Literature DB >> 29451381

From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein.

Yoann Cote1,2, Patrice Delarue2, Harold A Scheraga3, Patrick Senet2,3, Gia G Maisuradze3.   

Abstract

α-Synuclein (αS) is a major constituent of Lewy bodies, the insoluble aggregates that are the hallmark of one of the most prevalent neurodegenerative disorders, Parkinson's disease (PD). The vast majority of experiments in vitro and in vivo provide extensive evidence that a disordered monomeric form is the predominant state of αS in water solution, and it undergoes a large-scale disorder-to-helix transition upon binding to vesicles of different types. Recently, another form, tetrameric, of αS with a stable helical structure was identified experimentally. It has been shown that a dynamic intracellular population of metastable αS tetramers and monomers coexists normally; and the tetramer plays an essential role in maintaining αS homeostasis. Therefore, it is of interest to know whether the tetramer can serve as a means of preventing or delaying the start of PD. Before answering this very important question, it is, first, necessary to find out, on an atomistic level, a correlation between tetramers and monomers; what mediates tetramer formation and what makes a tetramer stable. We address these questions here by investigating both monomeric and tetrameric forms of αS. In particular, by examining correlations between the motions of the side chains and the main chain, steric parameters along the amino-acid sequence, and one- and two-dimensional free-energy landscapes along the coarse-grained dihedral angles γ and δ and principal components, respectively, in monomeric and tetrameric αS, we were able to shed light on a fundamental relationship between monomers and tetramers, and the key residues involved in mediating formation of a tetramer. Also, the reasons for the stability of tetrameric αS and inability of monomeric αS to fold are elucidated here.

Entities:  

Keywords:  Monomeric alpha-synuclein; Parkinson’s disease; all-atom molecular dynamics simulations; dihedral principal component analysis; free-energy landscape; tetrameric alpha-synuclein

Mesh:

Substances:

Year:  2018        PMID: 29451381      PMCID: PMC5955826          DOI: 10.1021/acschemneuro.7b00446

Source DB:  PubMed          Journal:  ACS Chem Neurosci        ISSN: 1948-7193            Impact factor:   4.418


  54 in total

1.  Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures.

Authors:  Andrew S Thomas; Adrian H Elcock
Journal:  J Am Chem Soc       Date:  2004-02-25       Impact factor: 15.419

2.  Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations.

Authors:  Yoann Cote; Patrick Senet; Patrice Delarue; Gia G Maisuradze; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-02       Impact factor: 11.205

3.  Energy landscape of a small peptide revealed by dihedral angle principal component analysis.

Authors:  Yuguang Mu; Phuong H Nguyen; Gerhard Stock
Journal:  Proteins       Date:  2005-01-01

4.  Structure and dynamics of micelle-bound human alpha-synuclein.

Authors:  Tobias S Ulmer; Ad Bax; Nelson B Cole; Robert L Nussbaum
Journal:  J Biol Chem       Date:  2004-12-22       Impact factor: 5.157

5.  How main-chains of proteins explore the free-energy landscape in native states.

Authors:  Patrick Senet; Gia G Maisuradze; Colette Foulie; Patrice Delarue; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-10       Impact factor: 11.205

6.  Local vs global motions in protein folding.

Authors:  Gia G Maisuradze; Adam Liwo; Patrick Senet; Harold A Scheraga
Journal:  J Chem Theory Comput       Date:  2013-07-09       Impact factor: 6.006

7.  Molecular cloning of cDNA encoding an unrecognized component of amyloid in Alzheimer disease.

Authors:  K Uéda; H Fukushima; E Masliah; Y Xia; A Iwai; M Yoshimoto; D A Otero; J Kondo; Y Ihara; T Saitoh
Journal:  Proc Natl Acad Sci U S A       Date:  1993-12-01       Impact factor: 11.205

8.  The conformational ensembles of α-synuclein and tau: combining single-molecule FRET and simulations.

Authors:  Abhinav Nath; Maria Sammalkorpi; David C DeWitt; Adam J Trexler; Shana Elbaum-Garfinkle; Corey S O'Hern; Elizabeth Rhoades
Journal:  Biophys J       Date:  2012-11-07       Impact factor: 4.033

9.  α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation.

