Instantaneous normal modes and the protein glass transition

Area of Science:

• Computational chemistry
• Biophysics
• Materials science

Background:

• Instantaneous normal mode (INM) analysis characterizes local potential energy surface anharmonicities.
• Understanding protein dynamics is crucial for comprehending their function and transitions.

Purpose of the Study:

• To apply INM analysis to molecular dynamics simulations of a scorpion toxin protein.
• To identify INM characteristics correlating with protein dynamical (glass) transition behavior.

Main Methods:

• Performing INM analysis on instantaneous configurations from molecular dynamics simulations.
• Filtering INM based on eigenvalue properties and eigenvector characteristics (e.g., double-well potentials).
• Utilizing energy minimization on selected configurations to assess configurational space exploration.

Main Results:

• The number of negative eigenvalues did not show a temperature-dependent transition for the protein.
• Filtering for double-well potentials revealed a transition in hydration water, but not the protein.
• Additional filtering of protein double-well modes, focusing on modes escaping to different configurational spaces upon minimization, identified a clear protein dynamical transition.

Conclusions:

• Specific characteristics of negative instantaneous normal modes provide insights into local diffusive dynamics.
• The study demonstrates a method to identify protein dynamical transitions through refined INM analysis.
• Refined INM analysis, combined with energy minimization, offers a physical picture of protein glass transition dynamics.