Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The graphical determination of K m and K i .

ABSTRACT: The principle of Dixon (1965) has been extended to give rapid graphical methods for determining enzyme constants for substrates (K(m)) and inhibitors (K(i)). It does away with the sometimes questionable assumption that the amounts of substrate or inhibitor bound by the enzyme are negligible in comparison with the total amount added, and is therefore valid even for cases of high affinity, where the usual methods fail. Besides doing away with the need for calculation, it enables the concentrations of the various components of the system to be read off directly for any point of the velocity curve.

SUBMITTER: Dixon M

PROVIDER: S-EPMC1174056 | biostudies-other | 1972 Aug

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

GRAPHICAL DETERMINATION OF EQUILIBRIUM CONSTANTS.

Project description:1. A rapid graphical method is described for determining equilibrium constants of combinations of the type A+Bright harpoon over left harpoonAB. The method can be extended to give other quantities for the system.

| S-EPMC1206613 | biostudies-other

A modified graphical method for determination of equilibrium constants.

Project description:A modification is described of the method of Dixon (1965) for determining equilibrium constants (K) of combinations of the type A+Bright harpoon over left harpoonAB. The method obviates drawing of a tangent to the curve at the origin.

| S-EPMC1265141 | biostudies-other

The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.

Project description:XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

| S-EPMC5349439 | biostudies-literature

Assessment of Graphical Methods for Determination of the Limiting Current Density in Complex Electrodialysis-Feed Solutions.

Project description:Electrodialysis (ED) is a promising technology suitable for nutrient recovery from a wide variety of liquid waste streams. For optimal operating conditions, the limiting current density (LCD) has to be determined separately for each treated feed and ED equipment. LCD is most frequently assessed in the NaCl solutions. In this paper, five graphical methods available in literature were reviewed for LCD determination in a series of five feed solutions with different levels of complexity in ion and matrix composition. Wastewater from microbial fermentation was included among the feed solutions, containing charged and uncharged particles. The experiments, running in the batch ED with an online conductivity, temperature, and pH monitoring, were conducted to obtain data for the comparison of various LCD determination methods. The results revealed complements and divergences between the applied LCD methods with increasing feed concentrations and composition complexity. The Cowan and Brown method had the most consistent results for all of the feed solutions. Online conductivity monitoring was linearly correlated with the decreasing ion concentration in the feed solution and corresponding LCD. Therefore, the results obtained in this study can be applied as a base for the automatized dynamic control of the operating current density-voltage in the batch ED. Conductivity alone should not be used for the ED control since LCD depends on the ion exchange membranes, feed flow, temperature and concentration, ionic species, their concentration ratios, and uncharged particles of the feed solution.

| S-EPMC8875246 | biostudies-literature

A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers.

Project description:High-resolution structure determination of homo-oligomeric protein complexes remains a daunting task for NMR spectroscopists. Although isotope-filtered experiments allow separation of intermolecular NOEs from intramolecular NOEs and determination of the structure of each subunit within the oligomeric state, degenerate chemical shifts of equivalent nuclei from different subunits make it difficult to assign intermolecular NOEs to nuclei from specific pairs of subunits with certainty, hindering structural analysis of the oligomeric state. Here, we introduce a graphical method, DISCO, for the analysis of intermolecular distance restraints and structure determination of symmetric homo-oligomers using residual dipolar couplings. Based on knowledge that the symmetry axis of an oligomeric complex must be parallel to an eigenvector of the alignment tensor of residual dipolar couplings, we can represent distance restraints as annuli in a plane encoding the parameters of the symmetry axis. Oligomeric protein structures with the best restraint satisfaction correspond to regions of this plane with the greatest number of overlapping annuli. This graphical analysis yields a technique to characterize the complete set of oligomeric structures satisfying the distance restraints and to quantitatively evaluate the contribution of each distance restraint. We demonstrate our method for the trimeric E. coli diacylglycerol kinase, addressing the challenges in obtaining subunit assignments for distance restraints. We also demonstrate our method on a dimeric mutant of the immunoglobulin-binding domain B1 of streptococcal protein G to show the resilience of our method to ambiguous atom assignments. In both studies, DISCO computed oligomer structures with high accuracy despite using ambiguously assigned distance restraints.

| S-EPMC3104227 | biostudies-literature

<i>FXD-CSD-GUI</i>: a graphical user interface for the X-ray-diffraction-based determination of crystallite size distributions.

