Předpověď 3 D-struktury a topologie bílkovin, strukturní a funkční klasifikace
Předpověď 3D-struktury/ foldu
• Klasifikace proteinů
• Předpověď funkce
• Vytvoření modelu pro další studium
Metody pro predikci funkce
^ „klasické" metody: vícenásobné aminokyselinové přiložení pozitivní alignment pouze mezi sekvencemi stejné rodiny
G£ty<^i>4-j^fi}£i|ýzaL2D ^StmktiCD     1 vlvrds tp dtd gdnwl acid
Glca1,3-Glj:g-R|^j^jgal -E. c^^j^j^ APKVLYLDAD11CQGT IE PL INFSFPDDKVAMWT ca-K typu
Gala1,3-Glca Glcal .2-Glca-R Galal
Glcal ,TlvIana-K SpsA
typ.
Rfeul E. coli
Dssn
LpcA R.le DUGT D
QIKVLYLDADIACKGSIQELIDLN AENEIAAWA LfaJ E.coll        LDRLLYLDADWCKGDISQLLHLGLN-GAVAAWK
«T<ossmann- or
IERLLYLDADVLAVS PVDELFTKNFQGKALAAVDD i, VRKIIFVDADAIVRTDIKELYDMDLGGAPYAYTPF
YFNAGVLLINLKKWR YFNSGFLLINTAQWA YFNAGFILIXIPLWT YFNSGWYLDLKKWA YFNAGVLLFDWSACR YHISALYWDLKRFR
GnTI
EDD
p4-GalT
DVD
Dvě pozorované topologie 3D struktur glykosyltransferas
SpsA-fold
?
)Stem
term
Golgi lumen...
TMĎ Cytoplasm
(Procaryotes/Phage)
ß-GIcT (BGT, phage T4) n.c.
ß4-GlcNAcT (MurG, E.coli) GT28
ß-GIcT (GtfB, M. orientalis) GT1
(Procaryotes)
SpsA (B. subtilis) GT2 a4-GalT (LgtC, N.meningitis) GT8 (Eucaryotes)
p4-GalT1 (bovine) GT7 p2-GlcNAcT (GnT I, rabbit) GT13 p3-GlcAT I (human) GT43 a3-GalT (bovine) GT6 Glycogenin (rabbit) GT8 oc3-GalNacT (GTA, human) GT6 cc3-GalT (GTB, human) GT6
inv inv inv
inv ret
inv inv inv ret ret ret ret
N-term
Nadrodina s BGT foldem
MurG (ß-GIcNAcT) GtfB (ß-GIcT) BGT (ß-GIcT)
GT28 GT1 n.c.
E. coli A. orientalis Phage T4
Ha etaL, 2000 Mulichak etal, 2001 Vrielink etat, 1994
Nadrodina s SpsA foldem
Společná NBD
SpsA [GT2] Charnok era/, 1999, 2001
Hum ß3-GlcAT [GT43] Pedersen er a/, 2000
Rabbit GnTI[GT13] Ünligil er al, 2000
Bovine ß4-GalT [GT7] Gastinel era/, 1999 Ramakrishnan er al, 2001, 200
LgtC (cc4-GalT) [GT8] Neisseria meningitidis Persson et al, 2001
Bovine cc3-GalT [GT6] Gastinel er al, 2001 Boix er al, 2001,2002
Předpověď 3D-struktury/ foldu
• Klasifikace proteinů
• Předpověď funkce
• Vytvoření modelu pro další studium
• Threading - „navlékání"
• Homology modeling
• Ab inicio metody
Threading
• „navlékání" = rozpoznání a přiřazení proteinového foldu aminokyselinové sekvenci
• sekvence je porovnávána s databází existujících foldů (3D profilů) a na jejich základě jsou konstruovány 3D- modely
• 3D profil - každému reziduu v 3D struktuře je přiřazena environmentálni proměnná (obsah polárních atomů v postranním řetězci, skrytá plocha, sekundární elementy, apod.) vycházející z předpokladu, že okolí rezidua je více konzervováno než aminokyselina samotná.
• Reziduum může být také popsáno pomocí svých interakcí
• Výsledná kvalita modelu shoda je popsána pomocí Z-skóre nebo energie
• U multidoménových struktur je potřeba aminokyselinovou sekvenci rozdělit na jednotlivé domény a analyzovat je separátně
PHYRE2 (3D-PSSM) http://www.sbg.bio.ic.ac.uk/phyre2 Threading at 2D level and scoring at 3D level :
matching of secondary structure elements, and propensities of the residues in the query sequence to occupy varying levels of solvent accessibility
The PSIPRED Protein Sequence Analysis Workbench http://bioinf.cs.ucLac.uk/psipred/
GenTHREADER Rapid fold recognition, matching your sequence
against a library of whole PDB chains.
pGenTHREADER Highly sensitive fold recognition using profile-profile comparison (whole chain library).
pDomTHREADER       Highly sensitive homologous domain recognition using profile-profile comparison (domain library).
