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- Title
Studying the Cu binding sites in the PrP N-terminal region: a test case for ab initio simulations.
- Authors
Furlan, S.; La Penna, G.; Guerrieri, F.; Morante, S.; Rossi, G. C.
- 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 103 electrons for as long as ∼2 ps. With a foreseeable forthcoming scaling up of the available CPU times by a factor 103, 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
- Subjects
MOLECULAR dynamics; CHEMICAL bonds; SOLID state physics; BIOPHYSICS; PROTEIN binding; COPPER
- Publication
European Biophysics Journal, 2007, Vol 36, Issue 7, p841
- ISSN
0175-7571
- Publication type
Article
- DOI
10.1007/s00249-007-0162-2