Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis.

Area of Science:

• Biophysics
• Computational Biology
• Molecular Dynamics

Background:

• Time-resolved Stokes shift measurements probe polar solvation dynamics in biological systems on picosecond to nanosecond timescales.
• Decomposing protein and solvent contributions in these measurements is challenging, necessitating computational approaches.
• Understanding molecular behavior requires detailed analysis of electrostatic interactions within biomolecules.

Purpose of the Study:

• To analyze computer simulations of electrostatic interactions in the immunoglobulin binding domain B1 of protein G.
• To elucidate the position-dependent and heterogeneous nature of polar solvation dynamics.
• To differentiate and quantify contributions from protein and solvent interactions.

Main Methods:

• Analysis of molecular dynamics simulations focusing on electrostatic interactions.
• Investigated 11 specific residues within the immunoglobulin binding domain B1 of protein G.
• Quantified protein and solvent contributions to polar solvation dynamics.

Main Results:

• Polar solvation dynamics were found to be position-dependent and highly heterogeneous.
• Solvent contributions ranged from negligible at picoseconds to dominant at hundreds of picoseconds.
• Dominant solvent contributions arise from coupled hydration and protein conformational dynamics.

Conclusions:

• The study provides a detailed microscopic picture of polar solvation dynamics in protein G.
• Interpretation of time-resolved Stokes shift measurements requires consideration of diverse molecular behaviors.
• Coupled protein and solvent dynamics significantly influence solvation processes over extended timescales.