Classificazione strutturale delle proteine e principali motivi strutturali

Classificazione strutturale delle proteine
e principali motivi strutturali
Protein Data Bank (PDB)
•
URL: http://www.rcsb.org/pdb/
•
Coordinate 3-D di strutture proteiche
•
Formato unico
•
Tutte le strutture risolte con i raggi X e NMR
•
Più vecchia della maggior parte degli altri database
•
Strutturata male a causa dello sviluppo storico
Il Protein Data Bank
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Crescita del PDB
Motivi strutturali depositati ogni anno
Motivi strutturali depositati ogni anno
Percentuale di nuovi motivi strutturali
Formato PDB I
HEADER
COMPND
COMPND
SOURCE
SOURCE
AUTHOR
AUTHOR
...
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
REMARK
...
SEQRES
SEQRES
SEQRES
...
ONCOGENE PROTEIN
06-JUN-91
121P
H-RAS P21 PROTEIN COMPLEX WITH GUANOSINE-5'-[B,G-METHYLENE]
2 TRIPHOSPHATE
HUMAN (HOMO SAPIENS) CELLULAR HARVEY-RAS GENE TRUNCATED AND
2 EXPRESSED IN (ESCHERICHIA COLI)
U.KRENGEL,K.SCHEFFZEK,A.SCHERER,W.KABSCH,A.WITTINGHOFER,
2 E.F.PAI
121P
121P
121P
121P
121P
121P
121P
2
3
4
5
6
7
8
1
1 REFERENCE 1
1 AUTH
U.KRENGEL,I.SCHLICHTING,A.SCHEIDIG,M.FRECH,J.JOHN,
1 AUTH 2 A.LAUTWEIN,F.WITTINGHOFER,W.KABSCH,E.F.PAI
1 TITL
THE THREE-DIMENSIONAL STRUCTURE OF P21 IN THE
1 TITL 2 CATALYTICALLY ACTIVE CONFORMATION AND ANALYSIS OF
1 TITL 3 ONCOGENIC MUTANTS
1 REF
NATO ASI SER.,SER.A
V. 220
183 1991
1 REFN
ASTM NALSDJ US ISSN 0161-0449
2002
121P
121P
121P
121P
121P
121P
121P
121P
121P
17
18
19
20
21
22
23
24
25
1
2
3
121P
121P
121P
56
57
58
166
166
166
MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY
VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN
HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SER
Formato PDB II
HELIX
HELIX
...
SHEET
SHEET
SHEET
...
TURN
TURN
TURN
...
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
...
HETATM
HETATM
HETATM
HETATM
...
1 A1
2 A2
LYS
SER
1 S
2 S
3 S
6 GLU
6 GLU
6 THR
1 T1
2 T2
3 T3
ALA
ILE
ALA
1
2
3
4
5
6
7
8
9
10
11
1324
1325
1326
1327
16
65
GLN
THR
37
49
2
11
46
83
25
74
ILE
THR
VAL
VAL
GLU
ASN
1
1
46 0
58 -1
9 1
O
N
LEU
LEU
53
6
N
O
LYS
ASP
42
54
14
49
86
121P
121P
80
81
121P
121P
121P
85
86
87
121P
121P
121P
91
92
93
104
105
106
107
108
109
110
111
112
113
114
N
CA
C
O
CB
CG
SD
CE
N
CA
C
MET
MET
MET
MET
MET
MET
MET
MET
THR
THR
THR
1
1
1
1
1
1
1
1
2
2
2
-7.176
-5.913
-5.903
-6.703
-4.712
-4.594
-3.193
-4.325
-4.966
-4.759
-4.312
32.630
31.928
30.860
30.881
32.869
33.420
34.558
35.886
29.934
28.930
29.597
-6.655
-6.676
-5.600
-4.654
-6.415
-4.990
-4.899
-4.618
-5.760
-4.751
-3.441
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
14.06
17.27
16.41
16.12
17.94
19.41
21.82
23.68
15.08
16.71
16.63
121P
121P
121P
121P
121P
121P
121P
121P
121P
121P
121P
PG
O1G
O2G
O3G
GTO
GTO
GTO
GTO
167
167
167
167
5.150
4.768
4.164
4.834
32.173
32.597
32.683
30.641
22.030
23.390
21.069
22.025
1.00
1.00
1.00
1.00
11.69
