scholarly journals Self-Assembling Cyclic Peptides:  Molecular Dynamics Studies of Dimers in Polar and Nonpolar Solvents†

2006 ◽  
Vol 110 (38) ◽  
pp. 18965-18972 ◽  
Author(s):  
Ekta Khurana ◽  
Steven O. Nielsen ◽  
Bernd Ensing ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Cyclic Peptides ◽  
Nonpolar Solvents ◽  
Self Assembling

scholarly journals Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations

2021 ◽  
Vol 121 (4) ◽  
pp. 2292-2324
Author(s):  
Jovan Damjanovic ◽  
Jiayuan Miao ◽  
He Huang ◽  
Yu-Shan Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Cyclic Peptides ◽  
Solution Structures ◽  
Dynamics Simulations

Molecular Pom Poms from Self-Assembling α,γ-Cyclic Peptides

2014 ◽  
Vol 20 (33) ◽  
pp. 10260-10265 ◽  
Author(s):  
Michele Panciera ◽  
Manuel Amorín ◽  
Juan R. Granja
Keyword(s):  
Cyclic Peptides ◽  
Self Assembling

COMPUTER SIMULATIONS TO INVESTIGATE STABILITY AND STRUCTURAL PROPERTIES OF PEPTIDE AMPHIPHILE NANOFIBERS

2007 ◽  
Vol 06 (03) ◽  
pp. 621-630
Author(s):  
RUO-YU CHEN ◽  
LING-YING WU ◽  
JUN-MIN LIAO ◽  
CHENG-LUNG CHEN
Keyword(s):  
Molecular Dynamics ◽  
Disulfide Bonds ◽  
Md Simulation ◽  
Intermolecular Hydrogen Bond ◽  
Intermolecular Distance ◽  
Peptide Amphiphile ◽  
Hydrogen Bond Interactions ◽  
Self Assembling ◽  
Polar Groups ◽  
The Stability

Molecular mechanics (MM) method followed by molecular dynamics (MD) simulation was carried out to investigate the stability of an aggregate formed by self-assembling of peptide amphiphile (PA) molecules. The MM + MD simulation confirms that the cylindrical shaped aggregate is very stable. The analysis showed that the remarkable stability of the aggregate was partly due to various intermolecular hydrogen-bond interactions between polar groups of PA molecules. The hydrophobic alkyl tails of PA molecules are packed loosely inside the interior of the aggregates. The packing of alkyl tails contribute further stability of the PA aggregate. Our simulations reproduce qualitatively experimental observations and support the fact that PA molecules are self-assembled within closed intermolecular distance to favor the forming of disulfide bonds.

scholarly journals Stability and growth mechanism of self-assembling putative antifreeze cyclic peptides

2017 ◽  
Vol 19 (29) ◽  
pp. 19032-19042 ◽  
Author(s):  
Z. Faidon Brotzakis ◽  
Mascha Gehre ◽  
Ilja K. Voets ◽  
Peter G. Bolhuis
Keyword(s):  
Growth Mechanism ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Growth Mechanisms ◽  
Self Assembling ◽  
Peptide Nanotube ◽  
Cyclic Peptide Nanotube

From right to left: three distinct growth mechanisms of a pentamer to a hexamer putative antifreeze cyclic peptide nanotube.

scholarly journals Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations

2021 ◽  
Vol 17 (3) ◽  
pp. e1008771
Author(s):  
Min Wu ◽  
Lyudmyla Dorosh ◽  
Gerold Schmitt-Ulms ◽  
Holger Wille ◽  
Maria Stepanova
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Cyclic Peptides ◽  
Molecular Mechanisms ◽  
Surface Effect ◽  
Early Stage ◽  
Aβ Peptides ◽  
Hydrophobic Residues ◽  
Dynamics Simulations

Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14’s presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42–SST14, Aβ42–AVP, and Aβ40–SST14. The Aβ42–SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) the propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42–SST14 system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ42–SST14 oligomerization.

Sign in / Sign up

Export Citation Format

Share Document