Transcript Oxion_20Sep - Structural Bioinformatics and Computational

Novel vertebrate homologues detected for two families of mechanosensitive channels.
HYUN JI KIM and MARK S. P. SANSOM
Structural Bioinfomatics and Computational Biochemistry Unit, Department of Biochemistry, University of
Oxford, South Parks Road, Oxford, OX1 3QU, UK
A Genomic Landscape of Ion Channels
1
A)
500
400
300
200
100
0
Vibr_ch_pep_results
Sulf_to_pep_results
Stre_co_pep_results
Stap_au3_pep_results
Shig_fl1_pep_results
Pyro_ho_pep_results
Pire_sp_pep_results
Nano_eq_pep_results
Myco_pn_pep_results
Meth_th_pep_results
Meth_ja_pep_results
Halo_sa_pep_results
Cory_gl_pep_results
Chla_tr_pep_results
Baci_su_pep_results
Yeast_pep_results
Para_te_pep_results
Ence_cu_pep_results
Cand_gl_pep_results
Zebra1_results
Mouse4_results
Human4_results
Chimp4_results
Chick4_results
ues
Number of hom olog
600
Vert
ebra
tes
Gen
om
es
Sim
p
euka ler
ryot
P
es rokaryo
tes
NBD1SUR1
7TM_class1
ENaC
Kv1.2;S1-S4
Ca2+_beta4
Ca2+_beta1
nAChR;LBD
KcsA;S5-S6
clcA
KvB2
s
Chak
e
i
il
TRP
m
a
f
Na+_alpha
n
i
e
MscS
t
o
r
MscL
P
Bacteriorhodopsin
KvAP;S1-S4
A Vertebrate Homologue of Largeconductance MechanoSensitive Channel
TMH3
B)
The vertebrate homologues, detected for MscL and MscS, are predicted to encode three TM helices
(Pongo and Dr. Cuthbertson’s). Sequence conservation was measured and mapped onto corresponding
crystal structures, 2oau (MscL) and 2oar (MscS), in Chimera. Degree of conservation is expressed by
the thickness of worm-shaped presentation and also by the strength of blue shades.
A) Sequence alignment of MscS family, Gly (yellow) and Aln (sky blue), as in MscL-TMH1.
B) Pairwise comparison of two profile Hidden Markov Models, each representing MscSTMH3 (upper) and a consensus mechanosensitive TM helix (lower). The latter was coextracted from two additional protein families, which are two pore potassium channels
(K2P) and transient receptor potential (TRP) channels.
K2P
MscS
MscL
chick
MscS
mouse
MscS
C)
2oau
MscL_BACSU
MscS_mouse
MscL_CLOPE
Q51409_BOR
MscL_CHICK
Q55882_SYN
MscL_STAAW
Q34897_BAC
2oar
Q05781_MYC
MscL_MYCTU
MscS_EDWIC
MscL_SYNY3
MscS_SHIFL
MscL_ECOLI
SBCB website, http://sbcb.bioch.ox.ac.uk.
b)
MscL
MscS_ECO57
MscL_PSEFL
*For further information, contact Hyunji Kim Email: [email protected]
and Mark Sansom Email: [email protected]
A)
Phylogenetic Trees with Evolutionary
Distance combined.
4
MscL_HAEIN
A)Sequence alignment of MscL family, colour-coded for two conserved residues, Gly and Aln.
B) Pairwise comparison of profile Hidden Markov Models: Font in proportion to emission
probabilities, whilst letters shown per column correspond to symbols emitted from each state.
Mechanosensitivity is traced down to Gly & Aln.
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TRPV4
NOMPC
MscL
B)
MscS
MscL
A)
TMH1
3-D Mapping of Sequence Conservation
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Genomic landscape of ion channels
& related proteins
80 genomes in total, were screened for homologues of 17 ion channels and related
proteins. ‘WU-BLAST’ was employed as search-engine, and ‘blastp’ was executed
with 6 various amino acid substitution matrices, for enhanced sensitivity, whereas
‘MSPcrunch’ was plugged in our automation-script for removing spurious hits, thus
higher specificity.
2
3 A Mammalian Homologue of Smallconductance MechanoSensitive Channel
Evolutionary distances were calculated from pairwise sequence
comparison (using PHYLIP), based on the two alignments presented
for MscL and MscS. Identical pairs are lined in the central diagonal direction.
Each shade of blue increments 0.5 in the range of 0 to 3.5.
A)A consensus. mechanosensitive motif, detected from 4 protein families, which are MscL, MscS, two pore
potassium channel (K2P) and TRP channels. One transmembrane helix (TMH) was extracted from each
family, such as TMH1 of MscL, TMH3 of MscS, TMH2 of pore 1 and pore 2 of K2P, and TMH4 of TRP
channels.
B) Principal Component Analysis showing co-relationship amongst the above 4 protein families.
C) A profile Hidden Markov Model was constructed from the assembled alignment on the left, which was
subsequently visualised by HMM Logos. Notable are strong signals detected for conserved Gly and Aln,
despite a very low overall sequence identity across those ion channel families.
7 Conclusions
References
(1) Biggin PC, Sansom MSP (2003) Mechanosensitive Channels: Stress
Relief. Current Biology 13(5): R183-R185.
(2) Honore E (2007) The neuronal background K2P channels: focus on
TREK1. Nature Reviews Neuroscience 8:251- 261
1. Genomic scanning of mechanosensitive channels revealed unprecedented
vertebrate homologues of Large and Small conductance MS channels.
2. It is speculated that Gly and Aln may serve key residues accounting for
mechanosensation observed in families of 2 pore potassium channels, Transient
Receptor Potential channels and Large/Small mechanosensitive channels.