Glossary

ABC transporter: ATP-binding cassette transporter, important in AMP sensing and/or detoxification.

Abu-S-Ala: methyl lanthionines (cf. Ala-S-Ala, lanthionines)

AD: Atopic Dermatitis or /Eczema (AE), a diseased condition where expression of AMPs such as hCAP-18/LL-37 is suppressed.

AFM: Atomic Force Microscopy

Alarmins: structurally distinct peptide mediators that can recruit and activate antigen-presenting cells (APCs), thereby enhancing immune response. See also DAMP.

Amino-acids : A, Ala, alanine; C, Cys, cysteine; D, Asp, asparate; E, Glu, glutamate; F, Phe, phenylallanine; G, Gly, glycine; H, His, histidine; I, Ile, isoleucine; K, Lys,lysine; L, Leu, leucine; M, Met, methionine; N, Asn, asparagine; P, Pro, proline; Q, Gln, glutamine; R, Arg, arginine; S, Ser, serine; T, Thr, threonine; V, Val, valine; W, Trp, tryptophan; and Y, Tyr, tyrosine.

AMPs : antimicrobial peptides

AKT: v-akt murine thymoma viral oncogene homolog 1

AP-1: Activated Protein-1, a transcription factor

APC: Antigen Presenting Cell

APD : The Antimicrobial Peptide Database

API: Active Pharmaceutical Ingredient

Archaeocins : Proteinaceous antimicrobials from the domain archaea

Bacteriocins: Proteinaceous antimicrobials from the domain bacteria. For Gram-positive bacteria, class I bacteriocins are lantibiotics whose polypeptide chains are subject to extensive chemical modifications after translation. Type A has an elongated structure while type B has a more rigid and globular structure. Class II bacteriocins possess unmodified polypeptide chains. This class is further divided into class IIa (the pediocin-like bacteriocins), class IIb (the two-peptide chain bacteriocins, class IIc (cyclic peptides), and class IId (the leaderless peptide bacteriocins). Classes III are large proteins with lytic activity (Cotter P et al., 2005 Nature Rev Microbiol 3: 777). Bacteriocins from Gram-negative bacteria are called microcins (Class I < 5 kDa; Class II, 5-10 kDa; and class III(colicins) > 10 kDa (Duquesne et al. 2007 Nat. Prod. Rep. 24: 708-734).

BB codes for peptide binding partners : BBB, peptide self association; BBII, metal ions; BBL, LPS; BBMm, membranes; BBN, nucleic acids; BBPP, protein/enzyme; BBS, sugars. AMPs with such activities can be searched in the name field of the search interface of the APD by entering the code.

BLP: Bacterial LipoProtein, TLR2/1 ligand (agonist). This BLP binding to TLR2/1 upregulates the expression of vitamin D receptor and the vitamin D-1-hydroxylase genes, leading to the induction of human cathelicidin LL-37 to kill Mycobacterium tuberculosis.

Boman Index : defined by this database in 2003 in memory of Hans Boman who called it protein-binding potential. Boman index is the sum of the free energies of the respective side chains for transfer from cyclohexane to water taken from Radzeka and Wolfenden and divided by the total number of the residues of an antimicrobial peptide. The calculated values are negative ( except for the hybrid peptide), but the + and - are reversed [Boman, H.G.(2003)J.Inter.Med.254:197-215].

CAPA: Corrective Action, Preventative Action (FDA)

Cathelicidin: a family of antimicrobial peptides that share the common N-terminal cathelin domain in their precursor proteins

CD: Circular Dichroism, especially good at estimating helix formation with the change in conditions.

CF: Cystic Fibrosis

CFU: Colony-Forming Unit

Colicins : see microcins.

ChIP: Chromatin ImmunoPrecipitation assays

CMC: Critical Micelle Concentration

Core peptide: in the lantipeptide case, it is referred to the C-terminal region of the precursor that becomes the final product after processing

CpG-ODN: CpG-OligoDeoxyNucleotides (DNA), unmethylated, TLR9 ligand

CQAs: Critical Qaulity Attributes such as viscosity, pH, density, or content uniformity

Crohn's disease: a chronic inflammatory bowel disease due to a defect in intestinal innate immune responses to bacteria

CT: Computed Tomography

CTD: Common Technical Document

Cyclotides: Plant circular peptides that have no exposed N- or C-terminal residues.

