Скачать презентацию SH 2 domain Nuria Bonifaci Francesc Estanyol Structural Скачать презентацию SH 2 domain Nuria Bonifaci Francesc Estanyol Structural

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SH 2 domain Nuria Bonifaci Francesc Estanyol Structural Bio. Informatics BIOINFO, 2007 SH 2 domain Nuria Bonifaci Francesc Estanyol Structural Bio. Informatics BIOINFO, 2007

INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 domain Study of conservation – Sequence – Structure – Phylogenetic

Why are they called SH 2? • 1911 Peyton Rous discovers Sarcoma Rous Virus Why are they called SH 2? • 1911 Peyton Rous discovers Sarcoma Rous Virus • Tyrosine Kinase v-Src • 3 domains: – Src homolog 1 (Kinase) – Src homolog 2 (SH 2) – Src homolog 3 (SH 3)

INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 domain Study of conservation – Sequence – Structure – Phylogenetic

General traits of SH 2 domain 3 beta strands 2 alpha helix Protein-protein binding General traits of SH 2 domain 3 beta strands 2 alpha helix Protein-protein binding on PTyr

SH 2 domain SH 2 domain

Classification • • Class α/β Fold: SH 2 -like Superfamily: SH 2 Family: SH Classification • • Class α/β Fold: SH 2 -like Superfamily: SH 2 Family: SH 2

INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 domain Study of conservation – Sequence – Structure – Phylogenetic

Proteins with SH 2 domain Proteins with SH 2 domain

Find the protein function: Find the protein function:

Types of proteins with SH 2 -Kinases: Brk, Chk, Csk, Fyn, Hck, p 55 Types of proteins with SH 2 -Kinases: Brk, Chk, Csk, Fyn, Hck, p 55 (Blk), p 56(lck), Pl 3 Kinase, Proto. oncogen. TK, Src, Syk, Zap-70 - Phosphatases: Shp 2, Syp - Adapters: Aps, Crk Proto-oncogen, Gbr 2, Gbr 7, Gbr 10, Mona - Dna Bindings: Cbl, STAT 1, STAT 3 b, STAThomolog - Others: Eat 2, PLCgamma, Sap

INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 domain Study of conservation – Sequence – Structure – Phylogenetic

Sequence conservation • Clustal. W Multiple sequence alignment between the kinases – Low conservation Sequence conservation • Clustal. W Multiple sequence alignment between the kinases – Low conservation of the residues – High conservation of the characteristics

p. Tyr p. Tyr

Nitrogen (ARG) Phosphate Nitrogen (ARG) Phosphate

3, 45 A 3, 45 A

Polar pocket Polar pocket

But why one SH 2 domain does not bind to any PTyr ? But why one SH 2 domain does not bind to any PTyr ?

Hydrophobic pocket Hydrophobic pocket

Importance of the hydrophobic pocket Src Kinase PTyr-X-Asn Importance of the hydrophobic pocket Src Kinase PTyr-X-Asn

Grb 2 Ptyr- Val- Asn- Val Grb 2 Ptyr- Val- Asn- Val

INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 domain Study of conservation – Sequence – Structure – Phylogenetic

Structural alignment using STAMP kinases. mat. . . & lck ) Sc 7. 90 Structural alignment using STAMP kinases. mat. . . & lck ) Sc 7. 90 RMS 1. 01 Len 105 nfit 96 r the alignment and transformations & hck lck ) Sc 8. 40 RMS 1. 32 Len 108 nfit 96 r the alignment and transformations & blk hck lck ) Sc 7. 96 RMS 0. 95 Len 107 nfit 85 r the alignment and transformations & cskk blk hck lck ) Sc 7. 97 RMS 1. 31 Len 106 nfit 84 r the alignment and transformations & brk cskk blk hck lck ) Sc 2. 11 RMS 3. 52 Len 163 nfit 24 r the alignment and transformations & potk brk cskk blk hck lck ) Sc 2. 74 RMS 4. 67 Len 187 nfit With the hole protein !!! r the alignment and transformations & itk potk brk cskk blk hck lck ) Sc r the alignment and transformations & syk itk potk brk cskk blk hck lck ) Sc potk brk cskk blk hck r the alignment and transformations & pi 3 k syk itk potk 9 nfit 16 r the alignment and transformations & fyn pi 3 k syk itk 00 Len 661 nfit 1 LOW SCORE or the alignment and transformations 5. 44 RMS 2. 11 Len 2. 55 RMS lck

The solution • Cut manually ALL the PDB files selecting only the SH 2 The solution • Cut manually ALL the PDB files selecting only the SH 2 domain ? ? ? A LOT OF WORK!!!

