http://www.protein.osaka-u.ac.jp/rcsfp/pi/ http://www.pdbj.org/ Haruki Nakamura Institute for Protein Research, Osaka University Bioinformatics Training Course Shanghai, on April 21, 2010 Structural Bioinformatics: Databases and Analyses
Microsoft PowerPoint - Shanghai100421distr.pptOsaka
University
Structural Bioinformatics: Databases and Analyses
1. Protein Data Bank Japan (PDBj) at Osaka
2. Functional prediction from 3D structures 2-1: Similar backbone
structure search
2-2: Similar local functional site search
2-3: Similar molecular surface search
3. Structural modelling of protein-protein interactions:
surFitsurFit, A docking server for , A docking server for protein
molecular surfacesprotein molecular surfaces
4. Tutorials for 4. Tutorials for PDBjPDBj
Outline of the Talk
http://www.wwpdb.org/
E-MSD is supported by grants from the Wellcome Trust, the EU
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Kleywegt, G Berman, HM Markley, JL Nakamura, H
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We process 25-30 % deposited data of the entire world, mainly from
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Processed data numbers at PDBj and wwPDB
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– Mechanism for extension based on new demands • PDBML
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: :
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: :
Maintain Format Standards • PDB • PDB Exchange (mmCIF)
– Mechanism for extension based on new demands • PDBML
– Derived from mmCIF – All entries converted to XML – Automatic
translation from mmCIF data files
and dictionaries – 3-styles of translation released – PDBML: the
representation of archival
macromolecular structure data in XML.
mmCIF (macromolecular Crystallographic Information Format)
As mmCIF is a list of data items which consist of a name and value
pair.
_name value
_entry.id 1GOF _cell.length_a 98.000 _cell.length_b 89.400
_cell.length_c 86.700 _cell.angle_alpha 90.00 _cell.angle_beta
117.80 _cell.angle_gamma 90.00 _symmetry.space_group_name_H-M 'C 2
'
loop_ _atom_site.label_seq_id _atom_site.group_PDB
_atom_site.type_symbol _atom_site.label_atom_id
_atom_site.label_comp_id _atom_site.auth_seq_id
_atom_site.label_asym_id _atom_site.Cartn_x _atom_site.Cartn_y
_atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv
_atom_site.id 1 ATOM N N ALA 1 A 38.840 0.236 1.012 1.00 34.65 1 1
ATOM C CA ALA 1 A 38.356 -0.999 0.357 1.00 42.26 2 1 ATOM C C ALA 1
A 37.098 -1.547 1.056 1.00 41.25 3 1 ATOM O O ALA 1 A 36.619 -0.946
2.028 1.00 29.44 4 1 ATOM C CB ALA 1 A 39.398 -2.114 0.379 1.00
40.70 5 2 ATOM N N SER 2 A 36.610 -2.666 0.495 1.00 32.67 6 2 ATOM
C CA SER 2 A 35.411 -3.244 1.202 1.00 34.90 7 2 ATOM C C SER 2 A
35.683 -4.740 1.081 1.00 38.30 8 2 ATOM O O SER 2 A 36.827 -5.147
0.747 1.00 28.59 9 2 ATOM C CB SER 2 A 34.063 -2.660 0.823 1.00
24.49 10 2 ATOM O OG SER 2 A 33.031 -3.308 1.686 1.00 20.37
11
Example of mmCIF description
– Mechanism for extension based on new demands • PDBML
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General Advantages of XML description
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as the template. _name value → <tag> content
</tag>
2) For compatibility, use the name and structure of mmCIF as much
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<PDBx:atom_siteCategory> <PDBx:atom_site id="1">
</PDBx:atom_site>
<atom_record id="1">ATOM 1 A A 1 1 ? . THR THR N N N 17.047
14.099 3.625 1.00 13.79</atom_record>
Full-tag description
Separated file for coordinates
ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 PDB-format
Example of PDBML for an atom coordinate.
