???????

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????????? ? ???????????
3
????? ????? ?????????? ????????? ???? ????????
???????? ????????? ????????? ??????????? ?
?????????????????? ? ????? ? ??? ?? ??????? ?
???????? ???????????? ???? ????????? ?
???????????? ??????.
????????? ??? ???????? ??????????????????
????????? ????????? ????????? ? ?? ?????????
???????????? ? ????????????
??????? ??????? (folding) ? ?????????
(topology) ?????? ?????????? ??? ????????
4
????? ???????? ? ??????????? ??????????
????????? ???????????, ???? ? ????? ????????????
?? ???????
5
?????? ?????????? ?????????
6
????????? ????????? C-????????? ?????? ????????
1CFG
????????? ????????? ???????????? 1AG9
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???????????? ????????? ????????? ?????????
S4 H2 S5 - S1 S2 S3 H2 S2 H1 S1 - H1

S4 H2 S5 h1 - - S3 H2 S2 H1 S1 S1
H1 h1
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??????????? ??? ???????? ????????? ????????????
? ???????????? ????????? ????????? ????????? ???
????? ?? ?????????????????? ? ????????????? ????
?.?., ????? ? ?????????? ?????????? (????????)
????? ?????????? ???????????, ??
???????????. ???????? ?? ?????!
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???????
??????????? ????? 4? ???????????? ????????
????????? ????? ???????????? ???????? ?.?.
????????? ????? ???? ???????? ?????????? TOPS
????????? TOPS
????????? TOPS
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??? ????-????? (??.????) ????? ??????????
???????????, ?? ?????? ?????????
11

• ? ?????????, ?? ??????? ??????????? ??????????
  ????????????? ??????? ???????? ?????????
  ??????? ???????? ??????? ???????? ? ?????????
  ????, ????? ????????? ??????????? ? ??????,
  ??????? ?????? ????????? ? ?.?.

? ??????? ?? ????????????? ????????????? ?
????????? ????????? ????????? ????????? ???????
???????? ? ???????????!
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??????? ???????? ?????????. TOPS
?? ????? ????, ? ???? ?????? ??????? ?????????
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??????? ???????, ??????????
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?????????? ?????
?? ????? ?????????? ?????????!
15
???????????? ???????
??????? ?????????
???????????? ??????? ?????????????????? gt
????????? ????????????? ??????? ?????????????
????

• ???????? ?? ?????!

??? ??????????? ??????? ? ???????????
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?????, ?? ??????? ?????????? ?????
(Intrinsically unstructured proteins)
Peter Tompa and Peter Csermely FASEB J 18
1169-75 (2004)
(??. ????? ??????????? ?? kodomo)
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???????, ?????? ? ??????????? ??????

• ????-??????? (sandwich)
• ????-??????? (barrel)
• ????? (jelly roll) ?? ????????, ???????,
  ?????????? ????? ?????
• ????-??????? (beta-helix)
• 3? (4?) ?????????? ???? (3helical bundle)
• ????? ???????? (parrallel helical bundles)
• ??????????????? ???????
• ?????-???? ??????? (TIM barrel)
• ??????? ???????? (Rossman fold)

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????-???????????? ?????????? ????? ????????
????????????? ???? ???????
????????????
?????????????
??????????? ????? ???????? ????? ?????
????????? ????.
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????-???????
???????, ???????????? ????-??????. ????
?????????? ?????? ???? ??????, ?????????
???????? ? ???????. ? ???? ????????
???????????????? ??????? ? ????????? ?????????
???????????. ?????? - ???????????????
????? ??????? ???????? ????-????????????? ????????
???????????
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BIFUNCTIONAL PROTEIN (ACTS AS BIOTIN OPERON
REPRESSOR AND BIOTIN HOLOENZYME SYNTHETASE) 1BIA
???? ??????????? ??? ????-???????
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????-?????
???????-???????? ???????????. ??????? ?? ??????
?????? Jelly roll
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1timtriose phosphate isomerase TIM barrel
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??????? ???????? ????-????, ??????????
?????-????????? ? ???? ??????. ???????? ??
????????? ????-?????-????.
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????-?????????2bat neuraminidase
This fold is called a beta propellor there are
six 'blades' in neuraminidase
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????-????????? (2bat)
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2mhr
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?????-???? ???????placental ribonuclease
inhibitor 1bnh
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??????????? ????????????? ???????

• SCOP (Murzin, Benner, Hubbard, Chotia, 1995)
• CATH (Orengo et al., 1993, 1997)
• FSSP (HolmSander, 1993)
• ??????

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Structural Classification of Proteins, SCOP

• ?????????? ????????? ???????
• ?????????? ?????????????

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• ?????
• ??????? (fold) ??????? ?????????
• ?????????????? ??????????? ????????? (?)
• ????????? ???????? ??????????????????? ?/???
  ??????? ???????????????? ???????????? ?????
• ????? ?.?. ???????????? ???????? ??????
• ??? ?????????? ?????

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SCOP Structural Classification of Proteins
top
CLASS
FOLD
SUPERFAMILY
FAMILY
By Michael Schroeder, Biotec,
36
????????

• ?????-?????????? ?????? (218 ???????)
• ????-??????????? ?????? (144)
• ?????/???? ??????????? ?????? (a/b) (136)
  (????-?????-???? ??????????? ???????)
• ????????? ?????? (ab) (279)
  (??????????? ????? ?????????? ? ????-???????????
  ???????)

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????? ?????-?????????? ??????? ???????? ?
???????? ? 553 ?? BACILLUS PASTEURII (1c75)
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????? ????-??????????? ??????? OB-fold
?????, ??????????? ?????????????? ??? (3ull)
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??????? ????? a/b ? ab

• a/b - ??????? ? ???? ??????
• ???????? ???????
• ????? ??????? ????????? ??????? ??? ???????? ??
  ???. ????(????-?????-???? ?????)

1TPH Triosephosphate isomerase from Chicken
(Gallus gallus) 1TPH
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??????? ????? ab ? a/b
ab - ??????? ? ???? ????? ??? ????? ?????????
- ????? ??????? ???????? ???? ????????? ???? -
?????? ?-?-? ??????????? ?????
2ACT. ACTINIDIN (SULFHYDRYL PROTEINASE)
41
?????????????

• ????????????? ????? (46) (??????? ??????)
• ?????????? (47) (????? ?????? ????????
  ???????)
• ????????? (75)

??????????????? ??????? (6) ??????
?????????? (24) ???????,
????????? (116) ????????????? ?????
(42)
42
????????? ??? ???????????? ????? ??????????????
?????????!
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???????-???????? ?????? ????? (human) (1imx) S-S
??????? ???????? ???????
???????? ?????? C2H2 (mouse) (1ali) ????? Zn
????????? ??????
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SCOP Structural Classification of Proteins.
1.75 release38221 PDB Entries (23 Feb 2009).
110800 Domains.
Class Number of folds Number of superfamilies Number of families
All alpha proteins 284 507 871
All beta proteins 174 354 742
Alpha and beta proteins (a/b) 147 244 803
Alpha and beta proteins (ab) 376 552 1055
Multi-domain proteins 66 66 89
Membrane and cell surface proteins 58 110 123
Small proteins 90 129 219
Total 1195 1962 3902
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Class Architecture Topology Homologous
superfamily, CATH

• ????? ??????? ?? ?????? ????????????? ???
• ????????????? ??????????? ???? ??????????
• DETECTIVE (Swindells, 1995),
• PUU (Holm Sander, 1994)
• DOMAK (Siddiqui and Barton, 1995).
• ??? ???????????? ??????????? ??????????
  ??????? ? ??????? ?? ?????????

47
????????? ????????????? ?????????????? (????????
SSAP, Taylor Orengo 1989).??? ???????
????????? ??????? ????????? ???????
48
CATH ?????? ?????????????

• ????? ???????? all-alpha, all-beta, alpha-beta
• ??????????? ??????? ????????????????
  ???????????? ????????? ????????? ????????? ???
  ????? ?? ??????????????????
• ????????? (???????) ??????? ????????
  ???????????? ????? ???? ? ? ????????????
  ????????? ????????? ?????????
• ?????????????? ???????????????? ??? ??????????
  ???????????? ??????
• ????????? ??????? ?????????????????? (gt35
  identity ? ??????????? ??????? ????????? gt60
  ?????)

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? ?????? ??????????? ????????????? ????
???????
CATH ??? (?!!!) ?????? (?!!!) (??????? ?
???????) ? ????????? ??????? ?????????????? ? ??
?????????? ???????? Clostridium Perfringens (PDB
??? 1PFO)
Two-layer sandwich (?!)
??? ??? ????? ?????????? ?!
(? ???? SCOP ??? ???? ?????)
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SCOP ???? ?????????? ??? ??????????????? ???
???? ??????????? ????? ?????? all alpha (???)
(????? - ???????????????? ?????? ?? Listeria
monocytogenes, ???????????? ???????? ????
?????????????)
???????????? ?????? (?)
? ????????? ?????? ???????? ?? ??? ??????
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????????????? SCOP ? CATH ????? ?? ?????????
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Sandwich or barrel?
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In the same CATH architecture one can find
classical Ig-like fold according SCOP!
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CATH architectures
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CATH architectures (cont.)