ABSTRACT
BDNF Brain-derived growth factor BEBO An unsymmetrical cyanine dye for binding to the minor groove of DNA; 4-
[(3-methyl-6-(6-methyl-benzothiazol-2-yl)-2,3,-dihydro(benzo-1,3-thiazole)-2-methylidene)]-1-methyl-pyridinium iodide
BET An isotherm for adsorption phenomena in chromatography; acronym derived from Stephen Brunauer, Paul Emmet, and Edward Teller
B/F Bound/free bFGF Basic fibroblast growth factor BFP Blue fluorescent protein BGE Background electrolyte Bicine N,N-bis(2-hydroxyethyl)glycine BiFC Bimolecular fluorescence complementation BIND Biomolecular interaction network database BiP Immunoglobulin heavy chain-binding protein Bis-Tris 2,2-bis-(hydroxymethyl)-2,2′,2′′ nitriloethanol BLA Biologic license application BLAST Basic local alignment search tool BME 2-mercaptoethanol; β-mercaptoethanol BMP Bone morphogenic protein BopA Secreted protein required for biofilm formation BPTI Bovine pancreatic trypsin inhibitor BrdU Bromodeoxyuridine BRE-luc A mouse embryonic stem cell line used to study bone morphogenetic protein BRET Bioluminescence resonance energy transfer; see FRET Brig Polyoxyethylene lauryl ether BSA Bovine serum albumin bZIP Basic leucine zipper transcription factor C1INH C1 inhibitor; inhibitor of activated complement component 1, missing in
hereditary angioneurotic edema CA125 Cancer antigen 125; a glycoprotein marker used for prognosis in ovarian
cancer; also referred to as MUC16 CAD Multifunctional protein which initiates and regulates de novo pyrimidine
biosynthesis; caspases-activated DNAse CAK Cdk-activating kinase CALM Clathrin assembly lymphoid myeloid leukemia, as in CALM gene CAM (CaM) Calmodulin; cell adhesion molecule CAMK Ca2+/calmodulin-dependent protein kinase
CaMK Calmodulin kinase, isoforms I, II, III Can Acetonitrile CAN Bacterial cell wall collagen-binding protein CAPS Cleavable amplified polymorphic sequences; cationic antimicrobial peptide CArG A promoter element [CC(A/T)6G] gene for smooth muscle α-actin CASP Critical assessment of structural prediction CASPASE Cysteine-dependent aspartate-specific protease CAT Catalase; chloramphenicol acetyl transferase CATH Class, architecture, topology, homologous superfamily; hierarchical classi-
fication of protein domain structure cATP Chloramphenicol resistance gene; caged ATP; cation transporting P-type Cbl A signal transducing protein downstream of a number of receptors coupled
to tyrosine kinases; a product of the c-cbl proto-oncogene Cbs Chromosomal breakage sequence CBz Carbobenzoxy CCC Concordance correlation coefficient CCD Charge couple device CCK Choleocystokinin CCV Clathrin-coated vesicles CD Clusters of differentiation; circular dichroism; cyclodextrin CDC Complement-dependent cytotoxicity; complement-mediated cell death CDK (cDK) Cyclin-dependent kinase cDNA Complementary DNA Cdpk4 Ca2− protein kinase CDR Complementary determining region CDTA 1,2-cyclohexylenedinitriloacetic acid CE Capillary electrophoresis CEC Capillary electrochromatography CELISA Cellular enzyme-linked immunosorbent assay; enzyme-linked immunosorbent