Project description:Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.

| S-EPMC6878879 | biostudies-literature

The cluster graphical lasso for improved estimation of Gaussian graphical models.

Project description:The task of estimating a Gaussian graphical model in the high-dimensional setting is considered. The graphical lasso, which involves maximizing the Gaussian log likelihood subject to a lasso penalty, is a well-studied approach for this task. A surprising connection between the graphical lasso and hierarchical clustering is introduced: the graphical lasso in effect performs a two-step procedure, in which (1) single linkage hierarchical clustering is performed on the variables in order to identify connected components, and then (2) a penalized log likelihood is maximized on the subset of variables within each connected component. Thus, the graphical lasso determines the connected components of the estimated network via single linkage clustering. The single linkage clustering is known to perform poorly in certain finite-sample settings. Therefore, the cluster graphical lasso, which involves clustering the features using an alternative to single linkage clustering, and then performing the graphical lasso on the subset of variables within each cluster, is proposed. Model selection consistency for this technique is established, and its improved performance relative to the graphical lasso is demonstrated in a simulation study, as well as in applications to a university webpage and a gene expression data sets.

| S-EPMC4307846 | biostudies-literature

Graphical determination of pK values of the active-site groups of enzymes. An analysis of the bell-shaped curves.

Project description:Descriptions are given for the graphical determination of molecular pK values from the curves of logV and p(Km/V) against pH. The arguments are based on the model dissociation equilibria LAL in equilibrium (AL + LA) in equilibrium A, where A denotes a molecule having two binding sites for a ligand L.

| S-EPMC1161437 | biostudies-other

A Source of Systematic Errors in the Determination of Critical Micelle Concentration and Micellization Enthalpy by Graphical Methods in Isothermal Titration Calorimetry.

Project description:Isothermal titration calorimetry is frequently employed to determine the critical micelle concentration and the micellization enthalpy of surfactants in terms of geometrical characteristics of the titration curves. Previously we have shown theoretically that even for an infinitesimal injection, the heat per titrant mol depends on the stock solution concentration. In this work, we explore experimentally the influence of the stock solution concentration on the geometrical characteristics of the titration curve and its effect in determining the critical micelle concentration and the micellization enthalpy of surfactants. The systematic study of this phenomenology involves a great number of measurements at different temperatures with several repetitions carried out using a robotic calorimeter. As surfactant hexadecyltrimethylamonium bromide was used. The magnitude and shape of the heat titration depend on the stock solution concentration. As a consequence, the inflexion-point, break-point, and step-height decrease until a limiting value. A qualitative analysis suggests that the limiting value depends only on substance. This work shows that graphical methods could not be suitable for the calculation of the critical micelle concentration and micellization enthalpy because the magnitude and shape of the titration curve depend on the stock solution concentration. Micellar properties should be calculated by the application of theoretical models as in the ligand-binding studies.

| S-EPMC7922405 | biostudies-literature

GRAPE: GRaphical Abstracted Protein Explorer.

Project description:The region surrounding a protein, known as the surface of interaction or molecular surface, can provide valuable insight into its function. Unfortunately, due to the complexity of both their geometry and their surface fields, study of these surfaces can be slow and difficult and important features may be hard to identify. Here, we describe our GRaphical Abstracted Protein Explorer, or GRAPE, a web server that allows users to explore abstracted representations of proteins. These abstracted surfaces effectively reduce the level of detail of the surface of a macromolecule, using a specialized algorithm that removes small bumps and pockets, while preserving large-scale structural features. Scalar fields, such as electrostatic potential and hydropathy, are smoothed to further reduce visual complexity. This entirely new way of looking at proteins complements more traditional views of the molecular surface. GRAPE includes a thin 3D viewer that allows users to quickly flip back and forth between both views. Abstracted views provide a fast way to assess both a molecule's shape and its different surface field distributions. GRAPE is freely available at http://grape.uwbacter.org.

| S-EPMC2896102 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data