Cargando…

Alternative Structures of α-Synuclein

The object of our analysis is the structure of alpha-synuclein (ASyn), which, under in vivo conditions, associates with presynaptic vesicles. Misfolding of ASyn is known to be implicated in Parkinson’s disease. The availability of structural information for both the micelle-bound and amyloid form of...

Descripción completa

Detalles Bibliográficos
Autores principales: Dułak, Dawid, Gadzała, Małgorzata, Banach, Mateusz, Konieczny, Leszek, Roterman, Irena
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038196/
https://www.ncbi.nlm.nih.gov/pubmed/32019169
http://dx.doi.org/10.3390/molecules25030600
_version_ 1783500597899558912
author Dułak, Dawid
Gadzała, Małgorzata
Banach, Mateusz
Konieczny, Leszek
Roterman, Irena
author_facet Dułak, Dawid
Gadzała, Małgorzata
Banach, Mateusz
Konieczny, Leszek
Roterman, Irena
author_sort Dułak, Dawid
collection PubMed
description The object of our analysis is the structure of alpha-synuclein (ASyn), which, under in vivo conditions, associates with presynaptic vesicles. Misfolding of ASyn is known to be implicated in Parkinson’s disease. The availability of structural information for both the micelle-bound and amyloid form of ASyn enables us to speculate on the specific mechanism of amyloid transformation. This analysis is all the more interesting given the fact that—Unlike in Aβ(1–42) amyloids—only the central fragment (30–100) of ASyn has a fibrillar structure, whereas, its N- and C-terminal fragments (1–30 and 100–140, respectively) are described as random coils. Our work addresses the following question: Can the ASyn chain—as well as the aforementioned individual fragments—adopt globular conformations? In order to provide an answer, we subjected the corresponding sequences to simulations carried out using Robetta and I-Tasser, both of which are regarded as accurate protein structure predictors. In addition, we also applied the fuzzy oil drop (FOD) model, which, in addition to optimizing the protein’s internal free energy, acknowledges the presence of an external force field contributed by the aqueous solvent. This field directs hydrophobic residues to congregate near the center of the protein body while exposing hydrophilic residues on its surface. Comparative analysis of the obtained models suggests that fragments which do not participate in forming the amyloid fibril (i.e., 1–30 and 100–140) can indeed attain globular conformations. We also explain the influence of mutations observed in vivo upon the susceptibility of ASyn to undergo amyloid transformation. In particular, the 30–100 fragment (which adopts a fibrillar structure in PDB) is not predicted to produce a centralized hydrophobic core by any of the applied toolkits (Robetta, I-Tasser, and FOD). This means that in order to minimize the entropically disadvantageous contact between hydrophobic residues and the polar solvent, ASyn adopts the form of a ribbonlike micelle (rather than a spherical one). In other words, the ribbonlike micelle represents a synergy between the conformational preferences of the protein chain and the influence of its environment.
format Online
Article
Text
id pubmed-7038196
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-70381962020-03-10 Alternative Structures of α-Synuclein Dułak, Dawid Gadzała, Małgorzata Banach, Mateusz Konieczny, Leszek Roterman, Irena Molecules Article The object of our analysis is the structure of alpha-synuclein (ASyn), which, under in vivo conditions, associates with presynaptic vesicles. Misfolding of ASyn is known to be implicated in Parkinson’s disease. The availability of structural information for both the micelle-bound and amyloid form of ASyn enables us to speculate on the specific mechanism of amyloid transformation. This analysis is all the more interesting given the fact that—Unlike in Aβ(1–42) amyloids—only the central fragment (30–100) of ASyn has a fibrillar structure, whereas, its N- and C-terminal fragments (1–30 and 100–140, respectively) are described as random coils. Our work addresses the following question: Can the ASyn chain—as well as the aforementioned individual fragments—adopt globular conformations? In order to provide an answer, we subjected the corresponding sequences to simulations carried out using Robetta and I-Tasser, both of which are regarded as accurate protein structure predictors. In addition, we also applied the fuzzy oil drop (FOD) model, which, in addition to optimizing the protein’s internal free energy, acknowledges the presence of an external force field contributed by the aqueous solvent. This field directs hydrophobic residues to congregate near the center of the protein body while exposing hydrophilic residues on its surface. Comparative analysis of the obtained models suggests that fragments which do not participate in forming the amyloid fibril (i.e., 1–30 and 100–140) can indeed attain globular conformations. We also explain the influence of mutations observed in vivo upon the susceptibility of ASyn to undergo amyloid transformation. In particular, the 30–100 fragment (which adopts a fibrillar structure in PDB) is not predicted to produce a centralized hydrophobic core by any of the applied toolkits (Robetta, I-Tasser, and FOD). This means that in order to minimize the entropically disadvantageous contact between hydrophobic residues and the polar solvent, ASyn adopts the form of a ribbonlike micelle (rather than a spherical one). In other words, the ribbonlike micelle represents a synergy between the conformational preferences of the protein chain and the influence of its environment. MDPI 2020-01-30 /pmc/articles/PMC7038196/ /pubmed/32019169 http://dx.doi.org/10.3390/molecules25030600 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Dułak, Dawid
Gadzała, Małgorzata
Banach, Mateusz
Konieczny, Leszek
Roterman, Irena
Alternative Structures of α-Synuclein
title Alternative Structures of α-Synuclein
title_full Alternative Structures of α-Synuclein
title_fullStr Alternative Structures of α-Synuclein
title_full_unstemmed Alternative Structures of α-Synuclein
title_short Alternative Structures of α-Synuclein
title_sort alternative structures of α-synuclein
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038196/
https://www.ncbi.nlm.nih.gov/pubmed/32019169
http://dx.doi.org/10.3390/molecules25030600
work_keys_str_mv AT dułakdawid alternativestructuresofasynuclein
AT gadzałamałgorzata alternativestructuresofasynuclein
AT banachmateusz alternativestructuresofasynuclein
AT koniecznyleszek alternativestructuresofasynuclein
AT rotermanirena alternativestructuresofasynuclein