25D: 25-hydroxyvitamin D3, the major circulating form. Once converted to 1,25D, it can induce LL-37 expression in human cells.

1,25D: 1,25-dihydroxylvitamin D3, the active form of vitamin D that induces the expression of LL-37, hBD-2, and intracellular pattern recognition receptor called NOD2/CARD15 in humans.

DAMP: damage-associated molecular patterns. Examples are alarmins (defensins, cathelicidins, high-mobility group box-1 protein (HMGB1), and iron-binding proteins) and mitochondrial DNA of eukaryotic cells.

DCs: Dendritic Cells

Dha: 2,3-didehydroalanine, dehydrated serine (Ser), or occasionally Cys (Claesen and Bibb 2010 PNAS 107:16297)

Dhb: (Z)-2,3-didehydrobutyrine, dehydrated threonine (Thr)

DSC: Differential Scanning Calorimetry

eDNA: extracellullar DNA, i.e. genomic DNA released by bacteria, an important component required for the initial establishment of bacterial biofilm.

EST: Expressed Sequence Tag

EGFR: Epidermal Growth Factor Receptor

ER: Endoplasmic Reticulum

Eucaryocins : Proteinaceous antimicrobials from the domain eucarya

FADD: Fas (TNFRSF6)-associated via death domain

Firmicutes: the low-G+C-content gram-positive bacterial species, e.g. bacilli & clostridia.

FPRL1: Formyl Peptide Receptor-Like 1. Human Ll-37 chemoattracts human neutrophils, monocytes, T cells and multipotent mesenchymal stromal cells (stem cells) by binding to this cell surface receptor. This molecular process could be essential for cancer metastasis (see the minireview on the relationship between LL-37 and cancer, Wu W.K.K. et al. 2010 Int J cancer 127:1741-7).

FRET: Fluorescence Resonance Energy Transfer

FT-IR: Fourier Transform InfraRed spectroscopy

HIV-1: Human Immunodeficiency Virus type 1.

HSV-1: Herpes Simplex Virus type 1.

FXR: Farnesoid X Receptor

GCP: Good Clinical Practice (FDA)

GLP: Good Laboratory Practice (FDA)

Glycopeptides: glycolated peptides with antimicrobial activity (newly discovered from bacteria in 2011). These are regarded as examples for the class IV peptide (conjugated peptides) originally proposed by Klaenhammer (1993).

GMP: Good Manufacturing Practice (FDA)

GM-CSF: Granulocyte-Macrophage Colony Stimulating Factor

hBD: human Beta Defensin (28 genes in humans, most common are HBD-1, HBD-2, HBD-3, and HBD-4)

hCAP-18: human Cationic Antimicrobial Protein of 18 kDa (i.e., the precursor of human cathelicidins LL-37 and ALL-38, the mature antimicrobial peptides; originally thought FALL-39). The gene that encodes this protein is referred to as CAMP.

HDP: see "Host Defense Peptide"

HNP: Human Neutrophil Protein, HNP-1 to HNP-4 made in granulocytes, and human defensins 5 and 6 (HD-5 and HD-6) made in Paneth cells.

HNSCC: Head and Neck Suqmous Cell Carcinoma

Host Defense Peptide: An alternative name for antimicrobial peptides that emphasizes the immune modulation activities of AMPs.

HSP: Heat Shock Proteins, proposed target for Pro-rich AMPs

IND: Investigational New Drug (FDA)

IDR: Innate Defence Regulator, which may not kill bacteria directly.

IKK: Inhibitor of Kappa light polypeptide gene enhancer in B-cells, signaling molecules

IL: InterLeukin

INF: interferon

iNOS: inducible Nitric Oxide Synthase

IRAK: Interleukin-1 Receptor Associated Kinase

IRF3: Interferon Regulatory Factor 3, a transcription factor (activated by phosphorylation)

ITC: Isothermal Titration Calorimetry

LAB: Lactic Acid Bacteria that produce lantibiotics useful for food preservation.

