Problems in Obtaining Diffraction-Quality Crystals of Integral Membrane Proteins • Discussed in the context of 2 recently obtained structures of integral membrane protein (IMP) complexes: • (I) Hetero-oligomeric cytochrome b 6 f complex of oxygenic photosynthesis (8 gene products; dimer; 26 TM -helices; MW = 220 kDa); 3.0 Å. • (II) Complex between the 22 strand -barrel E. coli outer membrane vitamin B 12 receptor (BtuB) and the colicin E3 receptor (R) binding- domain; 2. 75 Å. (II) The complex between the 22 strand -barrel vitamin B 12 receptor and the colicin E3 R-domain.
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Problems in Obtaining Diffraction-Quality Crystals of Integral Membrane Proteins Discussed in the context of 2 recently obtained structures of integral.
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Problems in Obtaining Diffraction-Quality Crystals of Integral Membrane Proteins
• Discussed in the context of 2 recently obtained structures of integral membrane protein (IMP) complexes:
• (II) Complex between the 22 strand -barrel E. coli outer membrane vitamin B12 receptor (BtuB) and the colicin E3 receptor (R) binding-domain; 2. 75 Å.
(II) The complex between the 22 strand -barrel vitamin B12 receptor and the colicin E3 R-domain.
(I) Cytochrome b6f complex: functions in membrane energy transduction
(I) The Cytochrome b6f Complexwith H. Zhang, G. Kurisu, & J. L. Smith
(II) Structure of the complex between BtuB and R135, which functions in protein import
40º
323313 438
447
LPSLPS
OM
(II) complex of the vitamin B12 receptor and the colicin E3 R-domain
with Genji Kurisu, Stas Zakharov, Masha Zhalnina, &M. Wiener, S. Bano, Y. Antonenko (not shown)
Challenge for Membrane Protein Structure Determination
Presently, in the protein data bank, there are > 22,000 protein structures. Among these,and 20 years after determination of thefirst integral membrane protein structure, there are 46 independent IMP structures, and 10 hetero-oligomeric IMP at a resolution 3.0 Å (http://www.mpibp.frankfurt. mpg.de/michel/public/memprotstruct.html).
Some problems in the crystallization of IMP1
• Use of thermophilic sources• Detergents: (i) undecyl-maltoside (); (ii) LDAO ()
• Purity; don’t over-purify! lipid depletion (part I).• Activity• Stability (oligomeric state; integral proteases)• Ligands for soluble domains (part II)• Problem of storage.
• 1 Iwata, S. (Ed.) [2003] Methods and Results in
Crystallization of Membrane Proteins., IUL, pp. 355
Electron transport complexes in oxygenic photosynthesis: cytochrome b6f complex provides electron connection between photosystem II & photosystem I reaction centers and translocates H+ across the membrane.
p (lumen) -side
n (stromal) -side
2H2O O2 + 4H+
PQ
4H+ PC (cyt c6)
Fd FNR Cyclic e-pathway
NADPH
PSII: Zouni et al
(2001) Nature 409,739 PSI: Jordan et al (2001) Nature 411, 909
Cyt b6f
Cells of the Thermophilic Cyanobacterium, Mastigocladus laminosus
Cross-Section of the Protein-Detergent Micelle Complex
Michel, H. (1990) Crystallization of Membrane Proteins;Pebay-Peyroula, et al., (1995) Structure, 3: 1051-1059
Electron Transfer Activity of Cytochrome b6f Complex
Efficiency of Action of Inhibitor
-0.9
-0.8
-0.7
-0.6
-0.5
-0.4
0 10 20 30 40 50 60 70
Vo
lta
ge
(V
)
Time (sec)
MLbf + DOPC
MLbf+DBMIB
MLbf
MLbf+DBMIB+DOPC
Masses of Eight Polypeptide Subunits of b6f Complex from the Thermophilic
Cyanobacterium, Mastigocladus laminosus
Whitelegge et al. Molec. Cell Proteomics (2002),1: 816-826
Subunit Measured Mass (Da)
Cyt f 32,270 Cyt b6 24,710 (calc., 24, 268)Rieske ISP 19,295Sub IV 17,529PetG 4057PetM 3841PetL 3530PetN 3304
Dimer MW = 217,057 Da
Two problems:
(i) It turned out that the protein was very pure, except for the possibility of trace protease (see below), and in fact was over-purified because the lipid was depleted (< 1 lipid/monomer);
(ii) the protease activity has not, until now,
been inhibitable.
