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Example for the binding energy computation of phosphate ion on the surface of LDH from Lactococcus lactis type 1

Example for the binding energy computation of phosphate ion on the surface of LDH from Lactococcus lactis type 1
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Output files of phosphate probe binding on the surface of LDH from lactococcus lactis type 1. File with extension XPLOR can be visualized with a program VMD to identify the most favorable position for the phosphate binding. This relates to the Model "Part 4".

SEEK ID: https://fairdomhub.org/data_files/1126?version=1

Filename: LACTIS1-GRID.tar Zoom

Format: Tar archive

Size: 52.1 MB

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Views: 2353 Downloads: 155

Created: 7th May 2014 at 16:14

Last updated: 8th Nov 2017 at 15:21

Last used: 17th Feb 2019 at 07:16

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Anna Feldman-Salit

Projects: SysMO-LAB

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Heidelberg

SysMO-LAB

Comparative Systems Biology: Lactic Acid Bacteria

Programme: SysMO

Public web page: http://www.sysmo.net/index.php?index=57

Organisms: Streptococcus pyogenes, Enterococcus faecalis, Lactococcus lactis, Lactic Acid Bacteria

Investigation of glycolysis and pyruvate branching of three lactic acid bacteria

SysMO-LAB

All contributors

Martijn Bekker

Challenge: Comparative analyses, as demonstrated by comparative genomics and bioinformatics, are extremely powerful for (i) transfer of information from (experimentally) well-studied organisms to the other organisms, and (ii) when coupled to functional and phenotypic information, insight in the relative importance of components to the observed differences and simalities. The central principle of this proposal is that important aspects of the functional differences between organisms derive not
...

Snapshots: No snapshots

Studies: Comparative modeling and phosphate dependence flux distributions and glu..., Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis and L...., Reconstructing the metabolic pathways of S. pyogenes and E. faecalis fro..., Study of the physiological characterization of three lactic acid bacteri...

Assays: BIOLOG substrate utilization assay, Genome-Scale Model Enterococcus faecalis V583, Genome-scale model of Streptococcus pyogenes, Global sensitivity analysis, Glucose pulsed L. lactis, Glucose pulsed S. pyogenes, Kinetics of L-lactate dehydrogenase from L. lactis, Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis, and L..., Maximal specific growth rates of the three lactic acid bacteria and thei..., Model of L. lactis glycolysis, Physiological characterization of Lactic acid bacteria grown in C-limite..., Regulation of the activity of lactate dehydrogenases from four lactic ac...

Created: 15th Feb 2010 at 13:38, Last updated: 22nd Nov 2011 at 20:12

Comparative modeling and phosphate dependence flux distributions and glucose consumption rates of two lactic acid bacteria S. pyogenes and L. lactis

SysMO-LAB

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Martijn Bekker

The two lactic acid bacteria L. lactis and S. pyogenes were studied with respect to the concentration of intracellular metabolites involved in glycolysis in time upon a glucose pulse. Models that describe this behavior are also constructed

Person responsible: Martijn Bekker

Snapshots: No snapshots

Investigation: Investigation of glycolysis and pyruvate branch...

Assays: Global sensitivity analysis, Glucose pulsed L. lactis, Glucose pulsed S. pyogenes, Kinetics of L-lactate dehydrogenase from L. lactis, Model of L. lactis glycolysis, Regulation of the activity of lactate dehydrogenases from four lactic ac...

Created: 15th Feb 2010 at 13:43, Last updated: 11th May 2016 at 17:19

Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria

SysMO-LAB

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Anna Feldman-Salit

Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact)
...

Contributor: Anna Feldman-Salit

Biological problem addressed: Metabolism

Snapshots: No snapshots

Investigation: Investigation of glycolysis and pyruvate branch...

Study: Comparative modeling and phosphate dependence f...

Organisms: Lactococcus lactis, Streptococcus pyogenes, Enterococcus faecalis, Lactobacillus plantarum

Models: Part 1: Comparative modeling of 3D structures o..., Part 2: Computation of electrostatic potentials..., Part 3: Comparison of electrostatic potentials ..., Part 4: Activation / Inhibition Effect on LDHs ..., Part 5: Algorithm to computationally estimate t...

SOPs: No SOPs

Data files: 3D-sturctures of Lactate Dehydrogenase from 4 L..., Activation / Inhibition of 4 LDH enzymes in the..., Comparison of electrostatic potentials of LDH e..., Electrostatic potentials of four LDH enzymes fr..., Example for the binding energy computation of p..., Measurements on kinetics of L-LDHs from differe..., The effects of fructose-1,6-bisphosphate, phosp...

Created: 19th Feb 2014 at 14:08, Last updated: 8th Nov 2017 at 15:21