Understanding the Role of Solvent Polarity and Amino Acid Composition of Cyclic Peptides in Nanotube Stability DOI
Rimjhim Moral, Sandip Paul

The Journal of Physical Chemistry B, Journal Year: 2025, Volume and Issue: unknown

Published: March 27, 2025

Cyclic peptides (CPs) possess the ability to self-assemble into cyclic peptide nanotubes (CPNTs), which find extensive applications in nanotechnology. The formation and stability of these are influenced by multiple factors. present study explores CPNTs various solvents with varying polarity, focusing on three specific sequences: DK4, WL4, DLKL2. Using molecular dynamics simulations, effect solvent polarity composition is assessed through determination electrostatic, van der Waals, hydrogen-bonding interactions. binding free energy between adjacent rings analyzed via MM/GBSA MM/PBSA methods, revealing that DLKL2, an amphiphilic peptide, exhibits greater than DK4 WL4 nonpolar solvents. introduction leucine residues DLKL2 reduces intramolecular hydrogen bonding electrostatic interactions, promoting stronger interpeptide backbone bonds maintaining nanotube's structural integrity. Hydrogen bond lifetimes, computed using corresponding time correlation function, indicate longest-lasting occur all environments except water, further contributing nanotubes. Additionally, deformation from circularity rings, ellipticity values, highlights degree distortion across solvents, showing highest deviation due These findings offer valuable insights roles self-assembly CPNTs, have significant implications for their potential nanotechnology biomedicine.

Language: Английский

Origins of the Superiority of Oscillating Electric Fields for Disrupting Senile Plaques: Insights from the 7-Residue Fragment and the Full-length Aβ-42 Peptide DOI Creative Commons
Surajit Kalita, David Danovich, Sason Shaik

et al.

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Our recent molecular dynamics simulations of decomposing Alzheimer's disease plaques, under oscillating- and static external electric fields (Os-EEFs St-EEFs), revealed the superiority Os-EEF for plaques consisting 7-residue peptide segment. This conclusion is now reinforced by studying dimers short peptides trimers full-length Aβ-42 peptide. Thus, dispersed obtained following St-EEF applications reformed once subsided. In contrast, originating from application remained long time scales. The present study provides insights into these results modeling decomposition modes that transpire both field types. Additionally, this frequency effects on processes within THz–MHz regions. simulation shows in lower range (≤GHz) decomposes plaque a scale ∼50 ns, whereas higher Os-EEFs (≥THz) are less effective. As such, with moderate-to-low frequencies lead to an "explosion," whereby fly distantly apart inhibit reformation. By St-EEFs form parallel pairs, which stabilized EEF due large dipole moment ensemble. sluggish reversible processes. We further conclude impact maximal pulses, prevents propensity arrange pairs. over maintained irrespective peptides' length. A model formulated predicts dependence EEF.

Language: Английский

Citations

0
Understanding the Role of Solvent Polarity and Amino Acid Composition of Cyclic Peptides in Nanotube Stability DOI
Rimjhim Moral, Sandip Paul

The Journal of Physical Chemistry B, Journal Year: 2025, Volume and Issue: unknown

Published: March 27, 2025

Cyclic peptides (CPs) possess the ability to self-assemble into cyclic peptide nanotubes (CPNTs), which find extensive applications in nanotechnology. The formation and stability of these are influenced by multiple factors. present study explores CPNTs various solvents with varying polarity, focusing on three specific sequences: DK4, WL4, DLKL2. Using molecular dynamics simulations, effect solvent polarity composition is assessed through determination electrostatic, van der Waals, hydrogen-bonding interactions. binding free energy between adjacent rings analyzed via MM/GBSA MM/PBSA methods, revealing that DLKL2, an amphiphilic peptide, exhibits greater than DK4 WL4 nonpolar solvents. introduction leucine residues DLKL2 reduces intramolecular hydrogen bonding electrostatic interactions, promoting stronger interpeptide backbone bonds maintaining nanotube's structural integrity. Hydrogen bond lifetimes, computed using corresponding time correlation function, indicate longest-lasting occur all environments except water, further contributing nanotubes. Additionally, deformation from circularity rings, ellipticity values, highlights degree distortion across solvents, showing highest deviation due These findings offer valuable insights roles self-assembly CPNTs, have significant implications for their potential nanotechnology biomedicine.

Language: Английский

Citations

0