Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.

ABSTRACT: The kinetics of protein-DNA recognition, along with its thermodynamic properties, including affinity and specificity, play a central role in shaping biological function. Protein-DNA recognition kinetics are characterized by two key elements: the time taken to locate the target site amid various nonspecific alternatives; and the kinetics involved in the recognition process, which may necessitate overcoming an energetic barrier. In this study, we developed a coarse-grained (CG) model to investigate interactions between a transcription factor called the sex-determining region Y (SRY) protein and DNA, in order to probe how DNA conformational changes affect SRY-DNA recognition and binding kinetics. We find that, not only does a requirement for such a conformational DNA transition correspond to

SUBMITTER: Rogoulenko E 

PROVIDER: S-EPMC11229352 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature