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Literature DB >> 22976176

SSB binding to ssDNA using isothermal titration calorimetry.

Abstract

Isothermal titration calorimetry (ITC) is a powerful method for studying protein-DNA interactions in solution. As long as binding is accompanied by an appreciable enthalpy change, ITC studies can yield quantitative information on stoichiometries, binding energetics (affinity, binding enthalpy and entropy) and potential site-site interactions (cooperativity). This can provide a full thermodynamic description of an interacting system which is necessary to understand the stability and specificity of protein-DNA interactions and to correlate the activities or functions of different species. Here we describe procedures to perform and analyze ITC studies using as examples, the E. coli SSB (homotetramer with 4 OB-folds) and D. radiodurans SSB (homodimer with 4 OB-folds). For oligomeric protein systems such as these, we emphasize the need to be aware of the likelihood that solution conditions will influence not only the affinity and enthalpy of binding but also the mode by which the SSB oligomer binds ssDNA.

Entities: Chemical Disease Gene Mutation Species

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Year: 2012 PMID： 22976176 PMCID： PMC4336747 DOI： 10.1007/978-1-62703-032-8_3

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

25 in total

1. Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein.

Authors: A G Kozlov; T M Lohman
Journal: Proteins Date: 2000

2. E. coli SSB tetramer binds the first and second molecules of (dT)(35) with heat capacities of opposite sign.

Authors: Alexander G Kozlov; Timothy M Lohman
Journal: Biophys Chem Date: 2011-05-12 Impact factor: 2.352

3. Rapid measurement of binding constants and heats of binding using a new titration calorimeter.

Authors: T Wiseman; S Williston; J F Brandts; L N Lin
Journal: Anal Biochem Date: 1989-05-15 Impact factor: 3.365

4. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides.

Authors: C R Cantor; M M Warshaw; H Shapiro
Journal: Biopolymers Date: 1970 Impact factor: 2.505

5. Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects.

Authors: W Bujalowski; L B Overman; T M Lohman
Journal: J Biol Chem Date: 1988-04-05 Impact factor: 5.157

6. Large-scale overproduction and rapid purification of the Escherichia coli ssb gene product. Expression of the ssb gene under lambda PL control.

Authors: T M Lohman; J M Green; R S Beyer
Journal: Biochemistry Date: 1986-01-14 Impact factor: 3.162

7. Negative co-operativity in Escherichia coli single strand binding protein-oligonucleotide interactions. I. Evidence and a quantitative model.

Authors: W Bujalowski; T M Lohman
Journal: J Mol Biol Date: 1989-05-05 Impact factor: 5.469

8. Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage.

Authors: Douglas A Bernstein; Julie M Eggington; Michael P Killoran; Ana M Misic; Michael M Cox; James L Keck
Journal: Proc Natl Acad Sci U S A Date: 2004-05-24 Impact factor: 11.205

5. Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.

Authors: Nitzan Kutnowski; Fania Shmulevich; Geula Davidov; Anat Shahar; Dudy Bar-Zvi; Jerry Eichler; Raz Zarivach; Boaz Shaanan
Journal: Nucleic Acids Res Date: 2019-09-19 Impact factor: 16.971

5 in total

SSB binding to ssDNA using isothermal titration calorimetry.

1. Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein.

2. E. coli SSB tetramer binds the first and second molecules of (dT)(35) with heat capacities of opposite sign.

3. Rapid measurement of binding constants and heats of binding using a new titration calorimeter.

4. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides.

5. Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects.

6. Large-scale overproduction and rapid purification of the Escherichia coli ssb gene product. Expression of the ssb gene under lambda PL control.

7. Negative co-operativity in Escherichia coli single strand binding protein-oligonucleotide interactions. I. Evidence and a quantitative model.

8. Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage.

9. Large-scale purification and characterization of the Escherichia coli rep gene product.

10. The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA.

1. Is a fully wrapped SSB-DNA complex essential for Escherichia coli survival?

2. Probing E. coli SSB protein-DNA topology by reversing DNA backbone polarity.

3. Quantitative Determination of Ca²⁺-binding to Ca²⁺-sensor Proteins by Isothermal Titration Calorimetry.

Review 4. Choosing a suitable method for the identification of replication origins in microbial genomes.

5. Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.