Data Format update (v3.2) 1) New “SPLIT” record
Structure for Supramolecules
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http://www.wwpdb.org/ccd.html)
PDBj Mine
Encyclopedia of Protein Structures, eProtS (Kinjyo, Kudo, &
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Structures. MAFFTash (Kato. Toh & Standley
Homolog protein search, Sequence Navigator (Standley
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Folds and Sequences, SeSAW (Standley
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Nakamura
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Development of other Databases and Services
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Template: 1zsy A
Spanner model
New! Spanner Hybrid-Template Modeling http://www.pdbj.org/spanner/
Developed by Mieszko Lis (MIT), Daron M. Standley (iFREC, Osaka U),
Haruki Nakamura (IPR, Osaka U)
(http://www.pdbj.org/sfas/)
SFAS: Get homologs in PDB and have alignments with 3D models
Input your e-mail address
Side-chain modeling: Combinatorial problem
Dead End Elimination (DEE)
Multiple Alignment of Sequence and Structures (by Kato. Toh &
Standley
Procedure of Homology Modeling @PDBj
Homology modeling service (by Mieszko, Standley, Nakamura
1. Protein Data Bank Japan (PDBj) at Osaka
2. Functional prediction from 3D structures 2-1: Similar backbone
structure search
2-2: Similar local functional site search
2-3: Similar molecular surface search
3. Structural modelling of protein-protein interactions:
surFitsurFit, A docking server for , A docking server for protein
molecular surfacesprotein molecular surfaces
4. Tutorials for 4. Tutorials for PDBjPDBj
Sequence: represented by a series of Characters Discrete
information: ATGC-DNAPRTEIN
Query search to find similar sequence is suitable to a digital
computer. (e.g.) Are there any sequences, which are similar
to
my sequence?
Structure: represented by floating point numbers Analog
information:
Query should be analog: (e.g.) Are there any structures, which are
similar to
my structure?
Query Structure
d
i
eNER
2
0
0
Structural similarity is defined by the Number of Equivalent
Residues: NERd0
Standley, D. M. et al. (2004) PROTEINS, 57,381–391. Stanldey, D. M.
et al. (2005) BMC Bioinfo. 6,221. Standley, D. M. et al. (2008)
Brief. Bioinfo. 9, 276-285.
Structure Navigator Search of Similar Folds
PDBID: 2dc4 165aa long Hypothetical Protein by Bagautdinov &
Kunishima (RIKEN)
Sequence identity: 27% with 2fjt (Adenylyl Cyclase)
Sequence alignment
2dc4 -------MEIEVKFRVNFEDIKRKIEGL--GA-K-FFGI-EEQEDVYFE-----L-PSPK
:.:.:::: :. . . : . :.: . :
2fjT
SEHFVGKYEVELKFRVM--DL-TTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLADQQI
2dc4 LLRVRKINNTGKSYITYKE-ILDKRNEEFYELEFEVQDPEGAIELFKRLGFKVQGVVKKR .
.: .: .: : : : . : .. ::.. . :.
2fjT
SMVLREMNPSGIRLWIVKGPG-A----ER-E-ASNIEDVSKVQSMLATLGYHPAFTIEKQ
2dc4 RWIYKLNNVTFELNRVEKAGDFLDIEVIT-S--NPEEGKKIIWDVARRLGLKEEDVEPKL :
:: . . . .... ::: .: ..: . : :.: .::. .. ::.
2fjT
RSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRS
2dc4 YIELIN- : .:.
2fjt YRQLLGF
Structural alignment NER (Number of Equivalent residues): 124 (75
%) RMSD (Root-mean-square deviations of Cα): 2.0 Å
Blue: 2dc4 Red: 2fjt
Pfam mapping of 2dc4 1. Structural alignment
4. Combine the alignments for 2dc4 & 2fjt
Active site of 2fjt (Adenylyl Cyclase)
2. Pfam alignment of 2dc4
3. Pfam alignment of 2fjt (Adenylyl Cyclase)
Active sites of 2dc4 & 2fjt (adenylyl cyclase)
Glu
Glu
2dc4 should have a function to hydrolyze phosphate.
