scholarly journals eSPC: an online data-analysis platform for molecular biophysics

Author(s):  
Osvaldo Burastero ◽  
Stephan Niebling ◽  
Lucas A. Defelipe ◽  
Christian Günther ◽  
Angelica Struve ◽  
...  

All biological processes rely on the formation of protein–ligand, protein–peptide and protein–protein complexes. Studying the affinity, kinetics and thermodynamics of binding between these pairs is critical for understanding basic cellular mechanisms. Many different technologies have been designed for probing interactions between biomolecules, each based on measuring different signals (fluorescence, heat, thermophoresis, scattering and interference, among others). Evaluation of the data from binding experiments and their fitting is an essential step towards the quantification of binding affinities. Here, user-friendly online tools to analyze biophysical data from steady-state fluorescence spectroscopy, microscale thermophoresis and differential scanning fluorimetry experiments are presented. The modules of the data-analysis platform (https://spc.embl-hamburg.de/) contain classical thermodynamic models and clear user guidelines for the determination of equilibrium dissociation constants (K d) and thermal unfolding parameters such as melting temperatures (T m).

1985 ◽  
Vol 110 (1) ◽  
pp. 75-82 ◽  
Author(s):  
Dieter Ratge ◽  
Sabine Hansel-Bessey ◽  
Hermann Wisser

Abstract. We measured plasma catecholamines, α- and β-adrenoreceptor numbers and the accumulation of cyclic adenosine monophosphate (cAMP) in the unstimulated state and in response to 10 μmol/l (-) isoproterenol in blood cells from 29 euthyroid controls and from 18 patients with spontaneous hyperthyroidism. In the thyrotoxic patients plasma norepinephrine (1.14 ± 0.5 nmol/l) and epinephrine (0.3 ±0.14 nmol/l) were significantly decreased compared with plasma norepinephrine (1.87 ± 0.7 nmol) and epinephrine (0.41 ± 0.19 nmol/l) in the controls (P < 0.01 and P < 0.05, respectively) and the values obtained in subjects rendered euthyroid by antithyroid treatment (P < 0.001, respectively). α-adrenoceptor density in platelet membranes obtained from patients in the hyperthyroid state (114 ± 38 sites per cell) was significantly decreased when compared with controls (159 ± 48 sites per cell, P < 0.01) and the values from patients under effective antithyroid treatment (136 ± 35 sites per cell, P < 0.01). On the contrary, a significant increase in β-adrenoceptor density in mononuclear leucocyte (MNL) membranes was found in hyperthyroid patients (1751 ± 237 sites/cell) when compared with controls (1510 ± 351 sites/cell, P < 0.05) and the same patients following antithyroid treatment (1455 ± 260 sites/cell, P < 0.001). The equilibrium dissociation constants (KD) did not change in hyperthyroidism. Basal cAMP concentrations in MNL were higher in untreated thyrotoxicosis (45 ± 18 pmol/106 cells/10 min) than in patients in the euthyroid state (35 ± 9 pmol/106 cells/10 min, P < 0.05). Our data support the hypothesis that the balance of α- and β-adrenoceptors depends on the thyroid state. However, before the reputed catecholamine supersensitivity in hyperthyroid man can be accepted, the relationship between alterations in adrenoceptors and the biological responsiveness to catecholamines has to be demonstrated in different human tissues.


1997 ◽  
Vol 6 (8) ◽  
pp. 1771-1773 ◽  
Author(s):  
Chantal S. Morgan ◽  
James M. Holton ◽  
Barry D. Olafson ◽  
Pamela J. Bjorkman ◽  
Stephen L. Mayo

2018 ◽  
Author(s):  
Leandro Gabriel Roser ◽  
Fernán Agüero ◽  
Daniel Oscar Sánchez

AbstractBackgroundExploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.ResultsThis paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.ConclusionsFastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.


2011 ◽  
Vol 399-401 ◽  
pp. 1894-1897
Author(s):  
Jian Hua Li ◽  
Zong Jian Zheng ◽  
Shao Ping Fu ◽  
Jing Bo Zhu

Highly selective molecularly imprinted layer-coated silica nanoparticles for paclitaxel were synthesized by molecular imprinting technique with a sol–gel process on the supporter of silica nanoparticles. The morphology of the obtained polymers was characterized by scanning electron microscopy (SEM). The binding properties of the imprinted polymers were evaluated through the equilibrium rebinding experiments. Scatchard analysis revealed that two classes of binding sites were formed in the imprinted polymers with equilibrium dissociation constants of 0.0509 g•L-1and 0.0094 g•L-1, respectively. Paclitaxel and its analogue were employed for selectivity tests. The results indicated that the imprinted polymers exhibited good selectivity and specificity toward paclitaxel.


