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PubMed1967

Localization of structural polymers in the cell wall of Neurospora crassa.

The distribution and localization of structural polymers in the cell wall of Neurospora crassa has been studied by selective removal and light and electron microscope examination. Observations with the light microscope indicated that each polymer by itself can provide structural integrity to the cell wall. Examination by electron microscopy showed that the cell wall consists of an outer layer of thick fibrils, identified chemically as a glucan-peptide-galactosamine complex, and an inner layer made up of beta-1,3 glucan and thin fibrils of chitin.

Amino Sugars↗
PubMed2006

Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses.

UNLABELLED: Prelude&Fugue are bioinformatics tools aiming at predicting the local 3D structure of a protein from its amino acid sequence in terms of seven backbone torsion angle domains, using database-derived potentials. Prelude(&Fugue) computes all lowest free energy conformations of a protein or protein region, ranked by increasing energy, and possibly satisfying some interresidue distance constraints specified by the user. (Prelude&)Fugue detects sequence regions whose predicted structure is significantly preferred relative to other conformations in the absence of tertiary interactions. These programs can be used for predicting secondary structure, tertiary structure of short peptides, flickering early folding sequences and peptides that adopt a preferred conformation in solution. They can also be used for detecting structural weaknesses, i.e. sequence regions that are not optimal with respect to the tertiary fold. AVAILABILITY: http://babylone.ulb.ac.be/Prelude_and_Fugue.

Algorithms↗
PubMed2003

Development of an ab initio protein structure prediction system ABLE.

An ab initio protein structure prediction system called ABLE is described. It is based on the fragment assembly method, which consists of two steps: dividing a target sequence into overlapping subsequences (fragments) of short length and assigning a local structure to each fragment; and generating models by assembling the local structures and selecting the models with low potential energy. One of the most important problems in conventional fragment assembly methods is the difficulty of selecting native-like structures by energy minimization only. ABLE thus employs a structural clustering method to select the native-like models from among the generated models. By applying the unit-vector root mean square distance (URMS) as a measure of structure similarity, we achieve more robust, effective structural clustering. When no enough clusters of good quality are obtained, ABLE runs the energy minimization procedure again by incorporating structural restraint conditions obtained from the consensus substructures in the previously generated models. This approach is based on our observation that there is a high probability that the consensus substructures of the generated models have native-like structures. Another feature of ABLE is that in assigning local structures to fragments, it assigns mainchain dihedral angles (phi, psi) to the central residue of each fragment according to a probability distribution map built from candidate sequences similar to each fragment. This enables the system to generate appropriate local structures that may not already exist in a protein structure database. We applied our system to 25 small proteins and obtain near-native folds for more than half of them. We also demonstrate the performance of our structural clustering method, which can be applied to other protein structure prediction systems.

Cluster Analysis↗
PubMed2006

Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.

MOTIVATION: Algorithmic and modeling advances in the area of protein-protein interaction (PPI) network analysis could contribute to the understanding of biological processes. Local structure of networks can be measured by the frequency distribution of graphlets, small connected non-isomorphic induced subgraphs. This measure of local structure has been used to show that high-confidence PPI networks have local structure of geometric random graphs. Finding graphlets exhaustively in a large network is computationally intensive. More complete PPI networks, as well as PPI networks of higher organisms, will thus require efficient heuristic approaches. RESULTS: We propose two efficient and scalable heuristics for finding graphlets in high-confidence PPI networks. We show that both PPI and their model geometric random networks, have defined boundaries that are sparser than the 'inner parts' of the networks. In addition, these networks exhibit 'uniformity' of local structure inside the networks. Our first heuristic exploits these two structural properties of PPI and geometric random networks to find good estimates of graphlet frequency distributions in these networks up to 690 times faster than the exhaustive searches. Our second heuristic is a variant of a more standard sampling technique and it produces accurate approximate results up to 377 times faster than the exhaustive searches. We indicate how the combination of these approaches may result in an even better heuristic. AVAILABILITY: Supplementary information is available at http://www.cs.toronto.edu/~natasha/BIOINF-2005-0946/Supplementary.pdf. Software implementing the algorithms is available at http://www.cs.toronto.edu/~natasha/BIOINF-2005-0946/estimate_grap-hlets.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗
PubMed2001

Studies of impurities in magnetic semiconductors: an example of important XAFS applications.

