protein complex and protein-protein interaction 彭鲲鹏国家人类基因组北方研究中心...

Protein Complex and Protein Complex and Protein-protein InteractionProtein-protein Interaction

彭鲲鹏国家人类基因组北方研究中心Email: [email protected]

Central dogma: Central dogma: the story of lifethe story of life

RNA

DNA

Protein

Protein is the final player in cell lifeProtein is the final player in cell life

Proteins function in association with Proteins function in association with other proteins or biomolecules, but other proteins or biomolecules, but

not in isolationnot in isolation

Introduction to ProteomicsIntroduction to Proteomics

the analysis of genomic complements of proteins

dynamicsystematicdiscovery-driven

Goals of ProteomicsGoals of Proteomics

to discover protein function

to understand cellular processes

to understand disease states

to discover drug target

to identify biomarker

Types of ProteomicsTypes of ProteomicsExpression Proteomics

– Quantitative study of protein expression and their changes between samples that differs by some variable

Functional Proteomics– To study protein-protein interaction, 3-D

structures, cellular localization and PTMs in order to understand the physiological function of the whole set of proteome.

ApproachesApproaches

Genetic:yeast two-hybridphage display

Biochemical:Blue native PAGEFar Western Pull-downCoimmunoprecipitationTAPCrosslinking

Bioinformatic:Co-occurrenceNeighborhoodSurface patch

Biophysical:Mass SpectrometrySPRFRET

Blue Native PAGEBlue Native PAGE

separation of native proteins in complex.Coomassie Blue G: stable and negatively

charge multiprotein complex.6-aminocaproic acid: solubilize membrane

protein complex instead of salts.the resolution is not so high that the

prepurification is needed.

Anal Biochem 1991, 199:223-231


detergent

CBB

6-ACA

_

+


Sample Preparation

Blue Native PAGE

SDS-PAGE

Solubilization with nonionic detergent (laurylmaltoside, TX-100, CHAPS, Mega 9, octylglucoside, Brij 35, etc), supplemented with 6-aminocaproic acid

Separation gel: 6-13% gradientCathode buffer contains 0.02% Coomassie blue G250

Separation of members of multiprotein complex

Blue Native PAGE of chloroplast Blue Native PAGE of chloroplast thylakoid membranesthylakoid membranes

BBRC 1999, 259:569-575

BN-PAGE of solubilized chloroplast thylakoid membranes (a) followed by SDS–PAGE in the second dimension (b).CF0F1 ATP synthase was indicated.

Blue Native PAGE of chloroplast Blue Native PAGE of chloroplast thylakoid membranesthylakoid membranes

BBRC 1999, 259:569-575

lane 1: LMW marker

lane 2: CF0F1 ATP synthase, purified by density gradient centrifugation

lane 3: electroeluted protein from the intense band (Rf= 0.38) in BN-PAGE (a).

Blue Native PAGE of multiprotein Blue Native PAGE of multiprotein complex from whole cellular lysatecomplex from whole cellular lysate

MCP 3:176-182, 2004

Dialysis permits the analysis of multiprotein complexes of whole cellular lysates by BN-PAGE.

Identification and analysis of distinct proteasomes by WCL 2D BN/SDS-PAGE

A, WCL of HEK293 cells was separated by 2D BN/SDS-PAGE (5.5–14 and 10%, respectively), and immunoblotting was performed with specific antibodies recognizing either subunits of the 20S core complex (Mcp21 and 2), or a subunit of the 19S cap of the 26S proteasome (S4 ATPase), or a subunit of the PA28 regulatory subunit (PA28).

B, An identical sample was boiled in 1% SDS, resolved by 2D BN/SDS-PAGE, and immunoblotted as described in A.

MCP 3:176-182, 2004


Visualization of MPCs on a 2D WCL BN/SDS gel

B, WCL of HEK293 cells was boiled with 1% SDS before separation and staining.

A, WCL of HEK293 cells was prepared using Triton X-100 and separated by 2D BN/SDS-PAGE (5.5–17 and 10%, respectively).

