Protein analysis Flashcards
Why is it important to study protein-protein interactions?
• Reason for studying protein-protein interactions
o Many proteins need to interact with other proteins, ligands, nucleic acids to function
o The regulation of cell function is balanced by the relative affinities of the various protein partners contained within such complexes
o Where two or more proteins interact with each other they may temporarily or permanently form a complex
o A protein complex consists of several proteins and the complex itself provides the function- proteins within the complex may be structural (support or transport) or enzymatic
How do proteins interact?
o How do proteins interact-
PTMs and charge/charge interactions
Covalent interactions e.g. intermolecular disulfide bonds
Non-covalent interactions
What is the best known protein complex?
o The best known protein complex is the ribosome
How many proteins are ribosomes made of?
Comprises of more than 50 proteins, some which provide structural support and others which undertake the function
What is the E.Coli 70S ribosomal subunit made of and what is its function?
The E.coli 70S ribosomal subunit
• 29 individual proteins make up the 70S ribosomal subunit in E.coli
• Proteins may be involved in binding rRNA, providing structural integrity, or in translation processes
o Some proteins are physically separated from each other/don’t physically interact whilst some do- binary level of interactions
What is the largest protein complex in S.cerevisiae?
The ribosome
What is the mitochondrial protein complex?
o The mitochondrial NADH complex
45 individual proteins make up the complex I of the electron transport chain
• Not all proteins interact with each other
Proteins may be involved in complex assembly, providing structural integrity, with 7 encoded by mitochondrial DNA
On what chemical basis do proteins interact with each other?
• Protein-protein interactions-functional implications
o Proteins interact based on charge-charge basis, dissulfide bonds, structural folds, etc.
What are the biological implications of protein-protein interactions/what do they form?
o Receptors
o Interactions form chains as well as complexes
o Chaperones
What are chaperones and are they specific in their interactions?
o Chaperones- aid in maintaining correct folding, chaperon proteins to correct sub-cellular location
Tend to be promiscuous in terms of interactions
o Expect very main interactions
Describe GroEL in E.Coli:
- What it is
- What interactions it makes
- What information can be inferred from it and how this information can be obtained
E.g. GroEL in E.Coli
• GroEL is a chaperone-proteins that assist other proteins to fold-expect a lot of interactions
• Numerous diverse interactions, especially during stress
o Amino acid biosynthesis
o RNA polymerase
o Heat shock proteins
• PPI can provide information regarding protein function
• Pulls down more proteins when there’s been stress
o Stress causes proteins to unfold
• Looked at this using immunoprecipitation
What are methods for looking at protein-protein interactions/complexes? What do they specifically look at?
• Methods for looking at protein-protein interactions/complexes o Yeast-2-hybrid (interactions) o Immunoprecipitation (IP)/affinity chromatography (interactions and/or complexes) o Native PAGE (BN-PAGE) (complexes) o Chemical cross-linking (interactions) o Tandem Affinity Purification (TAP) (interactions and/or complexes)
What is the construction and process of yeast-2-hybrid to study protein-protein interactions?
o Yeast-2-hybrid (interactions)
Uses a report gene (e.g. gal1-lacZ- beta galactosidase) that is transcriptionally activated when two proteins interact
• Bait protein and prey protein
The transcriptional activator has 2 domains:
• A DNA-binding domain
• An activating domain that activates reporter gene
Find proteins (prey) that interact with a single bait on a genome-wide bases- binary interactions
• Limitation- a lot of work
Bait is fused to the DNA-binding domain; preys fuse to the activating domain
Activity is achieved when bait and prey interact- reporter gene is then transcribed
What are the advantages of yeast-2-hybrid?
- Rapid, high throughput
- Can test many 1:1 interactions- good first pass
What are the disadvantages of yeast-2-hybrids?
- False positives if the bait is a transcriptional activator as everything gets switched on
- The fusion proteins may not have in vivo conformation and therefore not bind with in vivo specificity
- Bait and prey may not fold correctly in yeast
- Fusions may be toxic to yeast host
- Weak interactions are amplified- hence increased number of false positives
- Gives no information about bigger complexes
What is the most commmonly used method to look at interactions?
o Immunoprecipitation (IP)/affinity chromatography (interactions and/or complexes)
How is immunoprecipitation/affinity chromatography used to study protein-protein interactions and/or complexes/ how does it work?
Uses an antibody against a protein-of-interest under non-denaturing/native conditions
Antibody binds the protein and any interacting partners as a complex (that is X binds to Y binds to X: XYZ will be captured)
Requires native and gentle conditions
The complex is then captured and subjected to SDS-PAGE or directly digested with trypsin and subjected to LC-MS/MS
Proteins within a complex, but not absolute interactions
• Not getting binary interactions
What is the immunoprecipitation workflow?
Immunoprecipitation- workflow
• Make antibody against protein-> do immune precipitation-> do a proteolytic digest or SDS-PAGE
o SDS-PAGE-> excise band-> digest-> MS/MS and identify
o Proteolytic digest-> LC-> MS/MS and identify
What is a disadvantage of immunoprecipitation?
Disadvantage-
• Non-specific binding to immunoglobin chain (will be pulled down because bound to immunoglobin instead of because bound to protein)-> lots of false positives
What is a variation of immunoprecipitation that overcomes its disadvantages of false positives?
Variation- no antibodies/use the protein-of-interest (affinity chromatography)
How is immunoprecipitation performed when the protein-of-interest is used instead of antibodies? How is it designed? What is the disadvantage of this?
• The protein of interest (in this case S14) is expressed as a fusion with a cleavable affinity tag
• S14 protein is immobilised onto agarose beads via a tag. Nuclear cell extracts are incubated with the beads and washed. Tag-specific proteases are used to cleave the tag, which results in elution of all proteins that are specifically bound to S14. The eluted proteins are resolved by 1D or 2DE. The bands are excised and analysed by MS
o The advantage is that proteins non-specifically bound to the matrix or the tag are not eluted
What are the types of tags that can be used with immunoprecipitation and what are their respective proteases?
o Types of tags and appropriate proteases
FLAG-tag- can be removed with enteropeptidase
His-tag- can be removed with endo/exopeptidase
GST-fusion- can be removed with thrombin
How can false positives be reduced with iDIRT/how does this immunoprecipitation technique work?
Reducing false positives- iDIRT
• 1:1 mix of light (tagged-protein) and heavy (wild-type) sample-> immunoisolation-> mass spectrometry
• If the peak is seen in both the light and heavy sample, means that it binds to the affinity support or tag, it will be seen in both the light and heavy samples (non-specific binding)
How does native PAGE work for analyses of protein complexes? What is it used for?
Non-reducing PAGE (non-denaturing)
Proteins are retained in complex
• Can resolve complexes spanning 15kDa to approximately 10 mDa
• Will migrate through the gel based on complex size, shape and charge
Coomassie G-250 acts as a charge shift molecule
• Imparts a negative charge that alters electrophoretic mobility
• Contained within cathode buffer and sample loading buffer
• Blue native PAGE
Can perform a secondary SDS-PAGE or directly digest complexes with trypsin and subject to LC-MS/MS
• Would take blue native PAGE gel ->then separate on a secondary SDS-PAGE
Resolves proteins within a complex, but not absolute interactions
Workflow- 2-dimensional BN/SDS-PAGE
• Preparation of total cellular lysate-> dialysis of the lysate against BN-bugger-> 1st dimension BN-PAGE-> 2nd dimension SDS-PAGE-> Immuno-blotting or silver staining