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--- experimental_systems [2018/07/27 16:35]
jenn [Genetic Interactions]
+++ experimental_systems [2018/08/06 09:16]
jenn [Physical Interactions]
@@ Line 22: / Line 22: @@
   *  **Co-localization** - An interaction is inferred from two proteins that co-localize in the cell by indirect immunofluorescence only when in addition, if one gene is deleted, the other protein becomes mis-localized. This also includes co-dependent association of proteins with promoter DNA in chromatin immunoprecipitation experiments (write "ChIP" in qualification text box), and in situ proximity ligation assays (write "PLA" in qualification text box).
-  *  **Co-purification** - An interaction is inferred from the identification of two or more protein subunits in a purified protein complex, as obtained by several classical biochemical fractionation steps, or else by affinity purification and one or more additional fractionation steps. Note that a Western may also be used to identify the subunits, but that this differs from "Affinity Capture-Western" because it involves at least one extra purification step to get rid of contaminants. Typically, TAP-tag experiments are considered to be affinity captures and not co-purification experiments. If there is no obvious bait-hit directionality to the interaction, then the co-purifying proteins should be listed as a complex (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15907469&query_hl=4&itool=pubmed_DocSum|PMID: 15907469]]). If only co-fractionation is demonstrated, i.e. if the interaction is inferred from the presence of two or more protein subunits in a partially purified protein preparation (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11294905&query_hl=4&itool=pubmed_DocSum|PMID: 11294905]], Fig. 9), then use "Co-fractionation" instead.
+  *  **Co-purification** - An interaction is inferred from the identification of two or more protein subunits in a purified protein complex, as obtained by several classical biochemical fractionation steps, or else by affinity purification and one or more additional fractionation steps. Note that a Western or mass-spec may also be used to identify the subunits, but that this differs from "Affinity Capture-Western" or "Affinity Capture-Mass Spec" because it involves at least one extra purification step to get rid of contaminants (e.g. [[https://www.ncbi.nlm.nih.gov/pubmed/19343713?dopt=Abstract|PMID: 19343713]]). Typically, TAP-tag experiments are considered to be affinity captures and not co-purification experiments. If there is no obvious bait-hit directionality to the interaction, then the co-purifying proteins should be listed as a complex. If only co-fractionation is demonstrated, i.e. if the interaction is inferred from the presence of two or more protein subunits in a partially purified protein preparation (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11294905&query_hl=4&itool=pubmed_DocSum|PMID: 11294905]], Fig. 9), then use "Co-fractionation" instead.
   *  **Far Western** - An interaction is inferred when a bait protein is immobilized on a membrane and a prey protein that is incubated with the membrane localizes to the same membrane position as the bait protein. The prey protein could be provided as a purified protein probe (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12857883&query_hl=4&itool=pubmed_DocSum|PMID: 12857883]], Fig. 7).

Experimental Evidence Codes

Differences