I-TASSER
https://zhanglab.ccmb.med.umich.edu/l-TASSER/
a hierarchical approach to protein structure and function prediction. It first identifies structural templates from the PDB by multiple threading approach LOMETS, with full-length atomic models constructed by iterative template fragment assembly simulations. Function insights of the target are then derived by threading the 3D models through protein function database BioLiP.
Threading
Protein Homology/analogY Recognition Engine
(nástupce 3D-PSSM)
•sekvenční „alignmenf s porovnávanou strukturou •Využívá PSSMs (position-specific scoring matrix) generovanou metodou PSI-Blast jak pro cílovou sekvenci tak sekvencemi ze známých struktur.
•Kopírování 3D souřadnic a přepis jednotlivých reziduí podle zkoumané sekvence
•Následně porovná shodu profilů cílové sekvence a porovnávané struktury společně se shodou jejich sekundárních struktur.
•Jediné zásahy do aminokyselinové páteře templátu jsou při modelování inzercí a delecí v sekvenci oproti porovnávané struktuře.
Phyre2
ARDLVIPMIYCGHG
User sequence
Homologous sequences
Search the 10 million known sequences for homologues using PSI-Blast.
Phyre2
ARDLVIPMIYCGHG
User sequence
HMM
PSI-Blast
Hidden Markov model
Capture the mutational propensities at each position in the protein
An evolutionary fingerprint
Phyre2
Phyre2
Phyre2
Phyre2
Phyre2
Hidden Markov model
for sequence of KNOWN structure
Phyre2
Phyre2
Phyre2
ARDLVIPMIYCGHG
HMM
PSI-Blast
Hidden Markov model
Capture the mutational propensities at each position in the protein
An evolutionary fingerprint
Phyre2
Alignments of user sequence to known structures ARDL- -VIPMIYCGHGY ranked by confidence. AFDLCDLIPV--CGMAY
Sequence of known structure
Phyre2
Phyre2
ARDLVIPMIYCGHG
PSI-Blast
HMM
Very powerful -
able to reliably detect extremely remote homology
Routinely creates accurate models even when sequence identity is <15%
Hidden Markov Model DB of
HMM-HMM matching
3D-Model
ARDL—VIPMIYCGHGY AFDLC DLIPV—CGMAY
Sequence of known structure
Knowledge-based Potentials used by Fold Recognition methods
Calculation of
Mean Force Potentials
Mean force potential Databank of derived from the
3D structures databank
Building up a proposed model from amino acid sequence that is based on a real protein structure
SDVDIEAGQTLVQVVNISNGETWVAIQLPAQYRSFDLVFENVSPSTSGSVLVAQMA PQSGGVYGSNYSGSGWGNDLGGGGFYGYSEAKWMCLWPANRSGPNSKTGIYG TCKLMNLNQSNAVPSVTSNLFAPTAYKNEPGYANVGGCCQKIRGLASSIQFAFALH GGNVPQNTDTFSGGTIKVYGWN
3D-fold calculation based on known structures
Model quality evaluation
surface
residue-residue interactions
residue-solvent interactions
residue-residue and residue-solvent interaction
"Quality" scores
2
Protein Homology/analogY Recognition Engine V 2.0
Subscribe to Phyre at Google Groups	
_	Subscribe
Vi<;it Phvrp at (innnlp firniin*;	
553492 submissions since Feb 14 2011
Glykogensynthasa - rodina GT3 (v rodině v době analýzy nebyla vyřešena 3D-struktura)
http://www.sba.bio.ic.ac.uk/phvre/gphvre output/95cbaa7600a9bfff/ summarv.html
results for job svnt      - Mozüa firefox
vy  Zobrazit  Historie  Záložky  Nástroje Nápověda
C    X    ^  ( f    http://www.sbg.bioJc.ac.ulc/phyre/qphyre_output/95cbaa76X)0a9bfff/summary.html ovanéjší ^ Jak začít      Přehled zpráv % http://www.ncbi.nlm.... _        http://www.glycoscie...   W CHMI Radar Departme.,
re results for job cand_        X     f Quickphyre results for job synt_ X     f Qukkphyre results for job synt_ X
<£f "    G " Googi
•   —   w- •------------— ■------------------------------------■ — cognition						
nments	SCOP Code	View Model	I E-value	Estimated Precision	BioText        Fold/PDB descriptor	Superfamily
		. >u				
|, |,	d2bisa1 ✓flefigTFmZ) 18% i.d. )		3.9e-36	100%	, UDP-Glycosyttransferase/glycogen a Phosphorylase	UDP-Glycosyltransferase/g Phosphorylase
						
6.1e-36
MDl
n/a
UDP-Glycosyttransferase/glycogen UDP-Glycosyttransferase/g Phosphorylase Phosphorylase
c3c48A
61e-31
n/a
PDB headentransferase
Chain: A: PDB Molecule: predicted glycosyltransferases;
A co protein, který nemá v sekvenčních databázích žádný homolog?
•Ľ) Qutckphyre results for job rs20      - Mozilla Firefox
Soubor   Úpravy  Zobrazit   Historie  Záložky   Nástroje Napovedá
0~
C    X    Ä ( f I http://www.sbg.bioJc.ac.uk/phyre/qphyre_output/964f07M3iy5953
ft
P Nejnavštěvovanéjší      Jak začít      Přehled zpráv % http://www.ncbi.nlm.... [j http://www.glycoscie...   " CHMI Radar Departme...