MCP 3:176-182, 2004


Far WesternFar Western

Max: functional cloning of a Myc-binding proteinMax: functional cloning of a Myc-binding protein

A. CKII, casein kinase II phosphorylation site; BR, basic region; HLH, helix-loop-helix; LZ, leucine zipper.

B. Plaques that express beta-galactosidase fusion prteins were screened for their ability to react with 125I-labeld GST-MycC92. Top left, secondary plating of five putative positive demonstrates the reactivity of two of the primary plaques, Max11 and Max14. Top right, as a negative control, GST was labeled to a similar specific activity and compared with GST-MycC92 for bidning to Max14 plaques. Bottom, binding of GST-MycC92 to Mzx14 plaques was assayed with or without affinity purified carboxyl terminal-specific anti-Myc (Ab) or peptide immunogen (peptide).

MycC92

Science 251:1211-7, 1991


Association of Rb with HIP1Association of Rb with HIP1

HeLa nulear extract (~100 ug) (lane 1, 2) and HIP1 (~200 ng) purified from HeLa (lane 3, 4) were electrophoresed, blotted, and renatured in situ. Adjacent strips were cut from the filters and probed with 32P-GST-RB(379-928) (lane 1, 3) or 32P-GST-RB(379-928;706F) (lane 2, 4)

Cell 70:351-364, 1992


GST PulldownGST Pulldown

Interactions of Cellular Polypeptides with the Cytoplasmic Domain of the Mouse Fas Antigen


JBC 271:8627-32, 1996

Fas: 45-kilodalton transmembrane receptor that initiates apoptosis;

The biochemical mechanisms responsible for Fas action are incompletely understood;

the cytoplasmic domain is clearly necessary for Fas to function as a receptor;

The cytoplasmic domain does not display any known enzymatic activities but is capable of interacting with a number of proteins.

GST-mFas fusion proteins


149 166 204 293 3061

306194

194

194

194

194

194

292

283

276

268

221

194 306

306221

GST-mFas-associated polypeptides from 32S-labeled HeLa, L929, and Jurkat cell lysates


Preclearation: 25 ug GST/50 ul GSH-Seph.

Incubation: 10 ug GST/GST-mFas-(194-306)

Wash: 0.5% NP-40, 20 mM Tris, pH 8.0, 200 mM NaCl

Elution: 50 ul 20 mM GSH in 50 mM Tris

GST-mFas-associated polypeptides GST-mFas-associated polypeptides are stable to high salt concentrationsare stable to high salt concentrations


HeLa cell lysates were screened with either GST or GST-mFas-(194–306) as described above except that the Sepharose-protein complexes were washed with Lysis Buffer containing different salt concentrations (as indicated). The eluted material was subjected to 12% SDS-PAGE and fluorography.

Association is blocked by preincubation with a polyclonal antibody against GST-mFas


A. the antibody recognized the Fas intracellular domain;

B. association of proteins from HeLa lysate with GST-mFas was blocked by anti-GST-mFas IgG;

C. anti-GST antibody had no effect up to 100 ug of IgG.

Differential association with mutant forms of GST-mFas


HeLa

L929

292 283 276 268 221

Schematic representation of the mouse Fas antigen and its binding proteins


Epitope taggingEpitope tagging1

2

3

4 5

6-9


Co-ImmunoprecipitationCo-ImmunoprecipitationIn the intact cell, protein X is present in a complex with protein Y. This complex is preserved after cell lysis and allows protein Y to be coimmunoprecipitated with protein X (complex 1). However, the disruption of subcellular compartmentalization could allow artifactual interactions to occur between some proteins, for example, protein X and protein B (complex 2). Furthermore, the antibody that is used for the immunoprecipitation may cross-react nonspecifically with other proteins, for example, protein A (complex 3). The key to identification of protein:protein interactions by coimmunoprecipitation is to perform the proper controls so as to identify protein Y but not protein A and B.

Co-ImmunoprecipitationCo-Immunoprecipitation

Antibody Identification

The protein against which the antibody was raised should be precipitated from cell lysate.

(1) Independent antibodies raised against the same protein recognize the same polypeptide;

(2) Target protein should not be identified with antibodies from cell lines without target protein;

False positive and controlFalse positive and control


1. Antibody controlMonoclonal Ab: another MoAb against similar proteinAntiserum: serum before immunization from the same animalPolyclonal Ab: purified PoAb against another protein

2. Multiple antibodiesdifferent Abs against different epitopes; the epitope may be the site for association with other proteins;

3. Cell lines depleted of target proteinControl experiment should be practised in depleted cell lines

4. Inactive biological mutant5. Interaction verification before and after cell lysis

unphysiological interaction

Reduction of nonspecific protein Reduction of nonspecific protein backgroundbackground


1. to increase ionic strength in wash buffer;

2. to reduce the amount of primary Ab;

3. to preclear cell lysate with control Ab.

