3D Structure of Antimicrobial Peptides

1. Structure annotation in the APD

The information on the three-dimensional (3D) structure of antimicrobial peptides was annotated in this database from the first version of the APD (Wang & Wang, 2004) based on the Pub-Med with a link to the Protein Data Bank (PDB). It includes unique structures of PDB-deposited and non-deposited AMPs free in water or in complex with its targets, usually membranes. The annotated information ranges from methods for structural determination, structural class and structural regions and critical residues to the type of membrane-mimetic environments, such as micelles and organic solvents. The structure can be viewed via the link to the Protein Data Bank (PDB) for each peptide entry when the coordinates are deposited. When there are multiple structures, the link is usually given to the structure with the highest resolution. Other structures solved for the same peptide under different conditions can be viewed via the PDB links. To study the structure in detail, you can download the coordinates and view the structure in your computer.

2. Structural determination of antimicrobial peptides

Both X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy can determine the structure of antimicrobial peptides to atomic resolution. According to the statistics of the APD database, most of the 3D structures of AMPs were determined by 2D solution NMR spectroscopy (Wuthrich K, 1986). For small peptides, this method is usually sufficient. It is also helpful to extend the observation to natural abundance heteronuclei 15N and 13C NMR spectroscopy, especially for amino acid rich short peptides. This improved 2D NMR method can be essential to avoid misleading structure or dynamics for some peptides (Reviewed by Wang, 2013). These heteronuclear 13C and 15N NMR chemical shifts are then used to validate proton assignments and refine the 3D structure of AMPs. For more complex molecules, 3D NMR methods are needed by using isotope-labeled peptides. For example, see the structure determination of human LL-37.

For large complexes, X-ray crystallography is preferred (e.g. ribosomes). Such structures can be viewed via the APD links.

Finally, other biophysical techniques are frequently utilized to shine light on the structure of AMPs, although at a low resolution. Since circular dichroism (CD) provides strong evidence for helix formation of short linear peptides, the APD also annotated such information into the database. Note that CD does not tell you where the helix starts or ends. Such annotations will be replaced when high resolution structures become available.

3. AI prediction of 3D structure of antimicrobial peptides

It is getting popular now to predict 3D structures of AMPs by Alphafold. The predicted structure can be regarded as a model since AI does not tell you under what conditions the structure is predicted. It is important to note that the structure of linear AMPs could depend on the environmental conditions (e.g., organic solvents, SDS, DPC and D8PG micelles).

4. Structural classification of antimicrobial peptides

3D structures of host defense antimicrobial peptides are classified into four families (Wang, 2017): alpha (α), beta (β), alphabeta (αβ), and non-alphabeta (non-αβ) based on the types of secondary structures. The α family consists of AMPs with helical structures (e.g. magainins and LL-37). The β family is composed of AMPs with beta-strands (e.g. human α-defensins). While the αβ family comprises both α-helices and β-strands in the 3D structure (e.g. β-defensins), the non-αβ family contains neither α-helical nor β-strands (e.g. indolicidin). These four families of AMP structures are represented in the main page of this database. Additional examples are provided below to illustrate diversity in structural scaffolds.

5. Structural viewing of antimicrobial peptides

You can rotate and view the 3D structure of each antimicrobial peptide in the APD via the PDB link if the coordinates are deposited in the PDB. For example, you can view the LL-37 structure here.

6. Structural statistics of antimicrobial peptides

A list of antimicrobial peptdes with a defined 3D structure can be obtained by searching the APD database. The statistics of a variety of structures is also provided in this database. Go to the Statistic Interface.

7. Structural citation

It takes a lot effort and time to solve a structure of antimicrobial peptide/protein. In the case of human LL-37, we had to obtain isotope-labeled peptides first for 3D NMR studies. As a consequence, we suggest the citation of the original article that reports the 3D structure (for examples, see below). The reference can be obtained from the same PDB link. It is also proper for you to cite the APD and PDB if you obtain multiple entries from these resources. The sufficient citations may include both the database IDs and references that generate the structures.

8. Structural diversity of antimicrobial peptides

Here are the PDB IDs and references for the structures above:

(A) Micelle-bound

from Australian Bell frogs (PDB ID 1VM5; Pub-Med Wang et al., 2005);

(B) Fish

(PDB ID 1XC0; Pub-Med Raimondo et al., 2005);

(C) Micelle-bound human cathelicidin

(PDB ID 2K6O; Pub-Med Wang G, 2008);

(D) Amphibian

(PDB ID 1XKM; Pub-Med Raimondo et al., 2005);

(E) Caenorhabditis elegans

(PDB ID 2JS9; Pub-Med Mysliwy et al., 2010);

(F) Micelle-bound

(PDB ID 1LFC; Pub-Med Hwang et al., 1998);

(G) Human alpha defensin 1

(PDB ID 3GNY; Pub-Med Wei et al., 2009);

(H) Human beta defensin 1

(PDB ID 1E4S; Pub-Med Bauer et al., 2001);

(I) Bacterial lasso peptide (PDB ID 3NJW ; Pub-Med Nar et al., 2010);

(J) Plant cyclotide

(PDB ID 1KAL; Pub-Med Saether et al., 1995);

(K) Rhesus theta defensin 1

(PDB ID 2LYF; Pub-Med Conibear et al., 2012);

(L) Bovine cathelicidin

(PDB ID 1G89; Pub-Med Rozek et al., 2000).


Wang, G.* (2017) In "Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies" (verions 2), CABI, 2017.
Wang, G.* (2013) Database-guided discovery of potent peptides to combat HIV-1 or superbugs. Pharmaceuticals 6, 728-758. View the colored figure in the review article.

Last updated: Jan 2024 | Copyright 2003-2024 Dept of Pathology, Microbiology and Immunology, UNMC All Rights Reserved