Repository of University of Nova Gorica

Show document
A+ | A- | SLO | ENG

Title:Distance-based configurational entropy of proteins from molecular dynamics simulations
Authors:Fogolari, Federico (Author)
Corazza, Alessandra (Author)
Fortuna, Sara (Author)
Soler, Miguel Angel (Author)
VanSchouwen, Bryan (Author)
Brancolini, Giorgia (Author)
Corni, Stefano (Author)
Melacini, Giuseppe (Author)
Esposito, Gennaro (Author)
Files:.pdf 10_Fogolari_Enropy.pdf (2,40 MB)
 
Language:English
Work type:Not categorized (r6)
Tipology:1.01 - Original Scientific Article
Organization:UNG - University of Nova Gorica
Abstract: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.
Keywords:entropy, protein, molecular dynamics, simulations, MD
Year of publishing:2015
Number of pages:26
Numbering:7, 10
COBISS_ID:4536315  Link is opened in a new window
URN:URN:SI:UNG:REP:2E8HAEOE
DOI:10.1371/journal.pone.0132356 Link is opened in a new window
License:CC BY 4.0
This work is available under this license: Creative Commons Attribution 4.0 International
Views:3166
Downloads:192
Metadata:XML RDF-CHPDL DC-XML DC-RDF
Categories:Document is not linked to any category.
:
  
Average score:(0 votes)
Your score:Voting is allowed only for logged in users.

Hover the mouse pointer over a document title to show the abstract or click on the title to get all document metadata.

Record is a part of a journal

Title:PLoS ONE
Publisher:Public Library of Science
ISSN:1932-6203
Year of publishing:2015

Back