Quantitative specificity of the Mnt repressor

• Published in: Journal of molecular biology 1997-08, Vol.271 (2), p.178-194
• Main Authors: Fields, Dana S, He, Yi-yuan, Al-Uzri, Ahmed Y, Stormo, Gary D
• Format: Article
• Language: English
• Subjects: Bacteriophage P22 - metabolism; Base Sequence; Binding Sites; Consensus Sequence; DNA - chemistry; DNA - metabolism; DNA-Binding Proteins - metabolism; DNA-protein interaction; DNA-protein specificity; information content; Kinetics; Ligands; Mnt protein; Molecular Sequence Data; Oligodeoxyribonucleotides - chemistry; Oligodeoxyribonucleotides - metabolism; quantitative DNA sequencing; Repressor Proteins - metabolism; Salmonella - virology; Sequence Alignment; Substrate Specificity; Templates, Genetic; Thermodynamics; Viral Proteins - metabolism; Viral Regulatory and Accessory Proteins
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1997.1171

The Mnt protein of Salmonella phage P22 binds site-specifically to its operator. To better understand this binding we used dideoxy DNA sequencing in a quantitative manner to determine the relative binding constants, and hence the relative free energies, of wild-type Mnt protein to a substantial number of variants of its operator. These measurements were supported by experiments which used the SELEX procedure to generate a set of operators from an initially randomized population. In the Discussion we show that the present model of Mnt protein/operator binding, due to Sauer and co-workers, along with the assumption of an independent contribution of each position in the operator to the total binding, provides a reasonably accurate description of the system. We also discuss the use of information content as a measure of DNA-protein binding specificity with the Mnt protein/operator system serving as an example and show again that the assumption of independence supports the current view of this case of site-specific binding.