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Property Based Conservation
Percolation in Transmembrane
Proteins
JKS SEMINAR
Oznur Tastan
November 21, 2005
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PERCOLATION
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Percolation Threshold, pc
Percolation theory deals with the connectivity of components a system.
p< pc there is no infinite cluster
p> pc there is one infinite cluster
White balls => nonconducting spheres
Black ball =>conducting spheres .
Only above a certain concentration pc of the conducting balls
the system conducts electrical current.
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Membrane Folding
Klein-Seetharaman,J., 2005
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So far…
 Three very initial points have been explored:
1. Membrane assignment of residues.
2. Build a data set of up-to-date membrane proteins of
structure known.
3. The calculation of hydrophobic percentage of
membrane proteins
4. Initial program of percolation
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PDBTM
 PDB-TM is a new database for tm proteins with known structures (Tusnady
et. al. 2004).
* weekly updated
http://pdbtm.enzim.hu/
Rhodopsin 1u19, A
Membrane approximation and
oriented structures with respect to the
menbrane
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Membrane proteins compiled
 There are 179 chains in the non-redundant alpha list of
PDB-TM
 Followings are excluded:
 structures with less than three transmembrane
helices.
 structures unusual very open
 theoretical models
54 membrane protein chains
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Hydrophobic percentage
The three differing amino acids for each set:
All 6 hydrophobicity sets share
the same six amino acids:
Ile, Leu, Val, Phe, Trp, Met.
Set 1
Set 1
[Cys,His,Tyr]
Set 2
[Cys,Pro,Tyr]
Set 3
[Cys,Ala,Tyr]
Set 4
[Pro,Ala,Tyr]
Set 5
[Cys,Ala,Gly]
Set 6
[Pro,Ala,Gly]
Set 2
Set 3
Set 4
Set 5
Set 6
Membrane <fprot>54
0.47
0.50
0.55
0.58
0.60
0.64
Soluble <fprot>103
0.35
0.37
0.42
0.44
0.47
0.49
As expected membrane proteins contains more hydrophobic residues on
the average.
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Finding clusters, a breadth first search
Start from an occupied cell.
Add the first neighbors of the origin to the cluster,
Add the first neighbors of children
Grow cluster until there is no neighbors
Continue until there is no occupied cell
Hydrophobic Clusters residues in Rhodopsin
Connectivity cutoff(Å)
Number of clusters
Size of largest cluster
End-to-end distance of the largest cluster(Å)
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6
161
61.55
6
16
104
55.76
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65
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15.12
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Largest cluster of
hydrophobic residues at
7 6 Å cutoff
The largest cluster of
hydrophobic residues
at 6 Å cutoff.
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Property Based Conservation
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Rhodopsin and MGluR6 PBC comparison
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23 Properties selected
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4 A contact number/Nishikawa-Ooi
8 A contact number/Nishikawa-Ooi
Average accessible surface area/Janin
Flexibility param for no rigid neighbors/Karplus-Schulz
Flexibility param for one rigid neighbor/Karplus-Schulz
Flexibility param for two rigid neighbors/Karplus Schulz7Hphob/Miyazawa/Roseman8
Hydropathy index/Kyte-Doolittle
Long range non-bonded energy per atom/Oobatake-Ooi
Normalized flexibility/B-values, average/Vihinen
Normalized frequency of alpha-helix/Chou-Fasman
Normalized frequency of beta-sheet/Chou-Fasman
Normalized frequency of coil/Nagano
Normalized frequency of turn/Crawford
Normalized van der Waals volume/Fauchere
Number of hydrogen bond donors/Fauchere
Percentage of buried residues/Janin
Polarity/Grantham
Short and medium range non-bonded energy per residue/Oobatake-Ooi
Side chain torsion angle phi/AAAR Levitt
Volume/Grantham
White Wimley Octanol Interface Scale
Helix-PackingScale
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Method
 The permutation test is not employed.
 Instead the results are normalized with background
probabilities, which are calculated class specific, by
taking the frequencies of amino acid in each of the
alignments
 Positions that exhibit similar properties are identified.
 normalized conservation ratio, r
 normalized conservation difference, d
 consider similar behavior if|r-1| <0.05 or |d|<0.01
 37 positions to be examined in the folding core
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Rho116 Phe Mglur6-650 Leu
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Rho116 Phe MGluR6-650 Leu
'Average accessible surface area/Janin'
0.075881
'Percentage of buried residues/Janin'
0.18762
'Hphob/Miyazawa/Roseman'
0.2938
'Flexibility param for two rigid neighbors/Karplus-Schulz'
0.33739
'8 A contact number/Nishikawa-Ooi'
0.39612
0.09896
0.25537
0.32786
0.42779
0.38902
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Bacteriodopsin and Rhodopsin
Green is bacteriorhodopsin
Blue is rhodopsin
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Rho116 Phe BacRho-85 Asp
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Rho116 Phe BacRho-85 Asp
'Average accessible surface area/Janin'
0.075881
0.15427
'Number of hydrogen bond donors/Fauchere'
0.084191
0.14124
'Percentage of buried residues/Janin'
0.18762
0.16367
'Hydropathy index/Kyte-Doolittle'
0.23445
0.18368
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T4 lyzosome mutations
 To be used in the PBC analysis.
T4 lyzosome mutations are started to be compiled
The full mutation list is obtained from ProTherm.
There are 1068 entries.
We collected all the available online papers that is
related to the mutations.
Summarizing the effect and the nature of the
mutations
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To be continued..
 Thanks to Naveena, Judith, Jaime and Hagai
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