Arasteh Shima, Bagheri Mojtaba
Department of Chemistry, Center for Biophysics and Computational Biology, Institute for Computational Molecular Science, Temple University, Philadelphia, PA, USA.
Peptide Chemistry Laboratory, Institute of Biochemistry and Biophysics, University of Tehran, 16 Azar Street, 14176-14335, Tehran, Iran.
Methods Mol Biol. 2017;1548:103-118. doi: 10.1007/978-1-4939-6737-7_8.
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.
为了发现具有未被开发作用机制的抗菌肽（AMPs），以应对与细菌耐药性相关的威胁健康的问题，人们已经进行了大量研究。AMPs的内在有效性受到它们与细菌细胞膜初始相互作用的强烈影响。从原子层面详细了解这些相互作用对于设计不易产生耐药性的肽很重要。然而，这些研究总是需要耗费大量人力且步骤困难。在这方面，对AMPs与简单脂质膜系统（如脂质双层）结合的建模研究具有很大优势。在本章中，我们提出了一个适用的分步方案，使用格罗宁根化学模拟机（GROMACS）软件包对环-RRWFWR（c-WFW）（一种小的环化AMP）与1-棕榈酰-2-油酰-sn-甘油-3-磷酸胆碱（POPC）脂质双层之间的相互作用进行分子动力学（MD）模拟。这里描述的方案可以很容易地针对其他感兴趣的肽-脂质系统进行优化。