1987 ◽  
Vol 253 (5) ◽  
pp. F1063-F1067
Author(s):  
P. R. Sundaresan ◽  
M. M. Guarnaccia ◽  
J. L. Izzo

The role of the adrenal medulla in the regulation of renal cortical adrenergic receptors was investigated in renal cortical particulate fractions from control rats and rats 6 wk after adrenal demedullation. The specific binding of [3H]prazosin, [3H]rauwolscine, and [125I]iodocyanopindolol were used to quantitate alpha 1-, alpha 2-, and beta-adrenergic receptors, respectively. Adrenal demedullation increased the concentration of all three groups of renal adrenergic receptors; maximal number of binding sites (Bmax, per milligram membrane protein) for alpha 1-, and alpha 2-, and beta-adrenergic receptors were increased by 22, 18.5, and 25%, respectively (P less than 0.05 for each). No differences were found in the equilibrium dissociation constants (KD) for any of the radioligands. Plasma corticosterone and plasma and renal norepinephrine levels were unchanged, whereas plasma epinephrine was decreased 72% by adrenal demedullation (P less than 0.01); renal cortical epinephrine was not detectable in control or demedullated animals. Our results suggest that, in the physiological state, the adrenal medulla modulates the number of renal cortical adrenergic receptors, presumably through the actions of a circulating factor such as epinephrine.


1983 ◽  
Vol 61 (7) ◽  
pp. 731-743 ◽  
Author(s):  
Thomas Sandor ◽  
Afzal Z. Mehdi ◽  
John A. DiBattista

The interaction of tritiated corticosterone with the nasal gland corticosterone receptor was investigated. Kinetic studies have shown that the association of [3H]corticosterone–receptor followed second-order reaction kinetics and the dissociation of the ligand from the receptor became "pseudo" first order in the presence of large excess of radioinert steroids at 0, 15, 25, and 35 °C. Similar data were obtained with an ammonium sulfate precipitate of the cytosol. Dissociation rate constants varied from 10−5 to 10−3 s−1 and the association rate constants varied from 0.5 × 104 to 3.8 × 105 M−1∙s−1, depending on the reaction temperature and the cytoplasmic receptor preparation. Equilibrium dissociation constants were in 10−8–10−9 M range. Equilibrium dissociation constants, calculated from kinetic data (kd/ka), showed a marked temperature dependence, while those obtained by saturation analysis varied much less with the reaction temperature. Data obtained in these experiments were used to calculate some thermodynamic parameters of the binding of corticosterone to the cytoplasmic receptor. The enthalpy of dissociation was 101.5 and 79.4 kJ∙mol−1 and the entropy of dissociation was 200 and 280 J∙mol−1∙degree−1 for the crude cytoplasmic receptor and the ammonium sulfate precipitate, respectively. From the equilibrium dissociation constants, the enthalpy and entropy of the equilibrium binding was calculated. Polynomial fitting of Ka values versus 1/T yielded enthalpy (ΔH) values from −0.9 to −88.8 kJ∙mol−1, depending on the nature of the receptor preparation. Entropy values were negative for kinetically derived equilibrium association constants from the crude cytosol at all temperatures and for 0 and 15 °C for the precipitate. Entropy values were positive for Ka values obtained from kinetic rates at 25 and 35 °C and for Ka's calculated from saturation analysis. Further experiments with the precipitate confirmed our previous contention that the nasal gland cytoplasmic corticosterone receptor metabolized the bound ligand to 11-dehydrocorticosterone, though the receptor preparation was corticosterone specific. The following hydrodynamic parameters were obtained on the binding macromolecule: molecular weight, 316 000; s20,w, 8.0; Stokes radius (rs), 77.3 Å (1 Å = 0.1 nm); total frictional ratio (f/f0), 1.71. The labeled receptor preparation translocated to homologous nuclear binding sites following heat activation and, at the nuclear binding sites, the ligand was almost exclusively in its oxidized form. Measurement of the nuclear steroid–receptor complex by exchange assay with [3H]corticosterone confirmed the presence of nuclear binding sites. From these studies, it was concluded that the nasal gland of the duck contains specific, glucocorticoid-type corticosterone receptors and that the effector steroid is probably 11-dehydrocorticosterone or a critical mixture of these two steroids, with the oxidized form predominating.


2011 ◽  
Vol 239-242 ◽  
pp. 2423-2426
Author(s):  
Lin Min Zhu ◽  
Shao Ping Fu ◽  
Lin Ying Li ◽  
Jing Bo Zhu

Molecularly imprinted polymers (MIPs) were synthesized by precipitation polymerization using salvianolic acid A (Sal A), acrylamide (AA), ethylene glycol dimethacrylate (EGDMA) and acetonitrile as template molecule, functional monomer, cross-linker and solvent, respectively. The morphology of the obtained polymers was characterized by scanning electron microscopy (SEM). The effect of different polymerization conditions (solvent volume, solvent and template amount) on the size and shape of particles was investigated. The binding properties of the imprinted polymers were evaluated through the equilibrium rebinding experiments. Scatchard analysis revealed that two classes of binding sites were formed in the imprinted polymers with equilibrium dissociation constants of 0.33 μmol·mL-1and 0.07 μmol·mL-1, respectively. Besides Sal A, two structurally related compounds, protocatechuic aldehyde (Pra) and salvianolic acid B (Sal B), were employed for molecular selectivity tests. The results indicated that the imprinted polymers exhibited good selectivity and specificity toward Sal A.


Sign in / Sign up

Export Citation Format

Share Document