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61.
Kujawa M Volc J Halada P Sedmera P Divne C Sygmund C Leitner C Peterbauer C Haltrich D 《The FEBS journal》2007,274(3):879-894
We purified an extracellular pyranose dehydrogenase (PDH) from the basidiomycete fungus Agaricus xanthoderma using ammonium sulfate fractionation and ion-exchange and hydrophobic interaction chromatography. The native enzyme is a monomeric glycoprotein (5% carbohydrate) containing a covalently bound FAD as its prosthetic group. The PDH polypeptide consists of 575 amino acids and has a molecular mass of 65 400 Da as determined by MALDI MS. On the basis of the primary structure of the mature protein, PDH is a member of the glucose-methanol-choline oxidoreductase family. We constructed a homology model of PDH using the 3D structure of glucose oxidase from Aspergillus niger as a template. This model suggests a novel type of bi-covalent flavinylation in PDH, 9-S-cysteinyl, 8-alpha-N3-histidyl FAD. The enzyme exhibits a broad sugar substrate tolerance, oxidizing structurally different aldopyranoses including monosaccharides and oligosaccharides as well as glycosides. Its preferred electron donor substrates are D-glucose, D-galactose, L-arabinose, and D-xylose. As shown by in situ NMR analysis, D-glucose and D-galactose are both oxidized at positions C2 and C3, yielding the corresponding didehydroaldoses (diketoaldoses) as the final reaction products. PDH shows no detectable activity with oxygen, and its reactivity towards electron acceptors is rather limited, reducing various substituted benzoquinones and complexed metal ions. The azino-bis-(3-ethylbenzthiazolin-6-sulfonic acid) cation radical and the ferricenium ion are the best electron acceptors, as judged by the catalytic efficiencies (k(cat)/K(m)). The enzyme may play a role in lignocellulose degradation. 相似文献
62.
The thermal denaturation of Lactobacillus confusus
l-2-Hydroxyisocaproate Dehydrogenase (l-HicDH) has been studied by Differential Scanning Calorimetry (DSC). The stability of this enzyme has been investigated at
different pH conditions. The results of this study indicate that the thermal denaturation of this enzyme is irreversible and
the T
m
is dependent on the scan-rate, which suggests that the denaturation process of l-HicDH is kinetically determined. The heat capacity function of l-HicDH shows a single peak with the T
m
values between 52.14°C and 55.89°C at pH 7.0 at different scan rates. These results indicate that the whole l-HicDH could unfold as a single cooperative unit, and intersubunit interactions of this homotetrameric enzyme must play a
significant role in the stabilization of the whole enzyme. The rate constant of the unfolding is analyzed as a first order
kinetic constant with the Arrhenius equation, and the activation energy has been calculated. The variation of the activation
energy values obtained with different methods does not support the validity of the one-step irreversible model. The denaturation
pathway was described by a three-state model, N → U → F, in which the dissociation of the tetramer takes place as an irreversible
step before the irreversible unfolding of the monomers. The calorimetric enthalpy associated with the irreversible dissociation
and the calorimetric enthalpy associated with the unfolding of the monomer were obtained from the best fitting procedure.
Thermal unfolding of l-HicDH was also studied using Circular Dichroism (CD) spectroscopy. Both methods yielded comparable values. 相似文献
63.
Distribution of haplotypes and microsatellite alleles among Asian elephants (<Emphasis Type="Italic">Elephas maximus</Emphasis>) in Thailand 总被引:1,自引:1,他引:0
Joerns Fickel Dietmar Lieckfeldt Parntep Ratanakorn Christian Pitra 《European Journal of Wildlife Research》2007,53(4):298-303
Habitat fragmentation often promotes increased inbreeding depression due to interrupted gene flow between populations. In
this study, we demonstrate that Asian elephants most likely also suffer from outbreeding depression due to cryptic speciation.
We analysed mitochondrial and nuclear DNA loci from 78 Asian elephants. Haplotype genealogy and analysis of molecular variance
revealed two matrilinear clades (α
h, β
h). Microsatellite analyses of individuals grouped according to their haplotype clade (corresponding group of nuclear genotypes
called α
nuc and β
nuc) revealed significant genotypic differentiation between α
nuc and β
nuc. Such genealogically differentiated forms in a morphologically uniform species are considered indicative of cryptic speciation.
The differentiation was caused by bulls, whereas considering cows only resulted in no differentiation. Such result is best
explained by Haldane’s rule whereby hybrid formation between genealogical forms causes lower viability and fertility of heterogametic hybrids. Although
the lack of hybrid-specific morphological characteristics renders direct testing of reduced hybrid fitness under natural conditions
unfeasible, the effects of Haldane’s rule are demonstrated by reduced male-mediated gene flow between genealogical forms under
sympatric conditions, as was indeed suggested by the data found in Asian elephants: male-mediated gene flow between groups
α
nuc and β
nuc was much lower than female-mediated gene flow.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
相似文献
Joerns FickelEmail: |
64.
65.
The prediction of protein 3D structures close to insertions and deletions or, more generally, loop prediction, is still one of the major challenges in homology modeling projects. In this article, we developed ranking criteria and selection filters to improve knowledge-based loop predictions. These criteria were developed and optimized for a test data set containing 678 insertions and deletions. The examples are, in principle, predictable from the used loop database with an RMSD < 1 A and represent realistic modeling situations. Four noncorrelated criteria for the selection of fragments are evaluated. A fast prefilter compares the distance between the anchor groups in the template protein with the stems of the fragments. The RMSD of the anchor groups is used for fitting and ranking of the selected loop candidates. After fitting, repulsive close contacts of loop candidates with the template protein are used for filtering, and fragments with backbone torsion angles, which are unfavorable according to a knowledge-based potential, are eliminated. By the combined application of these filter criteria to the test set, it was possible to increase the percentage of predictions with a global RMSD < 1 A to over 50% among the first five ranks, with average global RMSD values for the first rank candidate that are between 1.3 and 2.2 A for different loop lengths. Compared to other examples described in the literature, our large numbers of test cases are not self-predictions, where loops are placed in a protein after a peptide loop has been cut out, but are attempts to predict structural changes that occur in evolution when a protein is affected by insertions and deletions. 相似文献
66.
Fujita H Labeit D Gerull B Labeit S Granzier HL 《American journal of physiology. Heart and circulatory physiology》2004,287(6):H2528-H2534
We studied the effects of Ca2+ on titin (connectin)-based passive tension in skinned myocardium expressing either predominantly N2B titin (rat right ventricle, RRV) or predominantly N2BA titin (bovine left atrium, BLA). Actomyosin-based tension was abolished to undetectably low levels by selectively removing the thin filaments with a Ca2+-insensitive gelsolin fragment (FX-45). Myocardium was stretched in the presence and absence of Ca2+, and passive tension was measured. Ca2+ significantly increased passive tension during and after stretch in the BLA. The increase was insensitive to the actomyosin inhibitor 2,3-butanedione 2-monoxime, supporting the conclusion that the effect is titin based. Passive tension did not respond to calcium in the RRV, indicating that passive tension developed by N2B titin is calcium insensitive. Western blot analysis and immunofluorescence studies indicated that N2BA titin expresses E-rich PEVK motifs, whereas they are absent from N2B titin, supporting earlier single molecule studies that reported that E-rich motifs are required for calcium sensitivity. We conclude that calcium affects passive myocardial tension in a titin isoform-dependent manner. 相似文献
67.
Scaffold-based tissue engineering: rationale for computer-aided design and solid free-form fabrication systems 总被引:14,自引:0,他引:14
One of the milestones in tissue engineering has been the development of 3D scaffolds that guide cells to form functional tissue. Recently, mouldless manufacturing techniques, known as solid free-form fabrication (SFF), or rapid prototyping, have been successfully used to fabricate complex scaffolds. Similarly, to achieve simultaneous addition of cells during the scaffold fabrication, novel robotic assembly and automated 3D cell encapsulation techniques are being developed. As a result of these technologies, tissue-engineered constructs can be prepared that contain a controlled spatial distribution of cells and growth factors, as well as engineered gradients of scaffold materials with a predicted microstructure. Here, we review the application, advancement and future directions of SFF techniques in the design and creation of scaffolds for use in clinically driven tissue engineering. 相似文献
68.
Christoph?ScheichEmail author Dietmar?Leitner Volker?Sievert Martina?Leidert Brigitte?Schlegel Bernd?Simon Ivica?Letunic Konrad?Büssow Anne?Diehl 《BMC structural biology》2004,4(1):4
Background
High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. 相似文献69.
Manstein DJ 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2004,359(1452):1907-1912
Protein engineering and design provide excellent tools to investigate the principles by which particular structural features relate to the mechanisms that underlie the biological function of a protein. In addition to studies aimed at dissecting the communication pathways within enzymes, recent advances in protein engineering approaches make it possible to generate enzymes with increased catalytic efficiency and specifically altered or newly introduced functions. Here, two approaches using state-of-the-art protein design and engineering are described in detail to demonstrate how key features of the myosin motor can be changed in a specific and predictable manner. First, it is shown how replacement of an actin-binding surface loop with synthetic sequences, whose flexibility and charge density is varied, can be employed to manipulate the actin affinity, the catalytic activity and the efficiency of coupling between actin- and nucleotide-binding sites of myosin motor constructs. Then the use of pre-existing molecular building blocks, which are derived from unrelated proteins, is described for manipulating the velocity and even the direction of movement of recombinant myosins. 相似文献
70.
The His-tagged lipase BTL2 from Bacillus thermocatenulatus was expressed in Escherichia coli and purified to homogeneity by a simple, one-step purification protocol using immobilized metal affinity chromatography. The success of protein separation and purification was pH-dependent and increased with decreasing pH. The purified BTL2 lipase showed a strong tendency to aggregate upon concentration, which prevented a reproducible crystallization. Aggregation studies using dynamic light-scattering (DLS) analysis were performed to improve the purification and concentration of BTL2 lipase. Different chemical classes of additives were tested to manipulate the aggregation behaviour of BTL2 lipase with the aim of obtaining a monodisperse sample to use for crystallization. For the process of concentration of BTL2 lipase in monomeric form, the alcohol 2-propanol and the ionic detergent dodecyl dimethylamine-N-oxide (LDAO) were found to be necessary. For the concentrated lipase, the availability of 5% 2-propanol was sufficient to hold the lipase in monomeric form and no additional detergent was needed. 相似文献