1. Comparing and Classifying Domain Structures
Methods for comparing protein structures
Protein structural classifications
How do structures and functions diverge in protein superfamilies
What proportion of genome sequences can be predicted to belong to superfamilies of known structure?

2. Protein Domain Family Classifications
Known domain structures
Alexey Murzin, LMB, Cambridge
Predicted domain structures
Julian Gough, Bristol University
Known domain structures
Predicted domain structures
Christine Orengo, UCL
Domain sequences
Alex Bateman, Sanger

3. domains are important evolutionary units
60-80% of genes in genomes code for multidomain proteins

4. Evolution gives rise to families of proteins (homologues)
Domain Superfamily
human
yeast
human
M. tuberculosis
Th. thermophilus
structure is more highly conserved than sequence during evolution
At least 40-50% of the structure is conserved 4

5. Evolution gives rise to families of proteins (homologues)
orthologues
Domain Superfamily
human
yeast
human
M. tuberculosis
Th. thermophilus
structure is more highly conserved than sequence during evolution
At least 40-50% of the structure is conserved 5

6. Evolution gives rise to families of proteins
paralogues
Domain Superfamily
human
yeast
human
M. tuberculosis
Th. thermophilus
structure is more highly conserved than sequence during evolution
At least 40-50% of the structure is conserved 6

7. Structural diversity in the CATH Domain Family P-loop hydrolases
Cocaine esterase
Acetylcholinesterase
Cutinase
structure is more highly conserved than sequence during evolution
At least 40-50% of the structure is conserved

8. Challenges in comparing protein structures
residue substitutions due to single base mutations
insertions or deletions (indels) of residues - usually not in the secondary structures but in the connecting loops
Usually the structural cores are highly conserved
Although structure is much more conserved than the sequence there can still be considerable structural differences between relatives outside the core

9. residue insertions usually occur in the loops connecting secondary
residue insertions usually occur in the loops connecting secondary structures
substitutions can cause shifts in the orientations of secondary structures

11. Superposition of OB fold Structures

12. Related structures
RMSD usually < 3.5A

13. Coping with Insertions and Deletions
ignore the variable loop regions and only compare the secondary structures
use algorithms which can explicitly handle insertions/deletions e.g. dynamic programming, simulated annealing

14. Fast structure comparison by secondary structures

15. In this example the common graph contains 5 nodes.
Graphs can be compared using the Bron Kerbosch algorithm to find the largest common graph
In this example the common graph contains 5 nodes. E E E E E E H E H H H H H H H H H
Generallly ~1000 times faster than residue based methods

16. STRUCTAL Score distances between superposed residues in path matrix
Use dynamic programming to find best path
Align sequences
Superpose structures
Use equivalences given by the best path to re-superpose the structures

17. Structure Comparison Algorithms
Structure classification
Secondary structure based:
SSM Henrick PDB
GRATH Harrison & Orengo CATH
Residue based:
SSAP Taylor and Orengo CATH
DALI Holm and Sander SCOP
Comparer Sali and Blundell HOMSTRAD
FatCat Adam Godzik PDB
Structal Levitt PDB
Structural Bioinformatics, Ed: Phil Bourne, Wiley 2003
Bioinformatics: Genes, Proteins and Computers, Bios, 2003

18. Domain structure database
lass
Domain structure database A
Orengo & Thornton 1993
rchitecture T
opology or Fold Group H
omologous Superfamily
~200,000 domains
2600 domain superfamilies

19. C A T H 3 ~40 ~1200 ~200,000 domains Class Architecture Topology or
Fold 3
~40
~1200
domain database

20. CATH Architectures Orthogonal bundle Up-down bundle -horseshoe
a-solenoid
aa-barrel
b-ribbon
b-sheet
b-roll
b-barrel

21. CATH Architectures Clam 2-layer b-sandwich Trefoil Orthogonal b-prism
Parallel b-prism
3-layer b-sandwich
b-solenoid
ab-roll
b-propeller

22. CATH Architectures ab-barrel 2-layer (ab) sandwich
3-layer (aba) sandwich
3-layer (bba) sandwich
3-layer (bab) sandwich
4-layer (abba) sandwich
ab-prism
ab-box
ab-horseshoe

23. C A T H ~200,000 domain entries 40,000 domain entries Topology or
Fold Group
~1200
40,000 domain entries
~200,000 domain entries
Homologous
Superfamily
~2600
Sequence
Family
(30%)

24. Divergent Evolution Convergent Evolution Divergent Evolution
..VILST… ..KLST… ...SLTRF...
..VILST… ..KLST… ...SLTRF...
Convergent Evolution
Convergent Evolution

25. Homologous Structures
cholera toxin
pertussis toxin
SSAP score 97 81
79%
12%
Sequence identity
Heat labile enterotoxin
high structure similarity score, often < 4A
may have detectable sequence similarity e.g. by HMMs
related functions

26. Evolutionary Ancestry Uncertain
structural similarity
no sequence similarity
no functional similarity
Evolutionary Ancestry Uncertain

29. How do proteins evolve new functions?

30. Evolution of Protein Functions in Domain Superfamilies
domain duplication
residue mutations and domain structure embellishments
domain fusion,
change in domain partner
oligomerisation

31. Mutation of Residues TIM barrel glycosyl hydrolases
acid
chitinase A
Glu general acid
narbonin
Glu incorporated in a
salt-bridge and this blocks
substrate access

32. Changes in domain function in paralogous relatives
EC code:
binding site
binding site
Pantetheine-phosphate adenyltransferase
Glycerol-3-phosphate cytidylyl transferase
changes in the domain structure can modify the binding site
or domain surface

33. Pantetheine-phosphate adenyltransferase Arginyl-tRNA synthetase
binding site
Pantetheine-phosphate adenyltransferase
Arginyl-tRNA synthetase
1od6A00
1f7uA01

34. Arginyl-tRNA synthetase

35. changes in the domain partnerships can modify the binding site
Pantetheine-phosphate adenyltransferase
Asparagine synthetase B

36. Change in Oligomerisation
Thioredoxin superfamily
peroxidase
calsequestrin

37. The Mosaic Theory of Protein Evolution
Teichmann et al 2001,2003 Gerstein et al. 2001
60-80% of proteins are multi-domain
few thousand domain superfamilies
(< 10,000 CATH, SCOP and Pfam)
> Two million domain combinations (multi-domain architectures)

38. Similarity in Chemistry
conserved I P
19% P
semiconserved I
67% P P P
poorly conserved I 7% P P I’ P’ 7%
unconserved
nearly 90% of families show full or partial conservation of functions

39. chemistry is conserved or semi-conserved across the family but the substrate can change
cytochrome
P450s
FAD/NAD(P)(H)-dependent
disulphide oxidoreductases
hexapeptide
repeat proteins

40. blade domain

41. fulcrum domain 41

42. handle domain 42

44. How representative are these structural superfamilies (ie in CATH, SCOP) of all proteins in nature?

45. :Domain structure predictions in genome sequences
protein sequences
from UniProt
scan against
library of sequence patterns (HMM models) for
CATH
~ 26 million domain sequences assigned to
CATH superfamilies
~6000 annotated genomes

47. 10,340 curated families with annotation
Pfam-A
Pfam-B
Other
Pfam-A
10,340 curated families with annotation 47

48. CATH and Pfam coverage of genomes
NewFam?

49. Protein Family Databases
Each family is represented by a sequence profile or HMM