MCPep

MCPep performs Monte Carlo simulations to model interactions of helical peptides with lipid membranes and to predict peptide location, orientation, helical content, and membrane-association energetics.

Key Features:

• Monte Carlo simulation engine: Implements a Monte Carlo (MC) simulation model for peptide–membrane interactions that has been tested on various peptides and protein fragments.
• Implicit environment models: Employs an implicit description for both aqueous and membrane environments.
• Aqueous-phase sampling: Samples internal conformational changes of peptides in the aqueous phase.
• Membrane-phase motions: Incorporates external rigid-body rotational and translational motions of the peptide in each Monte Carlo cycle within the membrane environment.
• Peptide scope: Supports helical peptides of any amino acid composition.
• Membrane scope and parameters: Supports lipid membranes of various compositions and accepts membrane parameters including natural width and surface charge.
• Predictive outputs: Reports average peptide location and orientation within the membrane, free energy of membrane association, and helical content.
• Validation: Simulation model reproduces empirical data from tested peptides and protein fragments.
• Snapshot outputs: Produces example simulation snapshots for interpretation of simulation results.

Scientific Applications:

• Peptide–membrane interaction analysis: Quantifies preferred peptide positions and orientations and estimates membrane insertion energetics.
• Amino-acid contribution studies: Elucidates the role of individual amino acids in membrane association.
• Membrane protein and peptide design: Provides structural and energetic data to inform studies of membrane protein function, peptide therapeutics, and drug design.
• Model validation and benchmarking: Enables comparison of simulation results with empirical data for peptides and protein fragments.

Methodology:

Uses Monte Carlo simulations with implicit descriptions of aqueous and membrane environments; samples internal peptide conformations in water and applies external rigid-body rotational and translational moves each MC cycle in the membrane, with the model tested on various peptides and protein fragments.