The x-ray absorption fine structure (XAFS) technique has been employed to investigate the local structure and valency about Mn and Fe ions in the III-V diluted magnetic semiconductors In(1-x)Mn(x)As and Ga(1-x)Fe(x)As, prepared by molecular-beam-epitaxy under various growth conditions. These new systems are promising magnetic materials of considerable current interest and with important technical applications including photo-carrier induced magnetism and spin-polarized current devices. The local structure around the magnetic ions can play a pivotal role in affecting the magnetic properties of these semiconductors. Local structure information obtained from XAFS has provided the first direct evidence that the magnetic impurities can indeed substitute for the cation host atoms in samples prepared under appropriate conditions.

Journal Article↗
PubMed1993

Chromosomal localization and structure of the human type II IMP dehydrogenase gene (IMPDH2).

We determined the chromosomal localization and structure of the gene encoding human type II inosine 5'-monophosphate dehydrogenase (IMPDH, EC 1.1.1.205), an enzyme associated with cellular proliferation, malignant transformation, and differentiation. Using polymerase chain reaction (PCR) primers specific for type II IMPDH, we screened a panel of human-Chinese hamster cell somatic hybrids and a separate deletion panel of chromosome 3 hybrids and localized the gene to 3p21.2-->p24.2. Two overlapping yeast artificial chromosome clones containing the full gene for type II IMPDH (IMPDH2) were isolated, and a physical map of 117 kb of human genomic DNA in this region of chromosome 3 was constructed. The gene for type II IMPDH was localized and oriented on this map and found to span no more than 12.5 kb.

Animals↗
PubMed2006

Evaluating the quality of NMR structures by local density of protons.

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures.

Crystallography, X-Ray↗
PubMed1995

Analysis of the Hoxd-3 gene: structure and localization of its sense and natural antisense transcripts.

This study set out to investigate the structure and localized expression of the mouse homeobox-containing gene Hoxd-3. In addition to identifying a transcript of the type known from other Antennapedia (Antp)-like mammalian homeobox cDNAs, an antisense transcript was also detected. The antisense form of Hoxd-3 overlaps with 603 bp of the sense transcript including the homeobox. Active antisense transcription has been confirmed by RNA blot analysis with single-stranded probes and by the direction of splicing of an intron in the antisense transcript. The localized expression of sense and antisense transcripts was compared by in situ hybridization. Hoxd-3 expression was observed from 8.5 days p.c., in the neural tube with a sharp border in the hind brain at the level of rhombomeres 4-5. In contrast, the earliest antisense expression was detected at 10.5 days p.c. in cDNA libraries. At 12.5 days p.c., sense and antisense transcripts colocalized in the liver. The possible role of antisense homeobox transcripts during liver and the hematopoietic development is discussed.

Amino Acid Sequence↗
PubMed1999

Relationship between the subcellular localization and structures of catalytic domains of FKBP-type PPIases.

The Schizosaccharomyces pombe gene, fkp39(+), encoding a homolog of FKBP(FK506 binding protein)-type peptidyl prolyl cis-trans isomerase (PPIase), was isolated and the primary structure was determined. This gene product (SpFkbp39p) showed PPIase enzymatic activity in a chymotrypsin-dependent enzyme assay involving recombinant SpFkbp39p. Comparison of the primary structures of the catalytic domains of FKBPs, including SpFkbp39p, revealed that FKBPs could be classified into four groups. This categorization corresponding to the known subcellular localization of the FKBPs, makes the prediction of the subcellular localization of FKBPs based on their primary structures feasible. SpFkbp39p was considered to be a member of the nuclear-type FKBP group from this relationship between primary structure and subcellular localization. An immunofluorescence assay against HA-epitope-tagged SpFkbp39p revealed that SpFkbp39p is localized to the nucleus, as predicted. Residues conserved in a "group-specific" manner in the catalytic domain were mapped to their corresponding three-dimensional positions; these "group-specific" residues were located in close proximity in distinct regions mostly on the protein surface, which implies the presence of "group-specific" regulatory functional regions. We also found that nuclear-type FKBPs, including SpFkbp39p, have two highly conserved domains other than catalytic ones, with further basic and acidic charged regions, especially in the case of nuclear-type FKBPs. This is the first report indicating that there is a rule for the relationship between the subcellular localization and structure of the catalytic domain of a FKBP.

