ProBLM

ProBLM models membrane-protein complexes by embedding transmembrane proteins into lipid bilayers or pseudomembranes to enable structural analysis of protein–lipid interactions.

Key Features:

• Automatic Protein Insertion: A geometry-based approach automatically integrates known 3D protein structures into pre-generated lipid bilayers or pseudomembranes.
• Versatile Membrane Modeling: Supports POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine), POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine), artificial bilayers, and pseudomembranes constructed from pseudoatoms via the Protein Nano-Object Integrator to model desolvation effects and reduce incorrect protein–lipid contacts.
• Regeneration of Missing Atoms and Residues: Automatically regenerates missing residues and heavy atoms in protein coordinate data.
• Manual Position and Orientation Refinement: Provides options to adjust the position and orientation of the protein relative to the membrane for refined modeling.

Scientific Applications:

• Biophysical studies of membrane protein function: Enables analysis of how lipid environments influence membrane protein activity and stability.
• Structural dynamics and conformational analysis: Supports examination of protein stability and conformational changes within lipid bilayers.
• Protein–lipid interaction mapping: Facilitates investigation of specific contacts and interactions between membrane proteins and lipids.
• Hypothesis testing of membrane–protein interactions: Provides modeled membrane contexts for evaluating structural hypotheses about membrane-associated mechanisms.

Methodology:

Uses a geometry-based algorithm to calculate optimal insertion points and orientations for embedding proteins into lipid bilayers or pseudomembranes; constructs pseudomembranes from pseudoatoms via the Protein Nano-Object Integrator; automatically regenerates missing residues and heavy atoms.