Defined terms

Scientific Glossary

Alphabetical definitions for peptide chemistry, analytical science, pharmacology, and molecular-biology terminology used in the library.

Acetylation: Also: N-acetylation; Attachment of an acetyl group, most commonly to the N-terminal amino group of a peptide. It changes the molecular formula and mass and removes the terminal positive charge, so an acetylated peptide is a distinct molecule from its unacetylated form.; Related:N-terminus Terminal modification Amidation
Aggregation: Also: self-association; Association of peptide molecules with one another into larger assemblies, which may be reversible or irreversible. It affects apparent molecular mass in solution and can be a stability consideration.; Related:Stability Molecular mass
Agonist: A ligand that binds a receptor and promotes a measurable receptor response in a defined experimental system.; Related:Ligand G-protein-coupled receptor
Amidation: Also: terminal amidation; Formation of an amide group; in peptide nomenclature, the term commonly identifies a terminal carboxamide.; Related:Peptide analog
Amino acid residue: Also: residue; An amino acid as it exists within a peptide chain after peptide-bond formation, having lost the elements of water relative to the free amino acid.; Related:Peptide bond Sequence Proteinogenic amino acid
Antagonist: A ligand that binds a receptor without producing the response of an agonist, and that reduces the response to an agonist when both are present. Antagonists are used experimentally to establish which receptor mediates an observed effect.; Related:Agonist Ligand Receptor selectivity
Beta-arrestin: Also: β-arrestin, arrestin; An intracellular protein recruited to activated G-protein-coupled receptors that participates in receptor desensitization and internalization and can initiate its own signaling. Its recruitment is a commonly measured pathway in receptor characterization.; Related:G-protein-coupled receptor Biased agonism Receptor internalization
Biased agonism: Also: functional selectivity, signaling bias; The property of a ligand engaging one downstream signaling pathway of a receptor preferentially over another — for example favoring cyclic AMP generation over beta-arrestin recruitment. Characterized by comparing pathway responses at matched receptor occupancy.; Related:Agonist Beta-arrestin Cyclic AMP
Bibliographic review receipt: Also: review receipt; A record attached to a verified reference whose real published title contains result-descriptive or clinical wording. The receipt documents that the wording belongs to the cited source and is reproduced as bibliographic metadata, not as a statement by this library.; Related:Verified reference Monograph
C-terminus: Also: carboxyl terminus, C-terminal; The end of a peptide chain bearing a free or modified carboxyl group; by convention the end of the written sequence.; Related:N-terminus Amidation Sequence
CAS Registry Number: Also: CAS RN; A registry identifier assigned by Chemical Abstracts Service to a specific substance record.; Related:PubChem CID
Chromophore: Also: UV chromophore; A molecular group that absorbs light at a characteristic wavelength. In peptides, the aromatic residues tryptophan, tyrosine, and phenylalanine absorb near 280 nm; a peptide lacking them gives no useful signal at that wavelength and must be detected by other means.; Related:High-performance liquid chromatography Identity confirmation
Class B GPCR: Also: secretin-family receptor, class B1 receptor; A subfamily of G-protein-coupled receptors characterized by a large extracellular domain that binds the C-terminal portion of a peptide ligand while the transmembrane core engages the ligand's N-terminus. The incretin, glucagon, and growth hormone-releasing hormone receptors belong to this class.; Related:G-protein-coupled receptor Extracellular domain Transmembrane domain
Cryo-electron microscopy: Also: cryo-EM; A structural biology technique that images flash-frozen molecular specimens with an electron beam to reconstruct three-dimensional structures, commonly used to determine receptor-ligand complexes at near-atomic resolution.; Related:X-ray crystallography Structural biology
Cyclic AMP: Also: cAMP, cyclic adenosine monophosphate; An intracellular second messenger produced when certain G-protein-coupled receptors activate adenylyl cyclase. Its accumulation is a standard readout for agonist activity at Gs-coupled receptors.; Related:G-protein-coupled receptor Biased agonism
D-amino acid: The mirror-image stereoisomer of the naturally predominant L-amino acid. Written with a D- prefix in three-letter code. A sequence-only assay that assumes L-configuration will not distinguish a D-residue from its L-counterpart.; Related:Non-proteinogenic amino acid Three-letter code Stereochemistry
Deamidation: A degradation pathway in which an asparagine or glutamine side chain loses its amide group, altering the residue and typically introducing a negative charge. It changes molecular mass by approximately one dalton.; Related:Oxidation Stability
Development code: Also: compound code, research code; An alphanumeric identifier assigned to a compound during development, before or instead of a nonproprietary name — for example LY3298176 or NNC 26-0161. Development codes appear in early literature and are recorded to link a compound to its original characterization.; Related:International Nonproprietary Name CAS Registry Number
Dipeptidyl peptidase-4: Also: DPP-4, DPP-IV; An enzyme that cleaves the two N-terminal residues from peptides bearing an alanine or proline at the second position. Resistance to this cleavage is a characterized property of some peptide analogs and is assessed in vitro.; Related:Peptide analog Stability N-terminus
Disulfide bond: Also: disulfide bridge, cystine bridge; A covalent sulfur-sulfur bond between two cysteine residues, constraining the peptide's three-dimensional shape. Its presence or absence is part of the peptide's structural identity.; Related:Sequence Oxidation
Dual agonist: Also: co-agonist, multi-receptor agonist; A single molecule characterized as an agonist at two distinct receptors. A triple agonist engages three. Activity at each receptor is characterized separately and may differ in potency and signaling profile.; Related:Agonist Receptor selectivity Biased agonism
Extracellular domain: Also: ECD, N-terminal domain; The portion of a membrane receptor exposed outside the cell. In class B receptors it is a large structured domain that provides much of the ligand-binding affinity and specificity.; Related:Class B GPCR Transmembrane domain
Fragment: Also: peptide fragment; A contiguous subsequence of a longer peptide or protein, identified by residue numbers in parentheses. For example, GRF(1-29) denotes residues 1 to 29 of growth hormone-releasing factor.; Related:Sequence Peptide analog
G-protein-coupled receptor: Also: GPCR; A membrane receptor family whose conformational changes can couple extracellular ligand binding to intracellular G-protein signaling.; Related:Agonist Ligand
High-performance liquid chromatography: Also: HPLC; A separation technique that resolves the components of a sample by their differing interactions with a stationary phase under high pressure. Used to assess peptide purity by the fraction of total detected signal attributable to the main peak.; Related:Purity Liquid chromatography high-resolution mass spectrometry Chromophore
Identity confirmation: Also: identity testing; Establishing that a sample is the intended molecule, typically by mass spectrometry matching the expected molecular mass and, where necessary, sequence-level methods. Mass alone does not distinguish stereoisomers or molecules of identical formula.; Related:Liquid chromatography high-resolution mass spectrometry Purity Molecular mass D-amino acid
Incretin: A term used for gut-derived peptide signals including GLP-1 and GIP and for the receptor systems named from them.; Related:G-protein-coupled receptor
International Nonproprietary Name: Also: INN, generic name; A unique, globally recognized name assigned to a pharmaceutical substance by the World Health Organization. Where a compound has an INN, this library uses it as the canonical name; trade and literature names are listed as aliases.; Related:UNII Development code
Ligand: A molecule or ion characterized by its binding relationship with a molecular target.; Related:Agonist G-protein-coupled receptor
Lipidation: Also: lipid conjugation; Covalent attachment of a lipid-derived group to a peptide or protein molecular structure.; Related:Peptide analog
Liquid chromatography high-resolution mass spectrometry: Also: LC-HRMS; An analytical approach combining chromatographic separation with accurate-mass spectrometric measurement.; Related:Molecular mass
Lyophilization: Also: freeze-drying; Removal of water from a frozen solution by sublimation under vacuum, producing a dry solid. Most synthetic peptides are supplied in lyophilized form.; Related:Peptide content Salt form
Metal-peptide complex: Also: coordination complex; A molecular species formed when a peptide ligand coordinates a metal ion. The complex has a different formula, mass, and registry number from the free peptide and is recorded as a separate molecular identity.; Related:Ligand Molecular formula CAS Registry Number
Molecular formula: A notation reporting the elements and atom counts represented in a defined molecular record.; Related:Molecular mass
Molecular mass: Also: molecular weight; The mass associated with a defined molecular representation, reported here in daltons when an authoritative value is available.; Related:Molecular formula
Monograph: Also: compound monograph; In this library, a single-compound reference page presenting verified molecular identity, structural and nomenclature notes, receptor and class relationships, and a bibliography. Monographs describe what a compound is; they do not make claims about what it does.; Related:Verified reference Zero-reference monograph Non-stocked compound
N-terminus: Also: amino terminus, N-terminal; The end of a peptide chain bearing a free or modified alpha-amino group; by convention the start of the written sequence.; Related:C-terminus Acetylation Sequence
NMR spectroscopy: Also: nuclear magnetic resonance; A technique that characterizes molecular structure and dynamics in solution from the magnetic behavior of atomic nuclei. It is often used to study peptide conformation under conditions closer to those of a biological system than a crystal.; Related:X-ray crystallography Structural biology
Non-proteinogenic amino acid: Also: non-standard amino acid, unnatural amino acid; An amino acid not among the twenty encoded by the genetic code. Examples in this library include alpha-aminoisobutyric acid (Aib) and 2-naphthylalanine. Their presence affects analytical method selection and sequence notation.; Related:Proteinogenic amino acid Three-letter code D-amino acid
Non-stocked compound: A compound documented in this library that is not offered in the catalog. Such entries exist so that the reference covers a compound class or receptor completely rather than only the subset that is sold, and they carry no catalog link.; Related:Monograph
One-letter code: A notation assigning a single letter to each of the twenty proteinogenic amino acids. It cannot represent non-proteinogenic residues or D-amino acids, so peptides containing them are written in three-letter code instead.; Related:Three-letter code Proteinogenic amino acid Non-proteinogenic amino acid
Oxidation: Also: oxidative degradation; A degradation pathway in which a residue gains oxygen or loses electrons, most commonly affecting methionine, cysteine, and tryptophan. Peptides containing these residues are more susceptible than those without.; Related:Deamidation Disulfide bond Stability
Partial agonist: A ligand that produces a receptor response smaller than the maximal response achievable at that receptor, even at full receptor occupancy.; Related:Agonist Biased agonism
Peptide analog: A peptide designed with one or more sequence or chemical differences from a reference peptide.; Related:Lipidation Amidation
Peptide bond: Also: amide bond; The covalent amide linkage between the carboxyl group of one amino acid and the amino group of the next, forming the backbone of a peptide chain.; Related:Amino acid residue Sequence
Peptide content: Also: net peptide content; The mass fraction of a lyophilized sample that is peptide, as distinct from counterions, residual water, and other non-peptide mass. It is a separate measurement from purity and is not implied by it.; Related:Purity Salt form Lyophilization
Proteinogenic amino acid: Also: standard amino acid, canonical amino acid; One of the twenty amino acids encoded directly by the genetic code and incorporated into proteins during ribosomal synthesis.; Related:Non-proteinogenic amino acid One-letter code
PubChem CID: Also: CID; A numeric identifier for a compound record in the National Library of Medicine's PubChem database.; Related:CAS Registry Number
Purity: Also: chromatographic purity; The proportion of a sample's detected signal attributable to the intended compound, typically reported from HPLC as a percentage. Purity does not confirm identity: a highly pure sample of the wrong molecule is still the wrong molecule.; Related:High-performance liquid chromatography Identity confirmation Peptide content
Receptor desensitization: A reduction in receptor responsiveness following sustained or repeated agonist exposure, measured in a defined system.; Related:Receptor internalization Beta-arrestin
Receptor internalization: Also: endocytosis of receptor; Removal of a receptor from the cell surface into intracellular compartments following ligand binding. The degree of internalization differs between ligands at the same receptor and is one dimension along which agonists are compared.; Related:Beta-arrestin Receptor desensitization
Receptor selectivity: Also: selectivity; The degree to which a ligand engages one receptor in preference to related receptors, typically expressed as a ratio of potencies or affinities measured in defined assay systems.; Related:Agonist Antagonist Dual agonist