Fold Recognition
Fold/PDB
View Alignments
SCOP Code
View Model
E-value
Estimated Precision
BioText
descriptor
Superfamily
Goog
Fa
d1eh9a2 (length:67) 24% i.d.
1
c2fsdA (length: 142) 19% i.d.
c2ct4A (length:70) 11% i.d.
"1?
fa
__2k
50
50
56
n/a
n/a
n/a
Glycosyl
hydrolase domain
Glycosyl hydrolase domain
PDB Chain: A PDB
headenvirus viral Molecule:putative protein baseplate protein;
PDB Chain: A PDB
header:signaling  Molecule:cdc42-protein interacting protein 4;
alpha-
Amylas
C-termi
beta-sh
domain
PDBTil
commo the rece binding domain lactocoi phages crystal j of the hi domain phage t
PDBT11
solution strutcun sh3 dor the cdo interact protein
Homology modeling
•přiložení cílové sekvence se sekvencí homologního proteinu se známou 3D strukturou
• extrakce uhlíkové páteře ze struktury tem plátu a umístění postranních řetězců
•modelování otoček a smyček
• minimalizace energie •validace modelované struktury
MODELLER
Mostly used program in academic environment for serious homology modeling
SWISS-MODEL
An automated knowledge-based protein modelling server
- Start SMR-Pipeline in automated mode on BC2-cluster at Thu May    2 08:51:47 2013
- Start BLAST for highly similar template structure identification
- No suitable templates found!
- Run HHSearch to detect remotely relared template structures
- Unfortunately,  we could not identify useful template structures
- For troubleshooting,  please see our article in Nature Protocols:
- Bordoli,  L.,  Kiefer,   F.,  Arnold,  K.,  Benkert,   P.,  Battey,  J.  and Schwede,  T. (2009). Protein structure homology modelling using SWISS-MODEL Workspace.    Nature Protocols,   4, 1.
What are protein domains?
Since the first protein structures were solved, it was apparent that the polypeptide chain could often fold into one or more distinct regions of structure. Such substructures, or domains, are considered as the basic units of folding, function and evolution and often have similar chain topologies (Holm & Sander, 1994). Protein domains are often considered as independent or, at the least, semi-independent units, able to fold and in some cases retain function if separated from the parent chain. The independent, modular nature of many domains means that they can often be found in proteins with the same domain content, but in different orders, or in different proteins in combination with entirely different domain structures.
The concept of the protein domain is just as valid at the sequence level as the structural level. This can be shown by the fact that the alignment of sequences containing similar domains, but in different orders can result in poor and possibly misleading alignments.
However alignment of the shared domains if extracted from the parent sequence may reveal a high level of sequence similarity, demonstrating an evolutionary link between the domain sequences.
PLLSASIVSAPVVTSETYVDIPGLYLDVAKAGIRDGKLQVILNVPTPYATGNNFPGIYFAIATNQGVVADGCFTYSSKV PESTGRMPFTLVATIDVGSGVTFVKGQWKSVRGSAMHIDSYASLSAIWGTAAPSSQGSGNQGAETGGTGAGNIG GGGERDGTFNLPPHIKFGVTALTHAANDQTIDIYIDDDPKPAATFKGAGAQDQNLGTKVLDSGNGRVRVIVMANGR PSRLGSRQVDIFKKSYFGIIGSEDGADDDYNDGIVFLNWPLG
ERDGTFNLPPHIKFGVTALTHAANDQTIDIYIDDDPKPAATFKGAGAQDQNLGTKVLDSGNGRVRVIVMANGRPSR LGSRQVDIFKKSYFGIIGSEDGADDDYNDGIVFLNWPLGPLLSASIVSAPVVTSQTYVDIPGLYLDVAKAGIRDGKLQ VILNVPTPYATGNNFPGIYFAIATNQGVVADGCFTYSSKVPESTGRMPFTLVATIDVGSGVTFVKGQWKSVRGSAM HIDSYASLSAIWGTAAPSSQGSGNQGAETGGTGAGNIGGGGKLAAALEIKRASQPELAPEDPEDVEHHHHHH
emeoss_	001	:
	_o o:	i
exe :sí_	001	:
emb033_	001	51
	.-0 -	1
exe :zz_	001	101
emb033_	001	36
exec3 3_	001	151
embos3_	001	-.i
emboss_	001	201
emb033_	001	136
embos3_	001	251
emb033_	001	1b6
emb033_	001	272
exec3 3_	_o o:	236
emboss	001	2b4
51 řILGTKVTD3GNGRVRVTVMANGRP3RLG3RQ\tí iFKX3 yfgiIG3EEGAĽ
-PLL3A3IV3A PWT 3ETYVDIPGLYLDVAKAGIRD I I I I I I I I I I I I I I I: I I 111 I I I 11111 I I I I I I
I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I
I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I
I I I I I I I I I I I I I I I I I I I I I
I - I I: -KLAAA-
I I -leik----
----pas----
271
5C
D
100 35
150 85
-::
135 250 155 271 235 253
-qpe-
::.| I.. I.:.:. -lapedpedvekhh-
-hhh
302
domain boundary/disorder/globularity prediction:
LinkPred (at NIMR)
SnapDRAGON domain boundary prediction (at NIMR) PASS (at RIKEN)
Domain Guess by Size (DGS) (at NCBI)
UMA (Udwary-Merski Algorithm) (at Johns Hopkins Univ.)