LAM: LipoArabinoMannan, a glycolipid associated with the cell wall of Mycobacterium tubercolosis

Lan: meso-lanthionine

LanA: the peptide precursor to be processed by lantipeptide modification enzymes

Lantibiotics: lanthionine containing antibiotics which are extensively modified post-translationally.

Lantipeptides: lanthionine containing natural peptides with or without antimicrobial activity.

LBP: LPS-Binding Protein, its complex with LPS binds to CD14 high-affinity LPS receptor on the cell surface and induces cellular response via TLR4, the first mammalian homolog of Drosophila Toll. AMPs such as human LL-37 could compete with LBP, thereby suppressing, at least partially, the lethal effect of LPS-induced immune reponses. The structural basis for synnergistic binding of LPS by human LL-37 has been elucidated. Structurally, LL-37 contains two hydrophobic domains (Wang et al. 2011 Biochemistry 51:653-664). Abstract.

LC-MS: Liquid Chromatography-Mass Spectrometry

Leader peptide: in the case of lantibiotics, it refers to the N-terminal region of the precursor important for production but unmodified and removed after processing

Lipids: PC, diacyl phosphatidylcholines; PG, diacyl phosphatidylglycerols; PE, diacyl phosphatidylethanolamine

LPS: LipoPolySaccharides. Also called endotoxin from Gram-negative bacteria. A ligand for TLR4

LRR: Leucine-Rich Repeats

LTA: LipoTeichoic Acid from Gram-positive bacteria

LTP: Lipid Transfer Protein

LUV: Large unilamellar vesicles. e.g. DOPG=1,2-dioleoyl-sn-glycero-3-phosphocholine

Mal: see TIRAP

MALP-2: Macrophage Activating LipoPeptide-2

MAPK: Mitogen Activated Protein Kinase

MC: MelanoCortin

MCP-1: Monocyte Chemotactic Protein-1 (a marker cytokine the level of which is used as an indicator of immune modulation activity of AMPs)

MeLan: (2S,3S,6R)-3-methyllanthionine

MIC: (bacterial) Minimal Inhibitory Concentration

Microcins : Gene-encoded antibacterial peptides (<10 kDa) produced by enterobacteria to inhibit the growth of closely related species. Note that polypeptides (>10 kDa) are called colicins

Membrane-mimetic models: organic solvents such as TFE (trifluoroethanol), detergent micelles such as SDS (sodium dodecylsulfate) or DPC (dodecylphosphocholine), lipid micelles e.g. D8PG (dioctanoyl phosphatidylglycerol), bicelles, and lipid bilayers

MOA: Mechanism Of Action

MOI: Multiplicity Of Infection

MRI: Magnetic Resonance Imaging (Nobel Prize in 2003)

MRSA: Meticillin (Methicillin)-Resistant Stayphylococcus aureus, the difficult-to-kill superbug

MSR: the Macrophage Scavenger Receptor

MyD88: Myeloid Differentiation factor 88, a key adaptor protein in the TLR signaling pathways

NDA: New Drug Application

NFkB: Nuclear Factor kappa B, a transcription factor frequently involved in stress response of cells

NHBE cells: Normal Human Bronchial Epithelial cells

NMR: Nuclear Magnetic Resonance spectroscopy. While solution NMR is the major technique for structural and dynamics studies of membrane-bound AMPs, solid-state NMR provides complementary information such as peptide oligomerization and orientation in the membranes. (Nobel Prizes in 1952, 1991 and 2002)

NO: Nitric Oxide

NOD: nucleotide-binding oligomerization domain, an intracellular receptor responding to LPS

ORF: Open Reading Frame

PAMPs: Pathogen Associated Molecular Patterns

PBMC: Peripheral Blood Mononuclear Cells

PBS: Phosphate Buffered Saline

P/C properties: physio-chemical properties

PCR: Polymerase Chain Reaction

PD: Pharmacodynamics

pDCs: plasmacytoid Dendritic Cells

Peptaibol: fungi-derived short-length peptides (Pept ~15-20) rich in nonstandard amino acid residues such as aminoisobutyric acid (Aib) usually with a C-terminal hydroxyl group (OH).

