Role of Shape Deformation of DNA-Binding Sites in Regulating the Efficiency and Specificity in Their Recognition by DNA-Binding Proteins.

ABSTRACT: Accurate transcription of genetic information is crucial, involving precise recognition of the binding motifs by DNA-binding proteins. While some proteins rely on short-range hydrophobic and hydrogen bonding interactions at binding sites, others employ a DNA shape readout mechanism for specific recognition. In this mechanism, variations in DNA shape at the binding motif resulted from either inherent flexibility or binding of proteins at adjacent sites are sensed and capitalized by the searching proteins to locate them specifically. Through extensive computer simulations, we investigate both scenarios to uncover the underlying mechanism and origin of specificity in the DNA shape readout mechanism. Our findings reveal that deformation in shape at the binding motif creates an entropy funnel,

SUBMITTER: Sangeeta 

PROVIDER: S-EPMC11267559 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature