skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers

Abstract

We report that α-Synuclein (α-syn) is the major component of the intraneuronal inclusions called Lewy bodies, which are the pathological hallmark of Parkinson’s disease. α-Syn is capable of self-assembly into many different species, such as soluble oligomers and fibrils. Even though attempts to resolve the structures of the protein have been made, detailed understanding about the structures and their relationship with the different aggregation steps is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson’s disease. Here we report the structural flexibility of α-syn monomers and dimers in an aqueous solution environment as probed by single-molecule time-lapse high-speed AFM. In addition, we present the molecular basis for the structural transitions using discrete molecular dynamics (DMD) simulations. α-Syn monomers assume a globular conformation, which is capable of forming tail-like protrusions over dozens of seconds. Importantly, a globular monomer can adopt fully extended conformations. Dimers, on the other hand, are less dynamic and show a dumbbell conformation that experiences morphological changes over time. DMD simulations revealed that the α-syn monomer consists of several tightly packed small helices. The tail-like protrusions are also helical with a small β-sheet, acting as a “hinge”. Monomers within dimers have a largemore » interfacial interaction area and are stabilized by interactions in the non-amyloid central (NAC) regions. Additionally, the dimer NAC-region of each α-syn monomer forms a β-rich segment. Moreover, NAC-regions are located in the hydrophobic core of the dimer.« less

Authors:
 [1]; ORCiD logo [2];  [3]; ORCiD logo [4];  [5]; ORCiD logo [5]; ORCiD logo [2]
  1. University of Nebraska Medical Center, Omaha, NE (United States). Department of Pharmaceutical Sciences; Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Biology and Biotechnology Division, Physical and Life Sciences Directorate
  2. University of Nebraska Medical Center, Omaha, NE (United States). Department of Pharmaceutical Sciences
  3. University of Nebraska Medical Center, Omaha, NE (United States). Department of Pharmaceutical Sciences ; Bruker Nano Surfaces Division, Santa Barbara, CA (United States)
  4. Univ. of North Carolina, Chapel Hill, NC (United States). Curriculum in Bioinformatics and Computational Biology
  5. Univ. of North Carolina, Chapel Hill, NC (United States). Department of Biochemistry and Biophysics
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1458666
Report Number(s):
LLNL-JRNL-743994
Journal ID: ISSN 0021-9606; 898957; TRN: US1901496
Grant/Contract Number:  
AC52-07NA27344
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 148; Journal Issue: 12; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Atomic force microscopy; Polymers; Peptides; Thermodynamic properties; Diseases and conditions; Molecular dynamics; Biomolecules; Computational models; Lipids

Citation Formats

Zhang, Yuliang, Hashemi, Mohtadin, Lv, Zhengjian, Williams, Benfeard, Popov, Konstantin I., Dokholyan, Nikolay V., and Lyubchenko, Yuri L. High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers. United States: N. p., 2018. Web. doi:10.1063/1.5008874.
Zhang, Yuliang, Hashemi, Mohtadin, Lv, Zhengjian, Williams, Benfeard, Popov, Konstantin I., Dokholyan, Nikolay V., & Lyubchenko, Yuri L. High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers. United States. doi:10.1063/1.5008874.
Zhang, Yuliang, Hashemi, Mohtadin, Lv, Zhengjian, Williams, Benfeard, Popov, Konstantin I., Dokholyan, Nikolay V., and Lyubchenko, Yuri L. Thu . "High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers". United States. doi:10.1063/1.5008874. https://www.osti.gov/servlets/purl/1458666.
@article{osti_1458666,
title = {High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers},
author = {Zhang, Yuliang and Hashemi, Mohtadin and Lv, Zhengjian and Williams, Benfeard and Popov, Konstantin I. and Dokholyan, Nikolay V. and Lyubchenko, Yuri L.},
abstractNote = {We report that α-Synuclein (α-syn) is the major component of the intraneuronal inclusions called Lewy bodies, which are the pathological hallmark of Parkinson’s disease. α-Syn is capable of self-assembly into many different species, such as soluble oligomers and fibrils. Even though attempts to resolve the structures of the protein have been made, detailed understanding about the structures and their relationship with the different aggregation steps is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson’s disease. Here we report the structural flexibility of α-syn monomers and dimers in an aqueous solution environment as probed by single-molecule time-lapse high-speed AFM. In addition, we present the molecular basis for the structural transitions using discrete molecular dynamics (DMD) simulations. α-Syn monomers assume a globular conformation, which is capable of forming tail-like protrusions over dozens of seconds. Importantly, a globular monomer can adopt fully extended conformations. Dimers, on the other hand, are less dynamic and show a dumbbell conformation that experiences morphological changes over time. DMD simulations revealed that the α-syn monomer consists of several tightly packed small helices. The tail-like protrusions are also helical with a small β-sheet, acting as a “hinge”. Monomers within dimers have a large interfacial interaction area and are stabilized by interactions in the non-amyloid central (NAC) regions. Additionally, the dimer NAC-region of each α-syn monomer forms a β-rich segment. Moreover, NAC-regions are located in the hydrophobic core of the dimer.},
doi = {10.1063/1.5008874},
journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 12,
volume = 148,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 3 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: HS-AFM images of wild-type $\alpha$-syn monomers. Selected frames from movie S3 showing the structural transition of $\alpha$-syn monomer over time. The monomer starts in a globular conformation (0 s) and transitions to: one-tailed (13.8s, 26.0 s, 33.6 s, and 125.6 s), two-tailed (27.4 s, 62.6 s, 129.6 smore » and 132.6 s), and extended conformations (130.4 s and 136.6 s). Interspersed with the other conformations, the monomer transitions back to a globular conformation (16.8 s and 100.2 s).« less