Amino Acid Sequence↗
PubMed2005

Spatial chemical inhomogeneity and local electronic structure of Mn-doped Ge ferromagnetic semiconductors.

We have investigated the chemical distributions and the local electronic structure of potential diluted magnetic semiconductor Ge0.94Mn0.06 single crystals using scanning photoelectron microscopy (SPEM), x-ray absorption spectroscopy (XAS), and photoemission spectroscopy (PES). The SPEM image shows the stripe-shaped microstructures, which arise from the chemical phase separation between the Mn-rich and Mn-depleted phases. The Mn 2p XAS shows that the Mn ions in the Mn-rich region are in the divalent high-spin Mn2+ states but that they do not form metallic Mn clusters. The Mn 3d PES spectrum exhibits a peak centered at approximately 4 eV below E(F) and the negligible spectral weight near E(F). This study suggests that the observed ferromagnetism in Ge1-xMnx arises from the phase-separated Mn-rich phase.

Journal Article↗
PubMed2001

Quantitative analyses of anatomical and electrotonic structures of local spiking interneurons by three-dimensional morphometry in crayfish.

We quantitatively investigated the three-dimensional structure of the dendrites of local spiking interneurons using a confocal laser scanning microscope in the terminal abdominal ganglion of crayfish. We also studied their passive membrane properties electrophysiologically using the single-electrode current clamp techniques to analyze their electrotonic structure. All of the local spiking interneurons examined in this study lacked distinctive axonal structure and had a monopolar cell body that was connected with a fine primary process to a thick main segment. Numerous fine secondary processes projected from the main segment in the ganglionic neuropile. The average anatomical length of a secondary process from the main segment to its terminal was 261.9 +/- 15.2 microm. The average input resistance and membrane time constant of local spiking interneurons, obtained from their voltage responses to intracellular injection of step current pulses in the main segment, were 15.2 +/- 1.6 MOmega and 13.9 +/- 1.9 msec, respectively. Calculation of the electrotonic length of dendritic processes based on morphological and physiological data obtained in this study revealed that the average electrotonic length of secondary processes in local spiking interneurons was significantly longer than in local nonspiking interneurons, although both types of local interneurons showed apparently similar anaxonic structure. The steady-state voltage attenuation factors for the secondary processes of local spiking interneurons were significantly greater than those of local nonspiking interneurons in both centrifugal and centripetal directions. The larger electrotonic structure of local spiking interneurons compared to that of nonspiking interneurons appears to be compensated for by their excitable dendritic membrane.

Action Potentials↗
PubMed2001

XAFS study of LiCo1-xFexO2 cathode for rechargeable lithium battery by laboratory XAFS spectrometer.

The change of local structure in layered-rock-salt-type iron doped lithium cobaltate LiCo(1-x)Fe(x)O2 under electrochemical Li de-intercalation (charge) /re-intercalation (discharge) was studied by a laboratory type XAFS spectrometer. In Co K-XANES and Fe K-XANES of LiCo0.85Fe0.15O2 the absorption peak shifted to higher energy by 1.5-2eV for Co K-edge and by 2-2.5eV for Fe K-edge, respectively, after the first charge. The spectra returned close to initial position and had almost original shape after the first discharge. In Co K- and Fe K-EXAFS of LiCo0.85Fe0.15O2 during the first charge and discharge the reversible change of the local structure was observed mainly around the Co atoms although the partly irreversible change of the local structure was found around the Fe atoms. The variation of local structure occurred in similar manner for the samples with x=0.05 and 0.25. This indicates that both Co3+/Co4+ and Fe3+/Fe4+ redox reactions occur reversibly during the first charge and discharge.

