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Application of molecular dynamics simulations to design a dual-purpose oligopeptide linker sequence for fusion proteins

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Abstract

Proteins are often monitored by combining a fluorescent polypeptide tag with the target protein. However, due to the high molecular weight and immunogenicity of such tags, they are not suitable choices for combining with fusion proteins such as immunotoxins. In this study, we designed a polypeptide sequence with a dual role (it acts as both a linker and a fluorescent probe) to use with fusion proteins. Two common fluorescent tag sequences based on tetracysteine were compared to a commonly used rigid linker as well as our proposed dual-purpose sequence. Computational investigations showed that the dual-purpose sequence was structurally stable and may be a good choice to use as both a linker and a fluorescence marker between two moieties in a fusion protein.

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Acknowledgements

We would like to thank the Shiraz University of Medical Sciences School of Pharmacy for giving us the opportunity to perform this work on its server.

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Authors and Affiliations

  1. Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran

    Ehsan Rezaie & Mozafar Mohammadi

  2. Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran

    Ehsan Rezaie

  3. School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran

    Amirhossein Sakhteman

  4. Department of Immunology, Shiraz University of Medical Sciences, Shiraz, Iran

    Peyman Bemani

  5. Department of Pharmaceutical Biotechnology, Pharmaceutical Science Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran

    Sajjad Ahrari

Authors
  1. Ehsan Rezaie
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  2. Mozafar Mohammadi
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  3. Amirhossein Sakhteman
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  4. Peyman Bemani
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  5. Sajjad Ahrari
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Correspondence to Mozafar Mohammadi.

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Rezaie, E., Mohammadi, M., Sakhteman, A. et al. Application of molecular dynamics simulations to design a dual-purpose oligopeptide linker sequence for fusion proteins. J Mol Model 24, 313 (2018). https://doi.org/10.1007/s00894-018-3846-x

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  • DOI: https://doi.org/10.1007/s00894-018-3846-x

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