Conformational Fluctuations in GTP-Bound K-Ras: A Metadynamics Perspective with Harmonic Linear Discriminant Analysis

Area of Science:

• Biophysics
• Computational Biology
• Protein Dynamics

Background:

• Proteins undergo significant conformational changes during function, requiring extensive simulation times for accurate analysis.
• Enhanced sampling methods, utilizing collective variables, are crucial for studying these complex molecular rearrangements.
• Harmonic Linear Discriminant Analysis (HLDA) is a powerful tool for defining collective variables in complex systems.

Purpose of the Study:

• To apply HLDA for studying the free-energy landscape of the K-Ras protein bound to GTP.
• To analyze conformational rearrangements in flexible loops and oncogenic mutation regions.
• To compare simulation predictions with existing experimental and computational data.

Main Methods:

• Utilized microsecond-long biased molecular dynamics simulations.
• Applied Harmonic Linear Discriminant Analysis (HLDA) to identify collective variables.
• Studied wild-type K-Ras and G12C, G12D, G12V mutants.

Main Results:

• Observed rapid interconversion between open and closed K-Ras states with similar thermodynamic stability.
• Identified mutation-induced alterations in the relative stabilities of conformational states.
• Revealed the emergence of numerous microscopic metastable states due to mutations.

Conclusions:

• Demonstrated the applicability of the HLDA-based protocol for conformational sampling in folded proteins.
• HLDA effectively captures rearrangements across multiple flexible regions.
• The study provides insights into K-Ras functional dynamics and mutation effects.