DomPred (at UCL)
Domain boundary prediction based on entropy profile (at IPR, Moscow] GlobPlot (at EMBL) Prediction of protein disorder/order/globularity DisEMBL (at EMBL) Protein disorder prediction
Příklad: Předpověď spojovacích úseků mezi doménami -program DomCut
Předpovídání doménových a spojovacích oblastí v sekvencích proteinů
Domény = funkční jednotky, z nichž jsou bílkoviny složeny
Linker = spojovací úsek aminokyselinového řetězce spojujícího dvě sousední domény
DomCut
• Metoda programu DomCut vychází ze statisticky potvrzeného předpokladu odlišného složení doménových a linkerových úseku v řetězcích aminokyselin.
• Jestliže známe relativní frekvence výskytu jednotlivých AK v linkerových a doménových úsecích, můžeme u neznámé sekvence odhadnout zda je ten či onen úsek spíše linker nebo doména, podle toho, zda v něm převládají AK vyskytující se více v linkerech nebo v doménách.
• Pro vyjádření přednosti AK v linkerech je definován tzv. „linker index" 5
(^linker a^domainjg frekvence zastoupení aminokyseliny / v úsecích linkeru a domény)
	j linker
s,= - In -	j domain
Četnost výskytu jednotlivých aminokyselin
v doménách a linkerech
Záporná hodnota znamená, že daná AK se častěji vyskytuje v linkerových úsecích
Výjimku tvoří Gly, který je hojně zastoupený v doménách, ale je častým prvkem v linkerových oblastech - zajištuje „ohebnost"
Aminokyselina		ý linker (%)	ý domain (%)	S,	Aminokyselina		ý linker (%)	ý domain (%)	S,
Proline	Pro*	7.95	4.93	-0.478	Asparagine	As n	4.29	4.41	0.027
Serine	Ser*	8.32	6.97	-0.177	Isoleucine	lie	4.86	5.16	0.060
Threonine	Thr*	6.68	5.67	-0.163	Leucine	Leu*	7.62	8.75	0.138
Glutamic acid	Glu*	7.53	6.62	-0.128	Histidine	His*	2.13	2.59	0.195
Lysine	Lys*	6.30	5.64	-0.112	Phenylalanine	Phe*	2.92	3.71	0.240
Glutamine	Gin	4.35	4.04	-0.073	Methionine	Met*	1.47	1.94	0.275
Alanine	Ala	7.03	6.64	-0.058	Tyrosine	Tyr*	2.49	3.44	0.322
Valine	Val	7.33	6.96	-0.052	Glycine	Gly*	5.46	7.60	0.331
Arginine	Arg	5.39	5.39	0.000	Cysteine	Cys*	1.62	2.53	0.447
Aspartic acid	Asp	5.39	5.47	0.016	Thryptophan	Trp*	0.89	1.56	0.564
DomCut - grafické znázornění Sj faktoru
DomCut- příklad predikce spojovacích úseků
Aminokyselinová sekvence Q24372
- není podobná s žádnou z referenční množiny (podobnost <40%)
- úseky linkerů mezi doménami odpovídají jasně odhadům (prohlubně pod prahovou hodnotou -0,09)
Záznam trEMBL:
Lochesin, Contoins 2 lg-like C2-type domains, 1 lg-like V-type domoin.
	IGv		IGc2		IGc2	
						
ex	0.1 ij
"O	i
	I1
q3	o.o -
	
	
"O	-0.1 =
<D	
CD	
	-0.2 -
q3	
>	
<	0
100 200 300
Sequence position
Domény předpovídají i programy používané primárně pro jiné účely na základě podobnosti s dosud identifikovanými doménami/funkčními jednotkami
NCBI - Blast (Basic Local Alignment Search Tool) (National Centre for Biotechnology Information)
Prohledávání databází známých aminokyselinových sekvencí > celý protein
	Putative conserved domains have been detected, click on the image below for detailed results.	
1 1	50                                      10«                                      ISO                                      200 250 i       i       i       1            ^^^^   i       i        i                i        i       i        i                i       i                i            ^^^^m   iii ii	28* i 1
		
Superfanilies	[            PA-IIL superfamily	)
Hulti-donains M		
Distribution of 100 Blast Hits on the Query Sequence u<
Mouse over to see the defline. click to show alignments_
Color key for alignment scores
Query
	<40	40-50		80-200	>=200
I 1	I 50	I 100	I 150	I 200	I 250
NCBI-Blast
Prohledávání databází známých aminokyselinových sekvencí > celý protein
Conserved domains on [ici|i5iio]
Lo:al query sequence
Graphical summary show options »
