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41.
Aleksandra Czarna Rafael Sanjuán Fernando González-Candelas Borys Wróbel 《BMC evolutionary biology》2006,6(1):105-13
Background
The least squares (LS) method for constructing confidence sets of trees is closely related to LS tree building methods, in which the goodness of fit of the distances measured on the tree (patristic distances) to the observed distances between taxa is the criterion used for selecting the best topology. The generalized LS (GLS) method for topology testing is often frustrated by the computational difficulties in calculating the covariance matrix and its inverse, which in practice requires approximations. The weighted LS (WLS) allows for a more efficient albeit approximate calculation of the test statistic by ignoring the covariances between the distances. 相似文献42.
Wawrzkiewicz A Pawelek K Borys P Dworakowska B Grzywna ZJ 《European biophysics journal : EBJ》2012,41(6):505-526
Several approaches to ion-channel gating modelling have been proposed. Although many models describe the dwell-time distributions correctly, they are incapable of predicting and explaining the long-term correlations between the lengths of adjacent openings and closings of a channel. In this paper we propose two simple random-walk models of the gating dynamics of voltage and Ca(2+)-activated potassium channels which qualitatively reproduce the dwell-time distributions, and describe the experimentally observed long-term memory quite well. Biological interpretation of both models is presented. In particular, the origin of the correlations is associated with fluctuations of channel mass density. The long-term memory effect, as measured by Hurst R/S analysis of experimental single-channel patch-clamp recordings, is close to the behaviour predicted by our models. The flexibility of the models enables their use as templates for other types of ion channel. 相似文献
43.
Chekmenev EY Vollmar BS Forseth KT Manion MN Jones SM Wagner TJ Endicott RM Kyriss BP Homem LM Pate M He J Raines J Gor'kov PL Brey WW Mitchell DJ Auman AJ Ellard-Ivey MJ Blazyk J Cotten M 《Biochimica et biophysica acta》2006,1758(9):1359-1372
We studied amidated and non-amidated piscidins 1 and 3, amphipathic cationic antimicrobial peptides from fish, to characterize functional and structural similarities and differences between these peptides and better understand the structural motifs involved in biological activity and functional diversity among amidated and non-amidated isoforms. Antimicrobial and hemolytic assays were carried out to assess their potency and toxicity, respectively. Site-specific high-resolution solid-state NMR orientational restraints were obtained from (15)N-labeled amidated and non-amidated piscidins 1 and 3 in the presence of hydrated oriented lipid bilayers. Solid-state NMR and circular dichroism results indicate that the peptides are alpha-helical and oriented parallel to the membrane surface. This orientation was expected since peptide-lipid interactions are enhanced at the water-bilayer interface for amphipathic cationic antimicrobial peptides. (15)N solid-state NMR performed on oriented samples demonstrate that piscidin experiences fast, large amplitude backbone motions around an axis parallel to the bilayer normal. Under the conditions tested here, piscidin 1 was confirmed to be more antimicrobially potent than piscidin 3 and antimicrobial activity was not affected by amidation. In light of functional and structural similarities between piscidins 1 and 3, we propose that their topology and fast dynamics are related to their mechanism of action. 相似文献
44.
45.
Borys Szefczyk M. Natália D. S. Cordeiro Ricardo Franco José A. N. F. Gomes 《Journal of biological inorganic chemistry》2009,14(7):1119-1128
Molecular dynamics simulations of the wild-type and variant forms of the mouse ferrochelatase in complex with the product
(haem) have been performed using the GROMOS96 force field, in the NpT ensemble. Ferrochelatase, the last enzyme in the catalytic
pathway of the haem biosynthesis, catalyses the reaction of insertion of a ferrous ion into protoporphyrin IX by distorting
the planar geometry of the latter reactant. The simulations presented aim at understanding the role of active-site residues
in this catalytic process. Analysis of the simulation trajectories explains the consequences of the mutations introduced and
sheds more light on the role of the His209 residue in porphyrin macrocycle distortion. The function of residues coordinating
propionate groups of the haem molecule is discussed in terms of stability of the substrate and product complexes. 相似文献
46.
