Antimicrobial Peptides: Nature’s Defense Against Bacteria


AMP by polarityfSummary

Antimicrobial peptides (AMPs) are short protein segments produced by different organisms as a defense mechanism against biological pathogens (bacteria, viruses, parasites). AMPs act in various ways to destroy invading pathogens, one of which is to insert themselves into the pathogen’s cellular membrane and compromise its structural integrity. This quickly leads to the death of the foreign cell. Being short, AMPs usually have simple structure, like a spring or a loop. However, the specific distribution of amino acids of different types (hydrophobic, electrically charged, etc) over this structure confers AMPs unique physical characteristics, allowing them to attack bacteria but not human cells.

Since the molecular target of many AMPs is the lipid membrane rather than a protein, pathogens find it very difficult to acquire resistance to AMPs, as they normally do in the case of regular antibiotics (i.e., by undergoing genetic changes). This makes AMPs very attractive as potential therapeutics against antibiotics-resistant bacteria. Indeed, both the FDA and major pharmaceutical companies are showing interest in AMPs as antibiotics, as discussed in this Nature Biotechnology report.


What Are Peptides?

Peptides are protein fragments containing between 3 and 50 amino acids. Being short, peptides usually possess a simple structure, such as a helix (spring-like) or  beta-stand (extended stretch). Many peptides are naturally produced by organisms ranging from bacteria to humans and play diverse roles. For example, oxytocin and vasopressin act as hormones, and have dramatic physiological effects on the bodies of mammals. The structural simplicity of peptides also makes them an attractive model for proteins (e.g. 1, 2, 3).

The atomic structure of vassopresin (URL)


Antimicrobial Peptides (AMP)

1. Overview

AMP are natural substances produced by many organisms to fight bacterial infection. These peptides may kill bacteria in two main ways:


1.Disrupting the bacterial plasma membrane:

Electron micrographs of negatively stained E. coli untreated (left) and treated (right) with AMP LL-37


d2. Disrupting biochemical processes inside the bacterium:


2. Mechanisms of membrane disruption by AMP

AMP may disrupt the membrane of their target cell in two ways:

  1. By inserting into the membrane and undergoing polymerization inside it to form pores/channels (left side of the figure below). This leads to depolarization of the membrane and to cell death. (watch this nice YouTube animation)
  2. By partially penetrating the membrane and compromising its structural integrity (right side of the figure below. Also, watch molecular dynamics simulation of Melittin). This too leads to cellular death.


A direct visualization of Alamethicin channels formed in a phospholipid matrix has recently become available using electrochemical scanning tunneling microscopy (EC-STM). The images show clearly hexagonal pores of the peptide, as suggested before by various biochemical and computational studies:

Alamethicin channelSource: Pieta et al. (2012) PNAS 109: 21223-8

In a different study, the crystal structure of the human dermcidin channel in membranes was described. The structure is composed of zinc-connected trimers of antiparallel helix pairs. Data collected from NMR spectroscopy, electrophysiology, and MD simulations elucidate the high ion conductance of this antimicrobial channel.


Source: Song et al. (2013) PNAS 110:4586–91 


3. Membrane disruption: structure-function relationship

Both mechanisms of membrane disruption mentioned above rely on the AMP’s physico-chemical properties (e.g. 1, 2):


For example, many AMP carry a positive charge, which allows them to bind preferentially to membranes carrying a negative electric charge on their external surface. This includes mainly bacterial membranes, but also those of mammalian cancer cells. As a result, AMP are selective against both bacteria and cancer cells over normal mammalian cells.

Moreover, many AMP are α-helical and amphipathic, which means they have hydrophilic (usually basic) residues on one side, and hydrophobic residues on the other:

(hydrophobic residues – green, basic residues – blue)

Thus, these AMP are positively charged only on one side:


For example, the following image compares the amphipathicity of the helical-cationic AMPs melittin, magainin, and cecropin P1. The amphipathicity is denoted by the hydrophobic moment (μ): 

Amphipathicity of melittin, magainin, and cecropin

(Source: Dathe & Wieprecht [1999] Biochimica et Biophysica Acta – Biomembranes. 1462: 71-87 )

For each peptide, the image shows the 3D structure, helical wheel projection with hydrophobic moment (μ), amino acid sequence, number of residues (N), charge (Q), and mean residue hydrophobicity (H). Hydrophobic residues are shown in white, polar residues in gray and cationic residues in black circles.

The amphipathic nature of AMP is crucial to their mechanism of membrane disruption; it allows them to insert partly or completely into the lipid bilayer component of the membrane, where their hydrophobic side interacts with the lipid core of the bilayer, and their hydrophilic side interacts with the polar heads of membrane lipids:

(adapted from BMC Biochemistry 2005, 6:30)

By modulating the electric charge, conformation, hydrophobicity and amphipathicity of antimicrobial peptides, scientists can optimize their activity against different target cells (e.g. see 1, 2, 3, 4)


4. Medical advantages

Since the affected component of the host’s membrane is the lipid bilayer rather than proteins, bacterial resistanceto AMPs is uncommon. This makes them excellent candidates to be the next antibiotics, or at least to be used along with the existing drugs. As mentioned above, many AMP also possess anti-cancer activity (e.g. 1). This further increases the therapeutic potential of AMP. Indeed, despite past setbacks in the use of AMPs as pharmaceutical drugs, both FDA and major pharmaceutical companies are now showing renewed interest, as discussed in this Nature Biotechnology report.


5. Further reading

> More about the structure-function relationship in AMP is explained in my book, co-written with Prof. Nir Ben-Tal @ Tel-Aviv University


> To learn more about AMP research, see:

> Recent review articles:


Online AMP Research Tools


MCPep simulation of the AMP magainin in the membrane, along the x-z plane. Residue type is designated in circles. Hydrophobic residues (A, F, G, I, L, V) are orange, charged residues (K, R, E, D) are blue, and polar residues are green. The horizontal dotted line marks the location of the phosphate groups of the lipid polar heads in each frame.

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