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. CamilloniPrimo
;
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.Pubblicazioni consigliate
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