Signals in Sequences The number of sequences available for analysis rapidly approaches infinite. We need new ways to look at all this information.

Rule 1 First rule of sequence analysis: If a residue is conserved, it is important.

Rule 2 Second rule of sequence analysis: If a residue is very conserved, it is very important.

GPCR Project GPCR is THE drug target. Lots of data available. You have ~630 GPCRs. Little structure data sequences known. ‘Easy’ to align.

The GPCR (rhodopsin)

1 conserved aa / helix!

Laerte about modelling: “Use the sequence, Luke”

Conserved, CMA, variable QWERTYASDFGRGH QWERTYASDTHRPM QWERTNMKDFGRKC QWERTNMKDTHRVW Black = conserved White = variable Green = correlated mutations(CMA)

CMA and tree 1 ASASDFDFGHKM 2 ASASDFDFRRRL 3 ASLPDFLPGHSI 4 ASLPDFLPRRRV

CMA versus tree 1 ASASDFDFGHKMGHS 2 ASASDFDFRRRLRHS 3 ASLPDFLPGHSIGHS 4 ASLPDFLPRRRVRIT 5 ASASDFDFRRRLRIT 6 ASLPDFLPGHSIGIT Red : 1,2,5 vs 3,4,6 Black : 1,3,6 vs 2,4,5 Yellow: 1,2,3 vs 4,5,6

CMA on GPCR CMA on GPCR

CMA on GPCR

Florence Horn

Class B Ligands

Class B – ligand docking

G protein-coupling?

Sequence Signals Three classes of residues 1) Conserved 2) CMA 3) Variable

Conservation Artefacts Conservation can result from Not enough sequences Too conserved sequences Over-alignment

Variability Artefacts Variability can result from Wrong sequence choice Variable loops Alignment errors

CMA Artefacts CMA can result from Wrong sequence choice Poor sequence homogeneity Over-fitting

Recalcitrant residues

Sequence Entropy 20 E i =  p i ln(p i ) i=1

Sequence Variability Sequence variability is the number of residues that is present in more than 0.5% of all sequences.

Entropy - Variability Entropy = Information Variability = Chaos

Entropy - Variability Variability is result of evolution. Entropy is the protein’s break on evolutionary speed.

GPCR Entropy - Variability 11 Red 12 Orange 22 Yellow 23 Green 33 Blue

GPCR Location 11 Red 12 Orange 22 Yellow 23 Green 33 Blue

Ras Entropy - Variability

Ras Location 11 Red 12 Orange 22 Yellow 23 Green 33 Blue

Protease Entropy - Variability

Protease Location 11 Red 12 Orange 22 Yellow 23 Green 33 Blue

Globin Entropy - Variability GPCR

Globin Location 11 Red 12 Orange 22 Yellow 23 Green 33 Blue

GPCR Again….

GPCR Location (Again) 11 Red 12 Orange 22 Yellow 23 Green 33 Blue

GPCR signaling 11 Purple 12 Red 22 ‘Yellow’ 23 Green 33 Blue

Summary Given infinitely many sequences: Every residues role known. Signaling paths detectable. So, sequences contain many signals

Thanks to: Laerte OliveiraSao Paulo Wilma KuipersWeesp Florence HornSan Francisco Bob BywaterCopenhagen Nora vd WendenThe Hague Mike SingerNew Haven Ad IJzermanLeiden Margot BeukersLeiden Amos BairochGeneva Fabien CampagneNew York