Molecular dynamic simulations of nanomechanic chaperone peptide and effects of in silico His mutations on nanostructured function.
The nanoscale peptide YSGVCHTDLHAWHGDWPLPVK exhibits molecular chaperone activity and prevents protein aggregation under chemical and/or thermal stress. Here, His mutations of this peptide and their impact on chaperone activity were evaluated using theoretical techniques. Molecular dynamic (MD) simulations with simulated annealing (SA) of different mutant nanopeptides were employed to determine the contribution of the scaffolding His residues (H45, H49, H52), when mutated to Pro, on chaperone action in vitro. The in silico mutations of His residues to Pro (H45P, H49P, H52P) revealed loss of secondary ordered strand structure. However, a small part of the strand conformation was formed in the middle region of the native chaperone peptide. The His-to-Pro mutations resulted in decreased gyration radius (Rg) values and surface accessibility of the mutant peptides under the simulation times. The invariant dihedral angle (phi) values and the disrupting effects of the Pro residues indicated the coil conformation of mutant peptides. The failure of the chaperone-like action in the Pro mutant peptides was consistent with their decreased effective accessible surfaces. The high variation of Phi value for His residues in native chaperone peptide leads to high flexibility, such as a minichaperone acting as a nanomachine at the molecular level. Our findings demonstrate that the peptide strand conformation motif with high flexibility at nanoscale is critical for chaperone activity.
Barzegar
Abolfazl
A
Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Moosavi-Movahedi
Ali Akbar
AA
Mahnam
Karim
K
Bahrami
Homayoon
H
Sheibani
Nader
N
D000426:Alcohol Dehydrogenase / Q000737:chemistry; D003198:Computer Simulation; D005656:Fungal Proteins / Q000737:chemistry; D006639:Histidine / Q000737:chemistry; D018832:Molecular Chaperones / Q000737:chemistry; D008968:Molecular Conformation; D009154:Mutation; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011392:Proline / Q000737:chemistry; D017433:Protein Structure, Secondary; D012984:Software; D013997:Time Factors
D005656:Fungal Proteins; D018832:Molecular Chaperones; D010455:Peptides; D006639:Histidine; D011392:Proline; D000426:Alcohol Dehydrogenase