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1.
D J Neidhart V M Powers G L Kenyon A Y Tsou S C Ransom J A Gerlt G A Petsko 《The Journal of biological chemistry》1988,263(19):9268-9270
The recent development of a high-yield expression system and purification scheme for mandelate racemase has enabled us to produce sufficiently large quantities of pure enzyme to pursue x-ray crystallographic study. Large, single crystals of mandelate racemase have been grown from buffered polyethylene glycol (pH 8.0) in the presence of 10 mM magnesium chloride. The crystals grow in several habits, and we have identified two distinct tetragonal space groups in preliminary x-ray diffraction analysis. Crystals shaped as rectangular plates demonstrate 4/mmm Laue symmetry and systematic absences consistent with the space group I422. They have cell dimensions of a = b = 153 A and c = 181 A. Octahedrally shaped crystals of mandelate racemase display 4/m Laue symmetry and systematic absences consistent with the space group 14. Cell dimensions for these crystals are a = b = 113 A and c = 124 A. Based on estimates of Vm and on the measured density of the 1422 form, we suggest that two subunits of mandelate racemase (38,570 daltons/subunit) occupy the asymmetric unit in both crystal forms. Crystals of both forms diffract to beyond 3.0-A resolution. We are currently screening for isomorphous heavy-atom derivatives. 相似文献
2.
A mathematical model is presented which explains the symmetries observed for the protein coats of filamentous bacterial viruses. Three viruses (Ff, IKe, and If1) all have five-start helices with rotation angles of 36 degrees and axial translations of 16 A (Type I symmetry), and three other viruses (Pf1, Xf, and Pf3) all have one-start helices with rotation angles of approximately equal to 67 degrees and translations of approximately 3 A (Type II symmetry). The coat protein subunits in each group diverge from each other in amino acid sequence, and Type II viruses differ dramatically in DNA structure. Regardless of the differences, both Type I and Type II symmetry can be understood as direct, natural consequences of the close-packing of alpha-helical protein subunits. In our treatment, an alpha-helical subunit is modeled as consisting of two interconnected, flexible tubular segments that follow helical paths around the DNA, one in an inner layer and the other in an outer layer. The mathematical model is a set of algebraic equations describing the disposition of the flexible segments. Solutions are described by newly introduced symmetry indices and other parameters. An exhaustive survey over the range of indices has produced a library of all structures that are geometrically feasible within our modeling scheme. Solutions which correspond in their rotation angles to Type I and Type II viruses occur over large ranges of the parameter space. A few solutions with other symmetries are also allowed, and viruses with these symmetries may exist in nature. One solution to the set of equations, obtained without any recourse to the x-ray data, yields a calculated x-ray diffraction pattern for Pf1 which compares reasonably with experimental patterns. The close-packing geometry we have used helps explain the near constant linear mass density of known filamentous phages. Helicoid, rigid cylinder, and maximum entropy structure models proposed by others for Pf1 are reconciled with the flexible tube models and with one another. 相似文献
3.
At birth or after hatching from the egg, vertebrate brains still contain neural stem cells which reside in specialized niches. In some cases, these stem cells are deployed for further postnatal development of parts of the brain until the final structure is reached. In other cases, postnatal neurogenesis continues as constitutive neurogenesis into adulthood leading to a net increase of the number of neurons with age. Yet, in other cases, stem cells fuel neuronal turnover. An example is protracted development of the cerebellar granular layer in mammals and birds, where neurogenesis continues for a few weeks postnatally until the granular layer has reached its definitive size and stem cells are used up. Cerebellar growth also provides an example of continued neurogenesis during adulthood in teleosts. Again, it is the granular layer that grows as neurogenesis continues and no definite adult cerebellar size is reached. Neuronal turnover is most clearly seen in the telencephalon of male canaries, where projection neurons are replaced in nucleus high vocal centre each year before the start of a new mating season—circuitry reconstruction to achieve changes of the song repertoire in these birds? In this review, we describe these and other examples of adult neurogenesis in different vertebrate taxa. We also compare the structure of the stem cell niches to find common themes in their organization despite different functions adult neurogenesis serves in different species. Finally, we report on regeneration of the zebrafish telencephalon after injury to highlight similarities and differences of constitutive neurogenesis and neuronal regeneration. 相似文献
4.
Many proteins function in the crystalline state, making crystallography a tool that can address mechanism, as well as structure. By initiating biological turnover in the crystal, transient structural species form, which may be filmed by Laue diffraction or captured by freeze-trapping methods. Laue diffraction has now reached an unprecedented level of sophistication and has found a 'niche of excellence' in the study of cyclic, ultra-fast, light-triggered reactions. Trapping methods, on the other hand, are more generally applicable, but require care to avoid artifacts. New strategies have been developed and difficulties such as radiation damage have received particular attention. Complementary methods--mainly UV/visible single-crystal spectroscopy--have proven essential to design, interpret and validate kinetic crystallography experiments. 相似文献
5.
