LSM2104/CZ2251

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LSM2104/CZ2251 Essential Bioinformatics and
Biocomputing 
Protein Structure and Visualization (2)
Chen Yu Zong   csccyz_at_nus.edu.sg 6874-6877
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LSM2104/CZ2251 Essential Bioinformatics and
Biocomputing 
Lecture 10 Protein structure databases
visualization and classifications
1. Introduction to Protein Data Bank (PDB) 2.
Free graphic software for 3D structure
visualization 3. Hierarchical classification of
protein domains SCOP CATH DALI
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1. Protein Data Bank (PDB)

• Protein Data Bank maintained by the Research
  Collaboratory for Structural Bioinformatics
  (RCSB)
• http//www.rcsb.org/pdb/
• 30060 Structures 15-Mar-2005
• 27570 Structures 05-Oct-2004
• 23997 Structures 20-Jan-2004
• Also contains structures of other
  bio-macromolecules DNA, carbohydrates and
  protein-DNA complexes.

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1. Protein Data Bank (PDB)
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1. Protein Data Bank (PDB)
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PDB Content Growth
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PDB Presentation of Selected Molecules
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Deficiencies in our structural knowledge

• Only deposited data is actually available
• Many structures not deposited in PDB, why?
• Structures available for soluble proteins
• A few dozen entries for membrane protein
  domains, why?
• X-ray data only for those proteins that
  crystallize well or diffract properly.
• Why?
• NMR structures are usually for small proteins
• How to survey the size of NMR-determined
  proteins?
• Estimated that structural data available
• for only 10-15 of all known proteins.

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Alternative Source of Structure NCBI
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Protein Structure in PDB

• Text files
• Each entry is specified by a unique 4-letter code
  (PDB code) say 1HUY for a variant of GFP 1BGK
  for a 37-residue toxin protein isolated from sea
  anemone
• 1HUY and 1BGK
• Header information
• Atomic coordinates in Å (1 Ångstrom 1.0e-10 m)

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Header Details

• Identifies the molecule, modifications, date of
  release
• Host organism, keywords, method of study
• Authors, reference, resolution for X-ray
  structure
• Smaller the number, better the structure.
• Sequence, reference

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The Atomic Coordinates

• XYZ Coordinates for each atom (starting with
  ATOM, only heavy atom for X-ray structure) from
  the first residue to the last
• XYZ coordinates for any ligands (starting with
  HETATM) complexed to the bio-macromolecule
• O atoms of water molecules (starting with HETATM,
  normally at the last part of the xyz coordinate
  section)
• Usually, for X-ray structure, resolution is not
  high enough to locate H atoms hence only heavy
  atoms are shown in the PDB file.
• For NMR structure, all atoms (including hydrogen
  atoms) are specified in the PDB file.

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X-ray structure 1HUY
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NMR structure 1BGK
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2. Free Software for Protein Structure
Visualization

• RASMOL available for all platforms
• http//www.openrasmol.org
• Swiss PDB Viewer from Swiss-Prot
  http//www.expasy.ch/spdbv/
• Chemscape Chime Plug-in for PC and Mac
  http//www.mdl.com/downloads/downloadable/index.js
  p
• YASARA http//www.yasara.org/
• MOLMOL MOLecule analysis and MOLecule display
• http//129.132.45.141/wuthrich/software/molmol/in
  dex.html

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Ribbon representation by RasMol
1HUY
An Improved Yellow Variant Of Green Fluorescent
Protein From Tsiens group J.Biol.Chem. 276
29188 (2001)
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Ribbon representation by YASARA
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Ribbon representation by YASARA
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Ribbon representation by MOLMOL
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An ensemble of 15 structures (NMR, toxin
Bgk) Proton atoms also included
15 backbone structures of the sea anemone toxin
Bgk
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15 all-atom structures of the sea anemone toxin
Bgk
Line representation
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Ribbon representation
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Space-filling representation
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3. Hierarchical classification of protein
domains SCOP CATH

• SCOP Structural Classification of Proteins
• University of Cambridge, UK
• http//scop.mrc-lmb.cam.ac.uk/scop/
• Hyperlink in Singapore http//scop.bic.nus.edu.sg
  /
• CATH ClassArchitectureTopology
• --Homologous Superfamily
• Sequence family
• University College London, UK
• http//www.biochem.ucl.ac.uk/bsm/cath/

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Basis for protein classification

• Proteins adopt a limited number of topologies
• More than 50,000 sequences fold into 1000
  unique folds.
• Homologous sequences have similar structures
• Usually, when sequence identitygt30, proteins
  adopt the same fold. Even in the absence of
  sequence homology, some folds are preferred by
  vastly different sequences.
• The active site is highly conserved
• A subset of functionally critical residues are
  found to be conserved even the folds are varied.

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How many unique folds do organisms use to
express functions?
Sequence space gt 50,000
Conformational space
Many sequences to form one unique fold
1,000 ???????
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Growth of Protein Databases
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Structural Classification of Proteins SCOP

• University of Cambridge, UK http//scop.mrc-lmb.c
  am.ac.uk/scop/
• mirrored at Singapore http//scop.bic.nus.edu.sg/
  
• contains PDB entries grouped hierachically by
• Structural class,
• Fold,
• Superfamily,
• Family,
• Individual member
• (domain-based)

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Structural Classification of Proteins SCOP

• Family

• Proteins are clustered together into families on
  the basis of one of two criteria that imply their
  having a common evolutionary origin
• All proteins that have residue identities of 30
  and greater
• Proteins with lower sequence identities but whose
  functions and structures are very similar
• Example, globins with sequence identities of 15.

