lsm2104/cz2251 essential bioinformatics and biocomputing essential bioinformatics and biocomputing...

LSM2104/CZ2251 LSM2104/CZ2251 Essential Bioinformatics and Biocomputing Essential Bioinformatics and Biocomputing 

Protein Structure and Protein Structure and Visualization (2)Visualization (2)

Chen Yu Zong  csccyz@nus.edu.sg

6874-6877

Lecture 10

Protein structure databases; visualization; and classifications

LSM2104/CZ2251 LSM2104/CZ2251 Essential Bioinformatics and Biocomputing Essential Bioinformatics and Biocomputing 

1. Introduction to Protein Data Bank (PDB)2. Free graphic software for 3D structure

visualization3. Hierarchical classification of protein domains:

SCOP & CATH & DALI

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.

1. Protein Data Bank (PDB)

1. Protein Data Bank (PDB)

PDB Content Growth

PDB Presentation of Selected Molecules

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 proteinsHow to survey the size of NMR-determined proteins?

Estimated that structural data available for only 10-15% of all known proteins.

Alternative Source of Structure: NCBI

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)

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

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.

X-ray structure 1HUY

NMR structure 1BGK

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.jsp

• YASARA: http://www.yasara.org/

• MOLMOL: MOLecule analysis and MOLecule display

http://129.132.45.141/wuthrich/software/molmol/index.html

1HUY An Improved Yellow Variant Of Green Fluorescent Protein

From Tsien’s group J.Biol.Chem. 276 29188 (2001)

Ribbon representation by RasMol

Ribbon representation by YASARA

Ribbon representation by YASARA

Ribbon representation by MOLMOL

An ensemble of 15 structures (NMR, toxin Bgk);Proton atoms also included

15 backbone structures of the sea anemone toxin Bgk

15 all-atom structures of the sea anemone toxin Bgk

Line representation

Ribbon representation

Space-filling representation

• 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: Class—Architecture—Topology--Homologous SuperfamilySequence family

University College London, UKhttp://www.biochem.ucl.ac.uk/bsm/cath/

3. Hierarchical classification of protein domains: SCOP & CATH

Proteins adopt a limited number of topologiesMore than 50,000 sequences fold into ~1000 unique folds.

Homologous sequences have similar structures Usually, when sequence identity>30%, 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 conservedA subset of functionally critical residues are found to be conserved even the folds are varied.

Basis for protein classification

How many unique folds do organisms use to express functions?

Sequence space> 50,000

Conformationalspace

~1,000 ???????

Many sequences to form one unique fold

0

10000

20000

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40000

50000

60000

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1986

1988

1990

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1994

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Fo

ldsSequences

Structures

Folds

Growth of Protein Databases

• University of Cambridge, UK: http://scop.mrc-lmb.cam.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)

Structural Classification of Proteins SCOP

• Family

Structural Classification of Proteins SCOP

• 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%.

• Superfamily

Structural Classification of Proteins SCOP

• 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

• Fold

Structural Classification of Proteins SCOP

• 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.

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

SCOP Class: All- topologies

ferritin cytochrome b-562

SCOP Class: All- topologies

SCOP Class: All- topologies

SCOP Class: All- topologies

sandwiches -barrels

SCOP Class: All- topologies

SCOP Class: Topologies

horseshoe

barrels

SCOP Class: Topologies

SCOP Class: Topologies

SCOP Class: Alpha+Beta Topologies

SCOP Class: Alpha+Beta Topologies

Ubiquitin

1ubi

Ubiquitin

1ubi

Ubiquitin

1ubi

Ubiquitin

1ubi

CATH database

Orengo et al. CATH-a hierarchical classification of protein domain structures (1997) Structure 5, 1093-1108

Sequence identity >30% the same overall foldSequence identity >70% the same overall fold

+ the similar function

CATH: Class—Architecture—Topology--Homologous Superfamily--Sequence family

http://www.biochem.ucl.ac.uk/bsm/cath/

CATH databaseClassDerived from secondary structure content, is assigned for more than 90% of protein structures automatically.

ArchitectureDescribes 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 familiesStructures within each H-level are further clustered on sequence identity. Domains clustered in the same sequence families have sequence identities >35%.

Non-identical sequence domains, Identical sequence domains, Domains

CATH database

The class (C), architecture (A) and topology (T) levels in the CATH database

Class

Architecture

Topology

The class (C), architecture (A) and topology (T) levels in the CATH database

Homologous Superfamily

CATH – architecturesCATH – architectures

CATH – architectures (cont.)CATH – architectures (cont.)

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.

SCOP / CATH -> DALI

SCOP & CATHSCOP & CATH

• Hierarchical and based on abstractions• Include some manual aspects and are curated by

experts in the field of protein structure

Presentation of results of computer classification, where the methods that underlie the classification remain

internal

Structure comparison

Dali

DALI

anti parallel barrel

meander

More information about DALI

Touring protein fold space with Dali/FSSP: Liisa Holm and Chris Sander

Comparing protein structures in 3D

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

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.

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

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

Summary

Protein structure database (PDB)

Protein structure visualization software

Structural classification, databases and servers