journey of bacteriophage m13 major coat protein david stopar university of ljubljana slovenia...
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Journey of bacteriophage M13 major
coat protein
David Stopar
University of Ljubljana
Slovenia
Interactions in macromolecular
assemblies
• Replication cycle of the bacteriophage M13
• Structure of the major coat protein
• Topology of the major coat protein in the lipid bilayer
• Anchoring of the major coat protein in the lipid bilayer
Journey of bacteriophage M13 major coat protein
Schematic representation of bacteriophage M13 replication cycle
M13
E.coli
F-pilus
DNA
gp 5
gp 8
Gene 9 protein
Gene 6 protein
Gene 3 protein
Gene 8 protein
Circular ssDNA
Distal end
Proximal end
Gene 7 protein
Schematic structure of bacteriophage M13 filament
Model of the of bacteriophage M13 protein coat
Nearest-neighbour interactions between protein subunits in the phage particle
k=11 k=11
k=6 k=6
k=0 k=0
• Replication cycle of the bacteriophage M13
• Structure of the major coat protein
• Topology of the major coat protein in the lipid bilayer
• Anchoring of the major coat protein in the lipid bilayer
Journey of bacteriophage M13 major coat protein
Major coat protein structural domains in lipid bilayer
1-5 N-terminus
6-16 amphiphatic helix
17-23 loop
24-46 transmembrane helix
47-50 C-terminus
1
50
Amino acidresidue number
X-ray and NMR limitations for membrane proteins
X-ray: “no” crystals of membrane proteins
NMR: membranes are anisotropic systems
high-resolution NMR limited to micellar systems
solid-state NMR is needed for bilayer structure
13C and 15N-enrichment is needed (difficult and very
expensive!)
2D NMR & DG analysisPapavoine et al. (1998)J. Mol. Biol. 282, 401-419
M13 coat protein in SDS micelles
? ? ? ? ? ? ? ?
Structure not possible in a membrane
Molecular Dynamics (MD) Approach
Starting conformation for
protein in POPC membrane
from SDS (Papavoine et al.,
1998).
Snap Shots of Protein Backbone
0 ns 0.5 ns 1 ns 1.5 ns
41 H-bonds
41 H-bonds
42 H-bonds
43 H-bonds
The effects seen in MD are in the ESR time scale (ns)
Note: one label is measured at a time membrane-water
interface
M13 Coat Protein with Labels Attached
ESR Spin Label Information
Position withstructural restriction
Position with nostructural restriction
N
NOO
O
ESR spin label: 5-maleimido-proxyl
•
Sensitivity of spin labels for different protein sites
1
50
Amino acidresidue number
2Azz
Outer Splitting
Sensitivity of spin labels for different lipids
65
60
55
50
2Azz
(G
)
2422201816141210
amino acid residue
60
55
50
45
40
35
2A
zz (
G)
40302010
amino acid residue
65
60
55
50
2Azz
(G
)
424038363432302826
amino acid residue
PC22
PC14
• Replication cycle of the bacteriophage M13
• Structure of the major coat protein
• Topology of the major coat protein in the lipid bilayer
• Anchoring of the major coat protein in the lipid bilayer
Journey of bacteriophage M13 major coat protein
Spin label relaxation times in DOPC bilayers
0
0.5
1
1.5
2
2.5
3
3.5
0 10 20
Ni2+
(mM)
1/T
1 (se
c x
106 ) A49C
V31C
G38C
1
50
Amino acidresidue number
Relative quenching efficiency by oxygen and
Ni2+
Ni2+
1
50
Amino acidresidue number
0
10
20
30
40
50
60
70
20 30 40 50
residue number
rela
tive
quen
chin
g ef
fici
ency
oxygen
Ni2+
Dependence of spin labeled DOPC acyl
chains on the relaxation enhancement by
oxygen and Ni2+
0
10
20
30
40
50
60
70
-2 8 18 28 38
acyl carbon atom
rela
tive
rela
xatio
n en
hanc
emen
t
Ni2+
oxygen
1
50
Amino acidresidue number
Location of the protein in the lipid bilayer as determined by fluorescence labeling
470
475
480
485
490
495
500
505
510
0 20 40
Amino Acid Residue Number
Em
issi
on m
axim
um (
nm)
1
50
Amino acidresidue number
Trp 26Leu 14
NH3+
Phe 45
Interface
Interface
Hydrocarboncore
20 Å
Lys 40
Topology of the major coat protein in the lipid bilayer
• Replication cycle of the bacteriophage M13
• Structure of the major coat protein
• Topology of the major coat protein in the lipid bilayer
• Anchoring of the major coat protein in the lipid bilayer
Journey of bacteriophage M13 major coat protein
AEDANS max of the A7C protein mutants in lipid
bilayers
M13 major coat protein mutant Emission maximum (nm)
A7C 495
A7C/A10I 492
A7C/F11A 502
A7C/L14A 502
A7C/F11A/L14A 505
AEDANS max in DOPC lipid bilayers
488
489
490
491
492
493
494
495
496
497
T46C T46C/INS T46C/FA
AED
AN
S m
ax (n
m)
1
50
Amino acidresidue number
Tryptophane max in DOPC lipid bilayers
320
322
324
326
328
330
332
334
336
338
Wild type T46C/INS T46C/FA
Try
ptop
han
max
(nm
)
1
50
Amino acidresidue number
Bacteriophage M13 major coat protein anchors
in the lipid bilayer
C-terminus
N-terminus
Leu 14
Phe 11
Lys 8Trp 26
Lys 40Lys 43
Lys 44
Phe 42
Phe 45
Schematic representation of bacteriophage M13 replication cycle
M13
E.coli
F-pilus
DNA
gp 5
gp 8
Model of the major coat protein disassembly and assembly
(1)(3)(2)
N-terminus
C-terminus
Acknowledgements
Wageningen
Marcus Hemminga
Rob Koehorst
Ruud Spruijt
Werner Vos
Cor Wolfs
Göttingen Derek MarshKity A. Jansen
Szeged Tibor Páli
Ljubljana Ivan Mahne
Janez ŠtrancarMilan Schara