Query seq. Non-specif ic hits
Supci■ f.m i 1 i < ,
Hulti-donains
SC
View concise resuh
!)• 150 20« 2S0 268
PA-IIL PA-IIL superfamily
PixA
Ii
4			►
Search for similar doman architectures | ®      Refine search | ®			
1 List of domain hits ?			
[J Description	Pssmld	Multi-dom	E-value
[+lPA-IIL[pfam07472], Fucose-binding lectin II (PA-IIL): In Pseudomcnas aeruginosa the fucose-binding lectin II (PA-IIL) contributes to the ...	203639	no	3.60e-45
MPixA[pfam12306], Inclusion body protein; This family of proteins is found in bacteria Proteins in this family are typically...	204875	yes	4.88e43
NCBI- Blast
Prohledávání databází známých aminokyselinových sekvencí [protein
Conserved Domains
zzz
1
■er«?: PA-IIL
Fucoti-eindlng lectin II (PA-IIL)
B B B
■ •■■pnaefi of a mm - z •: —;- '.z- —
-stranded.anOearallcl bcta-aawdwch «rrar^s—-~- r--'_z
PubMed Referen
2.
•t jz\j z iisifc- r ~ —. z:.      c ■ zr zf • t jl.
«: JřjC 33 ."XT Dez íT.J-řír-
ie i a: -. z/r zz%i r f: Cc f 3r :
31 81038226 31 73463312 91 12346884; 31 123373383 gl 123383138 ZCUA.
2aax_A
31 137122883 It»V X
6 TTLSXSZXTZr.-ZXTl MIJ UJVLT3»
234 iffm—mp»na
7 raiJT^HJ^VIJLLT^l IMTJQT^-jm-xj
8 TTUMmU^ťl VLlMJJLlUaH,U l'UBI 2 TZl&Xůi .hz ZT-TZXTASZlIGilJ- •Wt'Llütll
.[23.
123.
[l].Las.	[2J-MB	PSS         SL2JC 83
[13.LSI.	[23 -an	iss      samt 84
LST.	[Í3-TSS	EST          SRTC 213
[ij.ni		ESB)         SK2X 71
[1].LT2	LBB	90S         SK2X 244
[13.LEI.	[23 -LOS	ZU. 233
[1].LSI.	[23 -LBS	- - 86
[1]-LEX.		iSS 83
[13 .IST.	[23 .MB	ESS. [13 .SrVQ 83
[13 ->U		ES9          SKIP 71
^21994
NCBI-Blast
Prohledávání databází známých aminokyselinových sekvencí > celý protein
z'z-: zPtxA					
Indu ston body protekl					
		" i ■1^9 i         9          1    9 r*C ^V99jC91 Vv	between 173 and 191 «rmric «Oda m IcnoC		k a a_     k_ _                    M__i* . .z . z i: : : zz
	I.JUB«	..... = -			
II  - "'S
PubMed Rtrferenceií 09
--c  n:'f z-:- rj.1 i-rtri1:- - ;x.ix-cbci; . íXřT   : i"? - T "ľ j~ ~.r ~'."
pfaml2306     äss *-sa as a Tooe t*«: - 2 :»i "O'efaTOTewan pfaml 2306 s ">d: ass iQBjsjd to at, ooT-a i s jzä-^t >.
--: — »-
MMOk»/: jo ta LO
	r act		TygTBirtin-:
	[4J	ac- m	.TnwxtwD. m.
■ i	[1]	■ Z-	Lnrxan. :::
• -	11]	■B	fjn.1' ľJtv. [7].
• :	[1]	•	QTLtVCZSS. [8] .
	[1]	ľSU	VKZXTTStV. IB] .
ť. v..	[1]	.se	rrtxsjCT. [71-
	iu	.stur	
■ P	[1]	■	imaa. IB].
	H]	.252:	fJTT.U 1B1P. [B] .
?	[1]		roacsTv
	123635821	2	-12].
«i	123«B«CIS	15	-[2].
í-	125152777	12	.12].
	55717882	B	.f2]-
í-	254248338	27	.12].
	17D75«53ľ	2	.f2]-
í-	8374BS82	:r	.12].
	154278423	22	.12].
	175722258	12	.12].
	236424278	22	.12].
rLX.117].s. 115] .81 112].2.
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InterPro protein sequence analysis & classification
InterPro is an integrated database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. European Bioinformatics Institute - http://www.ebi.ac.uk/
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InterProScan Visual Output
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InterProScan (version: 4S) Sequence Sequence.I Length 2S8
CRC64 3FAC4C40C24MS64
Launched Wed. May 16. 2012 at 17 II 03 finished Wed. May 16. 2012 at 17 3 5 39
Inter Pro Match
Query Sequence
.....I Description
2U
IPR010907
Caldum-medated lectin
C3DSA 2.60.120.400» ■ PT074 72» SVS2026»
U"characterised protein family PixA/AJdA
PF12J06K
I no detc ration I PA-MI
Caloum-me<*aMd iKbn
|*«A
■ PKOOOM □ HIM AT
□ MINTS
□ Mtosrri
I nit
ISUHft'AMlY
IflCNAU*
ISMMH ITH MM
|PANT>0
■ Mt OAK
■ CtMID
C Curopean fcenrrformjtici Institute 2006-2012. ÍB is an Outttation of the European Molecular Biology Laboratory.