Binding of pVHL to Elongin B and CBinding of pVHL to Elongin B and C


1. von Hippel-Lindau disease is a hereditary cancer 1. von Hippel-Lindau disease is a hereditary cancer syndrome characterized by the development of multiple syndrome characterized by the development of multiple tumors;tumors;

2. VHL susceptibility gene, mutated in the majority of 2. VHL susceptibility gene, mutated in the majority of VHL kindreds, is a tumor suppressor;VHL kindreds, is a tumor suppressor;

3. to elucidate the biochemical mechanisms underlying 3. to elucidate the biochemical mechanisms underlying tumor suppression by pVHL, search for cellular proteins tumor suppression by pVHL, search for cellular proteins that bound to wt pVHL, but not to tumor-derived pVHL that bound to wt pVHL, but not to tumor-derived pVHL mutants.mutants.

Science 269:1444-6, 1995

Identification of VHL-associated proteinsIdentification of VHL-associated proteins


Lysates from 786-O renal carcinoma cells, transfected with the indicated pVHL constructs, were immunoprecipitated with anti-HA (A and B) or with anti-VHL (C).

Detection by autoradiography (A, C) or by immunoblotting (B).

open arrows: exo pVHL

closed arrows: VHL-AP

pVHL(1-115): without residues frequently altered by naturally occurring VHL mutations and, unlike pVHL(wt), does not suppress tumor formation in vivo. pVHL(167W): the predicted product of a mutant VHL allele that is common in VHL families.

anti-VHL

Mapping the p14 and p18 binding Mapping the p14 and p18 binding site on pVHLsite on pVHL


a-HA

A. 786-O cells producing HA-VHL(wt) or HA-VHL(1-115) were labeled with 35S-methione, lysed, and immunoprecipitated with anti-HA. Parental 786-O cells were similarly labeled, lysed, and incubated with GSH Sepharose preloaded with GST-VHL(117-213) or GST alone.

B and C. 786-O cells were labeled, lysed, and incubated with GSH Sephorase preloaded with the indicated GST-VHL fusion protein. In (C), the indicated peptides (final conc. ~0.1, 1, or 10 uM) were added to the GST-VHL fusion protein before incubation with the radiolabeled extract. The wt peptide is TLKERCLQWRSLVKP (underlined residues are sites of germ-line missense mutations). The mutant peptide is TLKERFLQWRSLVKP.

the binding site for Elongin B and C the binding site for Elongin B and C in pVHLin pVHL


Distribution of germ-line VHL mutations. The shaded region represents the bidning site for Elongin B and C.

Binding of pVHL to Elongin B and Binding of pVHL to Elongin B and Elongin C in vivoElongin C in vivo


A. ACHN (VHL +/+), CAKI-1 (VHL +/+), 786-O (VHL -/-), and 293 (VHL +/+) cells were labeled with 35S-methione, lysed, and immunoprecipitated with anti-VHL or a control antibody. The immunoprecipitaes were washed under high-salt conditions. The identification of pVHL(wt) (open arrow) was confirmed by anti-pVHL immunoblot analysis. The ~19 kD protein immediately above p18 (*) in the ACHN, CAKI-1, and 293 cell anti-VHL immunoprecipitates reacts with a polyclonal antibody to VHL.

B. Comparison of peptides generated by partial proteolysis of Elongin B and C, translated in vitro, with p18 and p14.

TAP: tandem affinity purificationTAP: tandem affinity purification

Sequence and structure of the TAP tagSequence and structure of the TAP tag

CBP TEV Ig BDbait

TAPTAP

Overview of the TAP procedureOverview of the TAP procedureTAPTAP

Schematic representation of the split TAP tag strategy

TAPTAP

Schematic representation of the substraction strategy

TAPTAP

Protein composition of TAP-purified U1 snRNP

TAPTAP

Step-by-step analysis of the TAP strategy

TAPTAP

Proteins present in the final TAP fraction (lanes 7 and 8), or present after each of the single affinity purification steps (lanes 1–4), were analyzed. Snu71-TAP (lanes 1, 3, and 7) or wild-type extracts (lanes 2, 4, and 8) were used. Lane 5: molecular weight marker. Lane 6: an amount of TEV protease identical to the amount used to elute proteins bound to IgG beads (lanes 2, 3, 7, and 8). Right arrows indicate the U1 snRNP-specific proteins including the tagged Snu71p after TEV cleavage; the arrow on the left indicates the Snu71p protein fused to the TAP tag before TEV cleavage.

