title: Role of promoter DNA sequence variations on the binding of EGR1 transcription factor.
abstract: In response to a wide variety of stimuli such as growth factors and hormones, EGR1 transcription factor is rapidly induced and immediately exerts downstream effects central to the maintenance of cellular homeostasis. Herein, our biophysical analysis reveals that DNA sequence variations within the target gene promoters tightly modulate the energetics of binding of EGR1 and that nucleotide substitutions at certain positions are much more detrimental to EGR1-DNA interaction than others. Importantly, the reduction in binding affinity poorly correlates with the loss of enthalpy and gain of entropy-a trend indicative of a complex interplay between underlying thermodynamic factors due to the differential role of water solvent upon nucleotide substitution. We also provide a rationale for the physical basis of the effect of nucleotide substitutions on the EGR1-DNA interaction at atomic level. Taken together, our study bears important implications on understanding the molecular determinants of a key protein-DNA interaction at the cross-roads of human health and disease.
authors.affiliation: Department of Biochemistry & Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, United States.
authors.forename: David C
authors.initials: DC
authors.lastname: Mikles
authors.affiliation: Department of Biochemistry & Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, United States.
authors.forename: Brett J
authors.initials: BJ
authors.lastname: Schuchardt
authors.affiliation: Department of Biochemistry & Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, United States.
authors.forename: Vikas
authors.initials: V
authors.lastname: Bhat
authors.affiliation: Department of Biochemistry & Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, United States.
authors.forename: Caleb B
authors.initials: CB
authors.lastname: McDonald
authors.affiliation: Department of Biochemistry & Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, United States. Electronic address: amjad@farooqlab.net.
authors.forename: Amjad
authors.initials: A
authors.lastname: Farooq
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D051766:Early Growth Response Protein 1 / Q000737:chemistry / Q000378:metabolism*; D019277:Entropy; D006801:Humans; D008958:Models, Molecular; D059372:Nucleotide Motifs; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012997:Solvents / Q000737:chemistry
chemical_list: C497325:EGR1 protein, human; D051766:Early Growth Response Protein 1; D012997:Solvents; D004247:DNA
keywords: Enthalpy–entropy compensation; Protein–DNA thermodynamics; Single nucleotide polymorphisms; Zinc fingers