Table 3.
Glossary.
| Term | Definition |
|---|---|
| Accessible surface area | Also known as solvent-accessible surface area (SASA); the surface area of a biomolecule that is accessible to a solvent. Measurement is usually described in units of square Ångstroms |
| Adoptive T cell transfer | A type of immunotherapy in which T cells are given to a patient to improve immune functionality to fight diseases |
| Amino acid index database (AAindex) | A database of amino acid indices and amino acid mutation matrices. An amino acid index is a set of 20 numerical values representing various physicochemical and biochemical properties of amino acids. An amino acid mutation matrix is generally 20 ×20 numerical values representing similarity of amino acids |
| Clonal expansion | A process in which a small number of precursor cells recognize a specific antigen, proliferate into expanded clones, differentiate and acquire various effector and memory phenotypes |
| Combinatorial peptide library | A library typically comprised of millions to billions of random peptides covering possible combinations of amino acids in each position |
| Degeneracy | Ability to recognize diverse ligands |
| Electrostatic potential | The amount of work needed to move a unit of charge against an electric field |
| Featured peptide | A peptide with solvent-exposed, prominent side chains or harmonious bulged confirmations and typically correspond to a diverse repertoire of TCRs |
| Find Individual Motif Occurrence | A motif-based sequence analysis tool that scans a set of sequences for individual matches to each of the motifs provided by the users |
| Flexible docking | A macromolecular docking where the internal geometry of the interacting partners can be changed when a complex is formed |
| Heterologous immunity | An immunity that can develop to one pathogen after a host has had exposure to non-identical pathogens |
| Immunodominant peptide | A peptide having a strong affinity for binding with HLA and for stimulating a T cell response |
| Kidera factor | A set of orthogonal physicochemical properties that reflect 20 amino acids, which include helix/bend preference, side-chain size, extended structure preference, hydrophobicity, double-bend preference, partial specific volume, flat extended preference, occurrence in alpha region, pK-C and surrounding hydrophobicity |
| Molecular mimicry | A phenomena that sequence similarities between foreign and self-peptides are sufficient to trigger cross-activation of autoreactive T cells by pathogen-derived peptides |
| Peptide-MHC display system | A platform with engineered functional peptide-MHC complexes for high-throughput screening of immunogenic peptides against TCRs |
| Polarization | A process to adopt different functionality in response to the signals from their microenvironment |
| Positional specific scoring matrix | An amino acid scoring matrix in a 20 ×20 table such that position indexed with amino acids e.g., position (X, Y), gives the score of alignment or substitution of amino acid X with amino acid Y |
| Private TCR | A TCR unique to an individual |
| Public TCR | A TCR shared among different individuals |
| Rigid docking | A computational modeling of the quaternary structure of complexes formed by two or more interacting biological macromolecules, where the relative orientation of interacting partners was allowed to vary but the internal geometry of each of the partners was held fixed |
| Rosetta terms | A set of 19 terms comprising Rosetta Energy Function 2015 (REF15), a model parametrized from small-molecule and X-ray crystal structure data, used to approximate the energy associated with each biomolecule conformation |
| Tetramer-associated T cell receptor sequencing | A method to link TCR sequences to their cognate antigens in single cells at high throughput manner. Peptide-TCR binding is determined using a library of DNA-barcoded antigen tetramers |
| ZAFFI score | Abbreviation for Zlab affinity enhancement; an algorithm to predict the effect of point mutations on binding affinity of TCRs. Training of energy function was performed using a dataset of systematic point mutations at 10 positions on the ovomucoid turkey inhibitor (OMTKY) molecule in four enzyme-inhibitor complexes. The optimal terms and weights for the function was obtained to fit the energies of OMTKY point mutants and tested using point mutations of T cell receptor. The terms and weights making up the score are: van der Waals attractive (0.24), van der Waals repulsive (0.017), Lazaridis-Karplus solvation (0.24), intra-residue clash (0.073) and atomic contact energy (0.32) |