Theory of electrostatically regulated binding of T4 gene 32 protein to single- and double-stranded DNA

Ioulia Rouzina, Kiran Pant, Richard L. Karpel, Mark C. Williams

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

Abstract

Bacteriophage T4 gene 32 protein (gp32) is a single-stranded DNA binding protein, which is essential for DNA replication, recombination, and repair. In a recent article, we described a new method using single DNA molecule stretching measurements to determine the noncooperative association constants K ds to double-stranded DNA for gp32 and *1, a truncated form of gp32. In addition, we developed a single molecule method for measuring K ss, the association constant of these proteins to single-stranded DNA. We found that in low salt both Kds and Kss have a very weak salt dependence for gp32, whereas for *1 the salt dependence remains strong. In this article we propose a model that explains the salt dependence of gp32 and *1 binding to single-stranded nucleic acids. The main feature of this model is the strongly salt-dependent removal of the C-terminal domain of gp32 from its nucleic acid binding site that is in pre-equilibrium to protein binding to both double-stranded and single-stranded nucleic acid. We hypothesize that unbinding of the C-terminal domain is associated with counterion condensation of sodium ions onto this part of gp32, which compensates for sodium ion release from the nucleic acid upon its binding to the protein. This results in the salt-independence of gp32 binding to DNA in low salt. The predictions of our model quantitatively describe the large body of thermodynamic and kinetic data from bulk and single molecule experiments on gp32 and *1 binding to single-stranded nucleic acids.

Original languageEnglish (US)
Pages (from-to)1941-1956
Number of pages16
JournalBiophysical journal
Volume89
Issue number3
DOIs
StatePublished - Sep 2005

Bibliographical note

Funding Information:
Funding for this project was provided by National Institutes of Health (grant No. GM 52049 to R.L.K.; grant No. GM 072462 to M.C.W.), National Science Foundation (grant No. MCB-0238190 to M.C.W.), the Research Corporation (to M.C.W.), and Designated Research Initiative Fund support from the University of Maryland Baltimore County (to R.L.K.).

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