Signals in SequencesSignals in Sequences

The number of sequences The number of sequences available for analysis rapidly available for analysis rapidly approaches infinite.approaches infinite.

We need new ways to look at We need new ways to look at all this information.all this information.

Rule 1Rule 1

First rule of sequence First rule of sequence analysis:analysis:

If a residue is conserved, it is If a residue is conserved, it is important.important.

Rule 2Rule 2

Second rule of sequence analysis:Second rule of sequence analysis:

If a residue is very conserved, it is If a residue is very conserved, it is very important.very important.

GPCR ProjectGPCR Project

GPCR is THE drug target.Lots of data available.You have ~630 GPCRs.Little structure data.2000 sequences known.‘Easy’ to align.

The GPCR (rhodopsin)The GPCR (rhodopsin)

1 conserved aa / helix!1 conserved aa / helix!

Laerte about modelling:Laerte about modelling:

“Use the sequence, Luke”

Conserved, CMA, variableConserved, CMA, variable

QWERTYASDFGRGHQWERTYASDTHRPMQWERTNMKDFGRKCQWERTNMKDTHRVWBlack = conservedWhite = variableGreen = correlated mutations(CMA)

CMA and treeCMA and tree

1 ASASDFDFGHKM2 ASASDFDFRRRL3 ASLPDFLPGHSI4 ASLPDFLPRRRV

CMA versus treeCMA versus tree

1 ASASDFDFGHKMGHS2 ASASDFDFRRRLRHS3 ASLPDFLPGHSIGHS4 ASLPDFLPRRRVRIT5 ASASDFDFRRRLRIT6 ASLPDFLPGHSIGITRed : 1,2,5 vs 3,4,6Black : 1,3,6 vs 2,4,5Yellow: 1,2,3 vs 4,5,6

CMA on GPCRCMA on GPCR

CMA on GPCRCMA on GPCR

Florence HornFlorence Horn

Class B LigandsClass B Ligands

Class B – ligand dockingClass B – ligand docking

G protein-coupling?G protein-coupling?

Sequence SignalsSequence Signals

Three classes of residues

1) Conserved2) CMA3) Variable

Conservation ArtefactsConservation Artefacts

Conservation can result from

Not enough sequencesToo conserved sequencesOver-alignment

Variability ArtefactsVariability Artefacts

Variability can result from

Wrong sequence choiceVariable loopsAlignment errors

CMA ArtefactsCMA Artefacts

CMA can result from

Wrong sequence choicePoor sequence homogeneity Over-fitting

Recalcitrant residues Recalcitrant residues

Sequence EntropySequence Entropy

20

Ei = pi ln(pi) i=1

Sequence VariabilitySequence Variability

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

Entropy - VariabilityEntropy - Variability

Entropy = Information Variability = Chaos

Entropy - VariabilityEntropy - Variability

Variability is result of evolution.

Entropy is the protein’s break on evolutionary speed.

GPCR Entropy - VariabilityGPCR Entropy - Variability

11 Red12 Orange22 Yellow23 Green33 Blue

GPCR LocationGPCR Location

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Ras Entropy - VariabilityRas Entropy - Variability

Ras LocationRas Location

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Protease Protease Entropy - VariabilityEntropy - Variability

Protease LocationProtease Location

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Globin Globin Entropy - VariabilityEntropy - Variability

GPCR

Globin LocationGlobin Location

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GPCR Again….GPCR Again….

GPCR Location (Again)GPCR Location (Again)

11 Red12 Orange22 Yellow23 Green33 Blue

GPCR signalingGPCR signaling

11 Purple12 Red22 ‘Yellow’23 Green33 Blue

SummarySummary

Given infinitely many sequences:

Every residues role known.Signaling paths detectable.

So, sequences contain many signals

Thanks to:Thanks to:

Laerte Oliveira Sao PauloWilma Kuipers Weesp Florence Horn San Francisco

Bob Bywater CopenhagenNora vd Wenden The HagueMike Singer New HavenAd IJzerman LeidenMargot Beukers LeidenAmos Bairoch GenevaFabien Campagne New York