Izabela Rutkowska-Wlodarczyk Borys Kierdaszuk Jakub Wlodarczyk 《Biochimica et Biophysica Acta - Proteins and Proteomics》2010,1804(4):891-898
Mass spectrometry is used to probe the kinetics of hydrogen–deuterium exchange in lysozyme in pH 5, 6 and 7.4. An analysis based on a Verhulst growth model is proposed and effectively applied to the kinetics of the hydrogen exchange. The data are described by a power-like function which is based on a time-dependence of the exchange rate. Experimental data ranging over many time scales is considered and accurate fits of a power-like function are obtained. Results of fittings show correlation between faster hydrogen–deuterium exchange and increase of pH. Furthermore a model is presented that discriminates between easily exchangeable hydrogens (located in close proximity to the protein surface) and those protected from the exchange (located in the protein interior). A possible interpretation of the model and its biological significance are discussed. 相似文献
47.
Expression of the replication genes of bacteriophage lambda, O and P, is believed to be translationally coupled. However, it was previously noted that, under conditions of amino acid starvation, when O is not synthesized, P continues to be expressed at a relatively high level. The results presented in this report, contrary to the previously presented hypothesis, suggest that an AGACUGGAU sequence (an optimal context for translation initiation from non-AUG codons in eukaryotes, and present upstream the P cistron) is inactive in Escherichia coli. Comparative sequence analysis confirms that such a signal is unlikely to be important for P synthesis. Instead, a weak Shine-Dalgarno sequence may be present upstream the P cistron, and be active in the absence of O gene expression. 相似文献
48.
Ammonia affects the glycosylation patterns of recombinant mouse placental lactogen-I by chinese hamster ovary cells in a pH-dependent manner 总被引:1,自引:0,他引:1
The N-linked glycosylation of the recombinant protein mouse placental lactogen-I (mPL-I) expressed by Chinese hamster ovary (CHO) cells under nongrowth conditions was inhibited by increasing levels of ammonium chloride (3 and 9 mM) in a serum-free, protein expression medium. The effect of ammonia on glycosylation was dependent on the extracellular pH (pH(e)). In media containing 0 and 9 mM ammonium chloride, the percentage of the most heavily glycosylated forms of secreted mPL-I decreased from ca. 90% to ca. 25% at pH(e) 8.0, and from ca. 90% to ca. 65% at pH(e) 7.6, respectively. However, at pH(e) 7.2, the most heavily glycosylated forms of secreted mPL-I decreased from ca. 90% to ca. 80% in media containing 0 and 9 mM ammonium chloride, respectively. Inhibition of mPL-I glycosylation was found to correlate with the calculated concentrations of the ammonia species (NH(3)). Control experiments showed that the ammonia effect on mPL-I glycosylation could not be attributed to increased chloride concentration or osmolarity, or to extracellular events after secretion of the recombinant protein into the supernatant. Ammonium chloride, 9 mM, inhibited the expression rate of MPL-I by CHO cells at low pH(e). (c) 1994 John Wiley & Sons, Inc. 相似文献
49.
H.K. Borys 《Analytical biochemistry》1978,88(1):245-255
A new analytical procedure has been developed to facilitate the investigation of the 1-methyladenine (1-MeA) biosynthetic pathway in starfish ovarian tissue. When fragments of ovarian tissue from Pisaster ochraceus are incubated in a seawater solution containing either [methyl-3H]- or [methyl-14C]methionine and a radial nerve extract, radioactive 1-MeA is produced. The labeled product is separated from the amino acid by using a combination of small ion-exchange columns and the formation of a silver-1-MeA complex which is insoluble in dilute acetic acid. Subsequently, 1-MeA is extracted from the complex, and its radioactivity is measured in a liquid seintillation counter. With this procedure, the synthesis of 1-MeA can be monitored in many samples simultaneously, without the use of bioassay. The results of the present experiments indicate that there is a methionine-dependent component in the 1-MeA biosynthetic pathway. In addition, synthesis of 1-MeA occurs in ovarian fragments almost immediately after exposure to radial nerve extract. These observations correspond very well to previously published data for other starfish species. 相似文献
50.
Type II alveolar cells were isolated from fetal rabbit lungs and used to determine the effect of GTP-binding protein activation on release of surfactant-related material. Cells were prelabelled with [3H]choline for 24 hours. NaF, a G-protein activator and GTP gamma S, a nonhydrolysable analogue of GTP, both loaded by hypoosmotic shock treatment, stimulated release of radioactive disaturated phosphatidylcholine. Localization of the cellular binding of [alpha-32P]GTP in fetal type II cells which were induced to differentiate by exposure to fetal lung fibroblast conditioned medium showed that two proteins of apparent molecular weights of 39.6 kd and 17.9 kd bound [alpha-32P]GTP. These proteins were detected only in the cells exposed to the conditioned medium. These results suggest GTP-binding proteins are involved in DSPC secretion and differentiation of fetal type II cells is accompanied by changes in GTP binding characteristics. 相似文献