Hideki Tanaka Yasushi Sasajima Minoru Ichimura Masanori Itaba Satoru Ozawa 《Molecular simulation》2013,39(3-6):397-406
Abstract The quasicrystal structure is considered to be a new type of ordered phase because its Fourier transform has Laue spots with icosahedral symmetry, which is inconsistent with crystal structure. Computer simulation of the formation process of a quasicrystal was performed by the molecular dynamics method. On the basis of the Strandburg type of quasicrystal model, we developed an algorithm of the formation process of binary quasicrystal reflecting the procedure as realistically as possible. The Fourier transform of some of the obtained structures has shown decagonal symmetry although the spots are rather diffused. It has been shown that the potential parameter and experimental condition should be limited to produce a perfect quasicrystal structure. 相似文献
6.
GOR V server for protein secondary structure prediction 总被引:3,自引:0,他引:3
SUMMARY: We have created the GOR V web server for protein secondary structure prediction. The GOR V algorithm combines information theory, Bayesian statistics and evolutionary information. In its fifth version, the GOR method reached (with the full jack-knife procedure) an accuracy of prediction Q3 of 73.5%. Although GOR V has been among the most successful methods, its online unavailability has been a deterrent to its popularity. Here, we remedy this situation by creating the GOR V server. 相似文献
7.
《Enzyme and microbial technology》1987,9(5):303-307
Tagetes minuta (marigold) cells were entrapped under sterile conditions in agarose, κ-carrageenan, agar and alginate. The effects of different supports on the growth rate of the entrapped cells during incubation for one week under standard conditions [I] were studied. In the second part (weeks 2 and 3) of the experiment the effects of low temperature (10°C) [II], intermittent N2 gassing [III], and omission of carbohydrates from the medium [IV]—superimposed on that of entrapment—on growth rate and the production of non-polar secondary metabolites were investigated. Compared to free cells, the impact of agarose on growth during the first week was nil, while the inhibition of growth increased in the order κ-carrageenan, agar and alginate, probably as a result of increasing rigidity of the support. In the second period the plant cells clearly had reached the stationary phase of the growth cycle in all cases. Again the pattern of growth on agarose closely followed that of free cells, i.e. a small increase in cases I and III, and a small decrease under the other two conditions. Low temperature [II] had the greatest effect on cell growth and cell release, probably as a result of gel structure at this temperature. Similarly to the effects on growth, the impact on secondary metabolite production was most pronounced in the case of alginate combined with low temperature. Both the omission of carbohydrates, and Nin2 gassing resulted in low concentrations of non-polar compounds in the media. The major trend observed was a shift away from mainly intracellular compounds in the case of free cells to mainly extracellular compounds in the case of entrapped cells at 10°C. 相似文献
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10.
Dominique Bourgeois Friedrich Schotte Maurizio Brunori Beatrice Vallone 《Photochemical & photobiological sciences》2007,6(10):1047-1056
When polychromatic X-rays are shined onto crystalline material, they generate a Laue diffraction pattern. At third generation synchrotron radiation sources, a single X-ray pulse of approximately 100 ps duration is enough to produce interpretable Laue data from biomolecular crystals. Thus, by initiating biological turnover in a crystalline protein, structural changes along the reaction pathway may be filmed by ultra-fast Laue diffraction. Using laser-light as a trigger, transient species in photosensitive macromolecules can be captured at near atomic resolution with sub-nanosecond time-resolution. Such pump-probe Laue experiments have now reached an outstanding level of sophistication and have found a domain of excellence in the investigation of light-sensitive proteins undergoing cyclic photo-reactions and producing stiff crystals. The main theoretical concepts of Laue diffraction and the challenges associated with time-resolved experiments on biological crystals are recalled. The recent advances in the design of experiments are presented in terms of instrumental choices, data collection strategy and data processing, and some of the inherent difficulties of the method are highlighted. The discussion is based on the example of myoglobin, a protein that has traversed the whole history of pump-probe Laue diffraction, and for which a massive amount of data have provided considerable insight into the understanding of protein dynamics. 相似文献
11.