13.29
12.61
13.18
121P1427
121P1428
121P1429
121P1430
X
Y
Z
B-factor
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CA
C
O
N
CA
C
O
CB
OG
N
CA
C
O
CB
OG1
CG2
GLU
GLU
GLU
SER
SER
SER
SER
SER
SER
THR
THR
THR
THR
THR
THR
THR
225
225
225
226
226
226
226
226
226
227
227
227
227
227
227
227
-0.900
-0.185
-0.514
0.788
1.534
2.231
1.883
2.572
3.237
3.242
3.989
4.274
4.179
5.354
5.114
6.256
-1.002
0.146
1.329
-0.203
0.805
1.806
1.952
0.130
-0.941
2.478
3.417
2.705
3.296
3.797
4.682
4.492
39.233
39.970
39.758
40.823
41.594
40.681
39.514
42.515
41.848
41.223
40.410
39.080
38.022
41.074
42.172
40.065
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
70.00
70.00
70.00
70.00
70.00
68.89
70.00
70.00
70.00
65.51
70.00
56.25
44.63
70.00
70.00
70.00
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
1HXN
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
Classificazioni
strutturali
Manuale
Semiautomatica
Automatica
SCOP
CATH
FSSP
Structural
Classification
Of
Proteins
Class,
Architecture,
Topology,
Homology
Families of
Structurally
Similar
Proteins
Classificazione delle proteine:
• SCOP (Structural Classification of Proteins,
scop.mrc-lmb.cam.ac.uk/scop/, Murzin et. al.):
1195 folds (major structural similarity in terms of secondary
structures e.g. globin-like, Rossman fold); 3902 families (clear
evolutionary relationship or homology e.g. globins, Ras)
• CATH (Class, Architecture, Topology, Homologous Superfamily,
www.biochem.ucl.ac.uk/bsm/cath/, Orengo et. al):
40 architectures (gross arrangment of secondary structures e.g. nonbundle, sandwich); 1282 topologies (connectivity of secondary
structures e.g. globin-like, Rossman fold); 2549 families (clear
homology, same function)
Esempi di categorie di fold (CATH architectures)
SCOP
•
URL: http://scop.mrc-lmb.cam.ac.uk/scop/
•
Class
–
•
a, b, a/b, a+b, ...
(Common) Fold
– Similarità strutturale
•
Superfamily
– Omologia
•
Family
– Omologia e funzione
•
Principalmente annotata a mano
– Alexey Murzin
– “Gold standard“
Structural Classification Of Proteins
Structural Classification Of Proteins
•Class
Similar secondary structure content
All , all ,αβ alternating /αβ etc
•Fold (Architecture)
Major structural similarity
SSE’s in similar arrangement
•Superfamily (Topology)
Probable common ancestry
HMM family membership
•Family
Clear evolutionary relationship
Pairwise sequence similarity > 25%
CATH
• URL: http://www.biochem.ucl.ac.uk/bsm/cath/
•
•
•
•
Class
Architecture
Topology
Homologous superfamily
• Semiautomatica
– Solo Architecture viene assegnata manualmente
Topology
Human Chorionic Gonadotropin
CATH
Class 1 – Mainly Alpha
Class 2 – Mainly Beta
Class 2 – Mainly Beta
Class 2 – Mainly Beta
Class 3 – Mixed Alpha-Beta
Class 3 – Mixed Alpha-Beta
Class 4 – Few secondary structures
Esempi
The lone helix
There are a number of examples of
small proteins (or peptides) which
consist of little more than a single helix.
