refinement.

Melittin is the principal protein component of bee venom and is thought to function as a lytic agent. Despite its predominantly hydrophobic character, melittin is soluble as a tetramer in aqueous salt solutions. We report here on the determination of the crystal structure of tetrameric melittin at 2.8-A resolution by the method of multiple isomorphous replacement, followed by partial atomic refinement at 2.0-A resolution. The melittin tetramer contains a noncrystallographic 2-fold axis of symmetry in addition to a crystallographic 2-fold axis, so that the four polypeptide chains have nearly identical structures. The noncrystallographic 2-fold axis was utilized twice during the determination of the structure. The multiple isomorphous replacement electron density map was averaged over this 2-fold axis before model building and strict noncrystallographic symmetry was assumed during the initial stages of atomic refinement. The 2.8-A resolution electron density map suggests that the melittin monomer contains two alpha-helical regions separated by a non-alpha-helical segment at residues 11 and 12. Difference maps at 2.0-A resolution tend to confirm this structure and reveal that at least six solvent molecules are bound to the melittin tetramer in the crystal. The relatively high occupancies of four of these suggest that they are ions of crystallization rather than water molecules.

Bee Venoms↗
PubMed1993

Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.

The Src-homology 3 (SH3) region is a protein domain consisting of approximately 60 residues. It occurs in a large number of eukaryotic proteins involved in signal transduction, cell polarization and membrane--cytoskeleton interactions. The function is unknown, but it is probably involved in specific protein--protein interactions. Here we report the crystal structure of the SH3 domain of Fyn (a Src family tyrosine kinase) at 1.9 A resolution. The crystals have two SH3 molecules per asymmetric unit. These two Fyn SH3 domains are not related by a local twofold axis. The crystal structures of spectrin and Fyn SH3 domains as well as the solution structure of the Src SH3 domain show that these all have the same basic fold. A protein domain which has the same topology as SH3 is present in the prokaryotic regulatory enzyme BirA. The comparison between the crystal structures of Fyn and spectrin SH3 domains shows that a conserved surface patch, consisting mainly of aromatic residues, is flanked by two hairpin-like loops (residues 94-104 and 114-118 in Fyn). These loops are different in tyrosine kinase and spectrin SH3 domains. They could modulate the binding properties of the aromatic surface.

Bacterial Proteins↗
PubMed2000

Crystal structure of the NADP+-dependent aldehyde dehydrogenase from Vibrio harveyi: structural implications for cofactor specificity and affinity.

Aldehyde dehydrogenase from the bioluminescent bacterium, Vibrio harveyi, catalyses the oxidation of long-chain aliphatic aldehydes to acids. The enzyme is unique compared with other forms of aldehyde dehydrogenase in that it exhibits a very high specificity and affinity for the cofactor NADP(+). Structural studies of this enzyme and comparisons with other forms of aldehyde dehydrogenase provide the basis for understanding the molecular features that dictate these unique properties and will enhance our understanding of the mechanism of catalysis for this class of enzyme. The X-ray structure of aldehyde dehydrogenase from V. harveyi has been solved to 2.5-A resolution as a partial complex with the cofactor NADP(+) and to 2. 1-A resolution as a fully bound 'holo' complex. The cofactor preference exhibited by different forms of the enzyme is predominantly determined by the electrostatic environment surrounding the 2'-hydroxy or the 2'-phosphate groups of the adenosine ribose moiety of NAD(+) or NADP(+), respectively. In the NADP(+)-dependent structures the presence of a threonine and a lysine contribute to the cofactor specificity. In the V. harveyi enzyme an arginine residue (Arg-210) contributes to the high cofactor affinity through a pi stacking interaction with the adenine ring system of the cofactor. Further differences between the V. harveyi enzyme and other aldehyde dehydrogenases are seen in the active site, in particular a histidine residue which is structurally conserved with phosphorylating glyceraldehyde-3-phosphate dehydrogenase. This may suggest an alternative mechanism for activation of the reactive cysteine residue for nucleophilic attack.

