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101.
Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces
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Matthias Dietzen Olga V. Kalinina Katerina Taškova Benny Kneissl Anna‐Katharina Hildebrandt Elmar Jaenicke Heinz Decker Thomas Lengauer Andreas Hildebrandt 《Proteins》2015,83(10):1887-1899
Macromolecular oligomeric assemblies are involved in many biochemical processes of living organisms. The benefits of such assemblies in crowded cellular environments include increased reaction rates, efficient feedback regulation, cooperativity and protective functions. However, an atom‐level structural determination of large assemblies is challenging due to the size of the complex and the difference in binding affinities of the involved proteins. In this study, we propose a novel combinatorial greedy algorithm for assembling large oligomeric complexes from information on the approximate position of interaction interfaces of pairs of monomers in the complex. Prior information on complex symmetry is not required but rather the symmetry is inferred during assembly. We implement an efficient geometric score, the transformation match score, that bypasses the model ranking problems of state‐of‐the‐art scoring functions by scoring the similarity between the inferred dimers of the same monomer simultaneously with different binding partners in a (sub)complex with a set of pregenerated docking poses. We compiled a diverse benchmark set of 308 homo and heteromeric complexes containing 6 to 60 monomers. To explore the applicability of the method, we considered 48 sets of parameters and selected those three sets of parameters, for which the algorithm can correctly reconstruct the maximum number, namely 252 complexes (81.8%) in, at least one of the respective three runs. The crossvalidation coverage, that is, the mean fraction of correctly reconstructed benchmark complexes during crossvalidation, was 78.1%, which demonstrates the ability of the presented method to correctly reconstruct topology of a large variety of biological complexes. Proteins 2015; 83:1887–1899. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. 相似文献
102.
The influence of corticosterone during the period of tyrosine hydroxylase gene expression (16th–18th days of rat embryogenesis), which is sensitive to hormonal induction, on the ontogenesis of presynaptic markers of the noradrenergic system has been studied. It has been found that hormone-induced changes in the level of noradrenaline and dopamine in the brain cortex and brainstem had a transitive character and were eliminated in adulthood. At the same time, the hormone increased the activity of tyrosine hydroxylase in the cortex of 7- to 16-day-old rat pups and in the cortex and brainstem of adult animals. It has been shown that the level of glucocorticoids is an important factor in development of the noradrenergic system of the brain, able during critical periods of ontogenesis to cause sustained changes of its functioning in subsequent periods of life. 相似文献
103.
Sokolyanskaya L. O. Ivanov M. V. Ikkert O. P. Kalinina A. E. Evseev V. A. Glukhova L. B. Karnachuk O. V. 《Microbiology》2020,89(4):498-501
Microbiology - Micromycetes can precipitate metals in the form of insoluble oxalates, thus participating in metal removal from geochemical cycling and in secondary mineral formation. Metal... 相似文献
104.
The genetic control of the traits "plant height", "the number of lateral shoots" and "the number of lateral stems" has been studied in 3 pure lines and 1 variety of linseed according to the model 1 of Hayman method. It has been shown that the traits under investigation are inherited according to the additive-dominant model of genetic control in the absence of any interloci interactions. The higher plant height and numerous lateral shoots are recessive traits controlled by 2 blocks of polymeric genes, whereas the trait of numerous lateral stems is a dominant trait influenced by 1 to 3 blocks of genes. The linseed lines have been ranked according to the number of dominant alleles they have. Suggestions for selection using these parental genotypes have been made. 相似文献
105.
Background
The diversity of viruses, the absence of universally common genes in them, and their ability to act as carriers of genetic material make assessment of evolutionary paths of viral genes very difficult. One important factor contributing to this complexity is horizontal gene transfer.Results
We explore the possibility for the systematic identification of atypical genes within virus families, including viruses whose genome is not encoded by a double-stranded DNA. Our method is based on gene statistical features that differ in genes that were subject of recent horizontal gene transfer from those of the genome in which they are observed. We employ a one-class SVM approach to detect atypical genes within a virus family basing of their statistical signatures and without explicit knowledge of the source species. The simplicity of the statistical features used makes the method applicable to various viruses irrespective of their genome size or type.Conclusions
On simulated data, the method can robustly identify alien genes irrespective of the coding nucleic acid found in a virus. It also compares well to results obtained in related studies for double-stranded DNA viruses. Its value in practice is confirmed by the identification of isolated examples of horizontal gene transfer events that have already been described in the literature. A Python package implementing the method and the results for the analyzed virus families are available at http://svm-agp.bioinf.mpi-inf.mpg.de. 相似文献106.
Pairs of amino acid positions that evolve in a correlated manner are proposed to play important roles in protein structure or function. Methods to detect them might fare better with families for which sequences of thousands of closely related homologs are available than families with only a few distant relatives. We applied co-evolution analysis to thousands of sequences of HIV Gag, finding that the most significantly co-evolving positions are proximal in the quaternary structures of the viral capsid. A reduction in infectivity caused by mutating one member of a significant pair could be rescued by a compensatory mutation of the other. 相似文献
107.
108.
Leshchiner AD Minina EA Rakitina DV Vishnichenko VK Solovyev AG Morozov SY Kalinina NO 《Biochemistry. Biokhimii?a》2008,73(1):50-55
A 25-kD movement protein (25K protein) encoded by the first gene of the potexvirus Potato virus X triple gene block of transport genes is essential for the viral movement in infected plants. The 25K protein belongs to superfamily 1 of NTPase/helicases and exhibits in vitro RNA helicase, Mg2+-dependent NTPase, and RNA-binding activities. In the present work, the ability of 25K protein for homologous interactions was studied using the yeast two-hybrid system, protein chemical cross-linking in the presence of glutaraldehyde, far-Western blotting, and ultracentrifugation in sucrose density gradients. The 25K protein was shown to form homodimers and homooligomers. Sites of homologous protein-protein interactions were found in both the N- and C-terminal portions of the protein. 相似文献
109.
The gonadogenesis was studied in adult and juvenile females of Japanese mitten crab Eriocheir japonicus (Crustacea: Decapoda, Grapsida) inhabiting the rivers of the Maritime Territory. The morphometric parameters of oocytes at different stages of maturity were determined using the methods of computer morphometry and color characteristics were evaluated using the Munsell Book of Color. As a result, a color table was compiled for the ovaries from the beginning of development to gonad maturity, which included light yellow (sandy), yellow, beige, light purple, light brown, dark purple, brown (chocolate), and dark brown (brown). The regular changes in the ovary color of E. japonicus proved to closely correlate with the gonadogenesis, namely, with the composition of cells at each stage of gonad maturity. 相似文献
110.
The effects of antagonist of α2-adrenoceptors yohimbine and their agonist clonidine on Bax and Bcl-X L mRNA levels in neonatal rat brain were studied. Yohimbine decreased Bax mRNA level in the cerebellum, increased the ratio between Bcl-X L and Bax mRNA levels in the cerebellum, cortex, and hippocampus, and increased Bcl-X L mRNA level in the cortex and hippocampus of 6-day-old-rat pups 24 h after injection. Administration of clonidine 20 min after yohimbine administration abolished its effect on Bcl-XL mRNA level in the hippocampus. The data obtained indicate that the blockade of α2-adrenoceptors induces antiapoptotic changes in the developing rat brain, some of which can be abolished after coadministration with the agonist of these receptors. 相似文献