Myoglobins

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Myoglobins
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Adding a shark
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Adding 4 fish
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Adding hemoglobins
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Correct alignment
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Mass search
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Mass search
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Patterns
gtPDOC00001 PS00001 ASN_GLYCOSYLATION
N-glycosylation site pattern Warning pattern
with a high probability of occurrence. 19 - 22
NATS gtPDOC00003 PS00003 SULFATION Tyrosine
sulfation site rule Warning rule with a high
probability of occurrence. 336 - 350
ipeatekYlggtddt gtPDOC00005 PS00005
PKC_PHOSPHO_SITE Protein kinase C phosphorylation
site pattern Warning pattern with a high
probability of occurrence. 42 - 44 TnR 68 - 70
TkK 238 - 240 TlK 340 - 342 TeK 350 - 352 TvK
gtPDOC00006 PS00006 CK2_PHOSPHO_SITE Casein
kinase II phosphorylation site pattern
Warning pattern with a high probability of
occurrence. 63 - 66 TpaD 90 - 93 StyD 119 -
122 StgD 120 - 123 TgdE 230 - 233 TeeE 261 -
264 TviD 271 - 274 TpeE 426 - 429 SeeE
gtPDOC00007 PS00007 TYR_PHOSPHO_SITE Tyrosine
kinase phosphorylation site pattern Warning
pattern with a high probability of occurrence.
51 - 58 KlseDcl.Y gtPDOC00008 PS00008 MYRISTYL
N-myristoylation site pattern Warning pattern
with a high probability of occurrence. 34 - 39
GQllSE 83 - 88 GLmvGA 87 - 92 GAasTY ......
447 - 452 GNpnGE gtPDOC00112 PS00122
CARBOXYLESTERASE_B_1 Carboxylesterases type-B
serine active site pattern. 148 - 163
FGGnpgsVtIfGeSAG gtPDOC00112 PS00941
CARBOXYLESTERASE_B_2 Carboxylesterases type-B
signature 2 pattern. 54 - 64 EDCLYLNIYtP
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Three-dimensional structure of proteins

• Peter Højrup
• Dept. of Biochemisty and Molecular Biology
• University of Southern Denmark

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Types of Molecular Homology

• Homologs genes that are descended from a common
  ancestor (e.g., all globins)
• Orthologs homologs that have diverged after
  speciation events (e.g., human and chimp
  b-globins)
• Paralogs homologs that have diverged after gene
  duplication events (e.g., a and b globin).

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Ortholog vs Paralog
Duplication
2 genes, A and B
A
B
Speciation species 1 and species 2
A1
A2
B1
B2
A B Paralogs A1 B1 Orthologs A2 B2
Orthologs A1 B2 Neither (still homologs)
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Peptide bond
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Polypeptide chain
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Turning the peptidebond
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Steric hindrance
? -60 ? 30
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Ramachandran plot
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Amino acids and glycine
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Alpha-helix
N...O 2.8Å
? -57 ? -47
n 3.6 5.4Å
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Helices found in proteins
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Beta-sheet
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Antiparallel beta-sheet
C - grøn, N - blå, O - hvid, sidekæder - purpur
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Topoligy of the beta-sheet
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Beta-turn
0º
0º
-90º
90º
-30º
120º
-60º
-60º
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Classification

• Class a bundles of a-helices.
• Class b mainly antiparallel b-sheets.
• Class a/b mainly parallel b-sheets with
  intervening a-helices, mixed b-sheets, barrel
  structures surrounded by a-helices.
• Class a b segregated a-helices and
  antiparallel b-sheets.
• Multidomain (a and b).
• Membrane and cell-surface proteins and peptides.

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a class protein
Hemoglobin
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b class protein
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a/b class protein
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a b class protein
G-specific endonuclease
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Membrane protein
Light harvesting complex
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Protein structure classification databases

• SCOP structural classification of proteins.
• CATH classification by class, architecture,
  topology, and homology.
• FSST fold classification based on
  structure-structure alignment of proteins.
• MMDB molecular modelling database.
• SARF statial arrangement of backbone fragments.

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TIM barrel 1dos 1dox
Oxireductase
Aldolase
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CATH
Class Architecture Topology Homologous
super-family
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SCOP
md - multi domain m - membrane s - Small
proteins c - coiled coil l - low resolution p -
peptides d - designed
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SCOP classification of flavodoxin

• Root SCOP
• Class alpha and beta proteins (a/b)
• Fold Flavodoxin-like (3 layers, a/b/a parallel
  bsheets of 5 strands, order 21345)
• Superfamily Flavoproteins
• Family Flavodoxin-related binds FMN
• Protein Flavodoxin
• Species Clostridium beijerinckii

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Calnexin

• Root scop
• Class All beta proteins
• Fold Concanavalin A-like lectins/glucanases
  sandwich 12-14 strands in 2 sheets complex
  topology
• Superfamily Concanavalin A-like
  lectins/glucanases
• Family Calnexin/calreticulin
• Protein Calnexin
• Species Dog (Canis familiaris)

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Chou Fasman propensities
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Chou Fasman
Fire helixformere Ha eller ha (Ia tæller halvt)
ud af seks rester danner nucleus. Fortsætter så
længe Pa for tetrapeptider gt 1.00 Tre beta sheet
formere ud af fem. Fortsætter så længe Pb for
tetrapeptid gt 1.00 I overlappende regioner er
det højeste værdi. Turns forudsiges udfra
hydrofobicitets indices.
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b
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GPMAW
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CASP

• Critical Assesment of Structure Predictions
• Biannual blind tests of structure
  predictionsLast assessment was in Dec. 2002
• Structures that are solved but not published are
  submitted to crystallographers and NMR
  spectroscopists for prediction.
• Structures are available in three categories1)
  Comparative modelling2) Fold recognition3) New
  fold

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CASP5 results
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CAST5 target T0162