Aldehyde Dehydrogenase↗
PubMed2000

Virtual body structures: a 3D structure development tool from visible human data.

Understanding the visiospatial aspects of anatomic structures is one of the most important aspects of studying gross anatomy. In this paper we are describing a tool that self-constructs 3D virtual body structures (VBS) 'right in-front-of your-eyes'. Furthermore, manipulation capabilities, such as translucent visualization, interactive rotation, translation, and scaling, incorporated into VBS facilitate fundamental learning experience that leads one to 'build 3D models in the mind', providing a validation of computer-assisted individual learning. Creating 3-D virtual body structures from actual human data has long been a dream of many computer scientists and Medical doctors. Now, with the advances in computer hardware and software technologies, our Virtual Body Structure technique, and the Visible Human project, that dream is becoming a reality.

Anatomy, Cross-Sectional↗
PubMed1975

The covalent and three-dimensional structure of concanavalin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure.

The coordinates of the individual non-hydrogen atoms of the lectin concanavalin A have been determined from the molecular model at 2.0-A resolution and have been adjusted to make them consistent with the known stereochemistry of the constituent amino acid residues. From the coordinates, an analysis has been made of all intra- and intersubunit interactions in the molecule, yielding a description of the hydrogen-bonded structure of the monomer, including two extensive pleated sheet structures and other features of the folding of the polypeptide chain. The description of the noncovalent bonding is extended to include the interactions involved in stabilization of the dimeric and tetrameric structures of the molecule. The complete description of the molecular structure provides a basis for analysis of the biological activities of concanavalin A.

Binding Sites↗
PubMed2003

Structuring healthcare knowledge bases: an analysis of explicit and implicit structures in Arden Syntax and an XML schema representation of Arden Syntax.

The Arden Syntax for Medical Logic Modules (MLMs) is an ANSI and ISO recognized standard language for representing clinical knowledge bases. We analyzed the explicit and implicit structures in Arden Syntax MLMs and developed an information model represented as an XML schema. While the explicit structures were easily represented as XML, implicit structures require further explicit definition. In any future representation format, explicit structuring must be balanced with expressiveness and usability.

Artificial Intelligence↗
PubMed2005

[Structured documentation of patients' medical records. A new record structure for emergency admissions is coming].

INTRODUCTION: In recent years a range of efforts to shorten the length of stay (LOS) for patients admitted to hospitals has been tested. Some studies indicate that this might be accomplished by rigorous planning of patient pathways and structured documentation of medical records. In this study the effect of a structured case record model was tested. METHODS: The new record structure was developed using predefined requirements for content, placement and presentation of documentation. Instruction of staff was followed by a switch to the new model from one day to the next. Collection of data was carried out three months before and five to eight months after implementation of the model. RESULTS: The department succeeded in including well over 50% of all includable patients. However, the analysis encompassed all includable patients (''intention to treat'' principle). The number of cases analysed was 340 before and 353 after implementation of the model. Average LOS was reduced by 1.1 day from before implementation to after implementation. This was not statistically significant. However, the model was subsequently kept in use by the department. DISCUSSION: This pilot study shows a non-significant tendency to shotening of LOS by using a structured case record model. It is important to pay attention to the practical difficulties of implementing new documentation tools.

Aged↗
PubMed1992

Structural requirements for tRNA methylation. Action of Escherichia coli tRNA(guanosine-1)methyltransferase on tRNA(1Leu) structural variants.

