Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers

被引：3

作者：

Holmquist, Peter C. ^{[1
]}

Holmquist, Gerald P. ^{[2
]}

Summers, Michael L. ^{[1
]}

机构：

[1] Calif State Univ Northridge, Dept Biol, Northridge, CA 91330 USA

[2] City Hope Natl Med Ctr, Duarte, CA 91010 USA

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷 / 15期

基金：

美国国家科学基金会;

关键词：

CAMP RECEPTOR PROTEIN; CAP-DNA COMPLEX; ACTIVATOR PROTEIN; INDIRECT READOUT; SEQUENCE LOGOS; TRANSCRIPTION; GENOME; SPECIFICITY; RECOGNITION; PREDICTION;

D O I：

10.1093/nar/gkr369

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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).

引用

页码：6813 / 6824

页数：12