ElNemo

ElNemo predicts macromolecular movements and analyzes conformational changes and structural dynamics using Normal Mode Analysis (NMA) based on low-frequency normal modes.

Key Features:

• Elastic Network Model (ENM) implementation: Implements the Elastic Network Model to compute and analyze low-frequency normal modes of macromolecules.
• Rotation-Translation-Block (RTB) approximation: Employs the RTB approximation to enable analysis of proteins of virtually any size.
• Mode calculation from PDB structures: Computes the 100 lowest-frequency normal modes from Protein Data Bank (PDB) input structures.
• Quantitative output metrics: Reports degree of collectivity, residue mean square displacements, distance fluctuation maps, and correlations between observed atomic displacement parameters (B-factors) and normal-mode-derived displacements.
• Normal-mode-perturbed model generation: Produces large numbers of normal-mode-perturbed models for use in X-ray crystallography molecular replacement (MR) phasing.
• Conformational movement analysis: Identifies the normal modes that contribute most to observed movements when two conformations of the same or homologous proteins are provided.

Scientific Applications:

• Protein conformational changes upon ligand binding: Analysis of conformational changes associated with ligand binding.
• Membrane channel dynamics: Investigation of opening and closure dynamics of membrane channels.
• Ribosome movements: Analysis of potential conformational movements in ribosomes.
• Viral capsid maturation: Exploration of structural transitions during viral capsid maturation.
• Molecular replacement in X-ray crystallography: Use of normal-mode-perturbed models as templates for diffraction data phasing via molecular replacement.

Methodology:

Applies Normal Mode Analysis (NMA) using an Elastic Network Model (ENM) with the rotation-translation-block (RTB) approximation; calculates the 100 lowest-frequency modes from PDB structures; computes degree of collectivity, residue mean square displacements, distance fluctuation maps, and correlations with experimental B-factors; generates normal-mode-perturbed models and compares modes between two conformations.