We used our bioinformatic knowledge!!! • Do a Phyton script to cut the PDB We used our bioinformatic knowledge!!! • Do a Phyton script to cut the PDB files given a starting and ending residue numbers • Get the FASTA sequences of the resulting PDBs But…where we can find the start/end residues?

http: //sanger. ac. uk/software/Pfam http: //sanger. ac. uk/software/Pfam

cut. PDB. py cut. PDB. py

Aminoacid 2 simbol function Aminoacid 2 simbol function

NO LOW SCORES!!! NO LOW SCORES!!!

oing cluster analysis. . . luster: 1 ( lck & src ) Sc 9. oing cluster analysis. . . luster: 1 ( lck & src ) Sc 9. 14 RMS 0. 80 Len 83 nfit 80 See file sh 2. 1 for the alignment and transformations luster: 2 ( zap & zap 2 ) Sc 8. 94 RMS 1. 02 Len 78 nfit 75 See file sh 2. 2 for the alignment and transformations luster: 3 ( cskk & zap 2 ) Sc 8. 88 RMS 0. 85 Len 79 fit 65 See file sh 2. 3 for the alignment and transformations luster: 4 ( syk & cskk zap 2 ) Sc 8. 57 RMS 1. 17 en 80 nfit 63 See file sh 2. 4 for the alignment and transformations luster: 5 ( lck src & syk cskk zap 2 ) c 8. 52 RMS 0. 82 Len 85 nfit 61 See file sh 2. 5 for the alignment and transformations luster: 6 ( itk & lck src syk cskk zap ap 2 ) Sc 8. 07 RMS 1. 25 Len 89 nfit 60 See file sh 2. 6 for the alignment and transformations luster: 7 ( fyn & itk lck src syk cskk ap zap 2 ) Sc 6. 05 RMS 1. 07 Len 89 nfit 63 See file sh 2. 7 for the alignment and transformations

oing cluster analysis. . . luster: 1 ( lck & src ) Sc 9. oing cluster analysis. . . luster: 1 ( lck & src ) Sc 9. 14 RMS 0. 80 Len 83 nfit 80 See file sh 2. 1 for the alignment and transformations luster: 2 ( zap & zap 2 ) Sc 8. 94 RMS 1. 02 Len 78 nfit 75 See file sh 2. 2 for the alignment and transformations luster: 3 ( cskk & zap 2 ) Sc 8. 88 RMS 0. 85 Len 79 fit 65 See file sh 2. 3 for the alignment and transformations luster: 4 ( syk & cskk zap 2 ) Sc 8. 57 RMS 1. 17 en 80 nfit 63 See file sh 2. 4 for the alignment and transformations luster: 5 ( lck src & syk cskk zap 2 ) c 8. 52 RMS 0. 82 Len 85 nfit 61 See file sh 2. 5 for the alignment and transformations luster: 6 ( itk & lck src syk cskk zap ap 2 ) Sc 8. 07 RMS 1. 25 Len 89 nfit 60 See file sh 2. 6 for the alignment and transformations luster: 7 ( fyn & itk lck src syk cskk ap zap 2 ) Sc 6. 05 RMS 1. 07 Len 89 nfit 63 See file sh 2. 7 for the alignment and transformations

Structural alignment Structural alignment

Secondary structure highly conserverd High variability in the loops Secondary structure highly conserverd High variability in the loops

Structural alignment of all the SH 2 domains Rmsd = 1, 68 Sc= 3, Structural alignment of all the SH 2 domains Rmsd = 1, 68 Sc= 3, 27

Advanced options of STAMP - Guide the program to do the superposition giving an Advanced options of STAMP - Guide the program to do the superposition giving an initial alignment. – 1 -. Clustal. W of all the sequences. – 2 -. > alignfit – f sh 2. align –d sh 2. domains –out sh 2. trans > stamp –l sh 2. trans –prefix sh 2 Stamp We can’t do it : - alignfit ? - other. trans files didn’t work.

INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 INDEX • • Introduction General traits of SH 2 domain Proteins with SH 2 domain Study of conservation – Sequence – Structure – Phylogenetic

Phylogenetic analysis • Compare the same protein between species (c-src) Phylogenetic analysis • Compare the same protein between species (c-src)

Good alignment !!! Good alignment !!!

Is the Arginin conserved through the evolution ? Which Arginin is the one that Is the Arginin conserved through the evolution ? Which Arginin is the one that interacts directly with p. Tyr ?

The Arginin is very conserved between the species due to its critical function The Arginin is very conserved between the species due to its critical function

References - Bradshaw JM, Waksman G Molecular Recognition by SH 2 domains - Bhushan References - Bradshaw JM, Waksman G Molecular Recognition by SH 2 domains - Bhushan Nagar, Oliver Hantschel, Markus Seeliger, Jason M. Davies, William I. Weis, Giulio Superti-Furga and John Kuriyan Organization of the SH 3 -SH 2 Unit in Active and Inactive Forms of the c-Abl Tyrosine Kinase - The SRC kinases. http: //jkweb. mcb. berkeley. edu (Berkeley Univeristy)

That’s All Any questions? That’s All Any questions?