Save / Share:

Works referenced in this record:

Effective energy functions for protein structure prediction
journal, April 2000


Conserved C-Terminal Charge Exerts a Profound Influence on the Aggregation Rate of α-Synuclein
journal, August 2011

  • Levitan, Katerina; Chereau, David; Cohen, Samuel I. A.
  • Journal of Molecular Biology, Vol. 411, Issue 2
  • DOI: 10.1016/j.jmb.2011.05.046

Imaging of nucleic acids with atomic force microscopy
journal, June 2011


Defining Long-Range Order and Local Disorder in Native α-Synuclein Using Residual Dipolar Couplings
journal, December 2005

  • Bernadó, Pau; Bertoncini, Carlos W.; Griesinger, Christian
  • Journal of the American Chemical Society, Vol. 127, Issue 51
  • DOI: 10.1021/ja055538p

Conformational properties of α-synuclein in its free and lipid-associated states 1 1Edited by P. E. Wright
journal, April 2001

  • Eliezer, David; Kutluay, Esin; Bussell, Robert
  • Journal of Molecular Biology, Vol. 307, Issue 4
  • DOI: 10.1006/jmbi.2001.4538

Molecular-level secondary structure, polymorphism, and dynamics of full-length  -synuclein fibrils studied by solid-state NMR
journal, October 2005

  • Heise, H.; Hoyer, W.; Becker, S.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 44
  • DOI: 10.1073/pnas.0506109102

Evidence for a Partially Folded Intermediate in α-Synuclein Fibril Formation
journal, January 2001

  • Uversky, Vladimir N.; Li, Jie; Fink, Anthony L.
  • Journal of Biological Chemistry, Vol. 276, Issue 14
  • DOI: 10.1074/jbc.m010907200

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
journal, May 2004


Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials
journal, October 2003


Interplay of  -synuclein binding and conformational switching probed by single-molecule fluorescence
journal, March 2009

  • Ferreon, A. C. M.; Gambin, Y.; Lemke, E. A.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 14
  • DOI: 10.1073/pnas.0809232106

Role of α-synuclein penetration into the membrane in the mechanisms of oligomer pore formation: α-syn membrane penetration
journal, February 2012


The new mutation, E46K, of α-synuclein causes parkinson and Lewy body dementia: New α-Synuclein Gene Mutation
journal, December 2003

  • Zarranz, Juan J.; Alegre, Javier; Gómez-Esteban, Juan C.
  • Annals of Neurology, Vol. 55, Issue 2
  • DOI: 10.1002/ana.10795

Burden of illness in Parkinson's disease
journal, January 2005

  • Huse, Daniel M.; Schulman, Kathy; Orsini, Lucinda
  • Movement Disorders, Vol. 20, Issue 11
  • DOI: 10.1002/mds.20609

α-Synuclein Misfolding: Single Molecule AFM Force Spectroscopy Study
journal, December 2008

  • Yu, Junping; Malkova, Sarka; Lyubchenko, Yuri L.
  • Journal of Molecular Biology, Vol. 384, Issue 4
  • DOI: 10.1016/j.jmb.2008.10.006

Scanning Force Microscopy of DNA Deposited onto Mica: EquilibrationversusKinetic Trapping Studied by Statistical Polymer Chain Analysis
journal, December 1996

  • Rivetti, Claudio; Guthold, Martin; Bustamante, Carlos
  • Journal of Molecular Biology, Vol. 264, Issue 5
  • DOI: 10.1006/jmbi.1996.0687

