Journal
NUCLEIC ACIDS RESEARCH
Volume 39, Issue 15, Pages 6813-6824Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkr369
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Funding
- United States National Science Foundation [MCB 0093327]
- United States National Institute of Health [5 SO6 GM048680, 1 SC1 GM093998]
- College of Science and Mathematics, Biology Department, CSU Northridge
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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).
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