Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes.

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes.
Eur Biophys J. 2019 Jul 04;:
Authors: Saldaño TE, Tosatto SCE, Parisi G, Fernandez-Alberti S
Abstract
According to the generalized conformational selection model, ligand binding involves the co-existence of at least two conformers with different ligand-affinities in a dynamical equilibrium. Conformational transitions between them should be guaranteed by intramolecular vibrational dynamics associated to each conformation. These motions are, therefore, related to the biological function of a protein. Positions whose mutations are found to alter these vibrations the most can be defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. In a previous study, we have shown that these positions are evolutionarily conserved. They correspond to buried aliphatic residues mostly localized in regular structured regions of the protein like β-sheets and α-helices. In the present paper, we perform a network analysis of these key positions for a large dataset of paired protein structures in the ligand-free and ligand-bound form. We observe that networks of interactions between these key positions present larger and more integrated networks with faster transmission of the information. Besides, networks of residues result that are robust to conformational changes. Our...

Source: European Biophysics Journal : EBJ - July 3, 2019 Category: Physics Authors: Saldaño TE, Tosatto SCE, Parisi G, Fernandez-Alberti S Tags: Eur Biophys J Source Type: research