The free energy surface (FES) of three Poly-Alanine peptides is exhaustively reconstructed by using metadynamics. A specific collective coordinate has been introduced to account for the hydration of the N- terminal region of alpha-helical conformations. Calculations suggest that Poly-Alanine peptides mainly populate unfolded states. Interestingly FESs exhibit different properties among peptides thereby providing some hints on factors determining the conformational preferences of short Poly-Alanine sequences. Overall the calculations evidence the efficiency of Metadynamics in exploring free energy surfaces of biological relevant molecules.

Exploring the Free Energy Surface of Short Peptides by Using Metadynamics / C. Camilloni, A. De Simone - In: From Computational Biophysics to Systems Biology (CBSB08) : Proceedings of the NIC Workshop 2008 / [a cura di] U.H.E. Hansmann, J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann. - [s.l] : NIC, 2008. - ISBN 978-3-9810843-6-8. - pp. 77-80 (( convegno From Computational Biophysics to Systems Biology (CBSB08) tenutosi a Julich (Germany) nel 2008.

Exploring the Free Energy Surface of Short Peptides by Using Metadynamics

C. Camilloni
Primo
;
2008

Abstract

The free energy surface (FES) of three Poly-Alanine peptides is exhaustively reconstructed by using metadynamics. A specific collective coordinate has been introduced to account for the hydration of the N- terminal region of alpha-helical conformations. Calculations suggest that Poly-Alanine peptides mainly populate unfolded states. Interestingly FESs exhibit different properties among peptides thereby providing some hints on factors determining the conformational preferences of short Poly-Alanine sequences. Overall the calculations evidence the efficiency of Metadynamics in exploring free energy surfaces of biological relevant molecules.
2008
http://www.kfa-juelich.de/nic-series/volume40/de_simone.pdf
Book Part (author)
File in questo prodotto:
Non ci sono file associati a questo prodotto.
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/59166
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact