Comprehensive Analysis of Coupled Proline Cis-Trans States in Bradykinin Using ωBP-REMD Simulations

Area of Science:

• Biochemistry
• Computational Biology
• Structural Biology

Background:

• Proline (Pro) cis-trans isomerization is crucial for protein folding and stability.
• The interplay between different proline isomerization states in proteins remains poorly understood.

Purpose of the Study:

• To investigate the coupled cis-trans isomerization of three proline residues in bradykinin (BK) as a model system.
• To understand the conformational coupling between proline isomer states during protein adaptation.

Main Methods:

• Utilized an enhanced-sampling molecular dynamics method: ω-bias potential replica exchange molecular dynamics (ωBP-REMD).
• Exhaustively sampled all combinations of proline isomer states.
• Performed 885 ns of simulations to obtain converged probability densities for all eight state combinations.

Main Results:

• The all-trans state was identified as the preferred isomer for zwitterionic aqueous BK, consistent with experimental data.
• Other isomer combinations significantly contributed to the structural ensemble.
• Revealed interdependence of proline isomerization states, demonstrating coupling between different proline isomers.
• The cis/trans equilibrium of a proline residue can shift by up to 2.5 kcal·mol⁻¹, influenced by the states of other proline residues.

Conclusions:

• The ωBP-REMD methodology proved efficient for sampling proline isomerization states.
• Coupling of proline isomerization states may play a more significant role in larger, conformationally constrained proteins.
• Demonstrated that the cis state of Pro7 becomes favored when Pro2 switches to its cis state.