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At least 1,009 records · Page 56Linked to original sources
PubMed2006

Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.

Crystal structures are known for several glycosyl hydrolase family 10 (GH10) xylanases. However, none of them is from an alkalophilic organism that can grow in alkaline conditions. We have determined the crystal structures at 2.2 Angstroms of a GH10 extracellular endoxylanase (BSX) from an alkalophilic Bacillus sp. NG-27, for the native and the complex enzyme with xylosaccharides. The industrially important enzyme is optimally active and stable at 343 K and at a pH of 8.4. Comparison of the structure of BSX with those of other thermostable GH10 xylanases optimally active at acidic or close to neutral pH showed that the solvent-exposed acidic amino acids, Asp and Glu, are markedly enhanced in BSX, while solvent-exposed Asn was noticeably depleted. The BSX crystal structure when compared with putative three-dimensional homology models of other extracellular alkalophilic GH10 xylanases from alkalophilic organisms suggests that a protein surface rich in acidic residues may be an important feature common to these alkali thermostable enzymes. A comparison of the surface features of BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in the polyextremophilicity of proteins, where understanding the structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. The work brings to the fore the role of the nature and composition of solvent-exposed residues in the adaptation of enzymes to polyextreme conditions, as in BSX.

Adaptation, Biological↗
PubMed1985

Secondary structure of the pore-forming colicin A and its C-terminal fragment. Experimental fact and structure prediction.

Conformational investigations, using circular dichroism, on the pore-forming protein, colicin A (Mr 60 000), and a C-terminal bromelain fragment (Mr 20 000) were undertaken to estimate their secondary structure and to search for pH-dependent conformational changes. Colicin A and the bromelain peptide are mainly alpha-helical with an enrichment of the alpha-helical content in the C-terminal domain carrying the ionophoric activity. The non-negligible beta-sheet structure in the C-terminal domain is unstable and is easily transformed into alpha-helix upon decreasing the polarity of the solvent. No evidence of pH-dependent conformational modification, correlated with modification of colicin A activity, could be obtained. The secondary structure estimated on the basis of experimental data favoured a model in which the pore is built of a minimal number of six transmembrane alpha-helical segments. Search for such segments in the amino acid sequence of the C-terminal domain of colicin A was carried out by combining secondary structure prediction methods with hydrophobicity and hydrophobic movement calculations. Similar calculations on the C-terminal domains of colicin E1 and IB indicate a common structure of the pores formed by colicin A, E1 and IB. Only two or three putative transmembrane segments could be selected in the sequences of colicin A, IB or E1. As a result, it is concluded that the channel is probably not built by a single colicin molecule but more likely by an oligomer.

Chemical Phenomena↗
PubMed1992

The nucleotide and deduced amino acid structures of sheep and pig fetuin. Common structural features of the mammalian fetuin family.

This study was initiated to gain further insight into the structural features of the mammalian fetuin family. The cDNA structures of sheep and pig fetuin were determined. The cDNA insert encoding sheep (pig) fetuin comprised 1550 (1470) nucleotides, including 54 (46) nucleotides encoding a signal peptide of 18 (15) residues and 1038 (1041) nucleotides encoding the 346 (347) amino acids of the mature plasma protein. The predicted amino-terminal sequence of the mature pig fetuin was confirmed by the amino-terminal sequence of the purified protein. However, two alternative sheep amino-terminal sequences were found in fetuin purified from the plasma of a single sheep fetus; the minor product was the one predicted by comparison with other fetuin sequences while the major product was two amino acids longer. Comparison of the deduced amino acid sequences of sheep and pig fetuin showed an extensive sequence identity between them (75%) and with other proteins of the mammalian fetuin family, i.e. human alpha 2-HS glycoprotein, and bovine and rat fetuins. Twelve cysteine residues were found at invariant positions in all fetuin sequences, suggesting strongly that the arrangement of disulphide bridges identified in human alpha 2-HS glycoprotein is common to the members of the family. Further sequence comparisons revealed that the structures of mammalian fetuins are organised in three domains: two cystatin-like domains (D1 and D2) and a complex carboxyl-terminal domain (D3). The proposed three-domain structure of the protein is reflected in the organisation of the rat fetuin structural gene which has recently been published.

Amino Acid Sequence↗
PubMed1996

Structural vs non-structural flood-alleviation measures in the Yangtze Delta: a pilot survey of floodplain residents' preferences.

