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Challenges in Experimental Methods

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Computer Simulations of Aggregation of Proteins and Peptides

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2340))

Abstract

Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.

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Acknowledgement

This work was partially supported by the National Science Centre, Poland, Grant 2019/35/B/NZ2/03997(MGG) and Grant No. 2017/26/D/ST5/00341 (MS), National Centre for Research and Development, Poland under POWR.03.02.00-00-I003/16 (NS).

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Authors and Affiliations

  1. Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wrocław, Poland

    Marlena E. Gąsior-Głogowska & Natalia Szulc

  2. Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland

    Monika Szefczyk

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  1. Marlena E. Gąsior-Głogowska
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  2. Natalia Szulc
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  3. Monika Szefczyk
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Correspondence to Marlena E. Gąsior-Głogowska .

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Editors and Affiliations

  1. Division of Theoretical Physics, Polish Academy of Sciences, Warsaw, Poland

    Mai Suan Li

  2. Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH, USA

    Andrzej Kloczkowski

  3. Instutute of Physics, Polish Academy of Sciences, Warsaw, Poland

    Marek Cieplak

  4. Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH, USA

    Maksim Kouza

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Gąsior-Głogowska, M.E., Szulc, N., Szefczyk, M. (2022). Challenges in Experimental Methods. In: Li, M.S., Kloczkowski, A., Cieplak, M., Kouza, M. (eds) Computer Simulations of Aggregation of Proteins and Peptides . Methods in Molecular Biology, vol 2340. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1546-1_13

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