assay on live cells CEPH Centre d’Etude du Polymorphisme Humain CERT Ceramide transport protein CE-SDS Capillary electrophoresis in the presence of sodium dodecyl sulfate CEX Cation exchange CFA Complete Freund’s adjuvant CFP Cyan fluorescent protein CFTR Cystic fibrosis transmembrane conductance region Cfu Colony-forming unit CGE Capillary gel electrophoresis CGH Comparative genome hybridization CGN cis-Golgi network CH Calponin homology CHAPS 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonic acid CHCA α-cyano-4-hydroxycinnamic acid CHEF Chelation-enhanced fluorescence CHES 2-(N-cyclohexylamino)ethanesulfonic acid ChiP Chromatin immunoprecipitation CHO Chinese hamster ovary; carbohydrate CID Collision-induced dissociation; collision-induced dimerization CIDEP Chemically induced dynamic electron polarization CIDNP Chemically induced dynamic nuclear polarization
CIEEL Chemically initiated electron exchange luminescence CLIP Class II-associated invariant chain (Ii) peptide CLT Clotvinazole [1-(α2-chlorotrityl)imidazole] CLUSTALW A general purpose program for structural alignment of proteins and nucleic
acids: https://www.ebi.ac.uk/clustalw/ cM Centimorgan CM Carboxymethyl CMCA Competitive metal capture analysis CML Chronic myelogenous leukemia; carboxymethyl lysine Cn Calcineurin CNC Cap’n’Collar family of basic leucine zipper proteins CNE Conserved noncoding elements CoA Coenzyme A COACH Comparison of alignments by constructing hidden Markov models COFFEE Consistency-based objective function for alignment evaluation COFRADIC Combined fractional diagonal chromatography COG Conserved oligomeric Golgi; cluster of orthologous groups COPD Chronic obstructive pulmonary disease COX Cytochrome C oxidase Cp Ceruloplasmin CPA Carboxypeptidase A CPB Carboxypeptidase B CPD Cyclobutane pyrimidine dimer CPDK Calcium-dependent protein kinase CpG Cytosine-phosphate-guanine CpG-C Cytosine-phosphate-guanine class C CPP Cell-penetrating peptide; combinatorial protein pattern CPSase Carbamoyl-phosphate synthetase CPY Carboxypeptidase Y CRAC Calcium release-activated calcium (channels) CRE Cyclic AMP response element CREA Creatinine CREB cAMP response element-binding protein Cre1 Cytokine response 1; a membrane kinase CRM Certified reference material CRP C-reactive protein; also cAMP receptor protein CRY Chaperone CS Chondroitin sulfate CSF Colony-stimulating factor CSP Cold-shock protein CSR Cluster-situated regulator; class-switch recombination CSSL Chromosome segment substitution lines Cst3 Cystatin 3 Ct Chloroplast CT Charge transfer CTB Cholera toxin B subunit CTD C-terminal domain CTL Cytotoxic T lymphocytes CTLA Cytotoxic T lymphocyte-associated antigen CTLL Cytotoxic T-cell lines CTPSase CTP synthetase
CtrA A master regulator of cell cycle progression CV Coefficient of variation Cvt Cytosome to vacuole targeting CW Continuous wave (nonpulsed source of electromagnetic radiation) CYP Cytochrome P450 enzyme CZE Capillary zone electrophoresis 2D-DIGE Two-dimensional difference gel electrophoresis 2DE Two-dimensional electrophoresis D Diffusion Dax Axial dispersion coefficient DAB(p-dab) p-dimethyl amino azo benzene dABs Domain antibodies DABSYL N,N-dimethylaminoazobenzene-4′-sulfonyl — usually as the chloride, DABSYL
chloride DAD Diaphanous-autoregulatory domain DAF Decay accelerating factor DAG Diacyl glycerol DALI Distance matrix alignment: https://www.ebi.ac.uk/dali/ DANSYL 5-dimethylaminonapthalene-1-sulfonyl; usually as the chloride, DANSYL
chloride DAP DNAX-activation protein; diaminopimelic acid DAP12 DNAX-activating protein of 12kDa mass DAS Distributed annotated system; downstream activation site DBD-PyNCS 4-(3-isocyanatopyrrolidin-1-yl)-7-(N,N-dimethylaminosulfonyl)-2-
benzoxadiazole DBTC “Stains All”; 4,5,4′,5′-dibenzo-3,3′-diethyl-9-methylthiacarbocyanine bromide DC Dendritic cell DCC Dicyclohexylcarbodimide DCCD N,N′-dicyclohexylcarbodimide dCNE Duplicated CNE DDBJ DNA Data Bank of Japan: https://www.ddbj.nig.ac.jp DDR1 Discoidin domain receptor1, CAK, CD167a, PTK3, Mck10 DDR2 Discoidin domain receptor2, NTRK3, TKT, Tyro10 DDRs Discoidin domain receptors (DDR1, DDR2) DEAE Diethylaminoethyl DEG Differentially expressed gene(s) DEX Dendritic cell-derived exosomes DFF DNA fragmentation factor DFP Diisopropylfluorophosphate; diisopropylphosphorofluoridate DHFR Dihydrofolate reductase DHO Dihydroorotase domain DHOase Dihydroorotase DHPLC
(dHPLC) Denaturing HPLC DHS DNase I hypersensitivity site DIP Database of interacting proteins: https://dip.doe-mbi.ucla.edu; also dictionary
of interfaces in proteins: https://drug-redesign.de/superposition.html Dipso 3-[N,N-bis(2-hydroxyethyl)amino]-2-hydroxypropanesulfonic acid DLS Dynamic light scattering DM An accessory protein located in the lysosome associated with MHC class II
antigen presentation; located in the endosomal/lysosomal system of APC
DMBA 7,12-dimethylbenz[α]anthracene DMD Duchenne muscular dystrophy; also Doctor of Dental Medicine DMEM Dulbecco’s Modified Eagle’s Medium DMF Dimethylformamide; decayed, missing, filled (in dentistry) DMS Dimethyl sulfate DMSO Dimethyl sulfoxide DMT1 Divalent metal transporter 1 ssDNA Single-stranded DNA DNAa A bacterial replication initiation factor DNAX DNAase III, tau and gamma subunits dNPT Deoxynucleoside triphosphate DO An accessory protein located in the lysosome associated with MHC class II
antigen presentation; DO has an accessory role to DM DOTA Tetraazacyclodecanetetraacetic acid DPE Downstream promoter element DPI Dual polarization interferometry DPM Disintegrations per minute DPN Diphosphopyridine dinucleotide (currently NAD) DPPC Dipalmitoylphosphatidylcholine DPPE 1,2-dipalmitoyl-sn-glycerol-3-phosphoethanolamine DPTA Diethylenetriaminepentaacetic acid DRE Dehydration response element; dioxin response element DRT Dimensionless retention time (a value for chromatography) DSC Differential scanning calorimetry dsDNA Double-stranded DNA DSP Downstream processing dsRBD Double-stranded RNA binding domain dsRNA Double-stranded RNA DTAF Dichlorotriazinyl aminofluorescein DTE Dithioerythritol DTNB 5,5′-dithio-bis(2-nitrobenzoic acid) Ellman’s Reagent DTT Dithiothreitol DUP A duplicated yeast gene family DVDF Polyvinyl difluoride E1 Ubiquitin-activating enzyme E2 Ubiquitin carrier protein E3 Ubiquitin-protein isopeptide ligase E-64 Trans-epoxysuccinyl-L-leucylamino-(4-guanidino)-butane, proteolytic enzyme
inhibitor EAA Excitatory amino acid EBA Expanded bead adsorption EBV Epstein-Barr virus ECF Extracytoplasmic factor; extracellular fluid ECM Extracellular matrix EDC 1-ethyl-(3-dimethylaminopropyl)-carbodiimide EDC (EADC) 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide; N-ethyl-N′-(3-dimethyl-
aminopropyl) carbodiimide EDI Electrodeionization EDTA Ethylenediaminetetraacetic acid, Versene, (ethylenedinitrilo)tetraacetic acid EEO Electroendoosmosis EEOF Electroendoosmotic flow
EF Electrofiltration EGF Epidermal growth factor EGFR Epidermal growth factor receptor; Erb-1; HER1 EGTA Ethyleneglycol-bis(β-aminoethylether)-N,N,N′,N′-tetraacetic acid eIF Eukaryotic initiation factor EK Electrokinetic EKLF Erythroid Krüppel-like factor ELISA Enzyme-linked immunosorbent assay EMBL European Molecular Biology Laboratory EMCV Encephalomyocarditis virus EMF Electromotive force EMMA Enhanced mismatch mutation analysis EMSA Electrophoretic mobility shift assay ENaC Epithelial Na channel EndoG Endonuclease G ENTH Epsin N-terminal homology as ENTH-domain ENU N-ethyl-N-nitrosourea EO Ethylene oxide EOF Electroosmotic flow Eph A family of receptor tyrosine kinases; function as receptors/ligands for ephrins EPL Expressed protein ligation Epps 4-(2-hydroxyethyl)-1-piperazinepropanesulfonic acid EPR Electron paramagnetic resonance ER Endoplasmic reticulum ERAD Endoplasmic reticulum-associated protein degradation ErbB2 Epidermal growth factor receptor, HER2 ErbB3 Epidermal growth factor receptor, HER3 ErbB4 Epidermal growth factor receptor, HER4 ERK Extracellular-regulated kinase Erk ∫ P 42/44 extracellular signal-regulated kinase Ero1p A thiol oxidase that generates disulfide bonds inside the endoplasmic
reticulum ERSE Endoplasmic reticulum (ER) stress-response element ES Embryonic stem, as in embryonic stem cell ESI Electrospray ionization ESR Electron spin resonance; erthyrocyte sedimentation rate ESS Exonic splicing silencer EST Expressed sequence tag ETAAS Electrothermal atomic absorption 5,6-ETE 5,6-epoxyeicosatrienoic acid ETS Family of transcription factors EUROFAN European Functional Analysis Network: https://mips.gsf.de/proj/eurofan/;
European Programme for the Study and Prevention of Violence in Sport Exo1 Exonuclease 1 EXP1 Expansion gene FAAH Fatty acid amide hydrolase Fab Antigen-binding fragment from immunoglobulin FAB Fast atom bombardment FAB-MS/MS Fast atom bombardment-mass spectrometry/mass spectrometry FACE Fluorophore-assisted carbohydrate electrophoresis FACS Fluorescence-activated cell sorting
FAD Flavin adeninine dinucleotide FADD Fas-association death domain FAK Focal adhesion kinase FBS Fetal bovine serum Fc Fc region of an immunoglobulin representing the C-terminal region FCCP Carbonyl cyanide p-trifluoromethoxyphenyl-hydrazine FcγR Cell surface receptor for the Fc domain of IgG FDA Fluorescein diacetate FDC Follicular dendritic cells FEAU 2′-fluoro-2′-deoxy-β-D-arabinofuranosyl-5-ethyluracil FecA Ferric citrate transporter FEN Flap endonuclease FERM FERM-domain (four-point-one; ezrin, radixin, moesin) Fes Retroviral oncogene derived from ST and GA feline sarcoma FFAT Two phenylalanyl residues in an acidic tract FFPE Formalin-fixed, paraffin-embedded FGF Fibroblast growth factor FGFR Fibroblast growth factor receptor Fgr Retroviral oncogene derived from GR feline sarcoma FIAU 2′-fluoro-2′-deoxy-β-D-arabinofuranosyl-5-iodouracil FIGE Field-inversion gel electrophoresis FITC Fluoroscein isothiocyanate FLAG™ An epitope “tag” that can be used as a fusion partner for recombinant protein
expression and purification FlhB A component of the flagellum-specific export apparatus in bacteria FLIP Fluorescence loss in photobleaching FLK-1 Vascular endothelial growth factor receptor (VEGFR) FLT-1 Vascular endothelial growth factor receptor (VEGFR) fMLP(FMLP) N-formyl methionine leucine phenylalanine fMOC 9-fluorenzylmethyloxycarbonyl Fms Retroviral oncogene derived from SM feline sarcoma Fok1 A type IIS restriction endonuclease derived from Flavobacterium okeanokoites Fos Retroviral oncogene derived from FBJ murine osteosarcoma FOX Forkhead box FpA Fibrinopeptide A FPC Fingerprinted contigs Fps Retroviral oncogene from Fujiami avian sarcoma FRAP Fluorescence recovery after photobleaching FRET Fluorescence resonance energy transfer; Förster resonance energy transfer FSSP Fold classification based on structure alignment of proteins: https://www.ebi.
