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Analysis of Thylakoid Membrane Protein Complexes by Blue Native Gel Electrophoresis

Published: September 28th, 2018



1Molecular Plant Biology, Department of Biochemistry, University of Turku

A protocol for the elucidation of plant thylakoid protein complex organization and composition with blue native polyacrylamide gel electrophoresis (BN-PAGE) and 2D-SDS-PAGE is described. The protocol is optimized for Arabidopsis thaliana, but can be used for other plant species with minor modifications.

Photosynthetic electron transfer chain (ETC) converts solar energy to chemical energy in the form of NADPH and ATP. Four large protein complexes embedded in the thylakoid membrane harvest solar energy to drive electrons from water to NADP+ via two photosystems, and use the created proton gradient for production of ATP. Photosystem PSII, PSI, cytochrome b6f (Cyt b6f) and ATPase are all multiprotein complexes with distinct orientation and dynamics in the thylakoid membrane. Valuable information about the composition and interactions of the protein complexes in the thylakoid membrane can be obtained by solubilizing the complexes from the membrane integrity by mild detergents followed by native gel electrophoretic separation of the complexes. Blue native polyacrylamide gel electrophoresis (BN-PAGE) is an analytical method used for the separation of protein complexes in their native and functional form. The method can be used for protein complex purification for more detailed structural analysis, but it also provides a tool to dissect the dynamic interactions between the protein complexes. The method was developed for the analysis of mitochondrial respiratory protein complexes, but has since been optimized and improved for the dissection of the thylakoid protein complexes. Here, we provide a detailed up-to-date protocol for analysis of labile photosynthetic protein complexes and their interactions in Arabidopsis thaliana.

Large multisubunit protein complexes photosystem PSI and PSII, Cyt b6f and ATPase coordinate the production of NADPH and ATP in photosynthetic light reactions. In higher plant chloroplasts, the complexes are located in the thylakoid membrane, which is a structurally heterogeneous membrane structure, comprising appressed grana and non-appressed stroma thylakoids. Blue native polyacrylamide gel electrophoresis (BN-PAGE) is an extensively used method in the analysis of large multisubunit protein complexes in their native and biologically active form. The method was established for the dissection of mitochondrial membrane protein complexes1

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1. Preparing BN Gel1,2,3

  1. Set up the gel caster with 8 cm x 10 cm plates (rectangular glass and notched alumina plate) according to manufacturer's instructions using 0.75 mm spacers.
  2. Place a gradient mixer on a stir plate and connect it with the peristaltic pump by a tubing. Attach a syringe needle to the other end of the tubing and place the needle between the glass and.......

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A representative 2D-BN/SDS-PAGE system in Figure 1 demonstrates the separation of digitonin and β-DM-solubilized thylakoid protein complexes and their detailed protein subunit composition. The protein complex pattern of digitonin solubilized thylakoids (horizontal gel on the top on the top of Figure 1A) contains the PSII-LHCII-PSI megacomplex, two large PSII-LHCII supercomplexes (sc), PSI-LHCII supercomplex, PSI monomer (m),.......

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The photosynthetic energy conversion machinery is composed of large multisubunit protein complexes, which are embedded in the thylakoid membrane. This protocol describes a basic method for analysis of the plant thylakoid protein complexes from Arabidopsis thaliana with BN-PAGE combined with 2D-SDS-PAGE. The protocol is also suitable for the analysis of thylakoid protein complexes from tobacco and spinach thylakoids, but might require small adjustments.

For the solubilization of membra.......

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This research was financially supported by the Academy of Finland (project numbers 307335 and 303757) and Solar Energy into Biomass (SE2B) Marie Skłodowska-Curie grant agreement (675006). The protocol is based on reference3.


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Name Company Catalog Number Comments
6-aminocaproic acid (ACA) Sigma-Aldrich A2504
BisTris Sigma-Aldrich B4429
Sucrose Sigma-Aldrich S0389
Acrylamide (AA) Sigma-Aldrich A9099 Caution: Neurotoxic!
n-dodecyl-β-D-maltoside Sigma-Aldrich D4641
Tricine Sigma-Aldrich T0377
Tris Sigma-Aldrich T1503
SDS VWR 442444H
Urea VWR 28877.292
Glycerol J.T. Baker 7044
Sodium Fluoride (NaF) J.T. Baker 3688
EDTA disodium salt J.T. Baker 1073
Digitonin Calbiochem 300410 Caution:Toxic!
Pefabloc SC Roche 11585916001
Serva Coomassie Blue G Serva 35050
β-mercaptoethanol Bio-Rad 1610710
APS (Ammonium persulfate) Bio-Rad 161-0700
TEMED (Tetramethylethylenediamine) Bio-Rad 1610801
(N,N'-Methylene)-Bis-Acrylamide Omnipur 2610
Glycine Fisher G0800
Prestained Protein Marker, Broad Range (7-175 kDa) New England Biolabs P7708
Falcon, Conical Centrifuge Tubes 15 ml Corning 352093
Dual gel caster with 10 x 8 cm plates Hoefer SE215
Gradient maker SG5 Hoefer
0.75 mm T-spacers Hoefer SE2119T-2-.75
Sample gel comb, 0.75 mm Hoefer SE211A-10-.75
Mighty Small SE250 vertical electrophoresis system Hoefer SE250
IPC-pump Ismatec
Power supply, PowerPac HV Bio-Rad 164-5097
Centrifuge Eppendorf 5424R
Rocker-Shaker Biosan BS-010130-AAI

Bio-Rad 1651813

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