A striking example is alamethicin, a
transmembrane voltage gated ion
channel, acting as a peptide antibiotic.
Esempi
The helix-turn-helix motif
The simplest packing arrangement of a
domain of two helices is for them to lie
antiparallel, connected by a short loop.
This constitutes the structure of the
small (63 residue) RNA-binding protein
Rop , which is found in certain plasmids
(small circular molecules of doublestranded DNA occurring in bacteria and
yeast) and involved in their replication.
There is a slight twist in the
arrangement as shown.
.
Esempi
The four-helix bundle
The four-helix bundle is found in a
number of different proteins. In many
cases the helices part of a single
polypeptide chain, connected to each
other by three loops. In four-helixbundle proteins the interfaces between
the helices consist mostly of
hydrophobic residues while polar side
chains on the exposed surfaces interact
with the aqueous environment, as
indicated below:
.
Esempi
Cytokines
A number of cytokines
consist of four a-helices in a
bundle. Here is a diagram of
Interleukin-2, human Growth
Hormone, Granulocytemacrophage colonystimulating factor (GM-CSF)
and Interleukin-4.
Esempi
Transcription factors are proteins
which bind to control regions of DNA.
These regions are "upstream" of the
structural gene (the sequence which
actually codes for a protein) whose
transcription they regulate.
Transcription factors have a DNAbinding domain and a domain that
activates transcription.
A three-helix bundle forms the basis of
a DNA-binding domain which occurs in
a number of proteins- for example
homeodomain proteins.
Esempi
Helix-helix packing
When alpha-helices pack against each other,
the side-chains in their interface are buried.
The two interface areas should have
complementary surfaces. The surface of an ahelix can be thought of as consisting of
grooves and ridges, like a screw thread: for
instance, the side chains of every 4th residue
form a ridge (because there are 3.6 residues
per turn). The direction of this ridge is 26° from
the direction of the helix axisThe "i+4" ridge is
believed to be the most common because
residues at every 4th position have sidechains which are more closely aligned than in
"i+3" or "i+1" ridges as indicated below.
Esempi
Helix-helix packing
Two other types of packing do occur, however:
between an "i+4" ridge and an "i+3" ridge
(there is an angle of 23° between the 2 helix
axes) and between an "i+4" and an "i+1" ridge
(the helices are 105° apart). The "ridges and
grooves" model does not describe all the
helix-helix packings, as there are examples
with unusual inter-axial angles. For instance in
the globin fold a pair of helices (B and E) pack
such that their ridges cross each other, by
means of a notch formed at a pair of glycine
residues.
On the left there is a diagrams of the notch in
the ridges of helices B and H:
Esempi
Helix-helix packing
Two other types of packing do occur, however:
between an "i+4" ridge and an "i+3" ridge
(there is an angle of 23° between the 2 helix
axes) and between an "i+4" and an "i+1" ridge
(the helices are 105° apart). The "ridges and
grooves" model does not describe all the
helix-helix packings, as there are examples
with unusual inter-axial angles. For instance in
the globin fold a pair of helices (B and E) pack
such that their ridges cross each other, by
means of a notch formed at a pair of glycine
residues.
On the left there is a diagrams of the notch in
the ridges of helices B and H:
Esempi
β sandwiches and β barrels
The immunoglobulin fold the strands form two sheets packed against each other,
forming a "β sandwich".
Aligned and orthogonal β sandwiches
In the immunoglobulin and fibronectin type-3 folds,
the two sheets are approximately aligned. In fact
the mean angle between the 2 sheets is
approximately 30° (designated -30° because the
uppermost sheet is rotated clockwise with respect
to the lower). The two sheets are usually
independent in that the linking residues between
them are not in β sheet conformation. The angle
between the sheets is determined by their righthanded twist.