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Structural Classification of Proteins SCOP

• Superfamily

• Families, whose proteins have low sequence
  identities but whose structures and, in many
  cases, functional features suggest that a common
  evolutionary origin is probable, are placed
  together in superfamilies
• Example, actin, the ATPase domain of the
  heat-shock protein and hexokinase

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Structural Classification of Proteins SCOP

• Fold

• Superfamilies and families are defined as having
  a common fold if their proteins have same major
  secondary structures in same arrangement with the
  same topological connections.

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Structural Classification of Proteins SCOP

• Class
• For convenience of users, the different folds
  have been grouped into classes. Most of the folds
  are assigned to one of a few structural classes
  on the basis of the secondary structures of which
  they composed

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SCOP Class All-a topologies
cytochrome b-562
ferritin
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SCOP Class All-a topologies
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SCOP Class All-a topologies
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SCOP Class All-b topologies
b-barrels
b sandwiches
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SCOP Class All-b topologies
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SCOP Class a/b Topologies
a/b horseshoe
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SCOP Class a/b Topologies
a/b barrels
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SCOP Class a/b Topologies
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SCOP Class AlphaBeta Topologies
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SCOP Class AlphaBeta Topologies
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Ubiquitin
1ubi
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Ubiquitin
1ubi
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Ubiquitin
1ubi
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Ubiquitin
1ubi
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CATH database
http//www.biochem.ucl.ac.uk/bsm/cath/
CATH ClassArchitectureTopology--Homologous
Superfamily--Sequence family
Orengo et al. CATH-a hierarchical classification
of protein domain structures (1997) Structure 5,
1093-1108
Sequence identity gt30 the same overall
fold Sequence identity gt70 the same overall
fold the similar function
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CATH database
Class Derived from secondary structure content,
is assigned for more than 90 of protein
structures automatically. Architecture Describes
the gross orientation of secondary structures,
independent of connectivities, is currently
assigned manually. Topology Clusters
structures according to their topological
connections and numbers of secondary structures.
Homologous superfamilies Cluster proteins with
highly similar structures and functions. The
assignments of structures to topology families
and homologous superfamilies are made by sequence
and structure comparisons. Sequence
families Structures within each H-level are
further clustered on sequence identity. Domains
clustered in the same sequence families have
sequence identities gt35. Non-identical
sequence domains, Identical sequence
domains, Domains
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CATH database
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The class (C), architecture (A) and topology (T)
levels in the CATH database
Class Architecture Topology
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The class (C), architecture (A) and topology (T)
levels in the CATH database
Homologous Superfamily
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CATH architectures
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CATH architectures (cont.)
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The protein structure universe in the PDB (1997)
by a CATH wheel
The distribution of non-homologous structures
(i.e. a single representative from each
homologous superfamily at the H-level in CATH)
amongst the different classes (C), architectures
(A) and fold families (T) in the CATH database.
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SCOP / CATH -gt DALI

• SCOP CATH
• Hierarchical and based on abstractions
• Include some manual aspects and are curated by
  experts in the field of protein structure

Dali
Presentation of results of computer
classification, where the methods that underlie
the classification remain internal
Structure comparison
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DALI
Comparing protein structures in 3D
a b meander
anti parallel b barrel
a/b
a
b
More information about DALI Touring protein fold
space with Dali/FSSP Liisa Holm and Chris Sander
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Compare 3D protein structures by Dali
http//www.ebi.ac.uk/dali/
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Compare 3D protein structures by Dali
http//www.ebi.ac.uk/dali/

• The FSSP database (Fold classification based on
  Structure-Structure alignment of Proteins) is
  based on exhaustive all-against-all 3D structure
  comparison of protein structures currently in the
  Protein Data Bank (PDB).
• The classification and alignments are
  automatically maintained and continuously updated
  using the Dali search engine.
• Dali Domain Dictionary
• Structural domains are delineated automatically
  using the criteria of recurrence and compactness.
  Each domain is assigned a Domain Classification
  number DC_l_m_n_p , where
• l - fold space attractor region
• m - globular folding topology
• n - functional family
• p - sequence family

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Compare 3D protein structures by Dali
http//www.ebi.ac.uk/dali/

• Functional families
• Evolutionary relationships from strong
  structural similarities which are accompanied by
  functional or sequence similarities.
• Functional families are branches of the fold
  dendrogram where all pairs have a high average
  neural network prediction for being homologous.
• Sequence families
• Representative subset of the Protein Data Bank
  extracted using a 25 sequence identity
  threshold.
• All-against-all structure comparison was carried
  out within the set of representatives.
• Homologues are only shown aligned to their
  representative.

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Compare 3D protein structures by Dali
http//www.ebi.ac.uk/dali/

• Fold types
• Fold types are defined as clusters of structural
  neighbors in fold space with average pairwise
  Z-scores (by Dali) above 2.
• Structural neighbours of 1urnA (top left).
  1mli (bottom right) has the same topology even
  though there are shifts in the relative
  orientation of secondary structure elements

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Summary

• Protein structure database (PDB)
• Protein structure visualization software
• Structural classification, databases and servers