Team:KULeuven/Model/Kinetic Constants

{{:Team:KULeuven/Tools/Header}}

===ETHZ list of parameters===
* [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters ETHZ list of parameters]
===mRNA decay===
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]

===T7 RNAP===
*[http://www.jbc.org/cgi/reprint/267/4/2640 Initiation of Transcription by T7 RNA Polymerase at Its Natural Promoters]
*[http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]
*[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]
*[http://www.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]
*[http://www.jbc.org/cgi/content/full/279/5/3239#FIG2 Single molecule studies of T7 RNA polymerase]

===LacI - LuxI===
* [http://www.tam.cornell.edu/tam/cms/manage/upload/Strogatz_20coupled_repressilators_PNAS.pdf Coupled repressilators]

* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]

===LuxI, LuxR, mRNALuxI, mRNALuxR decay===

*[http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]

*[http://www.pnas.org/content/93/18/9505 LuxI kinetics]

===HSL stuff===

*[http://aem.asm.org/cgi/content/abstract/71/3/1291 Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils] Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h

*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D0X9-9&_user=877992&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000047079&_version=1&_urlVersion=0&_userid=877992&md5=36d07f326b2c2e55c4de05a1ab426e09 Kinetics of the AHL Regulatory System in a Model Biofilm System]

*[http://www.pnas.org/content/96/8/4360.full HSL lactone synthesis kinetics by a LuxI-related enzyme]

*[http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 Lactonase mediated HSL degradation (hydrolysis)]

====Diffusion====

*[http://jb.asm.org/cgi/content/full/185/5/1485 AHL diffusion model]

*[http://jb.asm.org/cgi/content/full/185/5/1485 AHL diffusion constants & stuff]

===OmpR, OmpF===
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=543474&blobtype=pdf A simulation model of Escherichia coli osmoregulatory switch using E-CELL system] (Relevance: High), bekijk pg.11/13
*[http://www.jbc.org/cgi/reprint/281/25/17114 Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR] (Relevance: Medium)
*[http://jb.oxfordjournals.org/cgi/reprint/111/6/707.pdf Transmembrane Signal Transduction and Osmoregulation in Escherichia coli: Functional Importance of the Transmembrane Regions of Membrane-Located Protein Kinase, EnvZ] (Relevance:?), geen toegang tenzij account
*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=209999 DNA-Binding Properties of the Transcription Activator (OmpR) for the Upstream Sequences of ompF in Escherichia coli Are Altered by envZ Mutations and Medium Osmolarity] (Relevance: Low)
*[http://jb.asm.org/cgi/reprint/176/5/1309 A Distant Upstream Site Involved in the Negative Regulation of the Escherichia coli ompF Gene] (Relevance: ?), voor repressor regulatie van OmpF door OmpR
*[http://jb.asm.org/cgi/reprint/176/16/5005.pdf micF Antisense RNA Has a Major Role in Osmoregulation of OmpF in Escherichia coli] (Relevance: Low), invloed ''''Antisense RNA'''' op OmpF regulatie, hmm...

===Psid met P2ogr promotor===
*[http://parts.mit.edu/igem07/index.php/Cambridge/Amplifier_project Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter]

*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 P<sub>sid</sub> promotor with different activators]

===Constitutive promoters===
*Estimated transcription rate for J23105:[http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters]
*Scale other transcription rate with table in parts registry.

* Estimate the rate of transcription from a constitutive promotor family member.
[[Image:Const_pro_strength.png|center|400px|thumb|Estimates for the rate of transcription from the constitutive promotor family members. X is the GFP fluorescence in arbitrary units according to the Registry. Y is the number of mRNA's produced per second from that promotor]]

===E. coli transcription rates===
[http://www.fasebj.org/cgi/content/summary/20/10/1721 Paper about the calculated transcription rates for every E.coli ORF] <br>
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]