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DC Muddiman AP Null JC Hannis 《Rapid communications in mass spectrometry : RCM》1999,13(12):1201-1204
Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd. 相似文献
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Kazius J Nijssen S Kok J Bäck T Ijzerman AP 《Journal of chemical information and modeling》2006,46(2):597-605
Substructure mining algorithms are important drug discovery tools since they can find substructures that affect physicochemical and biological properties. Current methods, however, only consider a part of all chemical information that is present within a data set of compounds. Therefore, the overall aim of our study was to enable more exhaustive data mining by designing methods that detect all substructures of any size, shape, and level of chemical detail. A means of chemical representation was developed that uses atomic hierarchies, thus enabling substructure mining to consider general and/or highly specific features. As a proof-of-concept, the efficient, multipurpose graph mining system Gaston learned substructures of any size and shape from a mutagenicity data set that was represented in this manner. From these substructures, we extracted a set of only six nonredundant, discriminative substructures that represent relevant biochemical knowledge. Our results demonstrate the individual and synergistic importance of elaborate chemical representation and mining for nonlinear substructures. We conclude that the combination of elaborate chemical representation and Gaston provides an excellent method for 2D substructure mining as this recipe systematically explores all substructures in different levels of chemical detail. 相似文献
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Summary In recent biochemical studies it was demonstrated that residue Asp113 of the-adrenoceptor (-AR) is an indispensable amino acid for the binding of-AR antagonists. Earlier fluorescence studies showed that a tryptophan-rich region of the-AR is involved in the binding of propranolol, the prototype-AR antagonist. Bearing these two biochemical findings in mind, we explored the-AR part containing Asp113, for an energetically favorable antagonist binding site. This was done by performing molecular docking studies with the antagonist propranolol and a specific-AR peptide which included, besides Asp113, two possibly relevant tryptophan residues. In the docking calculations, the propranolol molecule was allowed to vary all its internal torsional angles. The receptor peptide was kept in an-helix conformation, while side chains relevant to ligand binding were flexible to enable optimal adaptations to the ligand's binding conformation. By means of force-field calculations the total energy was minimized, consisting of the intramolecular energies of both ligand and receptor peptide, and the intermolecular energy. We found an antagonist binding site, consisting of amino acids Asp113 and Trp109, which enabled energetically favorable interactions with the receptor-binding groups of propranolol. According to these results, binding involves three main interaction points: (i) a reinforced ionic bond; (ii) a hydrogen bond; and (iii) a hydrophobic/charge transfer interaction. The deduced binding site shows a difference in affinity between the levo- and dextrorotatory isomers of propranolol caused by a difference in ability to form a hydrogen bond, which is in conformity with the experimentally observed stereoselectivity. Moreover, it also provides an explanation for the
1-selectivity ofp-phenyl substituted phenoxypropanolamines like betaxolol. Thep-phenyl substituent of betaxolol was shown to be sterically hindered upon binding to the
2-AR peptide, whereas this hindrance is very likely to be much less with the
1-AR peptide. Finally, the proposed antagonist binding site is discussed in the light of some recent biochemical findings and theories.Abbreviations
-AR
-adrenergic receptor
- cDNA
complementary DNA
- H-bond
hydrogen bond
- VdW
van der Waals
- QSAR
quantitative structure-activity relationship
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125I-pBABC
p-(bromoacetamido)benzyl-1-[125I]iodocarazol 相似文献
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KM Clauwaert Van Bocxlaer JF HJ Major JA Claereboudt WE Lambert Van den Eeckhout EM Van Peteghem CH De Leenheer AP 《Rapid communications in mass spectrometry : RCM》1999,13(14):1540-1545
This paper describes the investigation of the potential of a quadrupole orthogonal acceleration time-of-flight mass spectrometer (Q-TOF) equipped with an atmospheric pressure ionisation interface for quantitative measurements of small molecules separated by reversed phase liquid chromatography. To this end, the detection limits and linear dynamic range in particular were studied in an LC/MS/MS experiment using 3,4-methylenedioxymethamphetamine standards and 3,4-methylenedioxyethylamphetamine for internal standardisation. In a second phase, the experiment was repeated with real biological extracts (whole blood, serum, and vitreous humour). A calibration for 3,4-methylenedioxymethamphetamine and its metabolite 3,4-methylenedioxyamphetamine was prepared in each of these matrices again using 3,4-methylenedioxyethylamphetamine as internal standard. The resulting quantitative data were compared with those obtained by liquid chromatography with fluorescence detection for the same extracts. The Q-TOF results revealed excellent sensitivity and a linear dynamic range of nearly four decades (2-10 000 pg on-column, r(2) = 0.9998, 1/x weighting). Furthermore, all the calibration curves prepared in biological material were superimposable, LC/MS/MS and LC-fluorescence, and the quantitative results for actual samples compared very favourably. It was concluded that the Q-TOF achieves a linear dynamic range for quantitative LC/MS/MS work exceeding that of fluorescence detection and at much better absolute sensitivity. Copyright 1999 John Wiley & Sons, Ltd. 相似文献
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Munshi G Mustafa Sudhir Raniwala T Awes B Rai RS Bhalerao JG Contreras RV Gavai SK Ghosh P Jaikumar GC Mishra AP Mishra H Mishra B Mohanty J Nayak J-Y Ollitrault SC Phatak L Ramello R Ray PK Sahu AM Srivastava DK Srivastava VK Tiwari 《Pramana》2006,67(5):961-981
This is the report of Heavy Ion Physics and Quark-Gluon Plasma at WHEPP-09 which was part of Working Group-4. Discussion and
work on some aspects of quark-gluon plasma believed to have created in heavy-ion collisions and in early Universe are reported. 相似文献
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AP Balachandran 《Pramana》2002,59(2):359-368
We review certain emergent notions on the nature of space-time from noncommutative geometry and their radical implications.
These ideas of space-time are suggested from developments in fuzzy physics, string theory, and deformation quantization. The
review focuses on the ideas coming from fuzzy physics. We find models of quantum space-time like fuzzy S
4 on which states cannot be localized, but which fluctuate into other manifolds like CP3. New uncertainty principles concerning such lack of localizability on quantum space-times are formulated. Such investigations
show the possibility of formulating and answering questions like the probability of finding a point of a quantum manifold
in a state localized on another one. Additional striking possibilities indicated by these developments is the (generic) failure
of CPT theorem and the conventional spin-statistics connection. They even suggest that Planck’s ‘constant’ may not be a constant,
but an operator which does not commute with all observables. All these novel possibilities arise within the rules of conventional
quantum physics, and with no serious input from gravity physics. 相似文献
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