Helix Orientation and Displacement Analysis

Overview and Methodology

What It Does

This script tracks how a helical segment changes orientation and position over time in a molecular dynamics simulation. It quantifies bending, twisting, and translational movements relative to a reference frame.

How It Works

• Objective: Detect and characterize conformational changes of a helix over time.
• Process:
  • Tilt: Measures the angle between the helix axis and its orientation in a reference frame — useful for detecting bending or rocking motions.
  • Rotation: Tracks angular displacement of a side chain atom around the helix axis — ideal for detecting twisting.
  • Displacement: Measures spatial deviation of the helix from its reference position using either:
    • Centroid: Compares center-of-mass positions.
    • Closest Atom: Uses maximum per-atom displacement, sensitive to local deviations.

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Configuration and Inputs

Prerequisites

• Requires a loaded trajectory.

Key Configuration Options

• Selections:

  • helix_sel: Atom group defining the helix (e.g., segid VSD and resid 200-240).
  • rotation_ref_sel: Atom(s) in a specific residue to track rotational motion (e.g., name CB and resid 205).
  • helix_name: Label for plot output.

• Analysis Parameters:

  • ref_frame: Frame used as the reference state (default = begin_frame).
  • distance_method: Either 'Centroid' or 'Closest Atom' to define helix displacement.
  • plot_rolling_average: Whether to overlay a smoothed version of the data.

• Visualization Settings:

  • Titles, axis labels, dimensions, and rolling window size are customizable for all subplots.

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Outputs

• Combined Plot: *_Analysis.png — Three-panel figure showing:

  • Tilt Angle (°) over time.
  • Rotation Angle (°) relative to the helix axis (if a reference is provided).
  • Max Displacement (Å) of the helix from its reference state.

• Console Output:

  • Frame processing progress, selection details, and file save confirmation.

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Interpreting the Results

Tilt Angle

• Stable Tilt: Indicates consistent orientation.
• Fluctuating Tilt: Suggests bending or rocking motion of the helix axis.

Rotation Angle

• Monotonic Drift: Continuous rotation around the axis (e.g., twisting).
• Oscillating Rotation: Back-and-forth torsional movement.

Displacement

• Low Values: Minimal deviation from the initial structure.
• Sharp Spikes: Sudden structural shifts or kinks.

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Example Scenarios

Voltage-Sensing Domain Rotation

• Scenario: VSD rotates during membrane depolarization.
• Observation: Progressive increase in rotation angle, stable tilt.
• Interpretation: Consistent axial twist without reorienting the helix.

Helix Bending or Kinking

• Scenario: Local bending due to residue mutation or force application.
• Observation: Increasing tilt and displacement, with minimal rotation.
• Interpretation: Helix is bending rather than twisting.

Ligand-Induced Shift

• Scenario: Ligand binding displaces the helix.
• Observation: Step-like change in displacement plot at a specific time.
• Interpretation: Ligand causes repositioning of the helix.

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Usage Tips

• Rotation Reference: Use a stable side chain (e.g., CB) near the middle of the helix for best rotational tracking.
• Displacement Method:
  • Use 'Closest Atom' to detect localized changes like kinks.
  • Use 'Centroid' for smoother, overall drift tracking.
• Smoothing: Enable plot_rolling_average=True with a small rolling_window for noisy trajectories.
• Frame Selection: Ensure ref_frame is representative of the expected "rest" state.

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