Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

• Published in: PloS one 2015-07, Vol.10 (7), p.e0132356-e0132356
• Main Authors: Fogolari, Federico, Corazza, Alessandra, Fortuna, Sara, Soler, Miguel Angel, VanSchouwen, Bryan, Brancolini, Giorgia, Corni, Stefano, Melacini, Giuseppe, Esposito, Gennaro
• Format: Article
• Language: English
• Subjects: Algorithms; Amino acids; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; beta 2-Microglobulin - chemistry; beta 2-Microglobulin - metabolism; Binding; Biological activity; Carrier Proteins - chemistry; Carrier Proteins - metabolism; Citric acid; Computation; Computer simulation; Density distribution; Entropy; Gold; Guanine Nucleotide Exchange Factors - chemistry; Guanine Nucleotide Exchange Factors - metabolism; Ligands; Lipoproteins - chemistry; Lipoproteins - metabolism; Magnetic Resonance Spectroscopy; Methods; Molecular dynamics; Molecular Dynamics Simulation; Order parameters; Protein Binding; Protein Conformation; Protein Folding; Protein structure; Protein Unfolding; Proteins; Proteins - chemistry; Proteins - metabolism; Science & Technology - Other Topics; Secondary structure; Simulation; Trajectory analysis
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0132356

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.