SeSAW Sequence-derived Structure Alignment Weights
for identifying functional sites
• A way of comparing sequence and structure similarities between
proteins
• Structural similarities measured using ASH structural alignment
program
• Sequence similarities measured using position specific scoring
matrices (PSSMs) from psiBLAST
(by Standley, D. M.) Standley, D. M. et al., PROTEINS (2008) 72,
1333-1351.
Protein Functional Annotation
arg 2 0
m
= + − + ∑
Score for strucutural similarity Blosum62 score Score from PSSM
values
dm: distance between the Cα atom pairs in the aligned structures.
do: 4A
Identification of Protein Families/Superfamilies
Superposed structures
1x42A1v96A
1y4yA1th5A
1yz6A 1j27A
1orbA1wv9A
1me5B2cwqB
Standley, D. M. et al., PROTEINS (2008) 72, 1333-1351.
(There are other 37 structures in PROTEIN 3000 with STarget values
above 50.)
Superposed structures
2acjD1wj5A
1ii5A2czlA
1nm3B1wjkA
1j1iA 2dstB
2fa4B1v9wA
1udxA1wxqA
Standley, D. M. et al., PROTEINS (2008) 72, 1333-1351.
Nature (2009) 458, 1185-190
Structural superpositions allow you to see which conserved residues
are close in space
SeSAW: Protein Functional Annotation
2. Functional prediction from 3D structures 2-1: Similar backbone
structure search
2-2: Similar local functional site search
2-3: Similar molecular surface search
3. Structural modelling of protein-protein interactions:
surFitsurFit, A docking server for , A docking server for protein
molecular surfacesprotein molecular surfaces
4. Tutorials for 4. Tutorials for PDBjPDBj
c.39: EF-hand b.69: β-propeller b.1: β-sandwich
Similar local functional site search
2CCL
Ca2+
1TXV
Ca2+
1EDH
Ca2+
with Refined Alignment Finder (By Kinjo, A. R. )
Kinjo, A. R., Nakamura, H. (2007) Biophysics 3, 75-84. Kinjo, A.
R., Nakamura, H. (2009) Structure, 17, 234-246.
LBSML: Ligand Binding Site ML
Kinjo, A. R., Nakamura, H. (2007) Biophysics 3, 75-84.
Outline of the GI-IR algorithm For a given query with its own
Refset-query,
1. Search for Refsets-template in RDB that have similar shapes and
environments.
2. Count the number of overlapping atoms within 2 Å radius: cnt(
itref , iqref )
3. Compute the GI score:
4. Refine the alignments of highly scoring hits.
Basis set of a local coordinates system: Refset, by Delaunay
tetrahedron
Each LBS is composed of hundreds of Refsets, which are stored in
RDB. (atom geometry, atom type, environment)
186,485 LBS
Refset- query
GIRAF method
All-against-all search of Ligand-binding sites • All PDB entries as
of 2008/6/13: 51,289 entries. • All ligands except for water and
large ligands with > 1000 atoms. • A ligand binding site is a
set of protein atoms closer than 5 Å from the ligand: 186,485 sites
(8,161,398 refsets) in total. • All-against-all comparison: ∼ 60
hours using Xeon (3.2GHz) 160-cores.
Sequence identity and structural similarity of Ligand Binding Sites
are weakly correlated.
Structural motifs (total: 2959 motifs: 69,748 Ligand Binding Sites)
defined with P=10-15 and at least 10 sites
TIM barrelP-loop
Rossmann fold
1II8:c.37: Rad50 ABC-ATPase 1S7N:d.108: Coenzyme-A (CoA) binding
site of acetyl transferase
ATP(Phosphate) /CoA
Similarity network for 3000 motifs: Node (structural motif) is
connected if a member of one node is similar to a member of the
other nodes.
