Transcript Protein structure Classification Ole Lund, Associate professor, CBS, DTU. Why classify proteins     Number of solved structures grow rapidly Generate overview of structure types Detect similarities (evolutionary.

Protein structure Classification
Ole Lund,
Associate professor,
CBS, DTU.
Why classify proteins
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Number of solved structures grow rapidly
Generate overview of structure types
Detect similarities (evolutionary relationships)
Set up prediction benchmarks
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Classification schemes
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SCOP
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CATH
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Manual classification (A Murzin)
Semi manual classification (C orengo)
FSSP
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Automatic classification (L Holm)
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Levels in SCOP
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2.
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4.
Class
Folds
Superfamilies
Families
10
648
1007
1699
Murzin et al., 1995
http://scop.mrc-lmb.cam.ac.uk/scop/
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Major classes in scop
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Classes
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All alpha proteins
Alpha and beta proteins (a/b)
Alpha and beta proteins (a+b)
Multi-domain proteins
Membrane and cell surface proteins
Small proteins
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All alpha: Hemoglobin (1bab)
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All beta: Immunoglobulin (8fab)
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Alpha/beta: Triosephosphate
isomerase (1hti)
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Alpha+beta: Lysozyme (1jsf)
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Folds*
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Each Class may be divided into one or more folds
Proteins which have the same (>~50%) secondary
structure elements arranged the in the same order in
the protein chain and in three dimensions are
classified as having the same fold
*confusingly also called fold classes
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Superfamilies
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Superfamilies are a subdivisions of folds
A superfamily contains proteins which are thought to
be evolutionarily related due to
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Sequence
Function
Special structural features
Relationships between members of a superfamily
may not be readily recognizable from the sequence
alone
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Families
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Subdivision of supefamilies
Contains members whose relationship is
readily recognizable from the sequence
(>~25% sequence identity)
Families are further subdivided in to Proteins
Proteins are divided into Species
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The same protein may be found in several
species
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Families
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CATH
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Levels
Class
Architecture
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Topology
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This level is unique to CATH (~30 is defined)
~Fold(/superfamily) in SCOP
Homologous Superfamily
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~Superfamily(/family) in SCOP
http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html
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Architecture
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Same overall arrangement of secondary
structures
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Example: The architecture :Two layer beta sheet
proteins contains different folds each with a
distinct number and connectivity of strands
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FSSP
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Fully automated classification
Automatic update
Database contains structural alignments
Tree of protein structures
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FSSP classification (MHC molecules)
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Links
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PDB
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SCOP
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scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html
CATH
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www.rcsb.org/pdb/
www.biochem.ucl.ac.uk/bsm/cath_new/index.html
FSSP
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http://www.bioinfo.biocenter.helsinki.fi:8080/dali/index.html
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