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Exploring Protein Sequences - Part 2
Part 1:
Part 2:
Patterns and Motifs
Profiles
Hydropathy Plots
Transmembrane helices
Antigenic Prediction
Signal Peptides
Repeats
Coiled Coils
Linkers
Protein Domains
Domain databases
Celia van Gelder
CMBI
Radboud University
December 2005
©CMBI 2005
Definition of protein domains
• Group of residues with high contact density, number of contacts
within domains is higher than the number of contacts between
domains.
• A stable unit of protein structure that can fold autonomously
• A rigid body linked to other domains by flexible linkers
• A portion of the protein that can be active on its own if you remove
it from the rest of the protein.
©CMBI 2005
Protein Domains
• Domains can be 25 to 500 residues long; most are less than 200
residues
• The average protein contains 2 or 3 domains
• The total number of different types of domains ~1000 – 3000
• The same or similar domains are found in different proteins.
“Nature is a ‘tinkerer’ and not an inventor” (Jacob, 1977).
“Nature is smart but lazy”
• Usually, each domain plays a specific role in the function of the
protein.
©CMBI 2005
Linkers
Domain linkers link the protein domains together and have been found to
contain an amino acid signature that is distinct from the structurally
compact domains.
Average linker size 8-9 amino acids
Linkers are susceptible for protease attack and they are flexible.
©CMBI 2005
Protein Domain Databases
Even though the structure of a domain is not always known it is still
possible to define the domain boundaries from sequence alone
Many of the common domains have already been defined in domain
databases
Advantages:
• Pre-annotated domains
• Easy interpretation of domain structure
Problem:
• Not trivial to define domain boundaries unambiguously
©CMBI 2005
Protein Domains
http://ip30.eti.uva.nl/ember-demo/ch3
Domain databases (2)
Generation
#entries
PfamA
manual
7503 families
PfamB
automatic
>140,000 families
Prints
manual
11,170 motifs
Prosite Profiles
manual
577 profiles
Blocks
automatic
28,337 blocks, 5733 groups
SMART
manual
667 HMMs
ProDom
automatic
501,917 domain families
©CMBI 2005
PRINTS database
•
Most protein families are characterised not by one, but by several
conserved motifs
•
Fingerprints are groups of conserved motifs excised from sequence
alignments
•
Taken together, they provide diagnostic family signatures. They are
are the basis of the PRINTS database, and are stored in the form of
aligned motifs
•
Input about protein families is done manually
•
True members match all elements of the fingerprint in order, subfamily
members may match part of fingerprint
©CMBI 2005
PRINTS database
http://ip30.eti.uva.nl/ember-demo/ch3
PRINTS
©CMBI 2005
BLOCKS database
Blocks are multiply aligned ungapped segments corresponding to the most
highly conserved regions of proteins.
The blocks for the BLOCKs database are made automatically by looking
for the most highly conserved regions in groups of proteins documented in
InterPro.
Version 14.1 of the BLOCKS Database consists of 28,337 blocks
representing 5733 groups documented in InterPro 8.1 (february 2005)
To ensure complete coverage it is recommended that both the PRINTS
and the BLOCKS database be searched
©CMBI 2005
©CMBI 2005
©CMBI 2005
ProDom:
The Protein Domain Database
• ProDom is a comprehensive set of protein domain families
automatically generated
• Each entry provides a multiple sequence alignment of homologous
domains and a family consensus sequence.
• Current ProDom release:
ProDom 2004.1, June 2004, 501917 domain families
©CMBI 2005
©CMBI 2005
©CMBI 2005
Pfam
Pfam (Protein families) is a large collection of multiple sequence
alignments and hidden Markov models covering many common protein
domains and families.
For each family in Pfam you can:
•Look at multiple alignments
•View the domain organisation of proteins
•Examine species distribution
•Follow links to other databases
•View known protein structures
©CMBI 2005
Pfam
Two distinct parts:
–Pfam-A entries are manually curated
7503 families
–Pfam-B entries automatically generated clusters
>140,000
(not covered by Pfam-A)
New:
iPfam is a resource that describes domain-domain interactions
that are observed in known structures
©CMBI 2005
©CMBI 2005
©CMBI 2005
SMART
SMART - Simple Modular Architecture Research Tool
Domain families found in:
1) signalling
2) nuclear
3) extracellular
4) other
Current version 5.0: Number of SMART HMMs: 669
You can use SMART in two different modes: normal or genomic.
©CMBI 2005
Bacteriorhodopsin
Human serine protease
©CMBI 2005
Limitations of domain databases
• Patterns not present for all families of proteins
• Multiple sequence alignment to define patterns could be
inaccurate due to an automatic alignment
• Low number of sequences from different species could
result in inaccurate patterns
©CMBI 2005
Integrating Pattern databases
InterPro - Integrated Documentation Resource of Protein Families,
Domains and Functional Sites.
InterPro is a database of protein families, domains and functional
sites in which identifiable features found in known proteins can be
applied to unknown protein sequences.
The aim is to provide a one-stop-shop for protein family diagnostics
©CMBI 2005
InterPro
Member Databases
Prosite
(regular expressions and profiles)
Pfam, SMART, TIGRFAMs, PIRSF, PANTHER, Gene3D and
SUPERFAMILY
(hidden Markov Models - HMMs)
PRINTS
(groups of aligned, un-weighted motifs)
ProDom
(uses cluster analysis to group sequences)
Release 12.0 contains 12542 entries
Types of entries: Family, Domain, Repeat, PTM, Binding Site, Active Site
©CMBI 2005
©CMBI 2005
©CMBI 2005
©CMBI 2005
Summary
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Many different protein signature databases exist (from small
patterns to alignments to complex HMMs)
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The databases have different strengths and weaknesses. Some
databases can be better for your sequence than others
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Therefore: best to combine methods, preferably in an integrated
database
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The quality of a database/server is best tested with a sequence
you know very well
•
Always do control experiments: never trust a server
©CMBI 2005