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Updated: Jan 20, 2026

Comparing the Affinity of GTPase-binding Proteins using Competition Assays
Published on: October 8, 2015
Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding
Peter C Holmquist1, Gerald P Holmquist, Michael L Summers
1Department of Biology, California State University Northridge, 18111 Nordhoff St. Northridge, CA 91330, USA. peter_holmquist@yahoo.com
None:
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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