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LINKER: a program to generate linker sequences for fusion proteins.

C J Crasto1, J A Feng

  • 1Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA.

Protein Engineering
|June 2, 2000
PubMed
Summary

This study introduces the LINKER program, which automatically generates extended-conformation linker sequences for fusion protein construction. This tool aids researchers by providing reliable sequence selection based on crystallographic and NMR data.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Functional fusion protein construction relies on linker sequences that adopt extended conformations for maximal flexibility.
  • Current linker sequence selection is often intuitive and lacks reliable criteria, posing challenges for designing longer linkers.

Purpose of the Study:

  • To introduce the LINKER program, a computational tool for automatically generating linker sequences with extended conformations.
  • To provide a reliable selection criterion for linker sequences, particularly for complex fusion protein designs.

Main Methods:

  • The LINKER program utilizes X-ray crystallography and Nuclear Magnetic Resonance (NMR) data to identify sequences known to adopt extended conformations.
  • The program requires only the desired linker sequence length as input, with optional parameters for enhanced selection.

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  • The output is a set of sequences of the specified length.

    • Main Results:

    • The LINKER program successfully generates sets of linker sequences predicted to adopt extended conformations.
    • The program offers a systematic approach to linker design, moving beyond intuitive selection methods.

    Conclusions:

    • The LINKER program is a valuable tool for the biotechnology industry and biomedical research, simplifying the design of fusion proteins.
    • This automated approach enhances the efficiency and reliability of constructing functional fusion proteins requiring flexible linkers.