title: Peptide sequence and amyloid formation; molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs.
abstract: We present a combined experimental and theoretical investigation of the tendencies to form amyloid fibrils by a hexapeptide derivative of the human islet amyloid polypeptide, the NFGAIL (22-27) fragment and its mutants. We performed a complete alanine scan of this fragment and studied the capability of the wild-type and its mutant analogs to form ordered fibrils by ultrastructural and biophysical analyses. In parallel, we conducted a meticulous characterization of each sequence-complex at an atomistic level by performing nine independent molecular dynamics simulations for a total of 36 ns. These allowed us to rationalize the experimental observations and to establish the role of every residue in the fibrillogenesis. The main factor that determines the formation of regular fibrils is a coherent organization of the intersheet space. In particular, phenylalanine side chains cement the macromolecular assemblies due to their aromatic chemical character and restricted conformational flexibility when interacting with aliphatic residues.
authors.affiliation: Laboratory of Experimental and Computational Biology, NCI-Frederick, Building 469, Room 151, Frederick, MD 21702, USA.
authors.forename: David
authors.initials: D
authors.lastname: Zanuy
authors.forename: Yair
authors.initials: Y
authors.lastname: Porat
authors.forename: Ehud
authors.initials: E
authors.lastname: Gazit
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D000409:Alanine; D000682:Amyloid / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D003198:Computer Simulation; D003224:Congo Red; D006801:Humans; D006860:Hydrogen Bonding; D058228:Islet Amyloid Polypeptide; D008958:Models, Molecular; D009154:Mutation; D009842:Oligopeptides / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D011487:Protein Conformation
chemical_list: D000682:Amyloid; D058228:Islet Amyloid Polypeptide; D009842:Oligopeptides; C478380:amylin (22-27); D003224:Congo Red; D000409:Alanine