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Fuzzy Oil Drop Model Application—From Globular Proteins to Amyloids

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Part of the book series: Springer Series on Bio- and Neurosystems ((SSBN,volume 8))

Abstract

The fuzzy oil drop model asserts the presence of a monocentric hydrophobic core in a protein, generated by the influence of water which directs hydrophobic residues towards the center, while exposing hydrophilic molecules on the surface. Applying the model to a range of proteins which vary in terms of structure and function reveals globally accordant structures and locally discordant fragments which disrupt the hydrophobic core and appear to mediate the protein’s biological function. Solenoids provide an example of structural elements which diverge from the fuzzy oil drop model by adopting a linear distribution of hydrophobicity. Such linear propagation, while unbounded in principle, is arrested by terminal “caps”, which mediate contact with water and therefore prevent the solenoid from growing indefinitely. Amyloids—a group of misfolding proteins—follow the same principles but lack suitable “caps” and may propagate without bound. In light of the fuzzy oil drop model, the factor most directly responsible for this phenomenon is anomalous interaction with the aqueous environment, where the expected monocentric distribution of hydrophobicity is replaced by a distribution based on the intrinsic hydrophobicity of each residue, thus preventing a hydrophobic core from emerging. In this work we present a set of proteins which represent progressive departures from the fuzzy oil drop model (i.e. from the theoretical distribution of hydrophobicity expressed by a 3D Gaussian). We also discuss the biological function and/or disfunction of each protein.

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Acknowledgements

The work was financially supported by Jagiellonian University—Medical College grants system—grant #006363.

Authors are very thankful to Piotr Nowakowski for translation and to Anna Smietanska for technical support.

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Authors and Affiliations

  1. Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Łazarza 16, 31-530, Krakow, Poland

    M. Banach & I. Roterman

  2. Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348, Krakow, Poland

    M. Banach

  3. Chair of Medical Biochemistry, Jagiellonian University—Medical College, Kopernika 7, 31-034, Krakow, Poland

    L. Konieczny

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  1. M. Banach
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Correspondence to I. Roterman .

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  1. Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Adam Liwo

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Banach, M., Konieczny, L., Roterman, I. (2019). Fuzzy Oil Drop Model Application—From Globular Proteins to Amyloids. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series on Bio- and Neurosystems, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-95843-9_19

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