AlaSOPro mutation in the gene encoding α-synuclein in Parkinson's disease
journal, February 1998

  • Krüger, Rejko; Kuhn, Wilfried; Müller, Thomas
  • Nature Genetics, Vol. 18, Issue 2
  • DOI: 10.1038/ng0298-106

Effect of Spermidine on Misfolding and Interactions of Alpha-Synuclein
journal, May 2012


α-Synuclein: Membrane Interactions and Toxicity in Parkinson's Disease
journal, November 2010


Direct Observation of Heterogeneous Amyloid Fibril Growth Kinetics via Two-Color Super-Resolution Microscopy
journal, December 2013

  • Pinotsi, Dorothea; Buell, Alexander K.; Galvagnion, Celine
  • Nano Letters, Vol. 14, Issue 1
  • DOI: 10.1021/nl4041093

Structural disorder of monomeric α-synuclein persists in mammalian cells
journal, January 2016

  • Theillet, Francois-Xavier; Binolfi, Andres; Bekei, Beata
  • Nature, Vol. 530, Issue 7588
  • DOI: 10.1038/nature16531

Mutation in the -Synuclein Gene Identified in Families with Parkinson's Disease
journal, June 1997


MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening
journal, August 2008

  • Yin, Shuangye; Biedermannova, Lada; Vondrasek, Jiri
  • Journal of Chemical Information and Modeling, Vol. 48, Issue 8
  • DOI: 10.1021/ci8001167

Structure and Dynamics of Micelle-bound Human  -Synuclein
journal, December 2004

  • Ulmer, T. S.; Bax, A.; Cole, N. B.
  • Journal of Biological Chemistry, Vol. 280, Issue 10
  • DOI: 10.1074/jbc.m411805200

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis
journal, December 2015

  • Proctor, Elizabeth A.; Fee, Lanette; Tao, Yazhong
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 3
  • DOI: 10.1073/pnas.1516725113

Visualization of Intrinsically Disordered Regions of Proteins by High-Speed Atomic Force Microscopy
journal, September 2008

  • Miyagi, Atsushi; Tsunaka , Yasuo; Uchihashi , Takayuki
  • ChemPhysChem, Vol. 9, Issue 13
  • DOI: 10.1002/cphc.200800210

The Role of Stable α-Synuclein Oligomers in the Molecular Events Underlying Amyloid Formation
journal, February 2014

  • Lorenzen, Nikolai; Nielsen, Søren Bang; Buell, Alexander K.
  • Journal of the American Chemical Society, Vol. 136, Issue 10
  • DOI: 10.1021/ja411577t

Molecular dynamics simulations at constant pressure and/or temperature
journal, February 1980

  • Andersen, Hans C.
  • The Journal of Chemical Physics, Vol. 72, Issue 4
  • DOI: 10.1063/1.439486

Single Fibril Growth Kinetics of α-Synuclein
journal, March 2015

  • Wördehoff, Michael M.; Bannach, Oliver; Shaykhalishahi, Hamed
  • Journal of Molecular Biology, Vol. 427, Issue 6
  • DOI: 10.1016/j.jmb.2015.01.020

Early Stages for Parkinson’s Development: α-Synuclein Misfolding and Aggregation
journal, July 2008


Rapid Self-assembly of α-Synuclein Observed by In Situ Atomic Force Microscopy
journal, June 2004

  • Hoyer, Wolfgang; Cherny, Dmitry; Subramaniam, Vinod
  • Journal of Molecular Biology, Vol. 340, Issue 1
  • DOI: 10.1016/j.jmb.2004.04.051

Nanoprobing of α-synuclein misfolding and aggregation with atomic force microscopy
journal, April 2011

  • Yu, Junping; Warnke, Julia; Lyubchenko, Yuri L.
  • Nanomedicine: Nanotechnology, Biology and Medicine, Vol. 7, Issue 2
  • DOI: 10.1016/j.nano.2010.08.001

α-Synuclein misfolding and Parkinson's disease
journal, February 2012

  • Breydo, Leonid; Wu, Jessica W.; Uversky, Vladimir N.
  • Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1822, Issue 2
  • DOI: 10.1016/j.bbadis.2011.10.002

From The Cover: Release of long-range tertiary interactions potentiates aggregation of natively unstructured  -synuclein
journal, January 2005

  • Bertoncini, C. W.; Jung, Y. -S.; Fernandez, C. O.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 5
  • DOI: 10.1073/pnas.0407146102

Direct Detection of α-Synuclein Dimerization Dynamics: Single-Molecule Fluorescence Analysis
journal, April 2015

