Long-time mean-square displacements in proteins.

Area of Science:

• Biophysics
• Computational Chemistry
• Materials Science

Background:

• Molecular dynamics (MD) simulations provide insights into atomic and molecular motion.
• Finite-time MD simulations often yield mean square displacement (MSD) values that are still increasing, lacking a clear long-time limit.
• Determining the intrinsic, long-time MSD is crucial for understanding protein dynamics and material properties.

Purpose of the Study:

• To introduce a novel method for calculating the intrinsic, long-time mean square displacement (MSD) from finite-time molecular dynamics (MD) simulations.
• To enable accurate characterization of protein dynamics using limited simulation data.
• To provide a reliable parameter for understanding atomic and molecular motion in condensed matter systems.

Main Methods:

• Fitting a model to the incoherent intermediate neutron scattering function, I(inc)(Q,t), derived from MD simulations.
• Extracting the infinite-time MSD, denoted as , as a parameter from the model fits.
• Utilizing the Debye-Waller factor definition: I(Q,t=∞)=exp(-Q(2)/3) for parameter determination.

Main Results:

• The proposed method successfully obtains the intrinsic MSD from finite-time MD data.
• Application to hydrated lysozyme powder demonstrated the method's effectiveness over a range of temperatures.
• The intrinsic MSD derived from 1 ns and 10 ns simulation data remained consistent.

Conclusions:

• The developed method reliably determines the intrinsic, long-time MSD from short MD simulations.
• This technique provides a more accurate measure of protein dynamics than MSD values directly obtained from limited simulation times.
• The intrinsic MSD is approximately twice the MSD observed in 1 ns simulations, offering a more complete picture of molecular motion.