dorsal/arxiv
View SchemaStochastic dynamics of macromolecular-assembly networks
| Authors | Leonor Saiz, Jose M. G. Vilar |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0609044 |
| URL | https://arxiv.org/abs/q-bio/0609044 |
| DOI | 10.1038/msb4100061 |
| Journal | Nature/EMBO Molecular Systems Biology 2, art. no. msb4100061, pp. 2006.0024 (2006) |
Abstract
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage lambda induction switches, which rely on the formation of DNA loops by proteins and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes.
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"abstract": "The formation and regulation of macromolecular complexes provides the\nbackbone of most cellular processes, including gene regulation and signal\ntransduction. The inherent complexity of assembling macromolecular structures\nmakes current computational methods strongly limited for understanding how the\nphysical interactions between cellular components give rise to systemic\nproperties of cells. Here we present a stochastic approach to study the\ndynamics of networks formed by macromolecular complexes in terms of the\nmolecular interactions of their components. Exploiting key thermodynamic\nconcepts, this approach makes it possible to both estimate reaction rates and\nincorporate the resulting assembly dynamics into the stochastic kinetics of\ncellular networks. As prototype systems, we consider the lac operon and phage\nlambda induction switches, which rely on the formation of DNA loops by proteins\nand on the integration of these protein-DNA complexes into intracellular\nnetworks. This cross-scale approach offers an effective starting point to move\nforward from network diagrams, such as those of protein-protein and DNA-protein\ninteraction networks, to the actual dynamics of cellular processes.",
"arxiv_id": "q-bio/0609044",
"authors": [
"Leonor Saiz",
"Jose M. G. Vilar"
],
"categories": [
"q-bio.MN",
"cond-mat.soft",
"physics.bio-ph",
"q-bio.SC"
],
"doi": "10.1038/msb4100061",
"journal_ref": "Nature/EMBO Molecular Systems Biology 2, art. no. msb4100061, pp.\n 2006.0024 (2006)",
"title": "Stochastic dynamics of macromolecular-assembly networks",
"url": "https://arxiv.org/abs/q-bio/0609044"
},
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