Cross-fold similarity of ligand binding motif
5EST: b.47: porcin pancreatic elastase (β-barrel) 1PEK: c.41:
proteinase (Rossmann-like fold)
XAI/PAPF
Similarity network
Ca2+/Ca2+
2CCL: c.39: cellulosomal scaffolding protein A 1TXV: b.69: human
integrin alpha-IIb
Similarity network
Summary Nearly 3000 common ligand binding motifs (with at least 10
members) were identified. Most motifs are confined within
homologous (super) families. The similarity network seems
biologically meaningful. From our comprehensive structural
classification, many (4035 pairs of motifs) do not share the common
folds.
GIRAF service is available at PDBj. Kinjo, A. R., Nakamura, H.
(2009) Structure 17, 234-246.
1. Protein Data Bank Japan (PDBj) at Osaka
2. Functional prediction from 3D structures 2-1: Similar backbone
structure search
2-2: Similar local functional site search
2-3: Similar molecular surface search
3. Structural modelling of protein-protein interactions:
surFitsurFit, A docking server for , A docking server for protein
molecular surfacesprotein molecular surfaces
4. Tutorials for 4. Tutorials for PDBjPDBj
eF-site/eF-surf/eF-seek
(Kinoshita, K. & Nakamura, H.)
Kinoshita, K. et al., Nucl. Acids Res. (2007) 35, W398-W402.
Kinoshita, K. & Nakamura, H., Protein Sci (2005) 14, 711-718.
Kinoshita, K. & Nakamura, H., Bioinformatics (2004) 20,
1329-1330.
eF-site database: http://ef-site.hgc.jp
Almost all PDB entries are calculated. Individual subunits are
calculated.. Each model for NMR structure is calculated.
Kinoshita, K. & Nakamura, H., Bioinformatics (2004) 20,
1329-1330.
Structure Page for surface and structure browsing
Kinoshita, K. & Nakamura, H., Bioinformatics (2004) 20,
1329-1330.
Molecular surface and electrostatic potential Connolly surface
(Molecular surface) by MSROLL.
Probe sphere Solvent Accessible Surface
Protein core Re-entrant surface
Ionic strength: 0.1 M
Search of the similar molecular surfaces of hypothetical
proteins
E09(SAH) FAD (NADP)-(ADP-ribose)
= # of corresponding vertices # of vertices in each patch
coverage
Kinoshita, K. & Nakamura, H. (2005) Protein Science, 14.
711-718.
Similar molecular surfaces are found by graph theorem (Largest
clique search) and by geometric hashing algorithm.
coverage vs. Z-score plot.
Prediction of Ligand Binding Sites: eF-seek
http://ef-site.hgc.jp/eF-seek
Prediction of Functional sites by similarity search for eF-site
Search for representative ligand binding sites
For the uploaded PDB-formatted file, the putative functional sites
are predicted, and the assumed complex structures will be
replied.
PDBID: 1uan TT1542 Termus thermopilus HB8
3D structure was determined by N. Handa, S. Kuramitsu, S. Yokoyama
(RIKEN) Handa et al. (2003) Protein Science 12, 1621-1632.
• 227 residues • More than 100 homolog proteins are known,
although their 3D structures were not known. • Rossman-like
fold
• 31 putative functional surfaces are converged into 13 functional
sites.
• Among them, 10’th functional site is the most promising. – The
highest similarity of the molecular surfaces. – The most well
conserved resion
From reverse angle
Similar molecular surfaces are searched for 22,747 functional
molecular surfaces in eF-site.
Conserved region
4 protein molecular surfaces are similar. 1. a.43.1.2: 1mjq, 1mjl,
1mjq with SAM 2. d.92.1.11: 1b3d, 1d5j, 1d7x, 966c with MM3, SPC,
RS2, S27 3. b.47.1.2: 1f0r with 815 4. b.71.1.1: 1jdd with
GLC
O
O
Ligand binding mode at the 10’th functional site.
