Conformational preferences of the full chicken prion protein in solution and its differences with respect to mammals.
We investigate the conformations of the full chicken prion protein (ChPrP1-267) in solution at neutral pH with molecular dynamics simulations. We focus on the persistence of its secondary structure motifs using a recently proposed protein chirality indicator [A. Pietropaolo et al., Proteins 2008, 70, 667-677]. From this, we find a high rigidity of helix 2 (ChPrP178-195) and of the hexarepeat domain, which is turn rich, and a plasticity of the short beta-sheet, consistent with the available NMR structural details. We also determine the extent of solvation for each residue, revealing local minima for such structured regions. These features hint at a possible origin of the high resistance to proteolysis of the avian prion proteins and of its capability in preventing the aggregation in comparison to mammals.
Pietropaolo
Adriana
A
Dipartimento di Chimica Fisica ed Inorganica and INSTM, Università di Bologna, V.le Risorgimento, 4, I-40136 Bologna, Italy.
Muccioli
Luca
L
Zannoni
Claudio
C
Rizzarelli
Enrico
E
D000595:Amino Acid Sequence; D000818:Animals; D030161:Avian Proteins / Q000737:chemistry*; D002645:Chickens; D003198:Computer Simulation; D008969:Molecular Sequence Data; D011328:Prions / Q000737:chemistry*; D011487:Protein Conformation; D016415:Sequence Alignment; D012996:Solutions; D014867:Water / Q000737:chemistry
D030161:Avian Proteins; D011328:Prions; D012996:Solutions; D014867:Water