Paper Citing NAMD - Abstract
Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan
Exploring the inter-molecular interactions in amyloid-beta protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 145101, APR 14 2012
Aggregation of amyloid-beta (A beta) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between A beta protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in A beta(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the A beta(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the A beta(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of A beta as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between A beta monomers in A beta(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of A beta aggregation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3702195]
