Abstract:
:We show that the cAMP receptor protein (Crp) binds to DNA as several different conformers. This situation has precluded discovering a high correlation between any sequence property and binding affinity for proteins that bend DNA. Experimentally quantified affinities of Synechocystis sp. PCC 6803 cAMP receptor protein (SyCrp1), the Escherichia coli Crp (EcCrp, also CAP) and DNA were analyzed to mathematically describe, and make human-readable, the relationship of DNA sequence and binding affinity in a given system. Here, sequence logos and weight matrices were built to model SyCrp1 binding sequences. Comparing the weight matrix model to binding affinity revealed several distinct binding conformations. These Crp/DNA conformations were asymmetrical (non-palindromic).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Holmquist PC,Holmquist GP,Summers MLdoi
10.1093/nar/gkr369subject
Has Abstractpub_date
2011-08-01 00:00:00pages
6813-24issue
15eissn
0305-1048issn
1362-4962pii
gkr369journal_volume
39pub_type
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