Authors:  Tim Bartels; Joanna G Choi; Dennis J Selkoe
Journal:  Nature       Date:  2011-08-14       Impact factor: 49.962

10.  Structural basis of synaptic vesicle assembly promoted by α-synuclein.

Authors:  Giuliana Fusco; Tillmann Pape; Amberley D Stephens; Pierre Mahou; Ana Rita Costa; Clemens F Kaminski; Gabriele S Kaminski Schierle; Michele Vendruscolo; Gianluigi Veglia; Christopher M Dobson; Alfonso De Simone
Journal:  Nat Commun       Date:  2016-09-19       Impact factor: 14.919

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  13 in total

Review 1.  The metastable states of proteins.

Authors:  Debasish Kumar Ghosh; Akash Ranjan
Journal:  Protein Sci       Date:  2020-04-11       Impact factor: 6.725

2.  Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.

Authors:  Phuong H Nguyen; Philippe Derreumaux
Journal:  Methods Mol Biol       Date:  2022

3.  Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace.

Authors:  Shayon Bhattacharya; Liang Xu; Damien Thompson
Journal:  Methods Mol Biol       Date:  2022

4.  Exploring Structural Flexibility and Stability of α-Synuclein by the Landau-Ginzburg-Wilson Approach.

Authors:  Anatolii Korneev; Alexander Begun; Sergei Liubimov; Khatuna Kachlishvili; Alexander Molochkov; Antti J Niemi; Gia G Maisuradze
Journal:  J Phys Chem B       Date:  2022-09-02       Impact factor: 3.466

5.  Pathogenic Mechanisms of Cytosolic and Membrane-Enriched α-Synuclein Converge on Fatty Acid Homeostasis.

Authors:  Arati Tripathi; Heba Alnakhala; Elizabeth Terry-Kantor; Andrew Newman; Lei Liu; Thibaut Imberdis; Saranna Fanning; Silke Nuber; Nagendran Ramalingam; Dennis Selkoe; Ulf Dettmer
Journal:  J Neurosci       Date:  2022-01-27       Impact factor: 6.709

Review 6.  Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.

Authors:  Phuong H Nguyen; Ayyalusamy Ramamoorthy; Bikash R Sahoo; Jie Zheng; Peter Faller; John E Straub; Laura Dominguez; Joan-Emma Shea; Nikolay V Dokholyan; Alfonso De Simone; Buyong Ma; Ruth Nussinov; Saeed Najafi; Son Tung Ngo; Antoine Loquet; Mara Chiricotto; Pritam Ganguly; James McCarty; Mai Suan Li; Carol Hall; Yiming Wang; Yifat Miller; Simone Melchionna; Birgit Habenstein; Stepan Timr; Jiaxing Chen; Brianna Hnath; Birgit Strodel; Rakez Kayed; Sylvain Lesné; Guanghong Wei; Fabio Sterpone; Andrew J Doig; Philippe Derreumaux
Journal:  Chem Rev       Date:  2021-02-05       Impact factor: 60.622

Review 7.  Navigating the dynamic landscape of alpha-synuclein morphology: a review of the physiologically relevant tetrameric conformation.

Authors:  Heather R Lucas; Ricardo D Fernández
Journal:  Neural Regen Res       Date:  2020-03       Impact factor: 5.135

Review 8.  Implementing Complementary Approaches to Shape the Mechanism of α-Synuclein Oligomerization as a Model of Amyloid Aggregation.

Authors:  Marco Giampà; María J Amundarain; Maria Georgina Herrera; Nicolò Tonali; Veronica I Dodero
Journal:  Molecules       Date:  2021-12-24       Impact factor: 4.411

9.  Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic.

Authors:  Adrien Guzzo; Patrice Delarue; Ana Rojas; Adrien Nicolaï; Gia G Maisuradze; Patrick Senet
Journal:  Front Mol Biosci       Date:  2021-11-29

10.  Investigation of α-Synuclein Amyloid Fibrils Using the Fluorescent Probe Thioflavin T.

Authors:  Anna I Sulatskaya; Natalia P Rodina; Maksim I Sulatsky; Olga I Povarova; Iuliia A Antifeeva; Irina M Kuznetsova; Konstantin K Turoverov
Journal:  Int J Mol Sci       Date:  2018-08-23       Impact factor: 5.923

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