Proteolysis Problem in First Crystals of the Cytochrome b6f Complex
1 2 3 4
Lane 1, fresh cytochrome b6f complex
Lane 2, after 7 days at room temperature Lane 3, crystalLane 4, thermolysin treated complex
Proteolysis of Cytochrome b6f Complex in Different Detergents
NG OG UDM DM DG DDM
t = 0
NG OG UDM DM DG DDM
t = 14 days
NG OG UDM DM DG DDM
t =7 days
Protease activity could not inhibited.
Crystals of cytochrome b6f complex from M. laminosus made after augmentation with the lipid,
DOPC (10:1, DOPC: Cytochrome f )
Hexagonal crystals, 78 % solvent content[Zhang, H. et al. (2003) PNAS, 100: 5160-5163]
SDS-PAGE of Cytochrome b6f Crystals
1 2 3Lane 1, fresh cyt b6f complex
Lane 2, new crystal
Lane 3, old crystal
Cyt f
Cyt b6
Sub IVISP
Cyt f
proteolysed Cyt b6
proteolysed ISP and Sub IV
Structure of Cytochrome b6f Complex
2 b-type Hemes, 1 c-type Heme, 1 [2Fe-2S]1 new heme, chlorophyll a, -carotene
p-side
n-side
DOPC
+10 kT-10 kT
Crystal Structure of the Complex between BtuB and R135 at 2.75 Å Resolution
40º
323313 438
447
LPSLPS
OM
Kurisu et al., Nat Struct Biol,
10: 948-954, 2003;pdb: 1UJW)
Problem of protein-protein contacts for “squat“ IMP in detergent; increase soluble domain with mab.
Hunte, C., H. Michel (2002) Curr Opin Struct Biol, 12: 503-508.
Cytotoxic colicins: colicin E3, a ribosomal RNAase;
n. b., coiled-coil motif
Colicin Ia Colicin N
Colicin E3
N
C
Domains:
Translocation
Receptor-binding
Activity
Mol Cell,8, 1053, 2001
Nature, 385, 461, 1997
To try to solve the problem of the lipid depletion, the purified complex was augmented with pure synthetic lipid.
• The result: the rate of formation of
crystals of intact complex increased greatly; i. e., crystals appeared over-night!
• Thus, the protease problem could be solved, but only by winning the race against it.
The E. coli Cell Envelope: receptor-containing outer-membrane, periplasmic space, & metabolically active inner-membrane
How are proteins imported across double membranes? Colicins as test molecules
How does colicin bind to, or insert into receptor?How does colicin bind to, or insert into receptor?n. bn. b., N-terminal cork (green) domain ., N-terminal cork (green) domain
blocks insertionblocks insertion
E. coliE. coli outer membrane protein BtuB, cobalamin outer membrane protein BtuB, cobalamin translocator, 22-antiparallel translocator, 22-antiparallel -barrel-barrel
((Chimento et al., Nat Struct Biol, 10, 394-401, 2003)
Colicin E3 receptor-binding domain (R135); Crystallization strategy: use R135 as soluble ligand of BtuB colicin receptor
Crystal Structure of the Complex between BtuB and R135 at 2.75 Å Resolution
40º
323313 438
447
LPSLPS
OM
Kurisu et al., Nat Struct Biol,
10: 948-954, 2003;pdb: 1UJW)
7-8
5-6
7-8
3-4
323
313 438
447
Two receptor translocon for colicin import across the E. coli outer membrane
Colicin E3
Cork domain
Acrobat Reader 5.0.lnk
AcknowledgmentsCytochome complex BtuB/R135 ComplexJ. T. Bolin Y. Eroukova (Moscow St.)A. Friedman M. LindebergD. W. Krogmann S. Schendel*M. Ponamarev R. Taylor*G. M. Soriano L. A. Sherman
DiscussionsM. G. Rossmann K. Jakes (AECOM)W. Minor (Virginia) M. Shoham (CWRU)
Synchrotron Lines & StaffAPS SBC-19 (N. Duke, F. Rotella); BioCARS 14 [Argonne NL]Spring-8 (Hyogo, Japan)
Grant SupportNIH-GMS (WAC); *NIH-GMS Biophysics Training Grant; Japan
Ministry of Science & Education (GK); DOE, NIH (APS)