Chapter title |
Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptide–Lipid Bilayer Interactions
|
---|---|
Chapter number | 8 |
Book title |
Antimicrobial Peptides
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-6737-7_8 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6735-3, 978-1-4939-6737-7
|
Authors |
Shima Arasteh, Mojtaba Bagheri, Arasteh, Shima, Bagheri, Mojtaba |
Abstract |
A great deal of research has been undertaken in order to discover antimicrobial peptides (AMPs) with unexploited mechanisms of action to counteract the health-threatening issues associated with bacterial resistance. The intrinsic effectiveness of AMPs is strongly influenced by their initial interactions with the bacterial cell membrane. Understanding these interactions in the atomistic details is important for the design of the less prone bacteria-resistant peptides. However, these studies always require labor-intensive and difficult steps. With this regard, modeling studies of the AMPs binding to simple lipid membrane systems, e.g., lipid bilayers, is of great advantage. In this chapter, we present an applicable step-by-step protocol to run the molecular dynamics (MD) simulation of the interaction between cyclo-RRWFWR (c-WFW) (a small cyclic AMP) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer using the Groningen machine for chemical simulations (GROMACS) package. The protocol as described here may simply be optimized for other peptide-lipid systems of interest. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 35 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 6 | 17% |
Student > Bachelor | 4 | 11% |
Researcher | 4 | 11% |
Other | 3 | 9% |
Professor > Associate Professor | 3 | 9% |
Other | 3 | 9% |
Unknown | 12 | 34% |
Readers by discipline | Count | As % |
---|---|---|
Chemistry | 7 | 20% |
Biochemistry, Genetics and Molecular Biology | 4 | 11% |
Agricultural and Biological Sciences | 2 | 6% |
Engineering | 2 | 6% |
Materials Science | 2 | 6% |
Other | 6 | 17% |
Unknown | 12 | 34% |