APD: the Antimicrobial Peptide Database

Received August 11, 2003; Revised August 20, 2003; Accepted September 3, 2003

      Antimicrobial peptides have been identified in various species ranging from bacteria, frogs to mammals, including humans. They form the first line of host defense against pathogenic infections and are a key component of the ancient innate immune system. Most antimicrobial peptides possess 6–50 amino acid residues with net positive charges (1–3). It is generally accepted that these cationic peptides selectively interact with anionic bacterial membranes (4,5) although different mechanisms may be used by different peptides under different conditions for killing (6). Currently, there is great interest in antimicrobial peptides because these so‐called ‘nature’s antibiotics’ are promising to overcome the growing problems of antibiotic resistance (1–3).

      Until now, more than 500 antimicrobial peptides have been reported (1,2). Although some structural and sequence information of these peptides can be retrieved from PDB (7) and Swiss‐Prot (8), the majority of the other antimicrobial data are scattered in the literature. This is not convenient for a more comprehensive structural and functional study of these peptides. For this reason, we have created a database to store and analyze these interesting peptides.

DATABASE CONSTRUCTION
      APD was built on the Red Hat Linux operating system using the freeware Apache web server, PHP script language and MySQL relational database system. Antimicrobial peptides were collected from the literature by PubMed search using keywords such as ‘antimicrobial peptide’, ‘antibacterial peptide’, ‘antifungal peptide’, ‘anticancer peptide’ or ‘antitumor peptide’. The peptides collected in this version of APD are mainly from natural sources. For the purpose of database bookkeeping, a unique five‐digit identification number (ID) starting with AP was assigned to each peptide. Each entry was checked in PDB or Swiss‐Prot. If the peptide exists in the established databases, a web link was created in APD for that entry to facilitate consultation of the original databases. In addition, each entry also contains peptide name, sequence, length, hydrophobic percentage, net charge, structure (such as α‐helix or β‐strand), physical method for structural determination (e.g. NMR spectroscopy or X‐ray diffraction), biological activity (antibacterial, antiviral, antifungal or antitumor), critical residue for activity, and reference (including authors, article title, journal, page, volume and year).

DATABASE DESCRIPTION

      The database main page contains the following interfaces: About (introduction to APD), Database (the query interface), Prediction, Peptide design, Statistical data, Useful links and Contact information. There are also links for antibacterial peptides, antiviral peptides, antifungal peptides and anticancer peptides. Each link contains a list of the peptides with a specific function.

APD CURRENT HOLDINGS AND FINDINGS

      The current version of APD holds 525 antimicrobial peptides. Among them, 498 have an effect on bacteria, 155 on fungi, 28 on viruses and 18 on cancer cells. Note that a specific peptide may have different functions. Thus, it can be counted twice or more. Based on the structure and sequence features, these peptides have been classified into six groups in APD. Table 1 lists the number of the peptides in each group. Clearly, the most abundant peptides are those with disulfide bonds or those without known structures. Indeed, only 54 antimicrobial peptides were found to have known 3D structures deposited in the PDB. In our database, however, we collected 68 peptides that were studied by NMR spectroscopy in membrane‐mimetic environments or lipid bilayers, whereas only a few crystal structures were found, indicating that NMR is the major player in this game.

      In APD, 97％ of the peptides contain 50 residues or less with an average length of 28. The longest peptide (AP00404) collected has 84 residues and the shortest one (AP00027) merely six residues. The majority of peptides (96％) in the database have a net positive charge with the highest being +17 (AP00010). As a result, the average net charge of all peptides in APD is +4.6. (Note that the effect of chemical modification and pH on the peptide charge has not been programmed in this version.) Some antimicrobial peptides, however, have a net negative charge. The most negatively charged peptide contains a string of Asp residues with a net charge of –6 (AP00528). It requires zinc as a cofactor for activity (13). Another negatively charged peptide in APD is maximum H5, which does not require a cofactor (14). It contains both hydrophobic and three Asp residues but no cationic residues. This anionic antimicrobial peptide is promising to kill the human β‐defensin‐resistant Gram‐positive bacteriumStaphylococcus aureus, which escapes attacks from cationic peptides probably by incorporating positive charges on the membrane surface by adding Lys to lipids (15). In light of the ancient Chinese ying‐yang philosophy, the anionic antimicrobial peptides, although rarely documented (13,14), appear to complement the cationic antimicrobial peptides, offering us a complete spectrum of antimicrobial peptides.

      The average contents of hydrophobic residues in different functional groups of the peptides are similar, ranging from 41％ to 49％ (Table 2, italicized). Although the populations of antiviral and antitumor peptides are relatively small in the database, it is interesting to note that antiviral peptides have the highest Cys content (16.0 versus average 6.6), causing 78％ of the peptides in this class to have one or more disulfide bonds. Also, they have a lower ratio of Lys (2.2 versus average 10.6) but a higher ratio of Arg (16.0 versus average 7.3). In strong contrast, anticancer peptides have a lower Cys ratio but a relatively high content of Lys. Of note, antimicrobial peptides that showed a toxic effect on mammalian cells have slightly higher contents of Ile, Leu and Ala in the sequence, leading to the highest hydrophobic content (Table 2). These findings may be useful in improving natural peptide templates or designing novel peptides with minimal side effects on humans. 

AVAILABILITY

APD is created, maintained and updated by the NMR Structural Biology Group at Eppley Institute, the University of Nebraska Medical Center. It can be accessed via the Internet at the URL:http://aps.unmc.edu/AP/main.html. Researchers in this field are invited to use the database, make suggestions and submit their peptides by contacting the authors. The database will be expanded and improved in our next release.