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A major time-consuming step of protein NMR structure determination is the generation of reliable NOESY cross peak lists which
usually requires a significant amount of manual interaction. Here we present a new algorithm for automated peak picking involving
wavelet de-noised NOESY spectra in a process where the identification of peaks is coupled to automated structure determination.
The core of this method is the generation of incremental peak lists by applying different wavelet de-noising procedures which
yield peak lists of a different noise content. In combination with additional filters which probe the consistency of the peak
lists, good convergence of the NOESY-based automated structure determination could be achieved. These algorithms were implemented
in the context of the ARIA software for automated NOE assignment and structure determination and were validated for a polysulfide-sulfur
transferase protein of known structure. The procedures presented here should be commonly applicable for efficient protein
NMR structure determination and automated NMR peak picking.
Electronic supplementary material Electronic supplementary material is available for this article at
and accessible for authorised users. 相似文献
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Karthik V. Rajasekar Andrew L. Lovering Felician Dancea David J. Scott Sarah A. Harris Lewis E.H. Bingle Manfred Roessle Christopher M. Thomas Eva I. Hyde Scott A. White 《Nucleic acids research》2016,44(10):4947-4956
The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53. 相似文献
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O. Bârzu F. Eckstein S. Dancea I. Petrescu C. Tărmure L.D. Ngoc A. Hodârnău H.H. Mantsch 《BBA》1979,547(2):361-369
Various analogs of adenosine 5′-triphosphate with a modified terminal phosphate group have been tested in energy-requiring reactions with intact mitochondria and submitochondrial particles.It is shown that the fluorophosphate analog ATP(γF) is a strong inhibitor of mitochondrial respiration and of energy requiring reactions which involve the participation of high energy intermediates, generated aerobically by the respiratory chain. On the other hand, ATP(γF) does not affect the ATPase activity of intact or disrupted mitochondria and is less effective in inhibiting ATP-driven reactions.The imidophosphate analog AMP-P(NH)P also inhibits the partial reactions of oxidative phosphorylation, but does not affect ATP synthesis from ADP and Pi. In contrast to ATP(γF), it is a strong inhibitor of both soluble and membrane-bound mitochondrial ATPases.The biological implication of the complementary effects of ATP(γF) and AMP-P(NH)P on mitochondria-catalysed reactions is discussed while suggesting the use of such nucleotide analogs as specific tools for the study of ATP-forming and ATP-utilizing reactions in mitochondria. 相似文献
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Dancea Z. Baba A. Morar M. V. Catoi C. Macri A. Drochner W. Schollenberger M. 《Mycotoxin Research》2004,20(1):19-23
Investigations on the mycological quality of feeds from Transylvanian farms are presented. The investigations had two objectives:
More than 50% of the samples showed water contents exceeding 16%, due to inadequate harvesting and storage conditions. This
correlated with high my-cological contamination, with dominant species of the genusFusarium, Aspergillus, Alternaria,Penicillium andRhizopus. Feeding trials with broilers showed that live weight gain and digestibility coefficients of protein and fat in animals givenFusarium infested grain were depressed. As well N-retention and feed conversion rate (kg feeding stuff/ kg weight gain) were impaired. 相似文献
1. | survey for mycological contamination and related chemical composition; |
2. | the evaluation of effects ofFusarium graminearum Schw. infested wheat (8% in the diet) on productivity and digestibility of nutrients in broilers. |
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Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes 总被引:2,自引:0,他引:2
Knowles TJ Jeeves M Bobat S Dancea F McClelland D Palmer T Overduin M Henderson IR 《Molecular microbiology》2008,68(5):1216-1227
Membranes of Gram-negative bacteria, mitochondria and chloroplasts receive and fold beta-barrel transmembrane proteins through the action of polypeptide transport-associated (POTRA) domains. In Escherichia coli, folding substrates are inserted into the outer membrane by the essential protein YaeT, a prototypic Omp85 protein. Here, the articulation between tandem POTRA domains in solution is defined by nuclear magnetic resonance (NMR) spectroscopy, indicating an unprecedented juxtaposition. The novel solution orientations of all five POTRA domains are revealed by small-angle X-ray scattering of the entire 46 kDa periplasmic region. NMR titration studies show that strands from YaeT's canonical folding substrate, PhoE, bind non-specifically along alternating sides of its mixed beta sheets, thus providing an ideal platform for helping to fold nascent outer-membrane proteins. Together, this provides the first structural model of how multiple POTRA domains recruit substrates from the periplasmic solution into the outer membrane. 相似文献
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Wolf CA Dancea F Shi M Bade-Noskova V Rüterjans H Kerjaschki D Lücke C 《Journal of biomolecular NMR》2007,37(4):321-328
Megalin, an approx. 600 kDa transmembrane glycoprotein that acts as multi-ligand transporter, is a member of the low density lipoprotein receptor gene family. Several cysteine-rich repeats, each consisting of about 40 residues, are responsible for the multispecific binding of ligands. The solution structure of the twelfth cysteine-rich ligand-binding repeat with class A motif found in megalin features two short beta-strands and two helical turns, yielding the typical fold with a I-III, II-V and IV-VI disulfide bridge connectivity pattern and a calcium coordination site at the C-terminal end. The resulting differences in electrostatic surface potential compared to other ligand-binding modules of this gene family, however, may be responsible for the functional divergence. 相似文献
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Lin YJ Dancea F Löhr F Klimmek O Pfeiffer-Marek S Nilges M Wienk H Kröger A Rüterjans H 《Biochemistry》2004,43(6):1418-1424
The periplasmic polysulfide-sulfur transferase (Sud) protein encoded by Wolinella succinogenes is involved in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The polysulfide-sulfur is covalently bound to the catalytic Cys residue of the Sud protein and transferred to the active site of the membranous polysulfide reductase. The solution structure of the homodimeric Sud protein has been determined using heteronuclear multidimensional NMR techniques. The structure is based on NOE-derived distance restraints, backbone hydrogen bonds, and torsion angle restraints as well as residual dipolar coupling restraints for a refinement of the relative orientation of the monomer units. The monomer structure consists of a five-stranded parallel beta-sheet enclosing a hydrophobic core, a two-stranded antiparallel beta-sheet, and six alpha-helices. The dimer fold is stabilized by hydrophobic residues and ion pairs found in the contact area between the two monomers. Similar to rhodanese enzymes, Sud catalyzes the transfer of the polysulfide-sulfur to the artificial acceptor cyanide. Despite their similar functions and active sites, the amino acid sequences and structures of these proteins are quite different. 相似文献