? Outline Interface Prediction for GPCRs Oligomer -

 ? Outline    Interface Prediction for GPCRs Oligomer   -

? Outline Interface Prediction for GPCRs Oligomer

- 1. 1 2. 3. -

1. 1 2. 3. - 1. 1 1-1. 1-2. 2. 3.

- - 1. 1 1-1. 1-2. 2. 3.

1-1. Query ( ) DB 1 Blast, Fasta etc.

Query Query homologous 1-1.

DB 1-1. Identity or Similarity Score Matrix 1-1.

- - Identity: 1 LIESTAQRECTVNM 2 ILDSTAQKDCTVQM 10 8 L I

D E (810)/(1410) 57.1% 1-1. Identity:

1 LIESTAQRECTVNM 2 ILDSTAQKDCTVQM 8 80/140 57.1% Similarity: 1 LIESTAQRECTVNM 2 ILDSTAQKDCTVQM

8 6 57.1% % 1-1. 1 LIESTAQRECTVNM 2 ILDSTAQKDCTVQM 2

? Score Matrix: PAM250, BLOSUM62 etc 1-1. Identity or Similarity Score Matrix 1-1.

Score Matrix Score matrix (similarity)

A-A: +4 G-W: -2 L-I : +2 1 A G L 2 A W I (+4)+(-2)+(+2) = +4 Score matrix (similarity)

PAM BLOSUM GONNET i. DB ii. iii. Score matrix

1. 2. Score matrix ? ?

? Score mat m atrix Score mat mat rix

/ - 1. 1 1-1. 1-2. 2.

3. 1-2 Query ( )

Model ? 1-2

Query ( )

? 1-2 SOSUI ( ) http://sosui.proteome.bio.tuat.ac.jp/sosuimenu0.html Query

? 1-2

1. 2. 1-2

(window) window 1-2 - 1. 1 2. 2-1.

2-2. 2-3. 3. 2.

2.

3 2. 2-1.

2-1-1. 2-1-2. 2-1-3. PSSM (position specific scoring matrix) 2-1-4. 2-2. 2-2-1. 2-2-2. 2-3.

2-3-1. 2-3-2. 2-1-1.

2-1-1. ?

2-1-1. ? A W ? iv. v. ? vi. Taxonomic Bias i.

ii. iii. 2-1-1. Taxonomic bias

2-1-1. ? A W ? iv. v. ? vi. Taxonomic Bias

i. ii. iii. N N N N Wj Wk Mut(M(j, i), M(k, i)) j Cons(i) =

k> j N N N N Wj Wk Score matrix j k >j

Score(a, b) - Min(Score) Mut(a, b) = Max(Score) - Min(Score) 0 ab Gap

2-1-1. ? A W ? iv. v. ? vi. Taxonomic Bias i.

ii. iii. 2. 2-1.

2-1-1. 2-1-2. 2-1-3. PSSM (position specific scoring matrix) 2-1-4. 2-2. 2-2-1. 2-2-2.

2-3. 2-3-1. 2-3-2. 2. 2-1.

2-1-1. 2-1-2. 2-1-3. PSSM (position specific scoring matrix) 2-1-4. 2-2. 2-2-1. 2-2-2. 2-3. 2-3-1.

2-3-2. 2-2-1. + + + +

+ + +

+ A a b c

1 2 3 1 2 3 B d

e f 1 2 s(d, e) 3 s((d, f)s(e, f) s(a, b) s(a, c) s(b, c) 1 2

3 1 2 3 2.

2-1. 2-1-1. 2-1-2. 2-1-3. PSSM (position specific scoring matrix) 2-1-4. 2-2.

2-2-1. 2-2-2. 2-3. 2-3-1. 2-3-2. 2-2-2.

Suel GM et al. Nat Struct Biol. 2003;10:59-69

2. PSSM

http://idsc.tokyo-eiken.go.jp/influenz/0203/fig4-5.html ( 1959 ) (Triticeae) (Tritic um)

http://www.shigen.nig.ac.jp/wheat/komunet/index03/3a-1.html

Root Node (Rooted Tree) (Unrooted Tree)

(maximum parsimony method) (maximum likelihood approach) (distance method) (neighbor joining method, UPGMA) PAUP(http://paup.csit.fsu.edu/index.html) PHYLIP(http://evolution.genetics.washington.edu/phylip.html) MEGA(http://www.megasoftware.net/)

MEGA Olfactory R Prostaglandin R Cannabinoid R Adenosine R

Opsin R Amine R Class A GPCR Peptide R

P

2.

PSSM 2.

3 * 1

1 2.

catalic triad? Evolutionary Trace (ET) - 1 N L W--------- S E S A

N L W ---------T E S N?W----? E S N I W --------- GE S

B - G W--------- Q K P A S W--------- T K P ??W----?K P G T W--------- E K T C

A V W--------- G K T - V W--------- G K T ??W----?KT Evolutionary Trace (ET) - 2

A B

C

Evolutionary Trace (ET) - 3 A B C

Class Specific Residue ..W ----E S ..W ----K P ..W ----K T

Conserved Residue Trace Residue (TR) Evolutionary Trace (ET) - 4

Trace Residue (TR) Evolutionary Trace (ET) - 5 Trace Residue (TR) Evolutionary Trace (ET) - 6

Trace Residue (TR) Evolutionary Trace (ET) - 7 I II III IV V TR I TR II TR III

TR IV TR V Evolutionary Trace (ET) - 8 i. ii. TR conserved & class specific iii. TR iv. v. ET Pyruvate

decarboxylase 90 Evolutionary Trace (ET) - 8

i. ii. TR conserved & class specific iii. TR iv. v. ET Class

Specific Residue Evolutionary Trace (ET) - 9 ET Evolutionary Trace Server (TraceSuite II) http://www-cryst.bioc.cam.ac.uk/~jiye/evoltrace/evoltrace.html Consurf

http://bioinfo.tau.ac.il/ConSurf/ 01 PIC 10 PIC Trace Residue(TR) Evolutionary Trace (ET) - 10 ( ) Class specific residues( )

Trace Residue(TR) Evolutionary Trace (ET) - 11 Class specific residue Class Class

Specific Residue + Conserved Residue II TR

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