Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 2 de 2
Filter
Add more filters










Database
Language
Publication year range
1.
Methods Mol Biol ; 1945: 231-249, 2019.
Article in English | MEDLINE | ID: mdl-30945249

ABSTRACT

SRSim combines rule-based reaction network models with spatial particle simulations allowing to simulate the dynamics of large molecular complexes changing according to a set of chemical reaction rules. As the rule can contain patterns of molecular complexes and specific states of certain binding sites, a combinatorially complex or even infinitely sized reaction network can be defined. Particles move in a three-dimensional space according to molecular dynamics implemented by LAMMPS, while the BioNetGen language is used to formulate reaction rules. Geometric information is added in a specific XML format. The simulation protocol is exemplified by two different variants of polymerization as well as a toy model of DNA helix formation. SRSim is open source and available for download.


Subject(s)
DNA/chemistry , Nucleic Acid Conformation , Software , DNA/genetics , Models, Biological , Molecular Dynamics Simulation
2.
Mol Syst Biol ; 8: 582, 2012 May 08.
Article in English | MEDLINE | ID: mdl-22580890

ABSTRACT

The orientation of the mitotic spindle with respect to the polarity axis is crucial for the accuracy of asymmetric cell division. In budding yeast, a surveillance mechanism called the spindle position checkpoint (SPOC) prevents exit from mitosis when the mitotic spindle fails to align along the mother-to-daughter polarity axis. SPOC arrest relies upon inhibition of the GTPase Tem1 by the GTPase-activating protein (GAP) complex Bfa1-Bub2. Importantly, reactions signaling mitotic exit take place at yeast centrosomes (named spindle pole bodies, SPBs) and the GAP complex also promotes SPB localization of Tem1. Yet, whether the regulation of Tem1 by Bfa1-Bub2 takes place only at the SPBs remains elusive. Here, we present a quantitative analysis of Bfa1-Bub2 and Tem1 localization at the SPBs. Based on the measured SPB-bound protein levels, we introduce a dynamical model of the SPOC that describes the regulation of Bfa1 and Tem1. Our model suggests that Bfa1 interacts with Tem1 in the cytoplasm as well as at the SPBs to provide efficient Tem1 inhibition.


Subject(s)
Gene Expression Regulation, Fungal , Models, Theoretical , Saccharomyces cerevisiae/genetics , Spindle Apparatus/metabolism , Systems Biology/methods , Asymmetric Cell Division , Cell Cycle , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Computer Simulation , Cytoplasm/genetics , Cytoskeletal Proteins/genetics , Cytoskeletal Proteins/metabolism , GTP Phosphohydrolases/antagonists & inhibitors , GTP Phosphohydrolases/metabolism , GTPase-Activating Proteins/genetics , GTPase-Activating Proteins/metabolism , Microscopy, Fluorescence , Mitosis , Monomeric GTP-Binding Proteins/antagonists & inhibitors , Monomeric GTP-Binding Proteins/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/antagonists & inhibitors , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Spindle Apparatus/genetics
SELECTION OF CITATIONS
SEARCH DETAIL
...