Hind A. AL-Khayat Robert W. Kensler John M. Squire 《Journal of molecular biology》2010,403(5):763-776
The rods of anti-parallel myosin molecules overlap at the centre of bipolar myosin filaments to produce an M-region (bare zone) that is free of myosin heads. Beyond the M-region edges, myosin molecules aggregate in a parallel fashion to yield the bridge regions of the myosin filaments. Adjacent myosin filaments in striated muscle A-bands are cross-linked by the M-band. Vertebrate striated muscle myosin filaments have a 3-fold rotational symmetry around their long axes. In addition, at the centre of the M-region, there are three 2-fold axes perpendicular to the filament long axis, giving the whole filament dihedral 32-point group symmetry. Here we describe the three-dimensional structure obtained by a single-particle analysis of the M-region of myosin filaments from goldfish skeletal muscle under relaxing conditions and as viewed in negative stain. This is the first single-particle reconstruction of isolated M-regions. The resulting three-dimensional reconstruction reveals details to about 55 Å resolution of the density distribution in the five main nonmyosin densities in the M-band (M6′, M4′, M1, M4 and M6) and in the myosin head crowns (P1, P2 and P3) at the M-region edges. The outermost crowns in the reconstruction were identified specifically by their close similarity to the corresponding crown levels in our previously published bridge region reconstructions. The packing of myosin molecules into the M-region structure is discussed, and some unidentified densities are highlighted. 相似文献
12.
Norbert Deutsch Mátyás Pajkos Gábor Erdős Zsuzsanna Dosztányi 《Protein science : a publication of the Protein Society》2023,32(1):e4522
Intrinsically disordered proteins (IDPs) play important roles in a wide range of biological processes and have been associated with various diseases, including cancer. In the last few years, cancer genome projects have systematically collected genetic variations underlying multiple cancer types. In parallel, the number and different types of disordered proteins characterized by experimental methods have also significantly increased. Nevertheless, the role of IDPs in various types of cancer is still not well understood. In this work, we present DisCanVis, a novel visualization tool for cancer mutations with a special focus on IDPs. In order to aid the interpretation of observed mutations, genome level information is combined with information about the structural and functional properties of proteins. The web server enables users to inspect individual proteins, collect examples with existing annotations of protein disorder and associated function or to discover currently uncharacterized examples with likely disease relevance. Through a REST API interface and precompiled tables the analysis can be extended to a group of proteins. 相似文献
13.
Seaweed is more than the wrap that keeps rice together in sushi. Seaweed biomass is already used for a wide range of other
products in food, including stabilising agents. Biorefineries with seaweed as feedstock are attracting worldwide interest
and include low-volume, high value-added products and vice versa. Scientific research on bioactive compounds in seaweed usually
takes place on just a few species and compounds. This paper reviews worldwide research on bioactive compounds, mainly of nine
genera or species of seaweed, which are also available in European temperate Atlantic waters, i.e. Laminaria sp., Fucus sp., Ascophyllum nodosum, Chondrus crispus, Porphyra sp., Ulva sp., Sargassum sp., Gracilaria sp. and Palmaria palmata. In addition, Undaria pinnatifida is included in this review as this is globally one of the most commonly produced, investigated and available species. Fewer
examples of other species abundant worldwide have also been included. This review will supply fundamental information for
biorefineries in Atlantic Europe using seaweed as feedstock. Preliminary selection of one or several candidate seaweed species
will be possible based on the summary tables and previous research described in this review. This applies either to the choice
of high value-added bioactive products to be exploited in an available species or to the choice of seaweed species when a
bioactive compound is desired. Data are presented in tables with species, effect and test organism (if present) with examples
of uses to enhance comparisons. In addition, scientific experiments performed on seaweed used as animal feed are presented,
and EU, US and Japanese legislation on functional foods is reviewed. 相似文献
14.
St-Onge N C?té JN Preuss RA Patenaude I Fung J 《Journal of electromyography and kinesiology》2011,21(6):904-912
Postural reactions in healthy individuals in the seated position have previously been described and have been shown to depend on the direction of the perturbation; however the neck response following forward and backward translations has not been compared. The overall objective of the present study was to compare neck and trunk kinematic, kinetic and electromyographic (EMG) stabilization patterns of seated healthy individuals to forward and backward translations. Ten healthy individuals, seated on a chair fixed onto a movable platform, were exposed to forward and backward translations (distance = 0.15 m, peak acceleration = 1.2 m/s2). The head and trunk kinematics as well as the EMG activity of 16 neck and trunk muscles were recorded. Neck and trunk angular displacements were computed in the sagittal plane. The centers of mass (COMs) of the head (HEAD), upper thorax (UPTX), lower thorax (LOWTX) and abdomen (ABDO) segments were also computed. Moments of force at the C7-T1 and L5-S1 levels were calculated using a top-down, inverse dynamics approach. Forward translations provoked greater overall COM peak displacements. The first peak of moment of force was also reached earlier following forward translations which may have played a role in preventing the trunk from leaning backwards. These responses can be explained by the higher postural threat imposed by a forward translation. 相似文献
15.