MM3
GLC
SAM
S27
Structural alignment Sequence Identity: 27 % NER (Number of
Equivalent residues): 159 (70 %) RMSD (Root-mean-square deviations
of Cα): 1.9 Å
Blue: TT1542 (1uan) Red: 1q7t
Standley & Nakamura (2008) PNE, 53, 638-644.
Green: β-Octylglucoside
(BluePositive, RedNegative potential
Standley & Nakamura (2008) PNE, 53, 638-644.
NER (Number of Equivalent residues): 159 (70%) RMSD
(Root-mean-square deviations of Cα): 1.9
Blue: 1uan Red: 1q7t Green: β-Octylglucoside
TT1542 should have similar function to MshB (hydrolysis of
sugars).
Structural Alignment (Pfam mapping)
1. Protein Data Bank Japan (PDBj) at Osaka
2. Functional prediction from 3D structures 2-1: Similar backbone
structure search
2-2: Similar local functional site search
2-3: Similar molecular surface search
3. Structural modelling of protein-protein interactions:
surFitsurFit, A docking server for , A docking server for protein
molecular surfacesprotein molecular surfaces
4. Tutorials for 4. Tutorials for PDBjPDBj
E. Kanamori1,2, D.M. Standley3, S. Liang3, Y. Murakami4, A.R.
Kinjo5, Y. Tsuchiya6, K. Kinoshita6, H. Nakamura5
1Biomedicinal Information Research Center, Japan Biological
Informatics Consortium
2Hitachi Software Engineering Co.,Ltd. 3Systems Immunology
Laboratory, Immunology Frontier Research
Center, Osaka University 4National Institute of Biomedical
Innovation 5Institute for Protein
Research, Osaka University 6Institute of Medical Science,
University of Tokyo
surFit: A Docking server for protein molecular surfaces
Search of the Geometrical Complementarity with the weight of ET
score.
Maximize F by the optimization procedure.
RID of RalGDS
Surface Docking Procedure
∑
all vertex pairs
c
Query Sequences
surFit Pipeline
Scoring and re-computation of binding-site propensities
Clustering and Refinement by energy minimization
Submission
Binding interface prediction
Inhibitor (bound)
Two docking modes (CA and CB) [crystal structure (PDB code:
3E8L)]
Chain-A
Chain-B
Chain-C
Target
T40_P45 surFit Rank
f_nat L_rmsd I_rmsdbb
for CB M01 1 0.95 0.84 0.44 high M02 1 0.76 1.79 0.64 high M03 1
0.88 0.67 0.47 high M04 1 0.45 5.34 2.06 acceptable M05 1 0.76 1.23
0.80 high for CA M06 41 0.63 5.95 1.31 medium M07 41 0.88 2.82 1.26
medium M08 41 0.83 4.55 1.00 medium M09 41 0.89 1.00 0.45 high M10
41 0.86 2.31 0.71 high
surFit models
Homologous complex info.
surFit rank 1st and 41st models were selected for CB and CA
complex, respectively.
The 7th best structure among all 368 structures
M03 high quality model
M09 high quality model
1. Protein Data Bank Japan (PDBj) at Osaka
2. Functional prediction from 3D structures 2-1: Similar backbone
structure search
2-2: Similar local functional site search
2-3: Similar molecular surface search
3. Structural modelling of protein-protein interactions:
surFitsurFit, A docking server for , A docking server for protein
molecular surfacesprotein molecular surfaces
4. Tutorials for 4. Tutorials for PDBjPDBj
Get Entry Data from our XML-based browser
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PDBID (e.g. 12as) should be input in a box and GO
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Several Information for each Entry: Structural Details
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Result of BLAST search
Sequence Navigator is used.
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Conventional PDB header
Several Information for each Entry: Link
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Search of Similar Sequences: Sequence Navigator
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