title: Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein.
abstract: In this paper we present the results of mixed Monte Carlo/Molecular Dynamics (MC/MD) simulations of the D178N mutant of the human prion protein. We have used the MC moves for polypeptide sampling known as Concerted Rotations with Angles (CRA) to selectively sample the region of the prion protein comprising the β-sheet and one of the α-helices. The results indicate that the MC/MD simulations sample the phase space substantially faster than regular Molecular Dynamics simulations starting with the same initial conditions. This work further indicates the MC/MD technique as a potentially powerful simulation tool, allowing the selective sampling of a region of a physical system that is deemed important.
authors.affiliation: Instituto de Quimica, Universidade Federal do Rio de Janeiro sala 609, bloco A, Centro de Tecnologia, Cidade Universitaria, Ilha do Fundao, Rio de Janeiro, RJ 21941-909, Brazil. aastr@iq.ufrj.br
authors.forename: Andre A S T
authors.initials: AA
authors.lastname: Ribeiro
authors.forename: Ricardo B
authors.initials: RB
authors.lastname: de Alencastro
mesh_terms: D006801:Humans; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D050505:Mutant Proteins / Q000737:chemistry; D000072002:Prion Proteins; D011328:Prions / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D050505:Mutant Proteins; C512656:PRNP protein, human; D000072002:Prion Proteins; D011328:Prions