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31.
Background
Escherichia coli guanine-N2 (m2G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-terminus. Their C-terminal domain is related to the YbiN family of hypothetical MTases, but nothing is known about the structure or function of the N-terminal domain. 相似文献32.
Bujnicki JM Leach RA Debski J Rychlewski L 《Journal of molecular microbiology and biotechnology》2002,4(4):405-415
Functional analyses of the tRNA:(guanine 26, N2,N2)-dimethyltransferase (Trm1) have been hampered by a lack of structural information about the enzyme and by low sequence similarity to better studied methyltransferases. Here we used computational methods to detect novel homologs of Trm1, infer the evolutionary relationships of the family, and predict the structure of the Trm1 methyltransferase. The N-terminal region of the protein is predicted to form an S-adenosylmethionine-binding domain, which harbors the active site. The C-terminal region is rich in predicted alpha-helices and, in analogy to other nucleic acid methyltransferases, may constitute the target recognition domain of the enzyme. Interposing these two domains, most Trm1 homologs possess a highly variable inserted sequence that is delimited by a Cys4 cluster, likely forming a Zn-finger structure. The residues of Trm1 predicted to participate in cofactor binding, target recognition, and catalysis, were mapped onto a preliminary structural model, providing a platform for designing new experiments to better understand the molecular functions of this protein family. In addition, identification of novel, atypical Trm1 homologs suggests candidates for cloning and biochemical characterization. 相似文献
33.
Data retrieval, comprehension and sharing within and between plant-based databases are essential to exploit comparative genomic information to elucidate functional aspects of plant biology and to conduct studies of synteny and homology. However, the functionality is often hampered by the variability of terms used to describe comparable objects. The Zea mays Plant Structure Ontology database is designed to overcome this problem via the provision of a controlled vocabulary that facilitates knowledge sharing. It comprises international botanical terms, references, synonyms, and phylogenetic information and is open-source. 相似文献
34.
Kubisz L Mielcarek S Jaroszyk F 《International journal of biological macromolecules》2003,33(1-3):89-93
Determination of temperature dependencies of electric conductivity and thermal properties by differential scanning calorimetry (DSC) allow to analyse the processes of charge and heat transport in the bone being a complex collagen-hydroxyapatite (HAP)-water system. Modification of the bone structure by high doses of gamma-radiation changes the electrical and thermal properties of the bone. Electrical conductivity (sigma) of the bone decreases with consecutive heating runs. The decrease in sigma observed for irradiated samples was explained by the scission of the main chain of collagen macromolecule. Irradiation decreased the hydration level in the bone, its denaturation temperature and increased both enthalpy and entropy of the denaturation process. 相似文献
35.
The summer of every even year is considered by the protein structure prediction community as the Olympic Games season, because in addition to a number of continuous benchmarking experiments such as LiveBench, much effort is invested in the blind prediction experiments CASP and CAFASP. Here we report the major advances registered in the field since the last Games of 2000, as measured by the recently completed LiveBench-4 experiment. These results provide a timely measure of the capabilities of current methods and of their expected performance in the upcoming CASP-5 and CAFASP-3 experiments. We also describe the initiation of the two new, community-wide experiments, PDB-CAFASP and MR-CAFASP. These new experiments extend the scope of previous efforts and may have important implications for structural genomics. 相似文献
36.
Joanna Malicka Magorzata Groth Cezary Czaplewski Regina Kasprzykowska Adam Liwo Leszek ankiewicz Wieslaw Wiczk 《Letters in Peptide Science》1998,5(5-6):445-447
The probable conformations of two cyclic enkephalin analogs, DNS-cyclo[D-Dab-Gly-Trp-Leu] (I) and DNS-cyclo[D-Dab-Gly-Trp-D-Leu] (II) (DNS = dansyl), were determined by combining the results of NOE, vicinal coupling constant and fluorescence energy transfer measurements with theoretical calculations. The common feature of the conformations for both peptides is the presence of a -turn at residues 2 and 3. 相似文献
37.