Proč potřebujeme predikci domén?
•Prohledávání sekvenčních databází bez predikce domén může být neúspěšné
•Automatická predikce struktury se zaměří jen na nejlépe „definovanou" část
Phyre - whole protein
http://www.sbg.bio.ic.ac.uk/phvre2/phyre2 output/a 132b051273537c4/summary.htr
Template Information
PDB headercsugar-binding protein Chain: C: PDB Molecule:: : -
PDBTitle: crystal structure of bcla lectin from burkholderia2 cenocepacia in complex with alpha-methyl-mannoside at 1.73 angstrom resolution
PDB headercsugar binding protein Chain: A: PDB Molecule: e _
PDBTitle: c-terminal domain of bc2l-c lectin from burkholderia cenocepacia
Fold:Calcium-mediated lectin 37     Superfamily:Calcium-mediated lectin Family:Calcium-mediated lectin
NCBI-Blast
Prohledávání databází známých aminokyselinových sekvencí > celý protein
Conserved domains on [ici|i5iio]
Lo:al query sequence
Graphical summary show options »
Query seq. Non-specif ic hits
Supci■ f.m i 1 i < ,
Hulti-donains
sc
View concise resuh
!)• 150 20« 2S0 268
PA-IIL PA-IIL superfamily
PixA
Ii
4			►
Search for similar doman architectures | ®      Refine search | ®			
1 List of domain hits ?			
[J Description	Pssmld	Multi-dom	E-value
[+lPA-IIL[pfam07472], Fucose-binding lectin II (PA-IIL): In Pseudomcnas aeruginosa the fucose-binding lectin II (PA-IIL) contributes to the ...	203639	no	3.60e-45
MPixA[pfam12306], Inclusion body protein; This family of proteins is found in bacteria Proteins in this family are typically...	204875	yes	4.88e43
Phyre - C-term
http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/e332blecabb8d0a6/summary.html
Template        Alignment Coverage	3D Model			Confidence ■	% i.d.	Template Information
						PDB header:sugar binding protein Chain: A: PDB Molecule:lectin; PDBTitle: c-terminal domain of bc2l-c lectin from burkholderia cenocepacia
c2xr4A_                   i ^igr^gnj I 1      o □              ^-1				100.0 44		
_       c2vnvC                   i __     . i 2          0 g~                    1 Aignmer* |		□		100.0 62		PDB header:sugar-binding protein Chain: C: PDB Molecule:bcla; PDBTitle: crystal structure of bcla lectin from burkholderia2 cenocepacia in complex with alpha-methyl-mannoside at 1.73 angstrom resolution
		H		100.0	Fold:Calcium-mediated lectin 30     Superfamily:Calcium-mediated lectin Family:Calcium-mediated lectin	
						
Phyre -
n-term http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/e332blecabb8d0a6/summary.html
3D Model
Confidence
Template Information
Swissprot-whole protein
ES
BIOZENTRUM
UHKUUIIlMl »»C«ll» m Ma «uoi |H
SWISS-MODEL Workspace
Modelling Tools
[ myWorkspace ]
Repository Documentation [ login ]
Workunit: P000007 - Overview		
	288,	
		Print/Save this page as ^
Model Summary		
Model information:
Modelled residue range: Based on template: Sequence Identity [%]: Evalue:
Quality information: QMEAN Z-Score: -0.71
169 to 288 [2vnvDj> (1.7 A) 56.35 0 00e-1
[details]* I
logs: [Templates]* [Alignment]* [Modelling]*
display model: as [pdb]* - as [DeepView project]" - in [AstexViewer]*
download model: as [pdb]* - as [Deepview project]* - as [text]*
Global Model Quality Estimation © [+/-]
Quaternary structure information: [details]* Template (2vnv): DIMER Model built: SINGLE CHAIN
Ligand information: [details]* Ligands in the template: CA: 3. MMA: 1, S04: 1. Ligands in the model: CA: 2
http://swissmodel. expasy.org/workspace/index. php?userid=michaw(S)chemi. muni. cz&kev=0f449 e99bc0176edfa75fba19b2d96e4&func=workspace modellinq&priid=P000007
Swissprot - only N terminal part
Computation of this workunit has stopped.
Please see the following log report for details:_
Started: Thu May 17 15:21:24 2012 (3ms_automode_2011) Reading user input sequence
-  Start SMR-Pipeline in automated mode on BC2-cluster at Thu May 17  13:21:24 2012
- Start BLAST for highly similar template structure identification
- No suitable templates found!
- Run HHSearch to detect remotely related template structures
- Unfortunately,  we could not identify useful template structures
- For troubleshooting,  please see our article in Nature Protocols:
- Bordoli,  L.,   Kiefer,   F.,  Arnold,   K.,   Benkert,   P.,  Battey,   J.  and Schwede,  T. (2009). Protein structure homology modelling using SWISS-MODEL Workspace.     Nature  Protocols,   4, 1.
