PortEco logo

PMID:20156448

From EcoliWiki
Jump to: navigation, search

Contents

Citation

Szymanski, MR, Jezewska, MJ and Bujalowski, W (2010) Interactions of the Escherichia coli primosomal PriB protein with the single-stranded DNA. Stoichiometries, intrinsic affinities, cooperativities, and base specificities. J. Mol. Biol. 398:8-25

Abstract

Quantitative analysis of the interactions of the Escherichia coli primosomal PriB protein with a single-stranded DNA was done using quantitative fluorescence titration, photocrosslinking, and analytical ultracentrifugation techniques. Stoichiometry studies were done with a series of etheno-derivatives of single-stranded (ss) DNA oligomers. Interactions with the unmodified nucleic acids were studied, using the macromolecular competition titration (MCT) method. The total site-size of the PriB dimer-ssDNA complex, i.e. the maximum number of nucleotides occluded by the PriB dimer in the complex, is 12+/-1 nt. The protein has a single DNA-binding site, which is located centrally within the dimer and has a functionally homogeneous structure. The stoichiometry and photocrosslinking data show that only a single monomer of the PriB dimer engages in interactions with the nucleic acid. The analysis of the PriB binding to long oligomers was done using a statistical thermodynamic model that takes into account the overlap of potential binding sites and cooperative interactions. The PriB dimer binds the ssDNA with strong positive cooperativity. Both the intrinsic affinity and cooperative interactions are accompanied by a net ion release, with anions participating in the ion exchange process. The intrinsic binding process is an entropy-driven reaction, suggesting strongly that the DNA association induces a large conformational change in the protein. The PriB protein shows a dramatically strong preference for the homo-pyrimidine oligomers with an intrinsic affinity higher by about three orders of magnitude, as compared to the homo-purine oligomers. The significance of these results for PriB protein activity is discussed.

Links

PubMed PMC3226724 Online version:10.1016/j.jmb.2010.02.009

Keywords

Bacterial Proteins/metabolism; Base Sequence; Binding Sites; Crystallography, X-Ray; DNA, Bacterial/metabolism; DNA, Single-Stranded/chemistry; DNA, Single-Stranded/metabolism; Escherichia coli/metabolism; Escherichia coli Proteins/metabolism; Models, Chemical; Models, Molecular; Nucleic Acid Conformation; Physical Processes; Protein Binding; Protein Conformation; Spectrometry, Fluorescence; Thermodynamics; Ultracentrifugation

Significance

You can help EcoliWiki by summarizing why this paper is useful

Useful Materials and Methods

You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.

Annotations

Gene product Qualifier GO ID GO term name Evidence Code with/from Aspect Notes Status

EcoliWiki Links

Add links to pages that link here (e.g. gene, product, method pages)

See also

References

See Help:References for how to manage references in EcoliWiki.