This study was initiated to test if structural flood-alleviation measures were more popular than non-structural measures among the floodplain residents of the Yangtze Delta, because of the long tradition of "living with embankments and other flood control structures'. The results of a pilot questionnaire survey among 239 respondents from four sample villages of two typical floodplains of the delta indicated that, contrary to expectations, the non-structural measure of flood insurance attracted more favourable responses (97 per cent) than any one of the structural measures, although the latter were also frequently selected by the respondents (64-92 per cent). A number of multivariate logit regressions between each of the preferred flood-alleviation measures and the respondents' flood adaptations identified some of the determinants of these preferences. For a more complete explanation of the causes of popularity of various flood-alleviation measures, further research should incorporate a behavioural model with trade-offs for alternative measures.

Adult↗
PubMed1992

Comparison of the N-linked oligosaccharide structures of the two major human myelin glycoproteins MAG and P0: assessment and relative occurrence of oligosaccharide structures by serial lectin affinity chromatography of 14C-glycopeptides.

The N-linked oligosaccharide structures of human myelin-associated glycoprotein (MAG) and P0 have been characterized by serial lectin affinity chromatography (SLAC) of 14C-glycopeptides. 14C-Glycopeptides were prepared from purified MAG derivative and P0 by extensive proteolytic digestion and N-14C-acetylation. Assuming that all the 14C-glycopeptides were radiolabelled to the same specific radioactivity, the relative occurrence of the oligosaccharide structures was correlated to the amount of incorporated radioactivity. Sixteen and 15 fractions were generated by SLAC of MAG and P0 14C-glycopeptides, respectively. Despite this tremendous structural heterogeneity, the oligosaccharide "fingerprints" of MAG and P0 obtained by SLAC displayed similarities: (a) of the three types of N-linked oligosaccharides, the complex type accounted for 80.4% and 94.9% of MAG and P0 radioactivity, respectively; (b) biantennary complex oligosaccharides were the major structures present on MAG and P0; (c) approximately 60% of MAG and P0 oligosaccharides possessed a bisecting N-acetylglucosamine residue; and (d) large amounts of oligosaccharides with an alpha(1-6)fucose residue were found in both MAG and P0 and, noticeably, approximately 25% of the tri- and/or tetraantennary and approximately 90% of the bisected biantennary oligosaccharides of both glycoproteins contained alpha(1-6)fucose residues in the core. This study demonstrates that MAG and P0, both belonging to the immunoglobulin superfamily, display structural similarities in their N-linked oligosaccharide contents.

Carbon Radioisotopes↗
PubMed2006

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Arthrobacter↗
PubMed1999

Evidence for the distortion product frequency place as a source of distortion product otoacoustic emission (DPOAE) fine structure in humans. I. Fine structure and higher-order DPOAE as a function of the frequency ratio f2/f1.

Critical experiments were performed in order to validate the two-source hypothesis of distortion product otoacoustic emissions (DPOAE) generation. Measurements of the spectral fine structure of DPOAE in response to stimulation with two sinusoids have been performed with normal-hearing subjects. The dependence of fine-structure patterns on the frequency ratio f2/f1 was investigated by changing f1 or f2 only (fixed f2 or fixed f1 paradigm, respectively), and by changing both primaries at a fixed ratio and looking at different order DPOAE. When f2/f1 is varied in the fixed ratio paradigm, the patterns of 2 f1-f2 fine structure vary considerably more if plotted as a function of f2 than as a function of fDP. Different order distortion products located at the same characteristic place on the basilar membrane (BM) show similar patterns for both, the fixed-f2 and fDP paradigms. Fluctuations in DPOAE level up to 20 dB can be observed. In contrast, the results from a fixed-fDP paradigm do not show any fine structure but only an overall dependence of DP level on the frequency ratio, with a maximum for 2f1-f2 at f2/f1 close to 1.2. Similar stimulus configurations used in the experiments have also been used for computer simulations of DPOAE in a nonlinear and active model of the cochlea. Experimental results and model simulations give strong evidence for a two-source model of DPOAE generation: The first source is the initial nonlinear interaction of the primaries close to the f2 place. The second source is caused by coherent reflection from a re-emission site at the characteristic place of the distortion product frequency. The spectral fine structure of DPOAE observed in the ear canal reflects the interaction of both these sources.

Acoustic Stimulation↗
PubMed2001

Capturing a photoexcited molecular structure through time-domain x-ray absorption fine structure.

