Globular state in the oligomers formed by Abeta peptides.
Replica exchange molecular dynamics and implicit solvent model are used to study two oligomeric species of Abeta peptides, dimer and tetramer, which are typically observed in in vitro experiments. Based on the analysis of free energy landscapes, density distributions, and chain flexibility, we propose that the oligomer formation is a continuous transition occurring without metastable states. The density distribution computations suggest that Abeta oligomer consists of two volume regions-the core with fairly flat density profile and the surface layer with rapidly decreasing density. The core is mostly formed by the N-terminal residues, whereas the C-terminal tends to occur in the surface layer. Lowering the temperature results in the redistribution of peptide atoms from the surface layer into the core. Using these findings, we argue that Abeta oligomer resembles polymer globule in poor solvent. Abeta dimers and tetramers are found to be structurally similar suggesting that the conformations of Abeta peptides do not depend on the order of small oligomers.
Kim
Seongwon
S
Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia 20110, USA.
Takeda
Takako
T
Klimov
Dmitri K
DK
D016229:Amyloid beta-Peptides / Q000737:chemistry* / Q000378:metabolism*; D019295:Computational Biology; D056004:Molecular Dynamics Simulation; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D013696:Temperature; D013816:Thermodynamics
D016229:Amyloid beta-Peptides; D012997:Solvents