- Workspace Pipeline parameter
Cut-off parameters to model the target based on a BLAST target-template alignment
Evalue  : 0.0001
Minimum Template  size   (aa)   for ranking   : 25
Minimum Sequence identity  : 60
Cut-off parameters to model the target based on a HHSearch target-template alignment
Evalue  : 0.0001
Probability  : 50
MAC  : 0.3 Parameters for model selection
Minimal number of uncovered target
residues after BLAST to run HHSEARCH  : 50
Minimal number of uncovered target
residues to model an additional template   : 25
- Finish SMR-Pipeline in automated mode on BC2-cluster at Thu May 17  13:35:44 2012
Structural classes of proteins
Others:
Multi-domain, membrane and cell surface, small proteins, peptides and fragments, designed proteins,
Databases of Protein Folds
SCOP (http://scop.berkelev.edu/) - known domain structure
• Structural Classification of Proteins
• Class-Fold-Superfamily-Family
• Manual assembly by inspection
Superfamily (http://supfam.org/SUPERFAMILY/) - predicted domain structures
• HMM models for each SCOP fold
• Fold assignments to all genome ORFs
• Assessment of specificity/sensitivity of structure prediction
• Search by sequence, genome and keywords
CATH + Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/) - both
• Class - Architecture - Topology - Homologous Superfamily
• Manual classification at Architecture level
• Automated topology classification using SSAP (Orengo & Taylor) PDB eFold (http://www.ebi.ac.uk/msd-srv/ssm/)
• Fully automated using the DALI algorithm (Holm & Sander) Pfam (http://pfam.xfam.org)- domain sequences (MSA, HMM)
SCOP Structural Classification of Proteins (http://scop.mrc-lmb.cam.ac.uk/scop)
□
II (II RAI. C I.VSSII RATION Ol PROT
Welcome to SCOP: Structural Classification of Proteins. 1.75 release (June 2009)
38221 PDB Entries. 1 Literature Reference. 110800 Domains, (excluding nucleic acids and theoretical models). Folds, superfamilies, and families statistics here-New folds superfamilies families. List of obsolete entries and their replacements.
Authors. Alexey G. Murzin, John-Marc Chandonia, Antonina Andreeva, Dave Howorth, Loredana Lo Conte, Bartlett G. Alley, Steven E. Brenner Tim J. P. Hubbard, and Cyrus Chothia. scop@mrc-lmb.cam.ac.uk
Reference: Murzin A. G.: Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540. fPDF]
Recent changes are described in: Lo Conte L., Brenner S. E., Hubbard T.J.P., Chothia C, Murzin A. (2002). SCOP database in 2002: refinements accommodate structural genomics. Nucl. Acid Res. 30(1), 264-267. [PDF],
Andreeva A., Howorth D., Brenner S.E., Hubbard T.J.P., Chothia C, Murzin AG. (2004). SCOP database in 2004: refinements integrate structure and sequence family data. Nucl. Acid Res. 32:D226-D229. [PDF], and
Andreeva A., Howorth D., Chandonia J.-M.: Brenner S.E., Hubbard T.J.P., Chothia C, Murzin A.G. (2007). Data growth and its impact on the SCOP database: new developments. Nucl. Acid Res, advance access, doi: 10.1093 nargkm993. [PDF].
Access methods
Enter SCOP at the top of the hierarchy
Keyword search of SCOP entries SCOP parseable files (MRC site)
All SCOP releases and reclassified entry history (MRC site)
pre-SCOP - preview of the next release
SCOP domain sequences and pdb-style coordinate files (ASTRAL)
The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, http://scop.mrc-lmb.cam.ac.uk/scop
Family: Clear evolutionarily relationship
Proteins clustered together into families are clearly evolutionarily related. Generally, this means that pairwise residue identities between the proteins are
30% and greater. However, in some cases similar functions and structures provide definitive evidence of common descent in the absense of high sequence identity; for example, many globins form a family though some members have sequence identities of only 15%.
Superfamily: Probable common evolutionary origin
Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary origin is probable are placed
together in SUperfamilies. For example, actin, theATPase domain of the heat shock protein, and hexakinase together form a superfamily.
Fold: Major structural similarity
Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Different proteins with the same fold often have peripheral elements of secondary structure and turn regions that differ in size and conformation. Proteins
placed together in the same fold category may not have a common evolutionary origin: the structural similarities could arise just from the physics and chemistry of proteins favoring certain packing arrangements and chain topologies.
3 SCOP: Root scop - Mozilla Firefox
Soubor   Úpravy  Zobrazit   Historie  Záložky   Nástroje Nápověda
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Root: scop
Classes:
1. All alpha proteins [46456] (258) I
2. All beta proteins T487241 (165) f
3. Alpha and beta proteins (ab) [513491 (141) I Mainly parallel beta sheets (beta-alpha-beta units)
4. Alpha and beta proteins (a+b) T539311 (334) EB Mainly antiparallel beta sheets (segregated alpha and beta regions)
5. Muhi-domain proteins (alpha and beta) [56572] (53) EB Folds consisting of two or more domaim belonging to different classes
6. Membrane and cell surface proteins and peptides [56835] (50) I Does not include proteins in the immune system
7. Small proteins [56992] (85) ESI Usually dominated by metal liga>id, heme, andJor disulfide bridges
8. Coiled coil proteins [57942] (7) I Not a true class
. Low resolution protein structures T58117] (26) Not a true class
10. Peptides [58231] (120) I Peptides and fragments. Not a true class
11. Designed proteins T587881 (44) EB Experimental structures of proteins with essentially non-natural sequences. Not a true class
Laboratory of Molecular Biology
News
November,2013
During the development of SCOP2, we have identified a new, previously unrecognised type of alpha-alpha superhelix. Unlike other alpha-alpha superhelices.. More...
