Reference: George RA. and Heringa J. (2002) An analysis of protein domain linkers: their classification and role in protein folding. Protein Engineering 15, 871-879.
Linkers for gene fusion
Multi-functional enzymes are generally composed of a number of discrete domains
connected by inter-domain linkers. The use of protein domains in the creation of
novel protein and enzymic activities offers unlimited possibilities.
By the appropriate engineering of unnatural inter-domain linkers within modular
polyketide synthases, it was shown that the design of the linker is extremely
important in their 'assembly line' mechanism of catalysis (Gokhale et al, 1999 Science).
This has led to the 'Linker hypothesis': gene duplication is necessary
and sufficient for the evolution of multi-domain systems as long as linkers provide
suitable module connectivity. This provides a strategy of combinatorial
biosynthesis, in which modules are the building blocks of genetic manipulation.
Linker design is an obvious necessity in protein engineering. Linkers should be
invulnerable to host proteases, as they are often the targets for degradation.
They should be flexible, keeping domains apart while allowing
them to move as part of their catalytic function.
Linkers on the web
The inter-domain linker peptides of natural multi-domain proteins provide an
ample source of potential linkers for novel fusion proteins, these linkers provide
the conformation, flexibility and stability needed for a proteins biological function
in its natural environment.
The database is organised into four catagories;
- 1-linker : linkers connecting two continuous domains only.
- Helical : more than 30% of linker residues are involved in a helical structure.
- Non-helical : linkers with less than 30% of residues in a helical structure.
- All linkers : complete database.
The database can
be searched using several query types; PDB code, PDB header, linker length, C-alpha
extent, solvent accessibility, secondary structure or sequence. Searches using
regular expressions are possible and can be used to search for particular sequence
- use a '.' for any character.
example: searching 'P..P' in the sequence field will find sequences like 'PfdPa' or 'asdPrePa'.
- use  brackets to allow a combination of residues in one position.
example: 'A[D,E]R' will find sequences like 'fdADRtr' or 'aAERfp'.
- use a '^' to assign a starting residue.
Note: when using this you should specify the search field. In this case, for a starting residue search, select "Sequence"
example: '^P' will find all linkers starting with a Pro.
Each linker category may be queried individually or together.
The output from a search will display a list of linker identifier codes along
with their sequences. A hyperlink connects each linker identifier to an atomic
The Linker database was developed by Richard George.
Maintained by Bernd Brandt.