Molecular Dynamics Simulation Studies of Organizations of Melittin and Its Variants in Lipid Bilayer


Student thesis: Doctoral Thesis

View graph of relations


Related Research Unit(s)


Awarding Institution
Award date12 Oct 2023


Due to the development of antimicrobial resistance, pathogenic microorganisms have brought increasing threats to public health. With the emergence of multidrug-resistant (MDR) Gram-negative “superbugs,” it is more urgent to develop the next generation of antibiotics to combat drug resistance. Antimicrobial peptides (AMPs) have been attracted researchers’ attention as promising potential antimicrobial agents for the treatment of bacterial and fungal infections because the target of AMPs is cell membrane whose structure is unlikely to be changed by genetic mutations. However, a clear view of the detailed antimicrobial mechanism of AMPs at molecular level has not been discovered. Because through traditional experimental approaches, it is difficult to observe such phenomenon at molecule-level. MD simulations have been extensively used to explore the interactions between AMPs and lipid bilayers, because it is practical in revealing biomolecular structures and dynamics on the length scales of nanometers and the time scales from nanoseconds to microseconds. Until now, MD simulation has been employed to study the interactions between AMPs and cell membrane for about 15 years.

In this thesis, we use multiscale MD simulation (from coarse-grained modelling to all-atom modelling) methods to study the interactions between AMPs and DPPC/POPG hybrid lipid bilayer. Two types of well-studied AMPs, melittin and melp5 are simulated and compared in order to get some new insights of how peptide sequence can affect antimicrobial activities. We investigate many aspects of peptide-bilayer interactions, such as what concentration of peptides can lead spontaneous penetration of lipid bilayer; the organizations of peptides in the lipid bilayer; water permeability; contact map of some key amino acids.

In Chapter 1, drug resistance and antimicrobial peptides have been reviewed. Then applications of MD simulation in the investigation of actions of AMPs in cell membrane are introduced. In Chapter 2, the multiscale MD simulations including coarse-grained and all-atom simulation techniques are briefly introduced, which are the main simulation methods in the thesis. Then, the principles and methodologies of some analysis techniques in this thesis are introduced.

In Chapter 3, we construct a series of simulation systems with different concentrations of melittin interacting with lipid bilayer and investigate the pore formation on lipid bilayer, the disturbance of the lipid bilayer caused by melittin. Generally, the higher concentration of AMP, the higher efficiency of antimicrobial activity, but also causing higher toxicity to human cells. The concentration of melittin on antimicrobial activity and toxicity to human cell is discussed in this chapter.

In Chapter 4, we use coarse-grained and all-atom molecular MD simulations to investigate the organizations of melittin peptides during and after spontaneous penetration into DPPC/POPG lipid bilayers. We find that the peptides in lipid bilayers adopt either a transmembrane conformation or a U-shaped conformation, which are referred to as T-peptide and U-peptide, respectively. Several U-peptides and/or T-peptides aggregate to form stable pores. Different types of organizations of melittin peptides are discussed, especially, T-pore which consists of 4 T-peptides and U-pore which consists of 3 U-peptides and 1 T-peptide.

In Chapter 5, we study the role of amino acids in antimicrobial activity. The organizations of melittin and MelP5 peptides in cell membranes are simulated and compared. We find that the peptides in lipid bilayers adopt either a transmembrane conformation or some peptide can aggregate to form oligomers in the lipid bilayer. We find many types of oligomers are formed, from dimer to heptamer. While both melittin and MelP5 can form pores in the lipid bilayer, they differ in many aspects. First, the pore formed by melittin tetramer is larger than that of MelP5 tetramer, because the C-terminal residues exist strong electrostatic repulsions. Second, MelP5 peptides can form higher oligomers, such as hexamer and heptamer, while melittin peptides cannot form higher oligomers. Third, there are more contacts between MelP5 peptides in the tetramer than that of melittin tetramer. All the oligomers formed in the CG simulations are confirmed by 200 ns all-atom MD simulations. In all oligomers, the peptides maintain high helicity in atomistic simulations. The water permeability of the pores induced by peptide oligomers are verified in atomistic simulation.

Chapter 6 includes brief conclusions of the thesis and an outlook for future work. The peptide organizations obtained in this thesis should deepen the understanding of the stability, poration mechanism, and permeability of AMPs.