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Studying the Cu binding sites in the PrPN-terminal region: a test case for ab initio simulations (Articolo in rivista)

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Studying the Cu binding sites in the PrPN-terminal region: a test case for ab initio simulations (Articolo in rivista) (literal)

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Furlan, S; La Penna, G; Guerrieri, F; Morante, S; Rossi, GC (2007)
Studying the Cu binding sites in the PrPN-terminal region: a test case for ab initio simulations
in European biophysics journal
(literal)

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Univ Roma Tor Vergata, Dipartimento Fis, Ist Nazl Fis Nucl, Sez Roma Tor Vergata, I-00133 Rome, Italy; ISMAC, CNR, I-16149 Genoa, Italy; NRC, ICCOM, I-50019 Florence, Italy; Univ Roma La Sapienza, Dipartimento Fis, SOFT, CRS, I-00185 Rome, Italy (literal)

Titolo

Studying the Cu binding sites in the PrPN-terminal region: a test case for ab initio simulations (literal)

Abstract

First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as a test case a study of the Cu coordination mode at the Prion Protein binding sites localized in the N-terminal octarepeat region. Using medium size PC-clusters, we are able to deal with systems with up to about 350 atoms and 10(3) electrons for as long as similar to 2 ps. With a foreseeable forthcoming scaling up of the available CPU times by a factor 10(3), one can hope to be soon able to simulate systems of biological interest of realistic size and for physical times of the order of the nanosecond. (literal)

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