Evolution of the potential energy landscape with static pulling force for two model proteins

Area of Science:

• Biophysics
• Computational Biology
• Protein Folding

Background:

• Understanding protein folding mechanisms is crucial for molecular biology.
• Off-lattice bead models provide a simplified yet effective approach to study protein dynamics.
• External forces can significantly influence protein structure and function.

Purpose of the Study:

• To analyze the energy landscape of protein L and protein G under static pulling forces.
• To investigate how different attachment points affect protein folding pathways.
• To compare the effects of force on the folding mechanisms of protein L and protein G.

Main Methods:

• Utilized off-lattice bead models to simulate protein L and protein G.
• Applied static pulling forces to the models.
• Varied attachment points (residues 1/56 and 10/32) to analyze force application.
• Calculated energy landscapes and folding pathways.

Main Results:

• Terminal residue pulling (1/56) resulted in extended structures at high forces, with helical turns disappearing.
• Internal residue pulling (10/32) led to complex, frustrated energy landscapes with competing arrangements.
• Folding pathways changed dramatically under low static force, varying with protein and attachment points.
• Unforced folding pathways agreed with previous studies: N-terminal hairpin for protein L, C-terminal for protein G.

Conclusions:

• Static pulling forces significantly alter protein energy landscapes and folding mechanisms.
• Attachment points critically influence the response of proteins to external forces.
• The study provides insights into force-induced protein structural transitions and folding dynamics.