TAP in higher eucaryotesTAP in higher eucaryotesTAPTAP

Questions:

overexpression

endogenous expression

Solutions:

RNA interference

Knockin technique

Strengths and weaknesses of commonly used affinity approaches for the retrieval

of protein complexes

FRET: FRET: fluorescence resonance energy transferfluorescence resonance energy transfer

When will FRET occur?

1) Spectral overlap

Donor emission spectrum must significantly overlap the absorption spectrum of the acceptor (>30%)

2) Distance between the donor and acceptor is between 2 - 10 nm

3) Favorable orientation of fluorophores

2 ~ 10 nm

Donoremission

Acceptorabsorption

FRETFRET

E: energy transfer efficiency

R0: intermolecular distance when half of energy is transfered

r: distance between fluorophores

E = R06/(R0

6 + r6)

when r = 2R0, E = 1/65

R0 = 4.9 nm

Imaging protein phosphorylation by FRETImaging protein phosphorylation by FRET

target GFP Fab Cy3

transfection microinjectionor incubation

target GFP

Fab Cy3

activator

laser

FRETFRET

Detection of protein interaction by FRETDetection of protein interaction by FRET

target GFP

Fab Cy3Protein 1 CFP

Protein 2 YFP

FRETFRET

Protein 1 Cy3

Protein 2 FITC

in vitro phosphorylation in vivo

FRET reveals interleukin (IL)-1-FRET reveals interleukin (IL)-1-dependent aggregation of IL-1 type I dependent aggregation of IL-1 type I

receptors that correlates with receptors that correlates with receptor activationreceptor activation

FRETFRET

JBC 270:27562-8, 1995

AbbreviationAbbreviationFRETFRET

IL-1: interleukin 1

IL-1 RI: IL-1 type I receptor

IL-1ra: IL-1 receptor antagnist

CHO-mu1c: CHO-K1 cells stably transfected with wild-type IL-1 receptor

CHO-extn: CHO-K1 cells stably transfected with cytoplasmic tail-truncated IL-1 receptor

M5: noncompetitive anti-IL1 RI monoclonal antibody

FITC-M5: M5 labeled with a donor probe, FITC

Cy3-M5: M5 labeled with a acceptor probe, Cy3

IL-1IL-1a-dependent FRET between donor -dependent FRET between donor FITC-M5 and acceptor Cy3-M5 bound to FITC-M5 and acceptor Cy3-M5 bound to IL-1 RI on the surface of CHO-mu1c cellsIL-1 RI on the surface of CHO-mu1c cells

FRETFRET

A, a mixture of 5 nM FITC-M5 and 5 nM Cy3-M5 was incubated with CHO-mu1c cells (3 X 106 cells/ml) containing wild-type transfected receptors for 50 min at 22 °C. IL-1a or IL-1ra was added at a final concentration of 30 nM immediately after the time point at t = 0 min (arrow), and changes in the ratio of Cy3-M5 fluorescence to FITC-M5 fluorescence were monitored over time. Changes in this ratio were also monitored for the control sample to which no ligand was added. B, normalized fluorescence ratio for cells with added IL-1a or IL-1ra calculated from data in A.

IL-1a

IL-1ra

control

IL-1a

IL-1ra

IL-1a but not IL-1ra causes aggregation IL-1a but not IL-1ra causes aggregation between IL-1 RI-labeled with FITC and Cy3 between IL-1 RI-labeled with FITC and Cy3 Fab fragments of M5 as detected by FRETFab fragments of M5 as detected by FRET

FRETFRET

A mixture of 20 nM FITC-M5-Fab and 20 nM Cy3-M5-Fab was added to CHO-mu1c cells transfected with wild-type receptors and incubated at 22 °C for 50 min. IL-1a or IL-1ra was added to a final concentration of 10 nM immediately after the time point at 0 min. Changes in the normalized ratio of Cy3-M5 Fab fluorescence to FITC-M5 Fab fluorescence were monitored over time at 22 °C.

