Protein-protein/DNA interaction networks: Versatile macromolecular structures for the control of gene expression Journal Article
| Authors: | Saiz, L.; Vilar, J. M. G. |
| Article Title: | Protein-protein/DNA interaction networks: Versatile macromolecular structures for the control of gene expression |
| Abstract: | The assembly of macromolecular structures consisting of proteins and DNA lies at the core of many fundamental cellular processes, such as transcription, recombination and replication. A common theme to all these processes is DNA looping, which provides the backbone for the required long-range interactions on DNA and results in further complexity that is exceptionally difficult to tackle with traditional quantitative approaches. Here, recent advances in mathematical and computational methods to study the assembly of protein-protein/DNA complexes with loops and their effects in the cellular behaviour through gene regulation are reviewed. The interplay between multisite DNA looping and DNA bending regulatory proteins, such as the catabolite activator protein (CAP), and on its physiological consequences is focused on. It has become clear in the last few years that the complexity that looping brings about can actively control transcriptional noise and cell-to-cell variability. Here, it is shown that the DNA looping, through the effects of CAP, can also control the balance between robustness and sensitivity of the induction of gene expression. © The Institution of Engineering and Technology 2008. |
| Keywords: | signal transduction; dna-binding proteins; nonhuman; conference paper; proteins; genes; gene expression; models, biological; protein assembly; protein protein interaction; molecular dynamics; protein; genetic transcription; wild type; mathematical model; gene expression regulation; dna; transcription regulation; messenger rna; quantitative analysis; escherichia coli; nucleic acids; gene repression; bioactivity; transcription; computer simulation; thermodynamics; gene regulatory network; gene induction; organic acids; feedback; protein interaction mapping; stochastic model; gene regulations; protein dna interaction; macromolecule; macromolecular substances; dna binding motif; operon; laws and legislation; dna bending; interaction networks; macromolecular structures; flow interactions; computational methods; control theory; macromolecules; network protocols; sensor networks; activator proteins; cell variabilities; cellular processes; long-range interactions; multisite; quantitative approaches; regulatory proteins; cyclic amp binding protein; cyclic amp receptor protein |
| Journal Title: | IET Systems Biology |
| Volume: | 2 |
| Issue: | 5 |
| ISSN: | 1751-8849 |
| Publisher: | The Institution of Engineering and Technology 2008 |
| Date Published: | 2008-09-01 |
| Start Page: | 247 |
| End Page: | 255 |
| Language: | English |
| DOI: | 10.1049/iet-syb:20080091 |
| PUBMED: | 19045820 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 3" - "Export Date: 17 November 2011" - "Source: Scopus" |