January, 2014
SCOP2 article in NAR is published More...
January, 2014
The structure of the month
More...
Welcome to
Citation
Antonína Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey Murzin, SCOP2 prototype: a new approach to protein structure mining (2014) Nucl. Acid Res., 42 (Dl): D310-D314. [PDF]
Description of the SCOP2 database
SCOP2 is a successor of Structural classification of proteins (SCOP). Similarly to SCOP, the main focus of SCOP2 is on proteins that are structurally characterized and deposited in the PDB. Proteins are organized according to their structural and evolutionary relationships, but, in contrast to SCOP, instead of a simple tree-like hierarchy these relationships form a complex network of nodes. Each node represents a relationship of a particular type and is exemplified by a region of protein structure and sequence.
In SCOP2, we try to put in use the knowledge we acquired over the past years and the lessons we have learned during the classification of protein structures. We believe that there are many peculiarities of proteins and their structures that have been missed due to the constraints of the original SCOP hierarchical schema. We hope that our users will find the new resource useful and that it could open new avenues for protein analysis and research.
Search Browser
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Quick introduction on how to browse, search and download
SCOP2 offers two different ways for accessing data: SCOP2-browser, that allows navigation through the SCOP2 classification in a traditional way by browsing pages displaying the node information, and SCOP2-graph, which is a graph-based web tool for
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Display a menu
-02 © 2014 MRC Laboratory of Molecular Biology
http://scop2.mrc-lmbxam.ac.uk/front.html
CATH Protein Structure Classification (http:// www.cathdb.info )
CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis
CATH Classification Browser
Class (C), Architecture (A) - 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 (T) - the same overall shape and connectivity of the secondary structures in the domain core Homologous superfamily (H) - share a common ancestor (Similarities are identified either by high sequence identity or structure comparison)
Main Classification Levels
Class 1: Mainly Alpha
Class 3: Mixed Alpha-Beta
CATH Protein Structure Classification (http:// www.cathdb.info )
CATH Search -     Browse     Download     About Support
CATH by keywords or I
16 million protein domains classified into 2,626 superfamilies
Browse »
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Take the Toil
What's New?
The CATH website has recently undergone a big overhaul We really hope you find the new pages more useful, easier to use and quicker to load. Please get in touch and let us know what you think
Searching CATH
• Search by ID / keyword
• Search by FASTA sequence
• Search by PDB structure
Example pages
Latest News
Latest Release
PDB "2bop" Domain '"IcukAOT Relatives of "IcukAGT Superfamiry "HUPs"
Functional Family FunFam Alignment Search for "enolase" Superfamiry Comparison
CATH @ VIZBI 2013 March 21, 2013	
	
f-       • • tMii—ali i in, dmOmh	• ]
"Evolution of Protein Architecture" - Dr Sillitoe presents the CATH resource at VIZBI (Harvard/MIT)	
CATH v3.5 based on PDB dated Septemb	
173,536	CATH Domains
2,626	CATH Superfamilies
51,334	PDBs
	
Gene3D v11 released March 18, 2012	
1,639	Cellular Genomes
1,016	Viral Genomes
14,963,305 16,297,076	Protein Sequences
	CATH Domain Predict
CATH Protein Structure Classification (http:// www.cathdb.info )
Core classification files for the latest version of CATH-Plus (v4.2) are now available to download. Daily updates of our very latest classifications are also available.
We are currently working on generating the CATH-Plus database for v4.2 which comprises all the extra derived data from the classification data. This includes: incorporation of the latest Gene3D sequence and functional annotation data; updating the Functional Families (FunFams); creating new superfamily superpositions; producing structural clusters for each superfamily. We will update the web pages when this data is ready.
Fold Databases
SCOP Structural Classification of Proteins (http://scop.mrc-lmb.cam.ac.uk/scop/) Dali/FSSP (http://www.ebi.ac.uk/dali/)
CATH Protein Structure Classification (http:// www.cathdb.info ) Structural Alignment Tools
Vast (http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html) CE (http://cl.sdsc.edu/ce.html) DALI (http://www.ebi.ac.uk/dali)
Fold Prediction
3D-PSSM and PHYRE Protein Fold Recognition (http://www.sbg.bio.ic.ac.uk/~phyre/) CPHmodels homology modeling (http://www.cbs.dtu.dk/services/CPHmodels/) Geno3D (http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GEN03D/geno3d_home.html) 3D-JIGSAW (http://www.bmm.icnet.uk/~3djigsaw/) ESyPred3D (http://www.fundp.ac.be/urbm/bioinfo/esypred/)
Fully Automatic Homology Modelling
Robetta full-chain protein structure prediction server (http://robetta.bakerlab.org/) Swiss-Model (http://www.expasy.org/swissmod/SWISS-MODEL.html)