Solvent Shell Occupancy Analysis

Overview and Methodology

What It Does

This script quantifies solvent molecule occupancy near a defined molecular group over the course of a trajectory. It calculates solvent coordination numbers, residue-level solvent occupancy, solvent–group distance distributions, and water dwell times to provide a detailed picture of solvation dynamics. These metrics are especially useful in studying hydration patterns, binding interfaces, and dynamic solvent environments near protein or ligand surfaces.

How It Works

• Objective: Track the local solvent environment around a group of atoms or residues.
• Process:
  • Coordination Number: Counts how many solvent molecules are within a cutoff distance of the group at each frame.
  • Residue Occupancy (if applicable): Tracks how often each residue in the group is contacted by solvent.
  • Distance Distribution: Collects minimum solvent-to-group distances across all frames.
  • Dwell Time: Measures how long individual solvent molecules remain in the shell without interruption.
  • Output Summary:
    • Line plot of coordination number vs. time.
    • Bar plot of top residues by solvent occupancy.
    • Histogram of solvent–group distances.
    • Histogram of dwell times (if water-like solvent).

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Configuration and Inputs

Prerequisites

• Requires a loaded trajectory.

Key Configuration Options

• Selections:

  • group_sel: Target group (e.g., ligand, loop, or interface region).
  • group_name: Label used for outputs and figures.
  • solvent_sel: Solvent molecule selection (e.g., resname TIP3).
  • solvent_name: Label for solvent type.

• Cutoff:

  • cutoff: Defines the shell radius around the group (typically ~3.5 Å for water).

• Options:

  • show_distance_plot: Whether to generate a histogram of solvent–group distances.
  • show_occupancy_plot: Whether to show residue-level occupancy (only if group_sel includes residues).
  • show_dwell_plot: Whether to compute and plot solvent dwell times.
  • max_residues_plot: Maximum number of residues to show in occupancy bar plot.
  • show_progress: Whether to print progress updates.

• Processing:

  • num_threads: Number of CPU threads used for analysis.

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Output

• Plots:

  • {group_name}_Solvent_Coordination.png: Coordination number over time.
  • {group_name}_Solvent_Residue_Occupancy.png: Top residue occupancy (optional).
  • {group_name}_Solvent_Distances.png: Solvent–group distance histogram (optional).
  • {group_name}_Solvent_Dwell.png: Dwell time histogram for water molecules (optional).

• CSV File:

  • {group_name}_Solvent_Shell.csv: Contains time series of coordination number and optional per-residue occupancy tracking.

• Console Output:

  • Average coordination number.
  • Top residues by solvent exposure.
  • Solvent molecule tracking summaries.

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Interpreting the Results

• Coordination Number:

  • High values indicate strong or persistent hydration.
  • Fluctuations may reflect dynamic solvent exchange or conformational changes.

• Residue Solvent Occupancy:

  • Identifies surface-exposed or highly hydrated residues.
  • Useful for mapping hydration hotspots or solvent-accessible sites.

• Distance Histogram:

  • Shows typical range of solvent–group interactions.
  • Narrow peak at low distance = well-defined hydration shell.

• Dwell Times:

  • Long dwell = structured or trapped water.
  • Short dwell = bulk-like solvent dynamics.

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Example Scenarios

Toxin Hydration Analysis

• Scenario: Examine how solvent stabilizes a peptide toxin.
• Observation: Terminal residues show high occupancy; coordination number plateaus.
• Interpretation: Stable hydration at exposed termini.

Protein Interface Solvation

• Scenario: Identify hydration differences at a binding site.
• Observation: Decrease in coordination and dwell time upon ligand binding.
• Interpretation: Solvent displacement upon complex formation.

Hydrophobic Patch Detection

• Scenario: Detect poorly hydrated regions.
• Observation: Low solvent coordination and few residues with occupancy.
• Interpretation: Likely hydrophobic or buried region.

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Usage Tips

• Selection Strategy:

  • Use segid, resid, or resname to isolate a domain, ligand, or patch.
  • Confirm the group contains residues to enable occupancy analysis.

• Cutoff Distance:

  • Use ~3.5 Å for first hydration shell.
  • Adjust for larger probes or broader hydration layers.

• Solvent Choice:

  • Works best with water-like solvents (e.g., TIP3, WAT).
  • Other solvents (e.g., ions, cosolvents) can be analyzed with adjusted interpretation.

• Performance:

  • Use num_threads > 1 for large systems or long trajectories.
  • Disable optional plots to save runtime if not needed.

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