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Energy coupling between DNA binding and subunit association is responsible for the specificity of DNA‐Arc interaction
Author(s) -
Silva Jerson L.,
Silveira Cristina F.
Publication year - 1993
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560020608
Subject(s) - dna , protein subunit , repressor , chemistry , base pair , biophysics , operator (biology) , protein–dna interaction , crystallography , stereochemistry , microbiology and biotechnology , dna binding protein , biology , biochemistry , gene , transcription factor
The effects of several DNA molecules on the free energy of subunit association of Arc repressor were measured. The association studies under equilibrium conditions were performed by the dissociating perturbation of hydrostatic pressure. The magnitude of stabilization of the subunit interaction was determined by the specificity of the protein‐DNA interaction. Operator DNA stabilized the free energy of association by about 2.2 kcal/mol of monomeric unit, whereas poly(dG‐dC) stabilized the subunit interaction by only 0.26 kcal. Measurements of the stabilizing free energy at different DNA concentrations revealed a stoichiometry of two dimers per 21 bp for the operator DNA sequence and for the nonspecific DNA poly(dA‐dT). However, the maximum stabilization was much larger for operator sequence (Δ p = 1, 750 bar) as compared for poly(dA‐dT) (Δ p = 750 bar). The importance of the free‐energy linkage for the recognition process was corroborated by its absence in a mutant Arc protein (PL8) that binds to operator and nonspecific DNA sequences with equal, low affinity. We conclude that the coupling accounts for the high specificity of the Arc‐operator DNA interaction. We hypothesize a mutual coupling between the protein subunits and the two DNA strands, in which the much higher persistency of the associated form when Arc is bound to operator would stabilize the interactions between the two DNA strands.