Conserve Fibroblast growth

factor 8 (fgf 8) domains

Ana TomasJudith ParidaenSusana Domingues

Fibroblast growth factor 8

Member of the FGF family

Function:MitogenicChemotacticAngiogenic activityPromoting cell growth, differentiation and motility

Some Fgf 8 characteristics

N.º of a.a.: 233

Molecular weight: 26525.4

Theoretical p.i.: 10.44

Total n.º of negatively charged residues (Asp + Glu): 19

Total n.º of positively charged residues (Arg + Lys): 40

Formula: C1164H1877N363O330S9

Total n.º of atoms: 3743

Grand average of hydropathicity: -0.651 (soluble)

Estimated half-life:The N-terminal of the sequence considered is M (Met)The estimated half-life is:

30 hours (mammalian)

Instability index:The instability index (II) is computed to be 47.80

Unstable protein

ProtParam tool - ExPASy

Structure

6 chains present

913 residues

Structure and active sites

HBGF/FGFSP binding

ProSAT - Protein Structure Annotation Tool

Models

AxolotlChickenCiona S.CowDogDrosophilaFuguHouseshrewHuman

Japanese lampreyMouseOpossumOryziasRabbitRatRhesus macaqueShell turtleTetraodonZebrafish

Ciona

Phylogenetic tree

Cluster algorithm

Consensus domains

p85_SH2 SH2 KGAETGFYICMNKRG

InsR_Kin Y_kin

NARYEGWYMAFTRRG

ErkDD Kin_bind

RDCIFTEIVLENNYT  

Multalin – Multi alignment program

3D structure and consensus domains

ErkDD Kin_bind

RDCIFTEIVLENNYT  

InsR_Kin Y_kin

NARYEGWYMAFTRRG

p85_SH2 SH2 KGAETGFYICMNKRG

Rasmol

Fgf8 structure with receptor

Rasmol

Fgf

Receptor

Common regulatory elements in Fgf8

downstream targets

Anna Ferrer-VaquerAlisa Fuchs

Fgf8 signaling pathway

Elk

Ets

cJun

Fos

Myc

...

Fgf8 inducible genes

Sprouty1Pax3Otx2Tbx2ErmPea3Ptx1Lhx6SefAP2Flrt3 .... Many more

Sprouty1 > Mm, Gg, DrPax3 > Mm, Gg, DrOtx2 > Mm, Gg, DrTbx2 > Mm, Gg, DrErmPea3Ptx1Lhx6SefAP2Flrt3 .... Many more

Limitation:

1Kb of 5’UTR

Alignment

Alignment of sequences from different genes to find consensus

blocks

Not reliable

Promoter analysis

Sequence

(red: ci-value > 60

from - to capitals: core sequence)

V$MZF1/MZF1.02

Myeloid zinc finger protein MZF1 0.99 574 - 582 (-) 1.000 1.000 taGGGGaag

V$HOMF/DLX1.01

DLX-1, -2, and -5 binding sites 0.91 720 - 732 (-) 1.000 1.000 ttgtatAATTaaa

V$TALE/TGIF.01

TG-interacting factor belonging to TALE class of homeodomain factors 1.00 904 - 914 (+) 1.000 1.000 atgtGTCAatc

V$XBBF/RFX1.02

X-box binding protein RFX1 0.90 952 - 970 (-) 1.000 0.904 gcgcctctctgGCAActtt

V$CREB/CREBP1.01

cAMP-responsive element binding protein 1 0.85 581 - 601 (+) 1.000 0.905 tagcttTGACttaaatatttt

V$E2FF/E2F.02

E2F, involved in cell cycle regulation, interacts with Rb p107 protein 0.84 941 - 957 (+) 1.000 0.909 gtttgcgtCAAAaagtt

V$NKXH/HMX2.01

Hmx2/Nkx5-2 homeodomain transcription factor 0.83 109 - 123 (+) 1.000 0.914 gttCTTAagcacaaa

Position

Str. Core sim. Matrix sim.Family/ ma

trixFurther Information Opt.

Results of promoter analysis

Promotor/TF Elk vMyb ZBP-89

mSprouty1 + + +mPax3 +mOtx2 + + +mTbx2 + + +

Conclusion

Analysis of nucleotide sequences is much more difficult than amino acids