IL-1a

IL-1ra

IL-1-dependent energy transfer between IL-1 RI is temperature

FRETFRET

A mixture of 20 nM FITC-M5 Fab and 12 nM Cy3-M5 Fab was added to CHO-mu1c cells (3 X 106 cells/ml) with transfected wild-type IL-1 RI and preincubated at either 4 °C (A) or 22 °C (B) for 50 min. Immediately after the base-line data point at t = 0 min, IL-1a was added (arrow) at a final concentration of 10 nM to both samples. Changes in the normalized ratio of Cy3-M5 Fab fluorescence to FITC-M5 Fab fluorescence was monitored over time at the corresponding preincubation temperature. At t = 85 min, the temperature for sample (A) was changed from 4 to 22 °C, and the temperature for sample (B) was changed from 22 to 4 °C. Changes in the normalized fluorescence ratio continued to be monitored until t = 180 min.

A

B

IL-1a-dependent FRET can be detected between FITC-M5 Fab and Cy3-M5 Fab bound to the cytoplasmic tail

deleted mutant IL-1 RI on CHO-extn cells

FRETFRET

A mixture of 20 nM FITC-M5 Fab and 12 nM Cy3-M5 Fab was added to wild-type transfected receptors on CHO-mu1c cells and incubated at 22 °C for 50 min (A). A mixture of 20 nM FITC-M5 Fab and 12 nM Cy3-M5 Fab was added to CHO-extn cells (cytoplasmic tail deleted mutant IL-1 RI) and incubated at 22 °C for 50 min (B). IL-1a was added to a final concentration of 20 nM at the arrow, and changes in the normalized ratio of Cy3-M5 Fab fluorescence to FITC-M5 Fab fluorescence were monitored over time at 22 °C.

A

B

SPR: Surface Plasma ResonanceSPR: Surface Plasma Resonance

Diagram of BIAcoreDiagram of BIAcore

SPRSPR

Interactions betweenlectins and immobilized glycoproteins

SPRSPR

SPRSPR

Interactions betweenlectins and immobilized glycoproteins

An overlay plot of binding curves showing the interaction between lectins and immobilized thyroglobulin.

Lectin solutions (50 µg/ml in 10 mM HEPES, 0.5 mM MnCl2 , 0.5 M CaCl2 and 0.05% surfactant, pH 7.4) were injected. Bound lectin was dissociated by 100 mM HCl (15 µl, 5 µl/min).

Summary of the interaction of seven lectins of different nominal specificities with immobilized glycoproteins

Binding of lectin to the glycoprotein is indicated by “+” and lack of binding by “-” in the above table. As control experiments, the lectins were injected over (i) an immobilized non-glycosylated protein (recombinant HIV-1 reverse transcriptase expressed in E. coli) and (ii) a blank surface which was subjected to immobilizationchemistry in absence of a protein. The lectins did not show any binding in the control experiments.

SPRSPR

SPR-MS: SPR-MS: Ligand Fishing with Biacore 3000

SPRSPR

Selective binding, recovery and identification by MALDI MS of a specific interaction partner

SPR MS

Detection Identification

Other important techniques in Other important techniques in protein interaction researchprotein interaction research

Mass Spectrometry

Cross-linking

Ultracentrifuge

ChIP (Chromatin immunoprecipitation)

Mass spectrometry is indispensable for protein identification Mass spectrometry is indispensable for protein identification and will be in the center of proteomics research.and will be in the center of proteomics research.

Mass Spectrometry

High sensitivityHigh resolutionHigh throughput

Reference data basesReference data bases

Interactions– MIPS– DIP– YPD – Intact (EBI)– BIND/ Blueprint– GRID– MINT

Prediction server– Predictome (Boston U)– Plex (UTexas)– STRING (EMBL)

Protein complexes– MIPS– YPD

From defining the proteome

to understanding function

Thanks!

protein complex and protein-protein interaction 彭鲲鹏 国家人类基因组北方研究中心...

Documents

protein complex and protein-protein interaction 彭鲲鹏国家人类基因组北方研究中心...