Structural transitions in neutral and charged proteins in vacuo

Area of Science:

• Biophysics
• Computational Biology
• Protein Science

Background:

• Proteins in a vacuum (in vacuo) serve as simplified models for studying protein folding.
• Anhydrous protein studies, free from solvent effects, are crucial for understanding environmental influences on protein structure.
• Experimental characterization of these systems is emerging, necessitating complementary computational approaches.

Purpose of the Study:

• To investigate the fundamental principles of protein folding and unfolding transitions in anhydrous conditions.
• To explore the impact of sequence, temperature, charge, and initial configuration on protein folding.
• To complement experimental data with detailed molecular dynamics simulations for deeper insights.

Main Methods:

• Utilizing molecular dynamics (MD) simulations to model protein behavior.
• Employing protein shape analysis tools to examine folding-unfolding transitions.
• Analyzing trajectories based on global molecular shape features, including anisometry and chain entanglement complexity.

Main Results:

• Unfolding in lysozyme ions can be induced by Coulombic repulsion.
• Neutral lysozyme unfolding is triggered by centrifugal forces or weakened monomer-monomer interactions.
• Unfolded states serve as initial configurations for relaxation dynamics, allowing quantification of polymer collapse and large-scale folding features.

Conclusions:

• The study quantifies polymer collapse and large-scale folding features during unfolding and refolding.
• It provides insights into the nature of accessible conformational pathways for compact protein structures.
• Anhydrous protein dynamics, particularly hen egg-white lysozyme, can be effectively studied using MD simulations and shape analysis.