The Paxos algorithm requires a single correct coordinator process to operate. After a failure, the replacement of the coordinator may lead to a temporary unavailability of the application implemented atop Paxos. So far, this unavailability has been addressed by reducing the coordinator replacement rate through the use of stable coordinator selection algorithms. We have observed that the cost of recovery of the newly elected coordinator’s state is at the core of this unavailability problem. In this paper we present a new technique to manage coordinator replacement that allows the recovery to occur concurrently with new consensus rounds. Experimental results show that our seamless approach effectively solves the temporary unavailability problem, its adoption entails uninterrupted execution of the application. Our solution removes the restriction that the occurrence of coordinator replacements is something to be avoided, allowing the decoupling of the application execution from the accuracy of the mechanism used to choose a coordinator. This result increases the performance of the application even in the presence of failures, it is of special importance to the autonomous operation of replicated applications that have to adapt to varying network conditions and partial failures. 相似文献
16.
In our earlier work we established that stirred crystallization of achiral compounds that crystallize in enantiomeric forms result in spontaneous chiral symmetry breaking. The asymmetry thus spontaneously generated is confined to the solid state. In this article, we present a case in which the crystal enantiomeric excess (CEE) can be converted to molecular enantiomeric excess (EE) through a solid state reaction which relates the enantiomeric form of the crystal to the enantiomeric form of the product. Such a process not only provides a means of detecting the CEE generated in stirred crystallization but it is also a means through which chiral asymmetry generated spontaneously is "propagated" to generate chiral compounds with enantiomeric excess. 相似文献
17.
Molecular modelling of the interactions of tetra-(4-N-methylpyridyl) porphin with TA and CG sites on DNA. 总被引:1,自引:1,他引:0
The molecular structure of the DNA-intercalating ligand tetra-(4-N-methylpyridyl) porphin has been determined by X-ray crystallography. The porphyrin has a precise centre of symmetry; the central core is planar, with the N-methylpyridyl groups inclined to it at angles of 66-72 degrees. Molecular modelling of this structure into TpA and CpG sites of intercalated DNA, has been performed, and approximate energetics calculated. It has been shown that only the CpG site can have full ligand intercalation, since the thymine methyl group sterically hinders such geometry at TpA sites. Modelling indicates the importance of electrostatic effects in the low-energy forms of intercalated and part-intercalated complexes at both sequences. 相似文献
18.
Ohishi H Tozuka Y Da-Yang Z Ishida T Nakatani K 《Biochemical and biophysical research communications》2007,358(1):24-28
Several crystal structure analyses of complexes of synthetic polyamine compounds, including N(1)-(2-(2-aminoethylamino))ethyl)ethane-1,2-diamine PA(222) and N(1)-(2-(2-(2-aminoethylamino)ethylamino)ethyl)ethane-1,2-diamine PA(2222), and left-handed Z-DNA d(CGCGCG)(2) have been reported. However, until now, there have been no examples of naturally occurring polyamines bound to the minor groove of the left-handed Z-DNA of d(CGCGCG)(2) molecule. We have found that spermidine, a natural polyamine, is connected to the minor groove of left-handed Z-DNA of d(CGCGCG)(2) molecule in a crystalline complex grown at 10 degrees C. The electron density of the DNA molecule was clear enough to determine that the spermidine was connected in the minor groove of two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2). This is the first example that a spermidine molecule can form a bridge conformation between two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2) in the minor groove. 相似文献
19.
Organometallic complexes have unique physico-chemical properties, which have been widely used in homogenous catalysis, for example, for the synthesis of lead compounds and drug candidates. Over the past two decades, a few scientists from all over the world have extended the use of the specific characteristics of these compounds (e.g. structural diversity, possibility of ligand exchange, redox and catalytic properties) for medicinal purposes. The results are stunning. A few organometallic compounds have already entered clinical trials and it can be anticipated that several more will follow in coming years. In this short review, we present the specific advantages that organometallic metal complexes have over purely organic and also coordination compounds. Furthermore, using specific examples, we illustrate how these particular properties can be put to good use in medicinal chemistry. The examples we present have an emphasis on, but are not restricted to, anti-cancer activity. 相似文献
20.
R P Bywater C H Carlisle R B Jackson A L Mackay P A Timmins 《Journal of molecular biology》1975,91(3):293-300
Further details are given of crystals of glutamine synthetase prepared from Escherichia coli. Crystals of two kinds have been observed: (1) rhombic dodecahedra which correspond to the morphology of the crystals studied by Eisenberg et al. (1971) (and which were found by them to contain dodecamers), and (2) rhombohedra, reported here. Cell dimensions and packing considerations led to the consideration of two possible structures for the rhombohedral crystals. These we have called the “T = 7 structure” and the “B.C.C. structure”. The T = 7 structure would be related to that derived by Eisenberg and would contain dodecamers, but is inconsistent with our X-ray intensity data. The B.C.C. structure is considered more probable. It is built of cubic octomers or square tetramers. Electron micrographs of our glutamine synthetase preparations show a wide variety of aggregates, including dodecamers and tetramers. The unit cell dimensions of our crystals are , and . The Laue symmetry group is m P31. 相似文献