Index of papers in April 2015 that mention
  • kinetic parameters
Lorenza A. D’Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller
Ordinary differential equation modeling
With mass action kinetics and assuming pA catalyzes the formation of pB but is not consumed, we get the reaction B->pB with kinetic rate law k1*pA*B, where k1 denotes a kinetic parameter for this reaction.
Ordinary differential equation modeling
These parameters allow for a potential reduction of the kinetic parameters within a range of 0% to 100%.
Ordinary differential equation modeling
In addition to kinetic parameters , the ODE model is defined by scaling and noise parameters.
Supporting Information
Values of each kinetic parameter for model 4_8_12 are shown in SS Table.
Supporting Information
The second column shows the loglo value of each kinetic parameter involved in the model reactions shown in S4 Table.
kinetic parameters is mentioned in 7 sentences in this paper.
Topics mentioned in this paper:
Pedro Saa, Lars K. Nielsen
E-glc-atp
As previously mentioned, reaction mechanisms with branched steps can eXhibit apparent substrate inhibition depending on the kinetic parameter values and the substrate concentrations.
General framework for modelling metabolic reactions
In this article, we shall describe a general framework that enables parameterization and sampling of kinetic parameters consistent with thermodynamic constraints.
General framework for modelling metabolic reactions
An important feature of this parameterization is that it enables inclusion of fundamental thermodynamic relations between kinetic parameters , as it is compatible with the elementary reaction formalism.
Introduction
All use simplified kinetic expressions (loss of generality) and most ignore intrinsic thermodynamic constraints between kinetic parameters , hence they will sample infeasible parameter sets.
Introduction
An advantage is that the parameterization retains all intrinsic thermodynamic constraints between kinetic parameters .
Revealing the impact of thermodynamics on enzyme kinetics
For example, depending on the kinetic parameter values and the substrate concentrations, the reaction rate for the enzymes following this mechanism can display an apparent cooperative behaviour (sigmoidal reaction rate) upon addition of one substrate maintaining the other constant, while in the opposite situation they can exhibit substrate inhibition (the reaction rate pass through a maximum) [41].
kinetic parameters is mentioned in 6 sentences in this paper.
Topics mentioned in this paper:
Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff
A transcription (in)activation cycle model with realistic kinetics can reproduce experimentally observed population-level transcriptional cycHng
This experimental data (Fig 6B) can be reproduced fairly well by a 9-state cycle model with realistic kinetic parameters (Fig 6A).
A transcription (in)activation cycle model with realistic kinetics can reproduce experimentally observed population-level transcriptional cycHng
This could be explained by an even higher number of proteins and chromatin modifications involved serially in the initiation process than currently known experimentally, by more peaked waiting time distributions for individual cycle transitions, which could again be due to multi-step serial processes, or by differences in kinetic parameters .
Introduction
However, whether models with realistic kinetic parameters can also generate such slow dynamics remains unclear.
Introduction
Do the stochastic dynamics of the transcription cycle model agree with single-cell and population-level studies of transcription when realistic kinetic parameters are considered?
kinetic parameters is mentioned in 4 sentences in this paper.
Topics mentioned in this paper:
Tae J. Lee, Jeffrey Wong, Sena Bae, Anna Jisu Lee, Allison Lopatkin, Fan Yuan, Lingchong You
Characteristic power-law parameters describe uptake in different cell lines
Changes in many kinetic parameters associated with the Zipper mechanism can be mapped to changes in the power-law parameters (Fig 4A; simulated data in 84C Fig).
Characteristic power-law parameters describe uptake in different cell lines
For the same bacterial strain, different host cell types would likely lead to different kinetic parameters for the Zipper mechanisms, and thus different corresponding power-law parameters.
Supporting Information
(C) Mapping of kinetic parameters associated with the 3-stage model to power-law parameters.
kinetic parameters is mentioned in 3 sentences in this paper.
Topics mentioned in this paper: