|
|
 | a handle used to describe a protein identified by an antibody
|
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|
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| an immunoprecitiptate by an antibody to an acetylation site
|
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| an antibody that detects a specific acetylation site when it is acetylated
|
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|
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| a handle used to describe a protein identified by an antibody to a specific acetylation site
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| a modification used to represent acetylation
|
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|
| activated; used when a protein has been shown experimentally to be capable of catalyzing a reaction
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| a modification used to represent activation
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|
|
| a handle used to describe a protein or chemical immoblized on agarose
|
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| molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids.
|
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| a Treatment used when mixtures of amino acids are added to cells
|
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|
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| used when the substrate of a kinase reaction is the kinase itself
|
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|
|
| DNA in the B conformation
|
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|
|
| represented by Poly(dA-dT)-Poly(dT-dA) 17618271(M) 16785313(M)
|
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|
|
| the right-handed typical form of double helix DNA in which the chains twist up and to the right around the front of the axis of the helix and that has usually ten base pairs in each helical turn and two grooves on the external surface [Merriam-Webster Dictionary]
|
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|
|
| an ELISA performed on suspended beads and analysed by FACS
|
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|
|
| beta-Galactosidase Enzyme assay
|
|
|
|
| sample containing bGal is incubated with colorless substrate ONPG (o-nitrophenyl-beta-D-galactopyranoside). Active enzyme hydrolyzes subtrate to o-nitrophenyl which is yellow. The reaction is terminated with sodium carbonate and the absorbance at 420 nM is measured by spectrophotometry. [Promega catalog]
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|
| bimolecular fluorescence complementation
|
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|
 | A method of viewing the association of proteins inside living cells. The intact Green fluorescent protein (and its variants CFP, YFP, BFP, and RFP) is fluorescent. However, when the fluorescent protein is split into N and C-terminal halves, the molecule does not produce fluorescence. Fusing of each of the two non-fluorescent fragments to two putative interacting partners leads to restoration of fluorescence within a cell by reconstituting the split fluorophore. This fluorescence is detected via fluorescence microscopy, which can be recorded by a mounted camera. The advantage of the BiFC method over other methods of visualizing protein-protein interactions is that it gives an indication of interaction, as well as cellular localization of the complex. [Wiki]
|
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|
|
| Hu CD, Chinenov Y, Kerppola TK (2002) Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 9: 789-798
|
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|
|
| Hu CD, Grinberg A, Kerppola T (2005) Visualization of protein interaction in living cells using bimolecular fluorescence complementation (BiFC) analysis. In Current Protocol in Cell Biology, Bonifacino JS, Dasso M, Harford JB, Lippincott-Schwartz J, Yamada KM (eds), pp 21.3.1–21.3.21. Hoboken: John Wiley & Sons
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|
|
| Hu CD, Kerppola TK (2003) Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nat Biotechnol 21: 539–545
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| a streptavidin binding protein used as a protein tag
|
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|
|
| a handle used to describe a protein or chemical prebound to biotin
|
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|
|
| a detection method used for detecting protein surface expression
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|
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| Basal medium with low serum
|
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|
|
| same as BMS but serum concentration is <2% (or significantly lower than that in growth medium)
|
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|
|
| basal medium containing heat-inactivated serum
|
|
|
|
| Basal medium contains balanced salt solutions, amino acid, vitamins
|
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|
|
| any growth factor supplements should be listed separately
|
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|
|
| Serum can be Fetal bovine serum, calf serum, newborn calf serum, horse serum
|
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|
|
| The concentration of serum is > 5%
|
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|
|
| BMS is used when the medium used during an experiment is not explicitly stated
|
|
|
|
| A BProtein uses its Pathway Logic name as declared in proteinops.maude
|
|
|
|
| Any numbers used involving amino-acid sequence refer to the isoform chosen by UniProt as the 'canonical' sequence unless another splice variant is designated
|
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|
|
| does not contain serum or amino acids
|
|
|
|
| a residue located near the C-terminal end of Ras-family proteins
|
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|
|
| used in shorthand to describe a mutation - meaning that a CAAX box was added to protein to cause consitutive localization to membrane
|
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|
|
| an amino acid consensus sequence
|
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|
|
| C = cysteine to be prenylated
|
|
|
|
| A = any aliphatic amino acid (leucine (L), isoleucine (I), or valine (V))
|
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|
|
| Chloramphenicol AcetylTransferase Assay
|
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|
|
| a handle used to describe a protein or chemical identified using Commassie Blue stain
|
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|
| anything that is not a Protein or a Gene
|
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|
|
| Chromatin ImmunoPrecipitation Assay
|
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|
|
| cyclohexamide treatment followed by western blot
|
|
|
|
| Calf Intestine Alkaline Phosphatase
|
|
|
|
| an antibody that detects a the cleavage product of a Protein cleaved at a specific site
|
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|
|
| a handle used to identify a cleaved protein in a cleavage assay
|
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|
|
| a group of Proteins often referred to as one protein
|
|
|
|
| Composite declarations can be found in proteinops.maude
|
|
|
|
| a modification used for mono or poly ubiquitin conjugated to any protein
|
|
|
|
| anything seen by antibody FK2 Enzo cat# BML-PW8810-0500
|
|
|
|
| a caspase inhibitor 14739303(C)
|
|
|
|
| A serine-protease inhibitor encoded by cowpox virus 8034697(D)
|
|
|
|
| the cowpox viral protein crmA that blocks caspase-8-induced apoptosis by physically interacting with and inhibiting processing of caspase-8 precursor (20). 10753878(C)
|
|
|
|
| 20. Shu, H. B., Halpins, D. R., and Goeddel, D. V. (1997) Immunity 6, 751–763
|
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|
|
| a peptide substrate (GRPRTSSFAEG) used for kinase assays
|
|
|
|
| Cholera Toxin B-subunit used for visualizing GM1-gangliosides in lipid rafts
|
|
|
|
| a handle used to identify Golga2
|
|
|
|
| a fluorophore used for labeling proteins
|
|
|
|
| a handle used to identify proteins labeled with Cy3
|
|
|
|
| a fluorophore used for labeling proteins
|
|
|
|
| a handle used to identify proteins labeled with Cy5
|
|
|
|
| an expression that describes an experiment using a formal grammar
|
|
|
|
| DNA binding domain of a transcription factor
|
|
|
|
| a size separation method using centrifugation through glycerol or sucrose gradients: a detection method
|
|
|
|
| details in glossary - used when the mutations are too bulky to use in shorthand
|
|
|
|
| Deptor(T241A/S244A/S259A/T260A/S263A/S265A/S282A/S283A/S287A/S293A/S297A/S298A/S299A)
|
|
|
|
| Tp53(K319A/K320A/K321A/K370A/K372A/K373A/K381A/K382A/K386A)"9KR"
|
|
|
|
| Ubiq(K11R/K27R/K29R/K33R/K48R/K63R)
|
|
|
|
| Ubiq(K6R/K27R/K29R/K33R/K48R/K63R)
|
|
|
|
| Ubiq(K6R/K11R/K29R/K33R/K48R/K63R)
|
|
|
|
| Ubiq(K6R/K11R/K27R/K33R/K48R/K63R)
|
|
|
|
| Ubiq(K6R/K11R/K27R/K29R/K48R/K63R)
|
|
|
|
| Ubiq(K6R/K11R/K29R/K33R/K63R)
|
|
|
|
| Ubiq(K6R/K11R/K29R/K33R/K48R)
|
|
|
|
| Ubiq(K6R/K11R/K27R/K29R/K33R/K48R/K63R)
|
|
|
|
| detergent resistant membrane fraction
|
|
|
|
| DRM and non-DRM fractions were separated as described previously (Shima et al, 2003). Briefly, cells were lysed in buffer A (50 mM Tris–HCl (pH 7.4), 150 mM NaCl, 1 mM EDTA, 1 mM sodium orthovanadate, 50 mM NaF, 5 mM 2-mercaptoethanol and protease inhibitors) containing 0.25% Triton X-100 at 41oC. The lysate was separated on a discontinuous sucrose gradient (40–35–5%) by ultracentrifugation at 100000g for 16h at 4oC. The gradient was separated into 12 fractions collected from the top. The DRM proteins were solubilized in buffer A containing 2% N-octyl-b-D-glucoside (ODG) and 1% Nonidet P40 (NP40)
|
|
|
|
| dsDNA breaks caused by lasar scissors
|
|
|
|
| To analyze cellular responses to DSBs, including repair, at defined sites in human cells, we used the eukaryotic homing endonuclease I-PpoI, which has a 15 base pair recognition sequence7,8, to cleave endogenous DNA target sites in the human genome. Expression of I-PpoI in human cells results in cleavage of ~10% of the 200–300 I-PpoI genomic target sites9 to generate ~30 DSBs per cell (equivalent to that introduced by exposure to ~0.8 Gy irradiation).
|
|
|
|
| The system was improved by adding a mutant oestrogen receptor hormone-binding domain to I-PpoI to create a fusion protein that could be localized to the nucleus in response to 4-hydroxytamoxifen (4-OHT). Addition of 4-OHT to MCF7 cells infected with an oestrogen receptor–I-PpoI retrovirus resulted in time-dependent cleavage of the endogenous 28S rDNA I- PpoI site and ATM activation.
|
|
|
|
| transcribed in vitro from PCR products using T7 RNA polymerase 16625202(M)
|
|
|
|
| used as a ligand for TLR3
|
|
|
|
| Enzyme-Linked Immunosorbent Assay
|
|
|
|
| Electrophoretic Mobility Shift Assay
|
|
|
|
| Fluorescence Activated Cell Sorter
|
|
|
|
| a set of similar Proteins referred to by one name
|
|
|
|
| A Family is used in rules and datums instead of a Protein when it is not possible to distinguish between the family members studied.
|
|
|
|
| Family declarations can be found in proteinops.maude
|
|
|
|
| a method used to determine the direct binding of a substance to a denatured protein.
|
|
|
|
| soluble FasL trimer cross-linked either chemically or with an anti-Tag Ab
|
|
|
|
| required to induce apoptosis and cytotoxicity by FasL 12556501(D)
|
|
|
|
| a peptide tag used for identifying proteins
|
|
|
|
| a handle used to identify or isolate proteins labeled with Flag
|
|
|
|
| a handle used to identify proteins labeled with a fluorescent substance
|
|
|
|
| Förster resonance energy transfer
|
|
|
|
| any subspecies of Franciscella tularensis
|
|
|
|
| The DNA-binding domain of Gal4
|
|
|
|
| a handle used to enable activated transcription factors to interact with a Gal4-reporter
|
|
|
|
| guanosine 5'-[beta-thio]diphosphate
|
|
|
|
| a string of nucleotides that codes for a Protein
|
|
|
|
| Names of Genes in this model are derived from the Protein name (eg. the name of the gene for the protein Erk1 is Erk1-gene)
|
|
|
|
| used as a GTP analog by 16892055
|
|
|
|
| 5'-guanylylmethylenebisphosphonate
|
|
|
|
| used as a GTP analog by 9001246
|
|
|
|
| CID 36735 Guanylyl Imidodiphosphate
|
|
|
|
| A non-hydrolyzable analog of GTP, in which the oxygen atom bridging the beta to the gamma phosphate is replaced by a nitrogen atom. It binds tightly to G-protein in the presence of Mg2+. The nucleotide is a potent stimulator of adenylate cyclase. [PubChem]
|
|
|
|
| glutathione S-transferase
|
|
|
|
| a handle used to describe or isolate a protein fused to GST
|
|
|
|
| guanosine 5'-O-[gamma-thio]triphosphate
|
|
|
|
| nonhydrolyzable G-protein-activating analog of GTP
|
|
|
|
| a Sort used in curation shorthand to describe the way a protein is identified in an experiment
|
|
|
|
| TLR4 loss-of-function mutation in C3H/HeJ mice
|
|
|
|
| a method used to detect nuclear export
|
|
|
|
| a peptide tag containing multiple histidines used for identifying proteins
|
|
|
|
| a handle used to identify or isolate proteins labeled with His
|
|
|
|
| a Protein, Chemical, or nucleic acid used to "pull" Subject out of a lysate or reaction
|
|
|
|
| high performance liquid chromotography
|
|
|
|
| High Performance Liquid Chromatograph followed by Phosphoamino Acid Analysis and Edman Degradation.
|
|
|
|
| knockdown in a cell line by homologous recombination
|
|
|
|
| two promoterless targeting vectors containing either a geneticin or hygromycin resistance gene in place of genomic p53 sequences were sequentially transfected into HCT116 p53+/+ cells to disrupt both p53 alleles [30] 18324520
|
|
|
|
| [30]. Bunz F, Dutriaux A, Lengauer C, Waldman T, Zhou S, Brown JP, Sedivy JM, Kinzler KW, Vogelstein B. Requirement for p53 and p21 to sustain G2 arrest after DNA damage. Science 1998;282:1497–1501. [PubMed: 9822382]
|
|
|
|
| a prefix used to designate a protein expressed in insect cells and purified by immunoprecipitation or pulldown
|
|
|
|
| Inductively coupled plasma atomic emission spectroscopy
|
|
|
|
| Inductively coupled plasma atomic emission spectroscopy (ICP-AES), also referred to as inductively coupled plasma optical emission spectrometry (ICP-OES), is an analytical technique used for the detection of trace metals. It is a type of emission spectroscopy that uses the inductively coupled plasma to produce excited atoms and ions that emit electromagnetic radiation at wavelengths characteristic of a particular element.[1][2] The intensity of this emission is indicative of the concentration of the element within the sample. [Wikipedia]
|
|
|
|
| In Cell Western, a detection method
|
|
|
|
| fixed by the addition of 50 μL of a 5X Mirsky’s solution (National Diagnostics, Atlanta, GA) for 60 min
|
|
|
|
| washed in Tris-buffered saline, pH 7.4.
|
|
|
|
| incubated in TBS containing 0.1% Triton-X100 and 0.1% bovine serum albumin (blocking buffer) for 2 h
|
|
|
|
| incubated overnight at 4°C with primary antibodies diluted in blocking buffer
|
|
|
|
| incubated with europium-labeled secondary antibody for 90 min at room temperature in the dark
|
|
|
|
| incubated with Delphia Enhancement Solution for 120 min
|
|
|
|
| Fluorescence is quantified an Envision 2101 multilabel reader (Perkin Elmer, Waltham, MA).
|
|
|
|
| An activity assay performed on a kinase embedded in a polyacryamide gel.
|
|
|
|
| immunoprecipitate or pull-down
|
|
|
|
| The complex isolated from a lysate using an antibody against a protein or a protein-tag, or by pull down with things other than antibodies the bind to protein or protein-tag (such as GST:GSH, m7GTP, biotin:streptavidin)
|
|
|
|
| the source of an immunoprecipite used in a test-tube experiment
|
|
|
|
| used when cells are treated with an external agent (addition of a reagent or application of a stress)
|
|
|
|
| an assay used to determine the ability of the complex immunoprecipitated with a protein to phosphorylate a substrate
|
|
|
|
| a prefix used to designate a modified protein expressed from a knockin sequence driven by the endogenous promoter.
|
|
|
|
| a modification used for Ubiquitin polymerized via K48 linkages
|
|
|
|
| a modification used to for Ubiquitin polymerized via K63 linkages
|
|
|
|
| a modification used to describe a protein bound to Ubiquitin polymerized via K63 linkages
|
|
|
|
| a modification used to describe a protein bound to Ubiquitin polymerized via K48 linkages
|
|
|
|
| an antibody to K63-linked Ubiquitin
|
|
|
|
| an antibody that detects acetylated lysines
|
|
|
|
| an immunoprecipitation with an antibody that detects acetylated lysines
|
|
|
|
| the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome
|
|
|
|
| a tag derived from a bacterial repressor protein which activates transcription from a Lex operator-driven reporter gene when fused to activated transcription factors
|
|
|
|
| a handle used to enable activated transcription factors to interact with a LexA-reporter
|
|
|
|
| anything that binds to a receptor on the outside surface of a cell
|
|
|
|
| note: things that bind to nuclear receptors (eg estrogen binding to ERa) are classified as Ligands in this model.
|
|
|
|
| Epstsein-Barr virus latent membrane protein-1
|
|
|
|
| lipopolysaccaride from E.coli
|
|
|
|
| Lps-S.min: from Salmonella minnesota Re595
|
|
|
|
| Laser Scanning Fluorescence Cytometer
|
|
|
|
| 7-methyl-GTP Sepharose, a synthetic analog of the mRNA 7-methylguanosine cap complex
|
|
|
|
| a handle used to represent capped-mRNA
|
|
|
|
| a handle used to describe or isolate a protein fused to MalBP
|
|
|
|
| Mammalian Two Hybrid method
|
|
|
|
| In the mammalian two-hybrid system, protein-protein interactions are detected by fusing one test protein to the Gal4 DNA binding domain, fusing a second test protein to the strong transcriptional activation domain of the VP16 protein, and coexpressing these with the GAL4-dependent reporter. An interaction between these two proteins results in activation of a Gal4-dependent luciferase reporter by the VP16 activation domain.
|
|
|
|
| 3'-O-(N- methylanthraniloyl)guanosine 5'-diphosphate, a fluorescent analog of GDP
|
|
|
|
| 3'-O-(N- methylanthraniloyl)guanosine 5'-triphosphate, a fluorescent analog of GTP
|
|
|
|
| a microbial product, a component of petidoglycan
|
|
|
|
| a chemical modification of a protein after its translation
|
|
|
|
| a Sort used in curation shorthand to describe the modification of a protein
|
|
|
|
| a handle used when a protein is identified by Mass Spectroscopy
|
|
|
|
| bacteriophage MS2 coat protein
|
|
|
|
| a handle used to describe a protein fused to MS2
|
|
|
|
| Mycobacterium tuverculosis
|
|
|
|
| a change in the sequence of a protein
|
|
|
|
| a Sort used in curation shorthand to describe the mutation of a protein
|
|
|
|
| a handle used when a protein is identified by its migration on an SDS-PAGE gel
|
|
|
|
| a mutation that targets proteins to the cell membrane
|
|
|
|
| note: when myr is used as a mutation it means that a myristolyation site (usually from Src) is fused at the N-terminus of an expressed protein
|
|
|
|
| Proteins are separated by gel electrophoresis under non-denaturing conditions.
The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are detected using antibodies specific to the target protein.
|
|
|
|
| Lysates are run on non-denaturing PAGE gels, blotted, and stained for Subject.
|
|
|
|
| Note: If the dectected Protein complex is approximately twice the molecular weight of the uncomplexed Protein, then the assay is called "dimerization". Otherwise, "oligomerization" is used.
|
|
|
|
| Limitations: Does not distinquish between a complexes of Subject:Subject and Subject:OtherProtein (of a similar size).
|
|
|
|
| used for Ubiquitionation assays where noncovalent protei-protein interactions are disrupted by boiling lysates in 1% SDS before IP
|
|
|
|
| an method used to detect nuclear export
|
|
|
|
| a warning added to an extra to indicate that inhibition of a positive change may be due to inhibition of the basal state rather than the change in state
|
|
|
|
| Nonstructured-Protein-1 from Influenza Virus
|
|
|
|
| a modification used to with GTP-binding proteins that have been depleted of GTP and GDP
|
|
|
|
| a modification used to with genes that are actively expressing mRNA
|
|
|
|
| a prefix used to designate a purified protein
|
|
|
|
| In PL, a purified protein is an endogenous protein purified by biochemical techniques from cells or tissues
|
|
|
|
| P100 Fraction: a fraction containing cell membranes minus nuclei
|
|
|
|
| Lyse cells without detergent in hypotonic buffer
|
|
|
|
| Sonication, douncing, scraping
|
|
|
|
| a lectin that causes T cells to proliferate
|
|
|
|
| an antibody that detects a specific phosphorylation site when it is phosphorylated
|
|
|
|
| a handle used to describe a protein identified by an antibody to a specific phosphorylation site
|
|
|
|
| an immunoprecitiptate by anti-phosphorylation site antibody
|
|
|
|
| release of inorganic phosphate into solvent
|
|
|
|
| plasma membrane fraction (method #1)
|
|
|
|
| Lyse cells without detergent
|
|
|
|
| Sonication, douncing, scraping, freeze thaw
|
|
|
|
| Wash and resuspend pellet
|
|
|
|
| Layer on 38% sucrose cushion
|
|
|
|
| save interface and dilute
|
|
|
|
| ouabain-sensitive p-nitrophenylphosphatase
|
|
|
|
| decrease in sarcoplasmic reticulum marker EGTA-sensitive Ca++-ATPase
|
|
|
|
| plasma membrane fraction (method #2)
|
|
|
|
| Fractionation method [7479734, 11358964]
|
|
|
|
| Lyse cells without detergent
|
|
|
|
| Sonication, douncing, scraping, freeze thaw
|
|
|
|
| Low-speed spin (1000-500g)
|
|
|
|
| Layer on 30% Percoll cushion
|
|
|
|
| Spin 84,000-90,000g for 30 min
|
|
|
|
| save visible band and dilute
|
|
|
|
| Enrichment of plasma membranes was monitored by Western analysis for the plasma membrane marker protein, the ouabain-sensitive Na+/K+ ATPase versus the mitochondrial specific protein Porin. 11358964
|
|
|
|
| in some cases poly is followed by a number
|
|
|
|
| these are used to distinguish between different Ubiquitin polymers accorded to the Ubiquitin ligases used
|
|
|
|
| a symbol used in curation shorthand to describe the origin of a protein
|
|
|
|
| if the Protein has no prefix, then it is an endogenous protein
|
|
|
|
| if prefixed with "x" then it is a protein expressed ectopically in a eukaryotic cell
|
|
|
|
| if prefixed with "k" then it is a mutated protein expressed from a "knockin" sequence driven by the endogenous promoter.
|
|
|
|
| if prefixed with "r" then it is a protein expressed in a prokaryotic cell and purified
|
|
|
|
| if prefixed with "p" then it is a protein that has been purified from mammalian tissues
|
|
|
|
| extended (> 6 hr) pretreatment of cells with a stress or chemical
|
|
|
|
| Lps [preconditioning] causes endotoxin tolerance
|
|
|
|
| PMA [preconditioning] causes down regulation of cellular response to PMA
|
|
|
|
| a molecule made of amino-acids
|
|
|
|
| an antibody that detects phosphoserine
|
|
|
|
| an immunoprecipitate by anti-phosphoserine antibody
|
|
|
|
| an antibody that detects phosphoserine/threonine
|
|
|
|
| an immunoprecipitate by anti-phosposerine/threonine antibody
|
|
|
|
| an antibody that detects phosphoserine/threonine
|
|
|
|
| an immunoprecipitate by anti-phospothreonine antibody
|
|
|
|
| an antibody that detects phosphotyrosine
|
|
|
|
| an immunoprecipitate by anti-phosphotyrosine antibody
|
|
|
|
| a prefix used to designate a protein expressed in bacteria or by In Vitro Translation
|
|
|
|
| a handle used when a protein is identified by the DNA sequence it binds to
|
|
|
|
| re-expression of a protein in a knock-out cell
|
|
|
|
| any solid support bound to a recombinant protein
|
|
|
|
| used when a positive change is significantly increased in the absence of an endogenous protein
|
|
|
|
| reverse transcriptase PCR
|
|
|
|
| S100 Fraction: a fraction containing soluble cytoplasmic proteins
|
|
|
|
| Lyse cells without detergent in hypotonic buffer
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| Sonication, douncing, scraping
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| Selective amplification via biotin- and restriction-mediated enrichment
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| Lavery,D.J., Lopez Molina,L., Fleury,O.F. and Schibler,U. (1997) Selective amplification via biotin- and restriction-mediated enrichment (SABRE), a novel selective amplification procedure for detection of differentially expressed mRNAs. Proc. Natl Acad. Sci. USA, 94, 6831–6836.
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| Secreted Alkaline Phosphatase
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| a preparation of agarose used as a solid support for recombinant proteins
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| a handle used to describe a protein or chemical identified using Silver Stain
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| used when an antibody to a specific site on a protein is used as a detection method but the source does not report which site
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| used in activity assays (IVKA, IVLKA, IVGefA) when the source does not report the substrate used
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| a Maude expression that specifies the type or classification of a term
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| a streptavidin binding peptide used as a protein tag
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| a handle used to describe a protein tagged with SBP
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| Surface Plasmon Resonance
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| A protein tag derived from the N-terminus of RNaseA consisting of Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser. Binds to S-Protein RNaseA(21-124).
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| a handle used to describe a protein tagged with STag
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| something immunoprecipitated with anti-Sumo antibody
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| localizes to the same position but takes up less space
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| The first item in the first line of a datum - the focus of an experiment
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| In this model, the subject can be a Protein, a Family, a Composite, or a Gene.
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| the removal of bound ligand on the surface of a cell
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| an adverb used with extras to describe an effect two treatments which is greater than sum of the effect of each treatment alone.
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| an antibody to a fusion tag on an expressed or recombinant Protein
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| an experiment performed without cells or animals
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| Thin Layer Chromatography
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| used when the time of a Stimulus is not reported
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| the addition of something to cells or proteins to produce an observable change in state
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| an antibody to a tag on expressed Sumo
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| something immunoprecipitated with an antibody to a tag on expressed Sumo
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| an antibody to a tag on expressed Ubiquitin
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| something immunoprecipitated with an antibody to a tag on expressed Ubiquitin
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| something immunoprecipitated with anti-Ubiquitin antibody
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| a herpes simplex virus (HSV)-encoded transcriptional activator protein
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| Denatured proteins are separated using SDS-PAGE. The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are detected using antibodies specific to the target protein.
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| Western Blot Mobility Shift
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| Western Blot Mobility Shift before and after PPase treatment
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| in some cases proteins are given the designation WT to distinguish it from the mutated or modified version.
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| a prefix used to designate a expressed protein expressed in eukaryotic cells
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| a fluorescent protein fused to an expressed protein
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| a handle used to identify a protein fused to a fluorescent protein
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| chemical crosslinking that creates covalent bonds between proteins in close proximity
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| 2-Dimensional PhosphoPeptide Mapping
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| a method used to determine the oligomerization state of a protein
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| Cells are transfected with a plasmid expressing Subject1-tag1 and another plasmid expressing Subject2-tag2.
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| Subject2-tag2 is immunoprecipitated with anti-tag2 antibody
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| The amount of Subject1 in the immunoprecipitate is analyzed by WB using an anti-tag1 antibody.
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| Limitations: Does not provide information about the number of Subjects in the complex.
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| treatment of cells with 3H-acetate in the presence of cyclohexamade (CHX)
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| Guanosine diphosphate labeled with 3H
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| a handle used when 14C is used as a radiolabel
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| acetyl-CoA labeled with 14C
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| a handle used when 32P is used as a radiolabel
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| Adenosine triphosphate labeled with 32P
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| Guanosine triphosphate labeled with 32P.
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| metabolic labeling with 32P
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| Phosphoamino acid analysis on proteins labeled metabolically with 32P
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| release of 32P into solvent
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| a handle used when 35S is used as a radiolabel
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| Guanosine 5'-O-[gamma-thio]triphosphate, a nonhydrolyzable G-protein-activating analog of guanosine triphosphate (GTP), labeled with 35S.
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| a method for determining protein stability
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| a handle used when 125I is used as a radiolabel
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| A ligand labelled with 125I
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| a handle used to identify TgfbR1 and/or TgfbR2
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| 125I labeled Tgfb1 is added to cells and covalently crosslinked to the receptors it binds
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