The Escherichia coli enzyme tRNA(m1G)methyltransferase, one of a group of post-transcription tRNA-modifying enzymes, shows remarkable specificity in selecting the tRNA species and the specific guanosine base to be methylated. To examine the structural basis of this specificity, we synthesized a total of 15 modifications of tRNA(1Leu) and measured their methylation reaction kinetics in vitro. Elimination of any one of the three tRNA side loops, the V loop, the T loop, or the D loop, reduced the Vmax for methylation by about 1 order of magnitude. Elimination of all three side loops reduced Vmax by about 2 orders of magnitude. Clearly, gross tRNA structure is important for full enzyme activity. At the bottom of the stem proximal to the anticodon loop, in the pair at positions 31-39, substitution of a G-C for a C-G, a change that should not weaken the helical structure, had little effect on Vmax or Km. However, substitution of a G for a C increased Vmax and Km, whereas substitution of a C for G sharply reduced Vmax and, to a lesser extent, Km. These results appear to be a consequence of the principle that purines are better than pyrimidines in the stacking of adjacent bases for stability. Stacking in the stem structure appears to be important for methylation enzyme activity. In the anticodon loop itself, changing a U to a C had little effect, but changing the G of the anticodon to a C reduced Vmax over 20-fold, demonstrating the importance of the presence of the anticodon G adjacent to the G being methylated for enzyme recognition.

Anticodon↗
PubMed1990

Nucleotide sequence of the fadA gene. Primary structure of 3-ketoacyl-coenzyme A thiolase from Escherichia coli and the structural organization of the fadAB operon.

The DNA insert of plasmid pK52 contains the fadAB operon coding for the Escherichia coli fatty acid oxidation complex. Studies on the operon's structure and organization revealed that the initiator codon (ATG) of the structural gene for 3-ketoacyl-CoA thiolase, the fadA gene, is located 109 nucleotides 3' to the stop codon (TGA) of the fadB gene that encodes the alpha-subunit, a multifunctional polypeptide. The direction of transcription of this operon is thus from fadB to fadA. The orientation of the fadA and fadB genes is the reverse of what had been published previously. The structural gene for thiolase is 1,164 nucleotides long and starts six nucleotides downstream from a Shine-Dalgarno sequence. 109 nucleotides of 5'-noncoding and 321 nucleotides of 3'-noncoding regions are also reported. The 3-ketoacyl-CoA thiolase beta-subunit is composed of 388 residues and has a calculated Mr of 40,889. The alpha- and beta-subunits were separated by gel filtration in formic acid, and the sequence of the amino-terminal 10 amino acids of the beta-subunit coincided with that deduced from the nucleotide sequence data. Sequence comparisons suggest that Cys-91 of the E. coli enzyme is the active-site cysteine residue and that the consensus sequence of the active sites of 3-ketoacyl-CoA thiolases is Asn-Arg-X1-Cys-X2-Ser-X3-X4-Gln. Although the quaternary structure of E. coli 3-ketoacyl-CoA thiolase is different from that of other thiolases, the sequence is homologous to rat and human peroxisomal and rat mitochondrial 3-ketoacyl-CoA thiolases, to the extent of 42, 41, and 37%, identity, respectively. An evolutionary tree of thiolases was constructed; it suggests that the genes of E. coli and peroxisomal 3-ketoacyl-CoA thiolases diverged after the appearance of eukaryotic cells.

Acetyl-CoA C-Acyltransferase↗
PubMedDate not supplied

[Myxovirus structural investigations by spin probe methods. II. Influence of rimantadine on the structure of viral and artificial lipid membranes].

The lipid membrane structure of two myxoviruses (influenza and Sendai viruses), red blood cells and liposomes (prepared from total lipids of Sendai virus) have been investigated in the presence of rimantadine by means of two spin probes C5 and C6--the iminoxyl derivatives of stearic acids. Rimantadine was shown to penetrate the lipid membranes of myxoviruses and red blood sells and change the structure of the lipid phase no less than 0.8 nm apart from the viral surface. In the depth of 2.2 nm the structure of these lipid membranes remains unchanged after addition of rimantadine. Rimantadine also displaces the phase transition points of cell and viral lipid membranes to lower temperatures. Rimantadine does not change the lipid bilayer structure of liposomes 0.8 nm apart from its surface. These finding allow to suggest that rimantadine affects the cell and viral lipoprotein membranes.

Adamantane↗