dorsal/arxiv
View SchemaPhysical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction
| Authors | Ulrich Gerland, J. David Moroz, Terence Hwa |
|---|---|
| Categories | |
| ArXiv ID | physics/0112083 |
| URL | https://arxiv.org/abs/physics/0112083 |
| DOI | 10.1073/pnas.192693599 |
| Journal | Proc. Natl. Acad. Sci. USA 99 (2002) 12015-20 |
Abstract
We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (TF's) with the genomic background (i.e., the genome without the target sites). We introduce and motivate the concept of `programmability', i.e. the ability to set the threshold concentration for TF binding over a wide range merely by mutating the binding sequence of a target site. This functional demand, together with physical constraints arising from the thermodynamics and kinetics of TF-DNA interaction, leads us to a narrow range of ``optimal'' interaction parameters. We find that this parameter set agrees well with experimental data for the interaction parameters of a few exemplary prokaryotic TF's. This indicates that TF-DNA interaction is indeed programmable. We suggest further experiments to test whether this is a general feature for a large class of TF's.
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"abstract": "We study theoretical ``design principles\u0027\u0027 for transcription factor-DNA\ninteraction in bacteria, focusing particularly on the statistical interaction\nof the transcription factors (TF\u0027s) with the genomic background (i.e., the\ngenome without the target sites). We introduce and motivate the concept of\n`programmability\u0027, i.e. the ability to set the threshold concentration for TF\nbinding over a wide range merely by mutating the binding sequence of a target\nsite. This functional demand, together with physical constraints arising from\nthe thermodynamics and kinetics of TF-DNA interaction, leads us to a narrow\nrange of ``optimal\u0027\u0027 interaction parameters. We find that this parameter set\nagrees well with experimental data for the interaction parameters of a few\nexemplary prokaryotic TF\u0027s. This indicates that TF-DNA interaction is indeed\nprogrammable. We suggest further experiments to test whether this is a general\nfeature for a large class of TF\u0027s.",
"arxiv_id": "physics/0112083",
"authors": [
"Ulrich Gerland",
"J. David Moroz",
"Terence Hwa"
],
"categories": [
"physics.bio-ph",
"cond-mat.stat-mech",
"q-bio.BM"
],
"doi": "10.1073/pnas.192693599",
"journal_ref": "Proc. Natl. Acad. Sci. USA 99 (2002) 12015-20",
"title": "Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction",
"url": "https://arxiv.org/abs/physics/0112083"
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