The determination of the structure of transient molecules, such as photoexcited states, in disordered media (such as in solution) usually requires methods with high temporal resolution. The transient molecular structure of a reaction intermediate produced by photoexcitation of NiTPP-L2 (NiTPP, nickeltetraphenylporphyrin; L, piperidine) in solution was determined by x-ray absorption fine structure (XAFS) data obtained on a 14-nanosecond time scale from a third-generation synchrotron source. The XAFS measurements confirm that photoexcitation leads to the rapid removal of both axial ligands to produce a transient square-planar intermediate, NiTPP, with a lifetime of 28 nanoseconds. The transient structure of the photodissociated intermediate is nearly identical to that of the ground state NiTPP, suggesting that the intermediate adopts the same structure as the ground state in a noncoordinating solvent before it recombines with two ligands to form the more stable octahedrally coordinated NiTPP-L2.

Journal Article↗
PubMed2002

Crystal engineering: from structure to function.

Modern crystal engineering has emerged as a rich discipline whose success requires an iterative process of synthesis, crystallography, crystal structure analysis, and computational methods. By focusing on the molecular recognition events during nucleation and growth, chemists have uncovered new ways of controlling the internal structure and symmetry of crystals and of producing materials with useful chemical and physical properties.

Journal Article↗
PubMed1977

Threonyl-transfer ribonucleic acid synthetase from Escherichia coli: subunit structure and genetic analysis of the structural gene by means of a mutated enzyme and of a specialized transducing lambda bacteriophage.

Threonyl-transfer ribonucleic acid synthetase (ThrRS) has been purified from a strain of Escherichia coli that shows a ninefold overproduction of this enzyme. Determination of the molecular weight of the purified, native enzyme by gel chromatography and by polyacrylamide gel electrophoresis at different gel concentrations yielded apparent molecular weight values of 150,000 and 161,000, respectively. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate yields a single protein band of 76,000-dalton size. From these results an alpha(2) subunit structure can be inferred. A mutant with a structurally altered ThrRS, which had been obtained by selection for resistance against the antibiotic borrelidin, was used to map the position of the ThrRS structural gene (thrS) by P1 transductions. It was found that thrS is located in the immediate neighborhood of pheS and pheT, which are the structural genes for the alpha and beta subunits of phenylalanyl-transfer ribonucleic acid (tRNA) synthetase, the gene order being aroD-pheT-pheS-thrS. A lambda phage that was previously shown to specifically transduce pheS, pheT, and also the structural gene for the translation initiation factor IF3 can complement the defect of the altered ThrRS of the borrelidin-resistant strain. This phage also stimulates the synthesis of the 76,000, molecular-weight polypeptide of ThrRS in ultraviolet light-irradiated. E. coli cells. These results indicate that the genes for ThrRS, alpha and beta subunits of phenylalanyl-tRNA synthetase, and initiation factor IF3 are immediately adjacent on the E. coli chromosome.

Amino Acyl-tRNA Synthetases↗
PubMed2000

Structural fingerprinting: subgrouping of comoviruses by structural studies of red clover mottle virus to 2.4-A resolution and comparisons with other comoviruses.

Red clover mottle virus (RCMV) is a member of the comoviruses, a group of picornavirus-like plant viruses. The X-ray structure of RCMV strain S has been determined and refined to 2.4 A. The overall structure of RCMV is similar to that of two other comoviruses, Cowpea mosaic virus (CPMV) and Bean pod mottle virus (BPMV). The sequence of the coat proteins of RCMV strain O were modeled into the capsid structure of strain S without causing any distortion, confirming the close resemblance between the two strains. By comparing the RCMV structure with that of other comoviruses, a structural fingerprint at the N terminus of the small subunit was identified which allowed subgrouping of comoviruses into CPMV-like and BPMV-like viruses.

Amino Acid Sequence↗
PubMed2001

Structured drug-loaded bioresorbable films for support structures.

Bioresorbable films can serve simultaneously as anatomic support structures and as drug delivery platforms. In the present study, bioresorbable PLLA films containing dexamethasone were developed through solution processing. The effect of processing parameters on the film morphology and the resulting mechanical properties was studied. A model describing the structuring of these films is suggested. Generally, the solvent evaporation rate determines the kinetics of drug and polymer crystallization and thus, both the mode of drug dispersion in the polymer and the resulting mechanical properties. Two types of structured films were studied: (1) a polymer film with drug located on its surface, obtained due to drug skin formation accompanied by a later polymer core formation; and (2) a polymer film with small drug particles and crystals distributed within the bulk, obtained by parallel solidification of the two components. A prototypical application of these films is an expandable biodegradable support structure (stent). which we have developed. This stent demonstrated good initial mechanical properties. The film structure has only a minor effect on the stent radial compression strength, but more significantly affects the tensile mechanical properties.

