scholarly journals Cation−π Interactions Stabilize the Structure of the Antimicrobial Peptide Indolicidin near Membranes:  Molecular Dynamics Simulations

2007 ◽  
Vol 111 (1) ◽  
pp. 242-250 ◽  
Author(s):  
Himanshu Khandelia ◽  
Yiannis N. Kaznessis
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Π Interactions ◽  
Dynamics Simulations

scholarly journals Interaction of the Antimicrobial Peptide Cyclo(RRWWRF) with Membranes by Molecular Dynamics Simulations

2005 ◽  
Vol 89 (4) ◽  
pp. 2296-2306 ◽  
Author(s):  
Christian Appelt ◽  
Frank Eisenmenger ◽  
Ronald Kühne ◽  
Peter Schmieder ◽  
J. Arvid Söderhäll
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations

2003 ◽  
Vol 370 (1) ◽  
pp. 233-243 ◽  
Author(s):  
Craig M. SHEPHERD ◽  
Hans J. VOGEL ◽  
D. Peter TIELEMAN
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Helical Conformation ◽  
Constraint Forces ◽  
Surface Binding ◽  
Lipid Interactions ◽  
Area Per Lipid ◽  
Dynamics Simulations

Molecular-dynamics simulations covering 30ns of both a natural and a synthetic antimicrobial peptide in the presence of a zwitterionic lipid bilayer were performed. In both simulations, copies of the peptides were placed in an α-helical conformation on either side of the bilayer about 10Å (1Å = 0.1nm) from the interface, with either the hydrophobic or the positively charged face of the helix directed toward the bilayer surface. The degree of peptide—lipid interaction was dependent on the starting configuration: surface binding and subsequent penetration of the bilayer was observed for the hydrophobically oriented peptides, while the charge-oriented peptides demonstrated at most partial surface binding. Aromatic residues near the N-termini of the peptides appear to play an important role in driving peptide—lipid interactions. A correlation between the extent of peptide—lipid interactions and helical stability was observed in the simulations. Insertion of the peptides into the bilayer caused a dramatic increase in the lateral area per lipid and decrease in the bilayer thickness, resulting in substantial disordering of the lipid chains. Results from the simulations are consistent with early stages of proposed mechanisms for the lytic activity of antimicrobial peptides. In addition to these ‘free’ simulations, 25ns simulations were carried out with the peptides constrained at three different distances relative to the bilayer interface. The constraint forces are in agreement with the extent of peptide—bilayer insertion observed in the free simulations.

scholarly journals Self-assembly of glycerol monooleate with the antimicrobial peptide LL-37: a molecular dynamics study

RSC Advances ◽  
2020 ◽  
Vol 10 (14) ◽  
pp. 8291-8302 ◽  
Author(s):  
R. Innocenti Malini ◽  
M. Zabara ◽  
M. Gontsarik ◽  
K. Maniura-Weber ◽  
R. M. Rossi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Dynamics Simulations ◽  
Glycerol Monooleate

Molecular dynamics simulations of glycerol-monooleate (GMO)/LL-37 nanocarriers show that hydrophobic interactions among the molecules drive the formation of GMO/LL-37 micelles.

Solvation of diclofenac in water from atomistic molecular dynamics simulations – interplay between solute–solute and solute–solvent interactions

2018 ◽  
Vol 20 (13) ◽  
pp. 8629-8639 ◽  
Author(s):  
Mariana Kozlowska ◽  
Pawel Rodziewicz ◽  
Tillmann Utesch ◽  
Maria Andrea Mroginski ◽  
Anna Kaczmarek-Kedziera
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Aqueous Solubility ◽  
Solvent Interactions ◽  
Π Interactions ◽  
Self Association ◽  
Dynamics Simulations

Self-association of diclofenac in water via π–π interactions and C–H⋯π hydrogen bonds as a reason for its low aqueous solubility.

Molecular Dynamics Simulations of Pentapeptides at Interfaces:  Salt Bridge and Cation−π Interactions†

Biochemistry ◽  
2003 ◽  
Vol 42 (30) ◽  
pp. 8976-8987 ◽  
Author(s):  
Marcela P. Aliste ◽  
Justin L. MacCallum ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Salt Bridge ◽  
Π Interactions ◽  
Dynamics Simulations
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