Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to...

Area of Science:

• Molecular biology
• Structural biology
• Biophysics

Background:

• The N-terminal domain of phage lambda repressor dimerizes and binds to a specific DNA operator sequence.
• This domain contains a helix-turn-helix motif and a flexible N-terminal arm that wraps around DNA.
• Mutations in the arm or DNA operator significantly reduce repressor-operator binding affinity.

Purpose of the Study:

• To investigate the energetic contributions of the lambda arm to repressor-operator recognition.
• To model the effects of DNA mutations on protein-DNA complex conformation and energy.
• To assess the utility of computational methods for predicting mutagenesis outcomes in protein-DNA interactions.

Main Methods:

• Utilized a finite-difference Poisson-Boltzmann approach combined with conformational searching.
• Employed a simplified potential energy function for initial structure screening.
• Performed accurate electrostatic energy calculations on selected conformations.

Main Results:

• Identified low-energy conformations for the wild-type sequence with Lys4 side-chain mobility.
• Observed significant differences in lowest energy conformations upon introducing a C to T mutation at operator position 6.
• The mutation impacts the DNA sequence contacting the N-terminal arm.

Conclusions:

• The computational approach can estimate conformational and energetic effects of mutagenesis in protein-DNA complexes.
• The lambda arm plays a crucial role in the specificity and affinity of repressor-operator binding.
• Understanding these interactions aids in predicting the impact of genetic alterations.