Joanna Malicka Małgorzata Groth Cezary Czaplewski Regina Kasprzykowska Adam Liwo Leszek Łankiewicz Wieslaw Wiczk 《International journal of peptide research and therapeutics》1998,5(5-6):445-447
Summary The probable conformations of two cyclic enkephalin analogs, DNS-cyclo[d-Dab-Gly-Trp-Leu] (I) and DNS-cyclo[d-Dab-Gly-Trp-d-Leu] (II) (DNS=dansyl), were determined by combining the results of NOE, vicinal coupling constant and fluorescence energy transfer
measurements with theoretical calculations. The common feature of the conformations for both peptides is the presence of a
β-turn at residues 2 and 3. 相似文献
38.
Jasionowski Marek Łankiewicz Leszek Wiczk Wiesław Gwizdała Elwira Grzonka Zbigniew 《International journal of peptide research and therapeutics》1998,5(5-6):371-374
Summary Conformational features of the neuropeptide pituitary adenylate cyclase activating polypeptide (1–27) (PACAP(1–27)) and its
shorter fragments (1–5), (7–11) and (14–27) were studied by circular dichroism (CD) and fluorescence spectroscopy. The obtained
CD spectra revealed that only PACAP(1–27) and the fragment (14–27) possess some content of an organized structure — the α-helix.
This C-terminal, helical part of the peptides is important for receptor binding as it provides a stable structure that can
reside in the ordered lipid region of the receptor site in the membrane, while the primary biological function of the hormone
resides in the N-terminal, disordered part. Fluorescence studies have revealed that the tyrosine residue located in the helical
region of PACAP has a higher quantum yield and a longer average lifetime than the tyrosine in the N-terminus, probably due
to a ‘shielding’ effect of the hydrophobic cluster around Tyr22. 相似文献
39.
Abir U. Igamberdiev Leszek A. Kleczkowski 《BioEssays : news and reviews in molecular, cellular and developmental biology》2009,31(10):1091-1099
Here, we analyze how the set of nucleotides in the cell is equilibrated and how this generates simple rules that help the cell to organize itself via maintenance of a stable non‐equilibrium state. A major mechanism operating to achieve this state is thermodynamic buffering via high activities of equilibrating enzymes such as adenylate kinase. Under stable non‐equilibrium, the ratios of free and Mg‐bound adenylates, Mg2+ and membrane potentials are interdependent and can be computed. The adenylate status is balanced with the levels of reduced and oxidized pyridine nucleotides through regulated uncoupling of the pyridine nucleotide pool from ATP production in mitochondria, and through oxidation of substrates non‐coupled to NAD+ reduction in peroxisomes. The set of adenylates and pyridine nucleotides constitutes a generalized cell energy status and determines rates of major metabolic fluxes. As the result, fluxes of energy and information become organized spatially and temporally, providing conditions for self‐maintenance of metabolism. 相似文献
40.
Relationship between genotype and soil environment during colonization of poplar roots by mycorrhizal and endophytic fungi 总被引:1,自引:0,他引:1
Leszek Karliński Maria Rudawska Barbara Kieliszewska-Rokicka Tomasz Leski 《Mycorrhiza》2010,20(5):315-324
Poplars are among the few tree genera that can develop both ectomycorrhizal (ECM) and arbuscular (AM) associations; however,
variable ratios of ECM/AM in dual mycorrhizal colonizations were observed in the roots of a variety of poplar species and
hybrids. The objective of our study was to analyze the effect of internal and external factors on growth and dual AM and ECM
colonization of poplar roots in three 12–15-year-old common gardens in Poland. We also analyzed the abundance of nonmycorrhizal
fungal endophytes in the poplar roots. The Populus clones comprised black poplars (Populus deltoides and P. deltoides × Populus nigra), balsam poplars (Populus maximowiczii × Populus trichocarpa), and a hybrid of black and balsam poplars (P. deltoides × P. trichocarpa). Of the three sites that we studied, one was located in the vicinity of a copper smelter, where soil was contaminated with
copper and lead. Poplar root tip abundance, mycorrhizal colonization, and soil fungi biomass were lower at this heavily polluted
site. The total mycorrhizal colonization and the ratio of ECM and AM colonization differed among the study sites and according
to soil depth. The influence of Populus genotype was significantly pronounced only within the individual study sites. The contribution of nonmycorrhizal fungal endophytes
differed among the poplar clones and was higher at the polluted site than at the sites free of pollution. Our results indicate
that poplar fine root abundance and AM and ECM symbiosis are influenced by environmental conditions. Further studies of different
site conditions are required to characterize the utility of poplars for purposes such as the phytoremediation of polluted
sites. 相似文献