Journal Article↗
PubMed2006

Solitons in two-dimensional lattices possessing defects, dislocations, and quasicrystal structures.

Localized nonlinear modes, or solitons, are obtained for the two-dimensional nonlinear Schrödinger equation with various external potentials that possess large variations from periodicity, i.e., vacancy defects, edge dislocations, and quasicrystal structure. The solitons are obtained by employing a spectral fixed-point computational scheme. Investigation of soliton evolution by direct numerical simulations shows that irregular-lattice solitons can be stable, unstable, or undergo collapse.

Journal Article↗
PubMed2004

Integrated web service for improving alignment quality based on segments comparison.

BACKGROUND: Defining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and prediction of structure from only sequence information. Over many years the secondary structure elements were used as available building blocks with great success. Specially prepared sets of possible structural motifs can be used to describe similarity between very distant, non-homologous proteins. The reason for utilizing the structural information in the description of proteins is straightforward. Structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate. RESULTS: Here we provide a new fragment library for Local Structure Segment (LSS) prediction called FRAGlib which is integrated with a previously described segment alignment algorithm SEA. A joined FRAGlib/SEA server provides easy access to both algorithms, allowing a one stop alignment service using a novel approach to protein sequence alignment based on a network matching approach. The FRAGlib used as secondary structure prediction achieves only 73% accuracy in Q3 measure, but when combined with the SEA alignment, it achieves a significant improvement in pairwise sequence alignment quality, as compared to previous SEA implementation and other public alignment algorithms. The FRAGlib algorithm takes approximately 2 min. to search over FRAGlib database for a typical query protein with 500 residues. The SEA service align two typical proteins within circa approximately 5 min. All supplementary materials (detailed results of all the benchmarks, the list of test proteins and the whole fragments library) are available for download on-line at http://ffas.ljcrf.edu/darman/results/. CONCLUSIONS: The joined FRAGlib/SEA server will be a valuable tool both for molecular biologists working on protein sequence analysis and for bioinformaticians developing computational methods of structure prediction and alignment of proteins.

Computational Biology↗
PubMed1993

A variable-radius measure of local hospital market structure.

OBJECTIVE: To provide a radius measure of the structure of local hospital markets that varies with hospital characteristics and is available for all hospitals in the United States. DATA SOURCES: 1982 American Hospital Association (AHA) Survey of Hospitals, 1982 Area Resource File (ARF), and 1983 California Office of Statewide Health Planning and Development (OSHPD) discharge abstracts. STUDY DESIGN: The OSHPD data were used to measure the radii necessary to capture 75 percent and 90 percent of each hospital's admissions. These radii were used as the dependent variables in regression models in which the independent variables were from the AHA and ARF. To estimate predicted market radii, the estimated parameters from the California models were applied to all nonfederal, short-term, general hospitals in the continental United States. These radii were used to define each hospital's service area, and all other hospitals within the calculated radii were considered potential competitors. Using this definition, we calculated two measures of local market structure: the number of other hospitals within the radius and a Herfindahl-Hirschman Index based on the distribution of hospital bed shares in the market. DATA EXTRACTION METHODS: These measures were calculated for all nonfederal, short-term, acute care hospitals in the continental United States for whom complete data were available (N = 4,884). CONCLUSIONS: These measures are available from the authors on computer-readable diskette, matched to hospital identifiers.

Ancillary Services, Hospital↗
PubMed2006

EPR theoretical study of local molecular structure and thermal expansion coefficient for octahedral Mn2+ centers in zinc fluosilicate.

