Orientations of Proteins in Membranes database

Orientations of Proteins in Membranes database provides spatial positions and orientations of membrane-associated proteins and peptides within lipid bilayers to support structural, computational, and functional analyses.

Key Features:

• Content scope: Contains over 1,200 transmembrane and peripheral proteins and peptides from approximately 350 organisms, corresponding to around 3,800 Protein Data Bank entries.
• Structural classification: Systematically classifies proteins into classes, superfamilies, and families.
• Membrane type assignment: Assigns entries to one of 21 distinct membrane types.
• Orientation and topology data: Provides detailed spatial positions, topology, and intracellular localization of proteins within the lipid bilayer.
• PPM 2.0 energy model: Uses the PPM 2.0 method to optimize spatial positions relative to the lipid bilayer by accounting for hydrophobic interactions, hydrogen bonding, and electrostatic forces.
• Anisotropic environment characterization: Models the anisotropic water–lipid environment with specified dielectric constants and hydrogen-bonding profiles.
• Downloadable coordinates: Provides downloadable coordinates of proteins and peptides with defined membrane boundaries.
• PPM server calculations: Includes the PPM server to calculate spatial positions in membranes for newly determined protein structures or theoretical models.
• Visualization: Includes a gallery of protein images and integrated visualization tools to illustrate membrane orientations and interactions.

Scientific Applications:

• Structural analysis: Analyze orientations and positions of membrane proteins to inform structural interpretation.
• Computational studies: Provide coordinates and membrane boundary definitions for computational analyses and modeling.
• Model validation and refinement: Validate and refine spatial arrangements of new experimental structures and theoretical models using the PPM server.
• Protein–lipid interaction studies: Support investigation of protein–lipid interactions and orientation-dependent functional insights.
• Comparative classification: Enable comparative analyses across classes, superfamilies, families, and membrane types.

Methodology:

Spatial positions are computed with the PPM 2.0 method, which optimizes protein orientation by accounting for hydrophobic interactions, hydrogen bonding, electrostatic forces, and an anisotropic water–lipid environment characterized by dielectric constants and hydrogen-bonding profiles; the PPM server applies this method to new structures and theoretical models.