Physical constraints and functional characteristics of transcription factorâDNA interaction Export

@article{citeulike:235037, abstract = {10.1073/pnas.192693599 We study theoretical \^{a}€œdesign principles\^{a}€ for transcription factor (TF)\^{a}€“DNA interaction in bacteria, focusing particularly on the statistical interaction of the TFs 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\^{a}€“DNA interaction, leads us to a narrow range of \^{a}€œoptimal\^{a}€ interaction parameters. We find that this parameter set agrees well with experimental data for the interaction parameters of a few exemplary prokaryotic TFs, which indicates that TF\^{a}€“DNA interaction is indeed programmable. We suggest further experiments to test whether this is a general feature for a large class of TFs.}, address = {Department of Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA. gerland@physics.ucsd.edu}, archivePrefix = {arXiv}, author = {Gerland, Ulrich and Moroz, J. David and Hwa, Terence}, citeulike-article-id = {235037}, citeulike-linkout-0 = {http://arxiv.org/abs/physics/0112083}, citeulike-linkout-1 = {http://arxiv.org/pdf/physics/0112083}, citeulike-linkout-2 = {http://dx.doi.org/10.1073/pnas.192693599}, citeulike-linkout-3 = {http://www.pnas.org/content/99/19/12015.abstract}, citeulike-linkout-4 = {http://www.pnas.org/content/99/19/12015.full.pdf}, citeulike-linkout-5 = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2002PNAS...9912015G}, citeulike-linkout-6 = {http://view.ncbi.nlm.nih.gov/pubmed/12218191}, citeulike-linkout-7 = {http://www.hubmed.org/display.cgi?uids=12218191}, day = {17}, doi = {10.1073/pnas.192693599}, eprint = {physics/0112083}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {biophysics, dna\_binding, protein\_dna\_interactions}, month = {September}, number = {19}, pages = {12015--12020}, posted-at = {2009-11-04 18:53:31}, priority = {2}, title = {Physical constraints and functional characteristics of transcription factor\^{a}€“DNA interaction}, url = {http://dx.doi.org/10.1073/pnas.192693599}, volume = {99}, year = {2002} }

TY - JOUR ID - citeulike:235037 L3 - citeulike-article-id:235037 N2 - 10.1073/pnas.192693599 We study theoretical “design principles” for transcription factor (TF)–DNA interaction in bacteria, focusing particularly on the statistical interaction of the TFs 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 TFs, which 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 TFs. IS - 19 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 AD - Department of Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA. gerland@physics.ucsd.edu EP - 12020 TI - Physical constraints and functional characteristics of transcription factor–DNA interaction VL - 99 SP - 12015 KW - biophysics KW - dna_binding KW - protein_dna_interactions AU - Gerland, Ulrich AU - Moroz, David AU - Hwa, Terence PY - 2002/09/17/ UR - http://dx.doi.org/10.1073/pnas.192693599 ER -