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Protein—DNA recognition complexes: Conservation of structure and binding energy in the transition state
Author(s) -
JenJacobson Linda
Publication year - 1997
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(1997)44:2<153::aid-bip4>3.0.co;2-u
Subject(s) - chemistry , dna , transition (genetics) , state (computer science) , biophysics , computational biology , chemical physics , biochemistry , gene , algorithm , biology , computer science
This paper considers how enzymes that catalyze reactions at specific DNA sites have been engineered to overcome the problem of competitive inhibition by excess nonspecific binding sites on DNA. The formation of a specific protein—DNA recognition complex is discussed from both structural and thermodynamic perspectives, and contrasted with formation of nonspecific complexes. Evidence (from EcoRI and BamHI endonucleases) is presented that a wide variety of perturbations of the DNA substrate alter binding free energy but do not affect the free energy of activation for the chemical step; that is, many energetic factors contribute equally to the recognition complex and the transition‐state complex. This implies that the specific recognition complex bears a close resemblance to the transition‐state complex, such that very tight binding to the recognition site on the DNA substrate does not inhibit catalysis, but instead provides energy that is efficiently utilized along the path to the transition state. It is suggested that this view can be usefully extended to “noncatalytic” site‐specific DNA‐binding proteins like transcriptional activators and general transcription factors. © 1997 John Wiley & Sons, Inc. Biopoly 44: 153–180, 1997