PGN: PeptidoGlycaN, TLR2 ligand

PGRP: PeptidoGlycan Recognition Protein

PK: pharmacokinetics

PMN: PolyMorphonuclear Neutrophils

PRR: Pattern Recognition Receptors

PTMs: posttranslational modifications

QSAR: Quantitative Structure-Activity Relationship

QTPP: Quality Target Product Profile

RACE: Rapid Amplification of cDNA Ends. This technique produces cDNA from mRNA via reverse transcription, usually followed by PCR amplification.

RANA box: a C-terminal domain connected by a pair of cysteins discovered in amphibian AMPs.

RAR: Retinoic Acid Receptor

ROS: Reactive Oxygen Species

RP-HPLC: Reversed-Phase High-Performance Liquid Chromatography

SAXS: Small-Angle X-ray Scattering

SCVs: Small colony variants, a more resistant form of bacteria. For example, S. aureus can form SCVs in CF patients.

Sepsis or septicemia: a systemic inflamatory response syndrome in response to pathogenic bacteria or their components in the blood or tissues

SINE: Short Interspersed Element, or a repetitive DNA element (so called "junk DNA"). Note that such a vitamin D receptor binding element exists only in primate and human genomes.

siRNA: small interfering RNA

SNP: Single Nucleotide Polymorphism

SPR: Surface Plasmon Resonance

ssRNA: single-stranded RiboNucleic Acid, TLR7 ligand

STAT: the Signal Transducer and Activator of Transcription protein

Structure classification of antimicrobial peptides: alpha (peptides with alpha-helical structures); beta (AMPs with beta-sheet structure); alphabeta (AMPs with both alpha and beta structures; and non-AlphaBeta (AMPs that contain neither alpha nor beta structures) (Wang, G. 2010 Structural studies of AMPs. In Chapter 1, <"Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies" (edited by G. Wang). Read Chapter 1 here.

TB: tuberculosis

TCR: T Cell Receptor

TCRS: Two-component regulatory system

TEM: Transmission Electron Microscopy

Th1: T helper 1

TIR: Toll/Interleukin-1 Receptor domain

TIRAP: Toll-Interleukin 1 Receptor (TIR) domain containing Adaptor Protein; also known as MyD88-adaptor-like protein or Mal

TLRs: Toll-Like Receptors; sensors of both innate and adaptive immune systems for microbial products; 11 in humans. e.g. TLR2 for lipoteichoic acid from Gram-positive bacteria; TLR4 for LPS from Gram-negative bacteria. However, TLR3, TLR7, TLR8, and TLR9 are endosomal Toll-like receptors.

TNF-alpha: Tumor Necrosis Factor alpha, a cytokine. Some AMPs such as human LL-37 can suppress the release of TNF-alpha (part of the immune modulation activity)

TOCL: TetraOleoleoyl-CardioLipin

Tollip: Toll-interacting protein

TRAF: TNF Receptor-Associated Factor

TRAIL: TNF-Related Apoptosis Inducing Ligand

TRAM: Toll-like Receptor Adaptor Molecule 2

Tregs: regulatory T cells

UPLC: Ultra Performance Liquid Chromatography

UTR: UnTranslated Regions

UVB: solar UltraViolet-B

VDR: Vitamin D Receptor

VDRE: Vitamin D Receptor binding Element

VISA: vancomycin intermediate S. aureus strains, which increase basal resistance to vancomycin withour acqusition of any clearly defined resistance determinants.

VRE: Vancomycin-Resistant Enterococcus faecalis

XX codes for chemical modification: XXA, C-terminal NH2; XXC, cyclization; XXD, D-amino acids; XXG, glycosylation; XXO, oxidation; XXP, peptide phopsphorylation. AMPs with such activities can be searched in the name field of the search interface of the APD by entering the code.

ZZ codes: ZZH, anti-HIV; ZZP, anti-parasital; ZZS, spermicidal; ZZI, insecticidal. AMPs with such activities can be searched in the name field of the search interface of the APD by entering the code. Since the end of 2011, the ZZ codes have been replaced by more convenient icon search in the same manner as other activity functions created originally in the database.