Biocompatible Materials↗
PubMed2002

A structure-based approach to psychological assessment: matching measurement models to latent structure.

The present article sets forth the argument that psychological assessment should be based on a construct's latent structure. The authors differentiate dimensional (continuous) and taxonic (categorical) structures at the latentand manifest levels and describe the advantages of matching the assessment approach to the latent structure of a construct. A proper match will decrease measurement error, increase statistical power, clarify statistical relationships, and facilitate the location of an efficient cutting score when applicable. Thus, individuals will be placed along a continuum or assigned to classes more accurately. The authors briefly review the methods by which latent structure can be determined and outline a structure-based approach to assessment that builds on dimensional scaling models, such as item response theory, while incorporating classification methods as appropriate. Finally, the authors empirically demonstrate the utility of their approach and discuss its compatibility with traditional assessment methods and with computerized adaptive testing.

Bayes Theorem↗
PubMed2004

Structural characterization of genomes by large scale sequence-structure threading.

BACKGROUND: Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human) totaling 167,888 genes. RESULTS: The reported data represent first rather general evaluation of performance of full sequence-structure threading on multiple genomes providing opportunity to evaluate its general applicability for large scale studies. According to the estimated results the sequence-structure threading has assigned protein folds to more then 60% of eukaryotic, 68% of archaeal and 70% of bacterial proteomes.The repertoires of protein classes, architectures, topologies and homologous superfamilies (according to the CATH 2.4 classification) have been established for distant organisms and superkingdoms. It has been found that the average abundance of CATH classes decreases from "alpha and beta" to "mainly beta", followed by "mainly alpha" and "few secondary structures".3-Layer (aba) Sandwich has been characterized as the most abundant protein architecture and Rossman fold as the most common topology. CONCLUSION: The analysis of genomic occurrences of CATH 2.4 protein homologous superfamilies and topologies has revealed the power-law character of their distributions. The corresponding double logarithmic "frequency - genomic occurrence" dependences characteristic of scale-free systems have been established for individual organisms and for three superkingdoms.

Animals↗
PubMed2000

Analysis of human follistatin structure: identification of two discontinuous N-terminal sequences coding for activin A binding and structural consequences of activin binding to native proteins.

A primary physiological function of follistatin is the binding and neutralization of activin, a transforming growth factor-beta family growth factor, and loss of function mutations are lethal. Despite the critical biological importance of follistatin's neutralization of activin, the structural basis of activin's binding to follistatin is poorly understood. The purposes of these studies were 1) to identify the primary sequence(s) within the N-terminal domain of the follistatin coding for activin binding, and 2) to determine whether activin binding to the native protein causes changes in other structural domains of follistatin. Synthetic peptide mimotopes identified within a 63-residue N-terminal domain two discontinuous sequences capable of binding labeled activin A. The first is located in a region (amino acids 3-26) of follistatin, a site previously identified by directed mutagenesis as important for activin binding. The second epitope, predicted to be located between amino acids 46 and 59, is newly identified. Although the sequences 3-26 and 46-59 code for activin binding, native follistatin only binds activin if disulfide bonding is intact. Furthermore, pyridylethylation of Cys residues followed by N-terminal sequencing and amino acid analysis revealed that all of the Cys residues in follistatin are involved in disulfide bonds and lack reactive free sulfhydryl groups. Specific ligands were used to probe the structural effects of activin binding on the other domains of the full-length molecule, comprised largely of the three 10-Cys follistatin module domains. No effects on ligand binding to follistatin-like module I or II were observed after the binding of activin A to native protein. In contrast, activin binding diminished recognition of domain III and enhanced that of the C domain by their respective monoclonal antibody probes, indicating an alteration of the antigenic structures of these regions. Thus, subsequent to activin binding, interactions are likely to occur between regions of follistatin located in different domains and separated by considerable lengths of linear sequence. Such interactions could have important functional significance with respect to the structural heterogeneity of naturally occurring follistatins.

Activins↗
PubMed1993

The nuclear pore complex: three-dimensional surface structure revealed by field emission, in-lens scanning electron microscopy, with underlying structure uncovered by proteolysis.