Orthogonal b sheet packings consist of b sheets
folded on themselves; the two sheets make an
angle of -90°. The strands at one corner or 2
diagonally opposite corners go uninterrupted from
one layer to the other. Local coiling at the corner or
a b bulge facilitates the right-angled bend.
Esempi
β sandwiches and β barrels
The immunoglobulin fold the strands form two sheets packed against each other,
forming a "β sandwich".
Esempi
β sandwiches and β barrels
The immunoglobulin fold the strands form two sheets packed against each other,
forming a "β sandwich".
Esempi
β sandwiches and β barrels
The immunoglobulin fold the strands form two sheets packed against each other,
forming a "β sandwich".
Esempi
β barrels
Some antiparallel β -sheet domains are better described as β -barrels rather
than b-sandwiches, for example streptavadin and porin. Note that some
structures are intermediate between the extreme barrel and sandwich
arrangements.
Esempi
β propeller
The case of hemopexin
Esempi
The Greek Key topology
The Greek Key topology, named after a pattern that was common on Greek
pottery, is shown below. Three up-and-down b-strands connected by hairpins are
followed by a longer connection to the fourth strand, which lies adjacent to the
first.
TNF omotrimero
Esempi
The most regular and common domain
structures consist of repeating β-α-β
supersecondary units, such that the outer layer
of the structure is composed of α-helices
packing against a central core of parallel βsheets. Many enzymes, including all those
involved in glycolysis , are α/β structures. Most
α/β proteins are cytosolic.
The β-α-β is always right-handed. In α/β
structures, there is a repetition of this
arrangement, giving a β-α-β-α.....etc sequence.
The β strands are parallel and hydrogen bonded
to each other, while the α helices are all parallel
to each other, and are antiparallel to the strands.
Thus the helices form a layer packing against
the sheet. The β-α-β-α-β subunit, often present
in nucleotide-binding proteins, is named the
Rossman Fold, after Michael Rossman (Rao
and Rossman,1973).
Esempi
The most regular and common domain
structures consist of repeating β-α-β
supersecondary units, such that the outer layer
of the structure is composed of α-helices
packing against a central core of parallel βsheets. Many enzymes, including all those
involved in glycolysis , are α/β structures. Most
α/β proteins are cytosolic.
The β-α-β is always right-handed. In α/β
structures, there is a repetition of this
arrangement, giving a β-α-β-α.....etc sequence.
The β strands are parallel and hydrogen bonded
to each other, while the α helices are all parallel
to each other, and are antiparallel to the strands.
Thus the helices form a layer packing against
the sheet. The β-α-β-α-β subunit, often present
in nucleotide-binding proteins, is named the
Rossman Fold, after Michael Rossman (Rao
and Rossman,1973).
Esempi
α-β Barrels
Consider a sequence of eight β-α motifs: If the first strand hydrogen bonds to the
last, then the structure closes on itself forming a barrel-like structure. This is shown
in the picture of triose phosphate isomerase.
Esempi
α-β Sheets
In a structure which is open rather
than closed like the barrel, helices
would be situated on only one side of
the b sheet if the sheet direction did
not reverse. Therefore open a/b
structures must be doubly wound to
cover both sides of the sheet (e.g.,
lactate dehydrogenase). The chain
starts in the middle of the sheet and
travels outwards, then returns to the
centre via a loop and travels
outwards to the opposite edge
Esempi
α-β Sheets
In a structure which is open rather
than closed like the barrel, helices
would be situated on only one side of
the b sheet if the sheet direction did
not reverse. Therefore open a/b
structures must be doubly wound to
cover both sides of the sheet (e.g.,
lactate dehydrogenase). The chain
starts in the middle of the sheet and
travels outwards, then returns to the
centre via a loop and travels
outwards to the opposite edge
Esempi
α+β Topologies
This is where we collect
together all those folds which
include significant alpha and
beta secondary structural
elements, but for which those
elements are `mixed', in the
sense that they do NOT exhibit
the wound alpha-beta topology.