Research use only: Also: RUO, for research use only; A designation indicating that a material is supplied for laboratory and research purposes and is not intended for diagnostic, clinical, or any use in humans or animals. This library documents molecular identity and published characterization consistent with that designation.; Related:Monograph Non-stocked compound
Salt form: Also: counterion form; The ionic pairing in which a peptide is supplied, such as an acetate or trifluoroacetate salt. The counterion contributes to measured mass and must be accounted for when comparing an analytical result against a reference record for the free peptide.; Related:Trifluoroacetate Molecular mass
Sequence: Also: primary structure, amino acid sequence; The ordered list of amino acid residues in a peptide, written from the N-terminus to the C-terminus.; Related:N-terminus C-terminus One-letter code Three-letter code
Stability: Also: chemical stability; The tendency of a peptide to retain its molecular identity over time under defined conditions. Assessed by analytical methods that detect degradation products, not by observation of appearance.; Related:Oxidation Deamidation Aggregation
Stereochemistry: Also: chirality; The three-dimensional arrangement of atoms in a molecule. For peptides, principally the L or D configuration of each residue's alpha carbon.; Related:D-amino acid
Structural biology: The study of the three-dimensional shapes of biological molecules and how those shapes relate to function. Receptor-level structural studies are cited in this library because one such reference informs every ligand characterized at that receptor.; Related:Cryo-electron microscopy X-ray crystallography NMR spectroscopy
Terminal modification: Any chemical group attached at the N-terminus or C-terminus of a peptide, such as an N-terminal acetyl or a C-terminal amide. Terminal modifications are part of a peptide's declared molecular identity.; Related:Acetylation Amidation N-terminus C-terminus
Three-letter code: A notation abbreviating each amino acid to three letters, such as Gly or Lys. It accommodates non-standard residues and stereochemical prefixes, for example D-Phe or Aib.; Related:One-letter code Non-proteinogenic amino acid D-amino acid
Transmembrane domain: Also: TMD, seven-transmembrane bundle; The portion of a receptor embedded in the cell membrane. In G-protein-coupled receptors it comprises seven alpha-helices whose rearrangement on ligand binding transmits activation to the intracellular side.; Related:Class B GPCR Extracellular domain G-protein-coupled receptor
Trifluoroacetate: Also: TFA salt, TFA; A common counterion in synthetic peptides, carried over from trifluoroacetic acid used during purification. Some reference database records describe the trifluoroacetate salt rather than the free peptide, which changes the listed formula and mass.; Related:Salt form Molecular mass
Tripeptide: A peptide of exactly three amino acid residues. Terms of the same form — dipeptide, tetrapeptide, pentapeptide, hexapeptide — denote two, four, five, and six residues respectively.; Related:Sequence Amino acid residue
UNII: Also: Unique Ingredient Identifier; A ten-character alphanumeric identifier assigned by the FDA Global Substance Registration System to a specific substance. Where a UNII exists for a compound it is published; where none appears in the reference record, the field is left absent rather than inferred.; Related:CAS Registry Number PubChem CID International Nonproprietary Name
Verified reference: Also: verified citation; A bibliographic record in this library whose title, authors, journal, date, and identifiers have been independently confirmed against the PubMed record and sealed with a receipt. Every reference listed on a monograph is a verified reference; unverified sources are not listed.; Related:Monograph Bibliographic review receipt Zero-reference monograph
X-ray crystallography: Also: crystal structure; A structural biology technique that determines atomic positions from the diffraction pattern of X-rays passing through a crystallized molecule. A solid-state crystal structure does not always represent the molecule's conformation in solution.; Related:Cryo-electron microscopy Structural biology NMR spectroscopy
Zero-reference monograph: Also: identity-only monograph; A monograph whose molecular identity is fully verified but which lists no bibliography, because the available literature did not meet the library's inclusion standard. The absence is deliberate and recorded; it is not a gap awaiting citations.; Related:Monograph Verified reference