The structure of the nuclear pore complex (NPC) has been previously studied by many different electron microscopic techniques. Recently, scanning electron microscopes have been developed that can visualise biologically relevant structural detail at the same level of resolution as transmission electron microscopes and have been used to study NPC structure. We have used such an instrument to visualise directly the structure of both cytoplasmic and nucleoplasmic surfaces of the NPC of manually isolated amphibian oocyte nuclear envelopes that have been spread, fixed, critical point dried and coated with a thin fine-grained film of chromium or tantalum. We present images that directly show features of the NPC that are visible at each surface, including coaxial rings, cytoplasmic particles, plug/spoke complexes and the nucleoplasmic basket or fishtrap. Some cytoplasmic particles are rod-shaped or possibly "T"-shaped, can be quite long structures extending into the cytoplasm and may be joined to the coaxial ring at a position between each subunit. Both coaxial rings, which are proud of the membranes, can be exposed by light proteolytic digestion, revealing eight equal subunits each of which may be bipartite. We have determined that the nucleoplasmic filaments that make up the baskets are attached to the outer periphery of the coaxial ring at a position between each of its subunits. These filaments extend into the nucleoplasm and insert at the distal end to the smaller basket ring. The space left between adjacent basket filaments would exclude particles bigger than about 25 nm, which is consistent with the exclusion limit previously found for NPC-transported molecules.

Actin Cytoskeleton↗
PubMed2002

A randomized school-based jumping intervention confers site and maturity-specific benefits on bone structural properties in girls: a hip structural analysis study.

We compared 7-month changes in bone structural properties in pre- and early-pubertal girls randomized to exercise intervention (10-minute, 3 times per week, jumping program) or control groups. Girls were classified as prepubertal (PRE; Tanner breast stage 1; n = 43 for intervention [I] and n = 25 for control [C]) or early-pubertal (EARLY; Tanner stages 2 and 3; n = 43 for I and n = 63 for C). Mean +/- SD age was 10.0 +/- 0.6 and 10.5 +/- 0.6 for the PRE and EARLY groups, respectively. Proximal femur scans were analyzed using a hip structural analysis (HSA) program to assess bone mineral density (BMD), subperiosteal width, and cross-sectional area and to estimate cortical thickness, endosteal diameter, and section modulus at the femoral neck (FN), intertrochanter (IT), and femoral shaft (FS) regions. There were no differences between intervention and control groups for baseline height, weight, calcium intake, or physical activity or for change over 7 months (p > 0.05). We used analysis of covariance (ANCOVA) to examine group differences in changes of bone structure, adjusting for baseline weight, height change, Tanner breast stage, and physical activity. There were no differences in change for bone structure in the PRE girls. The more mature girls (EARLY) in the intervention group showed significantly greater gains in FN (+2.6%, p = 0.03) and IT (+1.7%, p = 0.02) BMD. Underpinning these changes were increased bone cross-sectional area and reduced endosteal expansion. Changes in subperiosteal dimensions did not differ. Structural changes improved section modulus (bending strength) at the FN (+4.0%, p = 0.04), but not at the IT region. There were no differences at the primarily cortical FS. These data provide insight into geometric changes that underpin exercise-associated gain in bone strength in early-pubertal girls.

Biomechanical Phenomena↗
PubMed1983

Structure and function of L-lactate dehydrogenases from thermophilic and mesophilic bacteria. III) The primary structure of thermophilic lactate dehydrogenase from Bacillus stearothermophilus. Hydroxylamine-, o-iodosobenzoic acid- and tryptic-fragments. The complete amino-acid sequence.

Based on the partial sequence of the cyanogen bromide fragments [Tratschin, J.D., Wirz, B., Frank, G. and Zuber, H. (1983) Hoppe-Seyler's Z. Physiol. Chem. 364, 879-892], the amino-acid sequence of thermophilic lactate dehydrogenase from B. stearothermophilus was completed by the preparation and sequencing (sequenator, carboxypeptidase A and Y) of further overlapping fragments. Suitable peptide fragments were obtained by lactate dehydrogenase cleavage with hydroxylamine, o-iodosobenzoic acid and trypsin. The polypeptide chain of thermophilic lactate dehydrogenase from B. stearothermophilus consists of 317 amino-acid residues. While sequence homology with mesophilic lactate dehydrogenase of higher organisms reaches 35%, it is substantially higher with this mesophilic enzyme of bacillae (greater than 60%, B. megaterium, B. subtilis). The secondary structure elements and amino-acid residues of the active site of thermophilic lactate dehydrogenase deducted from primary structure data were compared with those from the mesophilic enzyme, the same was done for the internal sequence homology at the nucleotide-binding units. A comparative structure analysis (matrix system) based on the primary structure data of thermophilic enzyme should provide insight into the characteristic structure differences between thermophilic and mesophilic lactate dehydrogenase.

Amino Acid Sequence↗