scholarly journals Sliding of a single lac repressor protein along DNA is tuned by DNA sequence and molecular switching

2018 ◽  
Vol 46 (10) ◽  
pp. 5001-5011 ◽  
Author(s):  
Alessia Tempestini ◽  
Carina Monico ◽  
Lucia Gardini ◽  
Francesco Vanzi ◽  
Francesco S Pavone ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Lac Repressor ◽  
Repressor Protein ◽  
Molecular Switching

scholarly journals Lysine 84 is at the subunit interface of lac repressor protein

1993 ◽  
Vol 268 (23) ◽  
pp. 17613-17622
Author(s):  
W.I. Chang ◽  
J.S. Olson ◽  
K.S. Matthews
Keyword(s):  
Lac Repressor ◽  
Repressor Protein ◽  
Subunit Interface

scholarly journals Novel method for identifying sequence-specific DNA-binding proteins.

1985 ◽  
Vol 5 (9) ◽  
pp. 2307-2315 ◽  
Author(s):  
D Levens ◽  
P M Howley
Keyword(s):  
Dna Binding ◽  
Fusion Protein ◽  
Dna Sequence ◽  
Binding Proteins ◽  
Binding Protein ◽  
Protein S ◽  
Dna Binding Proteins ◽  
Lac Repressor ◽  
Lac Operator ◽  
Beta Galactosidase

We developed a general method for the enrichment and identification of sequence-specific DNA-binding proteins. A well-characterized protein-DNA interaction is used to isolate from crude cellular extracts or fractions thereof proteins which bind to specific DNA sequences; the method is based solely on this binding property of the proteins. The DNA sequence of interest, cloned adjacent to the lac operator DNA segment is incubated with a lac repressor-beta-galactosidase fusion protein which retains full operator and inducer binding properties. The DNA fragment bound to the lac repressor-beta-galactosidase fusion protein is precipitated by the addition of affinity-purified anti-beta-galactosidase immobilized on beads. This forms an affinity matrix for any proteins which might interact specifically with the DNA sequence cloned adjacent to the lac operator. When incubated with cellular extracts in the presence of excess competitor DNA, any protein(s) which specifically binds to the cloned DNA sequence of interest can be cleanly precipitated. When isopropyl-beta-D-thiogalactopyranoside is added, the lac repressor releases the bound DNA, and thus the protein-DNA complex consisting of the specific restriction fragment and any specific binding protein(s) is released, permitting the identification of the protein by standard biochemical techniques. We demonstrate the utility of this method with the lambda repressor, another well-characterized DNA-binding protein, as a model. In addition, with crude preparations of the yeast mitochondrial RNA polymerase, we identified a 70,000-molecular-weight peptide which binds specifically to the promoter region of the yeast mitochondrial 14S rRNA gene.

A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein

1979 ◽  
Vol 131 (4) ◽  
pp. 669-680 ◽  
Author(s):  
A. Klug ◽  
A. Jack ◽  
M.A. Viswamitra ◽  
Olga Kennard ◽  
Z. Shakked ◽  
...  
Keyword(s):  
Lac Repressor ◽  
Specific Sequence ◽  
Repressor Protein ◽  
Sequence Dependent

An Elastic Rod Representation for the LacI-DNA Loop Complex

2011 ◽  
Author(s):  
Todd D. Lillian
Keyword(s):  
Gene Regulation ◽  
Large Range ◽  
Protein Flexibility ◽  
Lac Repressor ◽  
Elastic Rod ◽  
Repressor Protein ◽  
Dna Loop ◽  
Rod Model ◽  
Elastic Rod Model

The well-recognized Lac repressor protein (LacI) regulates transcription by bending DNA into a loop. In addition to the known role of DNA flexibility, there is accumulating evidence suggesting that the flexibility of LacI also plays a role in this gene regulation. Here we extend our elastic rod model for DNA (previously used to model DNA only) to represent LacI. Specifically, we represent sites of concentrated flexibility in the protein with flexible elastic rod domains; and we represent relatively rigid domains of the protein with stiff elastic rod domains. Our analysis shows the sensitivity of looping energetics to the degree of flexibility within the protein over a large range of DNA lengths. In addition, we show that the predicted energetically dominant binding topology (A) remains upon introducing protein flexibility.

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