Molecular Dynamics Simulations of the Helical Antimicrobial Peptide Ovispirin-1 in a Zwitterionic Dodecylphosphocholine Micelle:  Insights into Host-Cell Toxicity

2005 ◽  
Vol 109 (26) ◽  
pp. 12990-12996 ◽  
Author(s):  
Himanshu Khandelia ◽  
Yiannis N. Kaznessis
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Host Cell ◽  
Cell Toxicity ◽  
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 Elucidating Interactions Between SARS-CoV-2 Trimeric Spike Protein and ACE2 Using Homology Modeling and Molecular Dynamics Simulations

2021 ◽  
Vol 8 ◽  
Author(s):  
Sugunadevi Sakkiah ◽  
Wenjing Guo ◽  
Bohu Pan ◽  
Zuowei Ji ◽  
Gokhan Yavas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Molecular Dynamics Simulations ◽  
Host Cell ◽  
Tertiary Structure ◽  
Cell Receptor ◽  
Host Cells ◽  
Spike Protein ◽  
Receptor Protein ◽  
Dynamics Simulations

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). As of October 21, 2020, more than 41.4 million confirmed cases and 1.1 million deaths have been reported. Thus, it is immensely important to develop drugs and vaccines to combat COVID-19. The spike protein present on the outer surface of the virion plays a major role in viral infection by binding to receptor proteins present on the outer membrane of host cells, triggering membrane fusion and internalization, which enables release of viral ssRNA into the host cell. Understanding the interactions between the SARS-CoV-2 trimeric spike protein and its host cell receptor protein, angiotensin converting enzyme 2 (ACE2), is important for developing drugs and vaccines to prevent and treat COVID-19. Several crystal structures of partial and mutant SARS-CoV-2 spike proteins have been reported; however, an atomistic structure of the wild-type SARS-CoV-2 trimeric spike protein complexed with ACE2 is not yet available. Therefore, in our study, homology modeling was used to build the trimeric form of the spike protein complexed with human ACE2, followed by all-atom molecular dynamics simulations to elucidate interactions at the interface between the spike protein and ACE2. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) and in silico alanine scanning were employed to characterize the interacting residues at the interface. Twenty interacting residues in the spike protein were identified that are likely to be responsible for tightly binding to ACE2, of which five residues (Val445, Thr478, Gly485, Phe490, and Ser494) were not reported in the crystal structure of the truncated spike protein receptor binding domain (RBD) complexed with ACE2. These data indicate that the interactions between ACE2 and the tertiary structure of the full-length spike protein trimer are different from those between ACE2 and the truncated monomer of the spike protein RBD. These findings could facilitate the development of drugs and vaccines to prevent SARS-CoV-2 infection and combat COVID-19.

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.

scholarly journals Molecular dynamics simulations of a new branched antimicrobial peptide: A comparison of force fields

2012 ◽  
Vol 137 (21) ◽  
pp. 215101 ◽  
Author(s):  
Jianguo Li ◽  
Rajamani Lakshminarayanan ◽  
Yang Bai ◽  
Shouping Liu ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers

2018 ◽  
Vol 19 (4) ◽  
pp. 1186 ◽  
Author(s):  
Liling Zhao ◽  
Zanxia Cao ◽  
Yunqiang Bian ◽  
Guodong Hu ◽  
Jihua Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptide ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Dynamics Simulations
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