The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study

PLoS One. 2016 Mar 23;11(3):e0152002. doi: 10.1371/journal.pone.0152002. eCollection 2016.

Abstract

LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • DNA / metabolism*
  • Energy Metabolism / physiology
  • Escherichia coli / metabolism
  • Gene Expression Regulation / physiology
  • Hinge Exons / physiology*
  • Hydrogen Bonding
  • Lac Repressors / metabolism*
  • Static Electricity

Substances

  • Lac Repressors
  • DNA

Grants and funding

The calculations were performed in the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw (Grant Number: G53-19). This work was supported by the National Science Center UMO-2011/02/A/ST3/00143(Maestro grant). S.H. was supported by Project Sonata from UMO-2012/07/D/ST4/02183.