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Naslov:Distance-based configurational entropy of proteins from molecular dynamics simulations
Avtorji:ID Fogolari, Federico (Avtor)
ID Corazza, Alessandra (Avtor)
ID Fortuna, Sara (Avtor)
ID Soler, Miguel Angel (Avtor)
ID VanSchouwen, Bryan (Avtor)
ID Brancolini, Giorgia (Avtor)
ID Corni, Stefano (Avtor)
ID Melacini, Giuseppe (Avtor)
ID Esposito, Gennaro (Avtor)
Datoteke:.pdf 10_Fogolari_Enropy.pdf (2,40 MB)
MD5: 6DF5E4A2373ACD4EC5AD39DBE8766276
 
Jezik:Angleški jezik
Vrsta gradiva:Delo ni kategorizirano
Tipologija:1.01 - Izvirni znanstveni članek
Organizacija:UNG - Univerza v Novi Gorici
Opis: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.
Ključne besede:entropy, protein, molecular dynamics, simulations, MD
Leto izida:2015
Št. strani:26
Številčenje:10, 7
PID:20.500.12556/RUNG-2690 Novo okno
COBISS.SI-ID:4536315 Novo okno
DOI:10.1371/journal.pone.0132356 Novo okno
NUK URN:URN:SI:UNG:REP:2E8HAEOE
Datum objave v RUNG:12.10.2016
Število ogledov:6011
Število prenosov:224
Metapodatki:XML DC-XML DC-RDF
:
FOGOLARI, Federico, CORAZZA, Alessandra, FORTUNA, Sara, SOLER, Miguel Angel, VANSCHOUWEN, Bryan, BRANCOLINI, Giorgia, CORNI, Stefano, MELACINI, Giuseppe in ESPOSITO, Gennaro, 2015, Distance-based configurational entropy of proteins from molecular dynamics simulations. PLoS ONE [na spletu]. 2015. Vol. 10, no. 7. [Dostopano 7 april 2025]. DOI 10.1371/journal.pone.0132356. Pridobljeno s: https://repozitorij.ung.si/IzpisGradiva.php?lang=slv&id=2690
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Gradivo je del revije

Naslov:PLoS ONE
Založnik:Public Library of Science
Leto izida:2015
ISSN:1932-6203

Licence

Licenca:CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
Povezava:http://creativecommons.org/licenses/by/4.0/deed.sl
Opis:To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.
Začetek licenciranja:10.10.2016

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