Methods to investigate protein–protein interactions

identify binary protein interactionsmany methods
There are many methods to investigate protein–protein interactions which are the physical contacts of high specificity established between two or more protein molecules involving electrostatic forces and hydrophobic effects.wikipedia
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Protein–protein interaction

interactprotein-protein interactionsprotein-protein interaction
There are many methods to investigate protein–protein interactions which are the physical contacts of high specificity established between two or more protein molecules involving electrostatic forces and hydrophobic effects.
PPIs have been studied with many methods and from different perspectives: biochemistry, quantum chemistry, molecular dynamics, signal transduction, among others.

Biacore

Best known are Biacore instruments which were the first commercially available.
SPR is one of many methods for protein-protein and protein-ligand interaction assessment, see Methods to investigate protein–protein interactions.

Static light scattering

light scatteringStatic Light Scattering (SLS)Zimm method
Static light scattering (SLS) measures changes in the Rayleigh scattering of protein complexes in solution and can characterize both weak and strong interactions without labeling or immobilization of the proteins or other biomacromolecule.
A more sophisticated analysis known as 'composition-gradient static (or multi-angle) light scattering' (CG-SLS or CG-MALS) is an important class of methods to investigate protein–protein interactions, colligative properties and other macromolecular interactions as it yields, in addition to size and molecular weight, information on the affinity and stoichiometry of molecular complexes formed by one or more associating macromolecular/biomolecular species.

Coulomb's law

Coulomb forceelectrostatic forceCoulomb interaction
There are many methods to investigate protein–protein interactions which are the physical contacts of high specificity established between two or more protein molecules involving electrostatic forces and hydrophobic effects.

Hydrophobic effect

hydrophobichydrophobic interactionshydrophobic core
There are many methods to investigate protein–protein interactions which are the physical contacts of high specificity established between two or more protein molecules involving electrostatic forces and hydrophobic effects.

Sensitivity and specificity

sensitivityspecificitysensitive
Each of the approaches has its own strengths and weaknesses, especially with regard to the sensitivity and specificity of the method.

Epitope

epitopesantigenic determinantantigenic determinants
Co-immunoprecipitation is considered to be the gold standard assay for protein–protein interactions, especially when it is performed with endogenous (not overexpressed and not tagged) proteins.

Antibody

antibodiesimmunoglobulinimmunoglobulins
The protein of interest is isolated with a specific antibody.

Western blot

Western blottingimmunoblottingblotting, western
Interaction partners which stick to this protein are subsequently identified by Western blotting.

Bimolecular fluorescence complementation

BiFCBimolecular fluorescence complementation assaysimultaneously visualise multiple protein complexes in the same cell
Bimolecular fluorescence complementation (BiFC) is a new technique in observing the interactions of proteins.

Affinity electrophoresis

affinity immunoelectrophoresismacromolecular complexes
Affinity electrophoresis as used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding.

Binding constant

association constantaffinityassociates more tightly
Affinity electrophoresis as used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding.

Lectin

lectinslectin protein lectin
Affinity electrophoresis as used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding.

Glycan

glycansN-linked GlycanN-linked glycans
Affinity electrophoresis as used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding.

Ligand

ligandsligand exchangebidentate ligand
Affinity electrophoresis as used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding.

Immunoprecipitation

coimmunoprecipitationco-immunoprecipitationRNA immunoprecipitation
Co-immunoprecipitation is considered to be the gold standard assay for protein–protein interactions, especially when it is performed with endogenous (not overexpressed and not tagged) proteins. Pull-down assays are a common variation of immunoprecipitation and immunoelectrophoresis and are used identically, although this approach is more amenable to an initial screen for interacting proteins.

Immunoelectrophoresis

Rocket immunoelectrophoresisaffinity immunoelectrophoreisimmunochemical
Pull-down assays are a common variation of immunoprecipitation and immunoelectrophoresis and are used identically, although this approach is more amenable to an initial screen for interacting proteins.

Phage display

antibody phage display technologyphage display library
Phage display is used for the high-throughput screening of protein interactions.

Photo-reactive amino acid analog

photo-reactive amino acidphotoreactivePhotoreactive methionine
In-vivo crosslinking of protein complexes using photo-reactive amino acid analogs was introduced in 2005 by researchers from the Max Planck Institute In this method, cells are grown with photoreactive diazirine analogs to leucine and methionine, which are incorporated into proteins.

Diazirine

3''H''-diazirine
In-vivo crosslinking of protein complexes using photo-reactive amino acid analogs was introduced in 2005 by researchers from the Max Planck Institute In this method, cells are grown with photoreactive diazirine analogs to leucine and methionine, which are incorporated into proteins.

Leucine

LeuL-leucineL
In-vivo crosslinking of protein complexes using photo-reactive amino acid analogs was introduced in 2005 by researchers from the Max Planck Institute In this method, cells are grown with photoreactive diazirine analogs to leucine and methionine, which are incorporated into proteins.

Methionine

Metmethionine metabolismL-methionine
In-vivo crosslinking of protein complexes using photo-reactive amino acid analogs was introduced in 2005 by researchers from the Max Planck Institute In this method, cells are grown with photoreactive diazirine analogs to leucine and methionine, which are incorporated into proteins.

Angstrom

Åångströmangstroms
Upon exposure to ultraviolet light, the diazirines are activated and bind to interacting proteins that are within a few angstroms of the photo-reactive amino acid analog.

Tandem affinity purification

affinity purificationTAP tag library
Tandem affinity purification (TAP) method allows high throughput identification of protein interactions.

Cross-link

crosslinkingcross-linkedcrosslink
Chemical cross-linking is often used to "fix" protein interactions in place before trying to isolate/identify interacting proteins.