title: Binding of fullerenes to amyloid beta fibrils: size matters.
abstract: Binding affinity of fullerenes C20, C36, C60, C70 and C84 for amyloid beta fibrils is studied by docking and all-atom molecular dynamics simulations with the Amber force field and water model TIP3P. Using the molecular mechanic-Poisson Boltzmann surface area method one can demonstrate that the binding free energy linearly decreases with the number of carbon atoms of fullerene, i.e. the larger is the fullerene size, the higher is the binding affinity. Overall, fullerenes bind to Aβ9-40 fibrils stronger than to Aβ17-42. The number of water molecules trapped in the interior of 12Aβ9-40 fibrils was found to be lower than inside pentamer 5Aβ17-42. C60 destroys Aβ17-42 fibril structure to a greater extent compared to other fullerenes. Our study revealed that the van der Waals interaction dominates over the electrostatic interaction and non-polar residues of amyloid beta peptides play the significant role in interaction with fullerenes providing novel insight into the development of drug candidates against Alzheimer's disease.
authors.affiliation: Insitute of Computational Science and Technology, Quang Trung Software Center, Ho Chi Minh City, Vietnam.
authors.forename: Pham Dinh Quoc
authors.initials: PD
authors.lastname: Huy
authors.forename: Mai Suan
authors.initials: MS
authors.lastname: Li
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry* / Q000378:metabolism; D037741:Fullerenes / Q000737:chemistry* / Q000378:metabolism; D062105:Molecular Docking Simulation; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D016229:Amyloid beta-Peptides; D037741:Fullerenes; D010446:Peptide Fragments; D014867:Water; C086839:amyloid beta-protein (17-42)