proteins

1. Protein structure Classification
Ole Lund,
Associate professor,
CBS, DTU.

2. OL
Why classify proteins
 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
 SCOP
– Manual classification (A Murzin)
 CATH
– Semi manual classification (C orengo)
 FSSP
– Automatic classification (L Holm)

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Levels in SCOP
1. Class 10
2. Folds 648
3. Superfamilies 1007
4. Families 1699
Murzin et al., 1995
http://scop.mrc-lmb.cam.ac.uk/scop/

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Major classes in scop
 Classes
– 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*
 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
 Superfamilies are a subdivisions of folds
 A superfamily contains proteins which are thought to
be evolutionarily related due to
– 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
 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
– The same protein may be found in several
species

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Families

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CATH
 Levels
 Class
 Architecture
– This level is unique to CATH (~30 is defined)
 Topology
– ~Fold(/superfamily) in SCOP
 Homologous Superfamily
– ~Superfamily(/family) in SCOP
http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

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Architecture
 Same overall arrangement of secondary
structures
– 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
 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
 PDB
– www.rcsb.org/pdb/
 SCOP
– scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html
 CATH
– www.biochem.ucl.ac.uk/bsm/cath_new/index.html
 FSSP
– http://www.bioinfo.biocenter.helsinki.fi:8080/dali/index.html