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Molecular Dynamics Studies on Amyloidogenic Proteins

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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))

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Abstract

Molecular dynamics simulations, coupled with experimental investigations could improve our understanding of the protein aggregation and fibrillization process of amyloidogenic proteins. Computational tools are being applied to solve the protein aggregation and fibrillization problem, providing insight into amyloid structures and aggregation mechanisms. Experimental studies of the nature of protein aggregation are unfortunately limited by the structure of aggregates and their insolubility in water. The difficulties have stimulated the development of new experimental methods, and intensive efforts to match computational results with the results of experimental investigations. The number of papers published on simulations of amyloidogenic proteins has increased rapidly during the last decade. The simulation systems covered a range from simple peptides (Alzheimer Aβ peptides or peptides being fragments of amyloidogenic proteins), to large proteins (transthyretin, prion protein, cystatin C, β2-microglobulin etc.). In studies of aggregation, very important is the integration of experimental and computational methods. Computational simulations constitute an “analytical tool” for obtaining and processing biological information and to make useful explanations of the physicochemical principles of amyloidogenesis, as well as to understand the role amino-acid sequences in amyloidogenic proteins. Very efficient theoretical models for prediction of protein aggregation propensities from primary structures have been proposed. At a minimal computational cost, some of these models can determine putative, aggregation-prone regions (“hot-spots”) within a protein sequence. The in silico simulations increase our understanding of the protein aggregation process. In this chapter the molecular studies of amyloidogenic proteins like prion protein, transthyretin and human cystatin C are presented. The MD studies of these proteins show the first steps during amyloids formation. In addition in this chapter the MD studies of protein fibrils are presented. Based on MD simulations of fibril models it is possible to interpret some experimental results and suggest a mechanism of elongation for the fibril protofilament formation.

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Authors and Affiliations

  1. Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland

    Sylwia Rodziewicz-Motowidło & Emilia Sikorska

  2. Swiss Institute of Bioinformatics, Molecular Modeling Group, Bâtiment Genopode, Quartier Sorge, 1015, Lausanne, Switzerland

    Justyna Iwaszkiewicz

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    Adam Liwo

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Rodziewicz-Motowidło, S., Sikorska, E., Iwaszkiewicz, J. (2019). Molecular Dynamics Studies on Amyloidogenic Proteins. 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_14

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