Download BPM§1.2_Protein Struktur.key

Hierarchy of protein structure
Branden & Tooze, Introduction to Protein Structure
Rädler WS2009
BPM §1.1.2
1
Secondary structure elements
“Buchstaben”
α-helix  helix bundle
β-strand  β -sheet
Rädler WS2009
BPM §1.1.2
2
Main supersecondary structure elements
Rädler WS2009
BPM §1.1.2
“Worte”
3
Evolution from fragments - solenoid proteins
“Worte”
Quelle: Andrei Lupas, MPI Tuebingen
Rädler WS2009
BPM §1.1.2
4
Rubredoxin
Prealbumin
(greek key)
Phosphate
Isomerase
Rädler WS2009
BPM §1.1.2
5
Fold classification (protein taxonomy)
classification: clustering proteins into structural families
http://www.cathdb.info/latest/index.html
Class, C-level
Three major classes are recognised; mainly-alpha,
mainly-beta and alpha-beta.
Architecture, A-level
This describes the overall shape of the domain structure
as determined by the orientations of the secondary
structures but ignores the connectivity between the
secondary structures.
Topology (Fold family), T-level Structures are grouped into fold families at
this level depending on both the overall
shape and connectivity of the secondary
structures.
Homologous Superfamily, H-level
Rädler WS2009
This level groups together protein
domains which are thought to share a
common ancestor.
BPM §1.1.2
6
Class,
C-level
Architecture,
A-level
Topology (Fold family),
T-level
Rädler WS2009
BPM §1.1.2
7
The Hair: all-alpha structure
Keratin
Intermediärfilament
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BPM §1.1.2
8
The coiled-coil
double helix is
stabilized by
hydrophobic „stripes“
Rädler WS2009
BPM §1.1.2
9
Coiled-coil is a widespread motive
Quelle: Andrei Lupas, MPI Tuebingen
Rädler WS2009
BPM §1.1.2
10
Silk : all beta structure
Rädler WS2009
BPM §1.1.2
11
Antecedent domain segments
encoded by mini-genes
Extinct intermediates
Present-day proteins
N
N
N
DsbA
N
N N
Hetero-dimer
N
Fused dimer
N
N
Thioredoxin
N
Gottschalk/SS 2005
BPMPonting
§1.1.2 and Russell, J.Struct.Biol. 134:191-203 (2001)
Lupas,
Divergent evolution: Circular permutation IV
Circular permutation in four easy steps:
Tandem, in-frame gene duplication:
Loss of stop codon:
3' deletion:
Resolution through further deletion
I: Gene returns to previous state
II: Circular permutation
Quelle: Andrei Lupas, MPI Tuebingen
BPM §1.1.2
Divergent evolution: Deletions
Grishin N.V., J.Struct.Biol. 134:167-185 (2001)
BPM §1.1.2
Divergent evolution: Strand invasion I
Grishin N.V., J.Struct.Biol. 134:167-185 (2001)
BPM §1.1.2
Divergent evolution: Swaps I
Grishin N.V., J.Struct.Biol. 134:167-185 (2001)
BPM §1.1.2
Divergent evolution: Circular permutation I
Grishin N.V., J.Struct.Biol. 134:167-185 (2001)
BPM §1.1.2
Divergent evolution: Circular permutation II
Grishin N.V., J.Struct.Biol. 134:167-185 (2001)
BPM §1.1.2
TolC
Rädler WS2009
BPM §1.1.2
19Tuebingen
Quelle: Andrei Lupas, MPI