On the evolution of membrane
proteins
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Homology detection
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Blast, PSIBLAST are they good ?
SHRIMP (Bernsel, submitted)
Evolution of TM-helices
Internal duplications
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>50% of +6TM proteins
Arne Elofsson (arne@bioinfo.se)
Problems with homology
detection of TM proteins
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Methods optimized on globular proteins
High scoring false positives due to
similarity between unrelated TM regions
Hedman et al, 1998 (Pmembr):
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Fold recognition methods improve this fact
Globular detections improved by profileprofile (HMM-HMM) comparisons
Arne Elofsson (arne@bioinfo.se)
Profile-profile methods improve
detection of membrane proteins
Arne Elofsson (arne@bioinfo.se)
Classification of GPCRs at 1% FPR
Arne Elofsson (arne@bioinfo.se)
How does TM proteins evolve

Mutation rates any differences in
respect to the different compartments.
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Few “multi-domain” membrane proteins
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Many complexes
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Internal symmetry
Arne Elofsson (arne@bioinfo.se)
Slower evolution in the
membrane
Arne Elofsson (arne@bioinfo.se)
Internal duplications on sequence
level
Searched for internal duplication events in
87 prokaryotic genomes
Out of 38,124 membrane proteins, 377
duplication events could be detected
(~1%)
Internal duplications has been hard to
detect on sequence level
α
α
X
J. Mol. Biol. 2004, 339:1-15
α
α
A
α
B
Arne Elofsson (arne@bioinfo.se)
α
C
Lactose Permease
Arne Elofsson (arne@bioinfo.se)
1xqf (NH3-channel) Antiparallel
duplication
Arne Elofsson (arne@bioinfo.se)
12-TM chain from Cytochrome
C-oxidase(Triplication)
Arne Elofsson (arne@bioinfo.se)
Internal symmetry in α-helical
inner membrane proteins
N
Antiparallel:
LeuT
2-fold symmetry axis
SecY
BtuCD
 Parallel to membrane
CAQP1
GlpF
 Odd number of TMH
AmtB
ClC H+/Cl- exchange transporter
 Domains anti-parallel to
NhaA
each other
middle
C
Parallel:
LacY
GlpT
N
Sav1866
ABC
transporter
AcrB
EmrD
ADP/ATP carrier

In plane with membrane


Even number of TMH
Domains parallel to each
other
Arne Elofsson (arne@bioinfo.se)
Many (most) proteins have
internal duplications
Fraction of chains with internal duplications
Fraction containing a duplication
1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
6
8
10
Number of transmembrane helices (minimum)
Arne Elofsson (arne@bioinfo.se)
12
Duplications in TM proteins
Distribution of duplication size
100,00%
90,00%
80,00%
70,00%
60,00%
50,00%
40,00%
30,00%
20,00%
10,00%
0,00%
No duplic ation
6 T MH
5 T MH
4 T MH
3 T MH
6
7
8
9
10
11
³12
Number of transmembrane helices in chain
Arne Elofsson (arne@bioinfo.se)
Both parallel and antiparallel
duplications exist
Parallel / Antiparallel duplications
6
5
4
Antiparallel
3
Parallel
2
1
0
3
4
5
Number of duplicated helices
Arne Elofsson (arne@bioinfo.se)
6
But in order to have antiparallel domains, they
must be inserted with opposing topology!
C
N
inside
membrane
•
outside
C
In order for an antiparallel symmetry to be explained by a
duplication event, each subunit of the homodimer must be
inserted with opposite topology
•
That implies that a sequence can have dual topology, be
inserted either way in the membrane
•
Have been constructed in labs (Cell 62, 1135-1141 & Cell 77, 401412)
N
Arne Elofsson (arne@bioinfo.se)
Hypothesis for antiparallel
internal symmetry
Nat. Struct. Mol. Biol. 2006, 13: 94-96
Arne Elofsson (arne@bioinfo.se)
Detection of internal
duplications
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Structural alignments

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Sequence alignments
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
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Finds most of the manually detected
examples.
Sequence alignments do not find most.
Using SHRIMP about 80% can be found
Also finds a few extra.
Some problems defining exact duplication
unit
Genome scanning
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Ongoing.
Arne Elofsson (arne@bioinfo.se)
Acknowledgements



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
Erik Granseth
Anni Kauko
Jenny Falk
Andreas Bernsel
Kristoffer Illergård
Arne Elofsson (arne@bioinfo.se)
Final comments


Thanks to EMBRACE
Please fill out the questionaire..
Arne Elofsson (arne@bioinfo.se)