CCOMP

CCOMP compares overlapping fragments of protein complexes to identify amino acids with altered orientations and quantify structural deviations for functional interpretation.

Key Features:

• Sequence Alignment: Performs sequence alignment of receptors to ensure accurate residue correspondence for comparison.
• Residue Superimposition: Superimposes aligned residues to enable precise structural comparison between complexes.
• RMSD Calculation: Calculates root mean square deviation (RMSD) at individual-atom, per-amino-acid, and whole-protein-complex levels.
• Identification of Functionally Important Amino Acids: Uses RMSD-derived metrics to pinpoint amino acids that contribute to functional disparities between complexes.
• Solvent Accessibility and Interaction Assessment: Assesses changes in solvent exposure and potential interactions with co-activators.

Scientific Applications:

• VDR complex comparison: Applied to 1alpha,25-(OH)(2)D(3)-hVDR and 1alpha,25-(OH)(2)D(3)-rVDR-peptide complexes, revealing side chain conformational shifts in 35 amino acids upon peptide binding, with four directly contacting the co-activator-mimicking peptide KNHPMLMNLLKDN and all being essential for biological activity.
• Protein-ligand and peptide-binding analysis: Investigates structural changes and solvent exposure variations in protein-ligand and peptide-bound complexes to interpret binding-related functional effects.

Methodology:

Initial sequence alignment, residue superimposition, and RMSD analysis at atomic, amino acid, and complex levels.