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Title: Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

Abstract

Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atommore » simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in slowing down fibril elongation in vivo.« less

Authors:
;  [1];  [2];  [3];  [4];  [5]
  1. Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw (Poland)
  2. Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City (Viet Nam)
  3. (Viet Nam)
  4. Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris (France)
  5. Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)
Publication Date:
OSTI Identifier:
22415651
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 142; Journal Issue: 14; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; AGGLOMERATION; ATOMS; COMPARATIVE EVALUATIONS; COMPUTERIZED SIMULATION; ELONGATION; FLUCTUATIONS; IN VIVO; INTERMEDIATE STATE; KINETICS; MONOMERS; NERVOUS SYSTEM DISEASES; PARTITION; PEPTIDES; SLOWING-DOWN; WATER

Citation Formats

Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl, Kolinski, Andrzej, Co, Nguyen Truong, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Nguyen, Phuong H., and Li, Mai Suan, E-mail: masli@ifpan.edu.pl. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models. United States: N. p., 2015. Web. doi:10.1063/1.4917073.
Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl, Kolinski, Andrzej, Co, Nguyen Truong, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Nguyen, Phuong H., & Li, Mai Suan, E-mail: masli@ifpan.edu.pl. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models. United States. doi:10.1063/1.4917073.
Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl, Kolinski, Andrzej, Co, Nguyen Truong, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Nguyen, Phuong H., and Li, Mai Suan, E-mail: masli@ifpan.edu.pl. Tue . "Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models". United States. doi:10.1063/1.4917073.
@article{osti_22415651,
title = {Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models},
author = {Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl and Kolinski, Andrzej and Co, Nguyen Truong and Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City and Nguyen, Phuong H. and Li, Mai Suan, E-mail: masli@ifpan.edu.pl},
abstractNote = {Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in slowing down fibril elongation in vivo.},
doi = {10.1063/1.4917073},
journal = {Journal of Chemical Physics},
number = 14,
volume = 142,
place = {United States},
year = {Tue Apr 14 00:00:00 EDT 2015},
month = {Tue Apr 14 00:00:00 EDT 2015}
}
  • The present contribution analyzes the binding of ThT and neutral ThT derivatives to a β-sheet model by means of quantum chemical calculations. In addition, we study the properties of four molecules: (2-(2-hydroxyphenyl)benzoxazole (HBX), 2-(2-hydroxyphenyl)benzothiazole (HBT) and their respective iodinated compounds, HBXI and HBTI, in binding to amyloid fibril models and Aβ{sub 1-40}fibrils by using a combination of docking, molecular dynamics and quantum mechanics calculations.
  • No abstract prepared.
  • In this work we examine the consequences of incorporating the ab-initio derived monomer potential energy surface and non-linear dipole surface of Partridge and Schwenke [J. Chem. Phys. 106, 4618 (1997)] into the previously developed TTM2-R model of Burnham et al. [J. Chem. Phys. xx. yyyy (2001)] in order to develop a new, all-atom polarizable, flexible model for water (TTM2-F). We found that the use of the non-linear dipole surface is essential in modeling the change in the internal geometry of interacting water molecules and, in particular, the increase in the internal H-O-H bend angle with cluster size. This is themore » first demonstration of a flexible model which shows an increase in the bending angle in clusters. An explanation for this behavior is presented using the concept of geometric polarizabilities . The model furthermore reproduces the n=2-6 cluster binding energies to within an RMS deviation of 0.05 kcal/mol per hydrogen bond with respect to the MP2 complete basis set estimates.« less
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