A theoretical method for studying the inter-relation between electronic and molecular structure has been proposed by diagonalizing the complete energy matrices for a d(5) configuration ion in a trigonal ligand field and considering the second-order and fourth-order EPR parameters D and (a - F) simultaneously. As for ZnSiF(6).6H(2)O:Mn(2+) and ZnSiF(6).6D(2)O:Mn(2+) complex molecules, the local lattice distortion and local thermal expansion coefficient for the octahedral Mn(2+) centers in zinc fluosilicate have been investigated, respectively. The calculations indicate that the local lattice structure around an octahedral Mn(2+) center has an expansion distortion, whether the Mn(2+) ion is doped in ZnSiF(6).6H(2)O or ZnSiF(6).6D(2)O. Moreover, the total tendency of the local lattice expansion distortion will be more and more obvious with the temperature rising, apart from some slight variations at T = 60 K for the ZnSiF(6).6H(2)O. By simulating the two low-symmetry EPR parameters D and (a - F) simultaneously, the local lattice structure parameters R and theta have been determined to vary from 2.204 Angstroms to 2.256 Angstroms and from 53.417 degrees to 52.710 degrees, respectively, in the temperature range 19-297 K for ZnSiF(6).6H(2)O:Mn(2+) and to vary from 2.215 Angstroms to 2.255 Angstroms and from 53.346 degrees to 52.714 degrees, respectively, in the temperature range 50-300 K for ZnSiF(6).6D(2)O:Mn(2+). Subsequently the dependence of local thermal expansion coefficients on the temperature is studied and the corresponding theoretical values of the local thermal expansion coefficients are reported firstly. Some characteristics of local thermal expansion coefficients of Mn(2+) in ZnSiF(6).6H(2)O:Mn(2+) and ZnSiF(6).6D(2)O:Mn(2+) systems are also analyzed.

Journal Article↗
PubMed2005

Two-cistronic expression plasmids for high-level gene expression in Escherichia coli preventing translational initiation inhibition caused by the intramolecular local secondary structure of mRNA.

Two-cistronic expression plasmids for the wild-type solubilized domain of porcine NADPH-cytochrome P450 reductase (PsCPR) gene in Escherichia coli were systematically constructed using a solubilized domain of porcine cytochrome b5 gene (Psb5 gene) or a derivative of it as the first cistron to examine their utility for second gene expression preventing the translational inhibition caused by the intramolecular local secondary structure of mRNA at the ribosome-binding site (RBS). The mRNAs from the plasmids lacking an RBS for the second cistron (SD2) accumulated very low levels of PsCPR, while those from the plasmids having an SD2 accumulated higher levels of PsCPR. The level of accumulation of PsCPR by the mRNA from plasmid pCbSD-T-CPR-3, which has an SD2 upstream of the termination codon of the first cistron, was higher than for those with an SD2 in the intercistronic region. The predicted intramolecular local secondary structures at the SD2 of mRNAs from these plasmids were stable enough to cause translational initiation inhibition. These results indicate that the use of a two-cistronic expression plasmid is an effective way to overcome translational initiation inhibition. Improved plasmids, pCP1 and pCP2P, were constructed from pCbSD-T-CPR-3. Using these plasmids, the solubilized donain of porcine NADH-cytochrome b5 reductase was also highly accumulated on prevention of the translational initiation inhibition. These plasmids are expected to be useful tools for the comprehensive high-level expression of heterologous genes in E. coli cells.

Amino Acid Sequence↗
PubMed1996

Constructing amino acid residue substitution classes maximally indicative of local protein structure.

Using an information theoretic formalism, we optimize classes of amino acid substitution to be maximally indicative of local protein structure. Our statistically-derived classes are loosely identifiable with the heuristic constructions found in previously published work. However, while these other methods provide a more rigid idealization of physicochemically constrained residue substitution, our classes provide substantially more structural information with many fewer parameters. Moreover, these substitution classes are consistent with the paradigmatic view of the sequence-to-structure relationship in globular proteins which holds that the three-dimensional architecture is predominantly determined by the arrangement of hydrophobic and polar side chains with weak constraints on the actual amino acid identities. More specific constraints are imposed on the placement of prolines, glycines, and the charged residues. These substitution classes have been used in highly accurate predictions of residue solvent accessibility. They could also be used in the identification of homologous proteins, the construction and refinement of multiple sequence alignments, and as a means of condensing and codifying the information in multiple sequence alignments for secondary structure prediction and tertiary fold recognition.

Amino Acid Sequence↗