Primary Citation PubMed: 12051853
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A helical structural nucleus is the primary elongating unit of insulin amyloid fibrils.
(2007) PLoS Biol 5
PubMed: 17472440 | PubMedCentral: PMC1858711 | DOI: 10.1371/journal.pbio.0050134
The calculated scattering from a monomer of insulin (partially unfolded monomers at acidic pH, pdb-file 1GUJ) and the low-pass–filtered experimental scattering from the coherent unit of the fi... ril after 9-h incubation were employed.
Publication Year: 2007
Oligomerization of Peptides LVEALYL and RGFFYT and Their Binding Affinity to Insulin.
(2013) PLoS One 8
PubMed: 23805182 | PubMedCentral: PMC3689759 | DOI: 10.1371/journal.pone.0065358
Materials and Methods Crystal structures of insulin and peptide LVEALYL The crystal structure of full-length human insulin used in our simulations was taken from Protein Data Bank (PDB) with PDB ID 1G... J.
Docking result Using the Autodock Vina we dock LVEALYL to the PDB structure 1GUJ.
The PDB structure 1GUJ obtained at pH = 2.1 (blue), while red color refers to the most populated cluster structure.
Using the PDB structure (PDB ID: 1GUJ) obtained at pH = 2.1 as a initial conformation 300 ns MD simulation has been carried out at pH = 7 and = 300 K.
One can show that rmsd between this structure and PDB structure obtained at pH = 2.1 (PDB ID: 1GUJ) is 0.28 nm.
Moreover, rmsd between 1GUJ and 3I3Z is about 0.32 nm implying the weak dependence of insulin structure on pH. Thus we will use PDB structure 1GUJ for further docking and MD simulations at pH = 7.0.
Publication Year: 2013
PubMed ID is not available.
Published in 2014
The starting structures of +4 hIAPP include a β-sheet rich extended conformation and a helix-rich compact conformation, identified in our previous computational study 33 as well as in works by... Reddy et al. 43 and Qiao et al. 44 A starting structure for the IBC was obtained from a long MD simulation ( Figure S7 (SI) ) initiated from the conformation extracted from the X-ray solved crystal structure of insulin (PDB id: 1GUJ).
The binding between the two hIAPP conformers and the larger insulin monomer (PDB id: 1GUJ) was also modeled by MD simulations.
Publication Year: 2014
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