  • Lv, Zhengjian; Krasnoslobodtsev, Alexey V.; Zhang, Yuliang
  • Biophysical Journal, Vol. 108, Issue 8
  • DOI: 10.1016/j.bpj.2015.03.010

Applications of Discrete Molecular Dynamics in biology and medicine
journal, April 2016


Direct observation of the three regions in α-synuclein that determine its membrane-bound behaviour
journal, May 2014

  • Fusco, Giuliana; De Simone, Alfonso; Gopinath, Tata
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4827

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics
journal, July 2008


High Intrinsic Mechanical Flexibility of Mouse Prion Nanofibrils Revealed by Measurements of Axial and Radial Young’s Moduli
journal, March 2014

  • Lamour, Guillaume; Yip, Calvin K.; Li, Hongbin
  • ACS Nano, Vol. 8, Issue 4
  • DOI: 10.1021/nn5007013

A novel pathway for amyloids self-assembly in aggregates at nanomolar concentration mediated by the interaction with surfaces
journal, March 2017

  • Banerjee, Siddhartha; Hashemi, Mohtadin; Lv, Zhengjian
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep45592

Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing
journal, February 2011

  • Gambin, Yann; VanDelinder, Virginia; Ferreon, Allan Chris M.
  • Nature Methods, Vol. 8, Issue 3
  • DOI: 10.1038/nmeth.1568

α-Synuclein Misfolding Assessed with Single Molecule AFM Force Spectroscopy: Effect of Pathogenic Mutations
journal, October 2013

  • Krasnoslobodtsev, Alexey V.; Volkov, Ivan L.; Asiago, Josephat M.
  • Biochemistry, Vol. 52, Issue 42
  • DOI: 10.1021/bi401037z

A Combinatorial NMR and EPR Approach for Evaluating the Structural Ensemble of Partially Folded Proteins
journal, June 2010

  • Rao, Jampani Nageswara; Jao, Christine C.; Hegde, Balachandra G.
  • Journal of the American Chemical Society, Vol. 132, Issue 25
  • DOI: 10.1021/ja100646t

To be disordered or not to be disordered: is that still a question for proteins in the cell?
journal, June 2017

  • Pauwels, Kris; Lebrun, Pierre; Tompa, Peter
  • Cellular and Molecular Life Sciences, Vol. 74, Issue 17
  • DOI: 10.1007/s00018-017-2561-6

Prediction of “Aggregation-prone” and “Aggregation-susceptible” Regions in Proteins Associated with Neurodegenerative Diseases
journal, July 2005

  • Pawar, Amol P.; DuBay, Kateri F.; Zurdo, Jesús
  • Journal of Molecular Biology, Vol. 350, Issue 2
  • DOI: 10.1016/j.jmb.2005.04.016

α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation
journal, August 2011

  • Bartels, Tim; Choi, Joanna G.; Selkoe, Dennis J.
  • Nature, Vol. 477, Issue 7362
  • DOI: 10.1038/nature10324

NACP, A Protein Implicated in Alzheimer's Disease and Learning, Is Natively Unfolded
journal, January 1996

  • Weinreb, Paul H.; Zhen, Weiguo; Poon, Anna W.
  • Biochemistry, Vol. 35, Issue 43
  • DOI: 10.1021/bi961799n

α-Synuclein-Induced Membrane Remodeling Is Driven by Binding Affinity, Partition Depth, and Interleaflet Order Asymmetry
journal, July 2014

  • Braun, Anthony R.; Lacy, Michael M.; Ducas, Vanessa C.
  • Journal of the American Chemical Society, Vol. 136, Issue 28
  • DOI: 10.1021/ja5016958

Structural Intermediates during α-Synuclein Fibrillogenesis on Phospholipid Vesicles
journal, March 2012

  • Comellas, Gemma; Lemkau, Luisel R.; Zhou, Donghua H.
  • Journal of the American Chemical Society, Vol. 134, Issue 11
  • DOI: 10.1021/ja209019s

Dynamics of Nucleosomes Assessed with Time-Lapse High-Speed Atomic Force Microscopy
journal, September 2011

  • Miyagi, Atsushi; Ando, Toshio; Lyubchenko, Yuri L.
  • Biochemistry, Vol. 50, Issue 37
  • DOI: 10.1021/bi200946z

α-Synuclein in Lewy bodies
journal, August 1997

  • Spillantini, Maria Grazia; Schmidt, Marie Luise; Lee, Virginia M. -Y.
  • Nature, Vol. 388, Issue 6645
  • DOI: 10.1038/42166

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations
journal, November 2006

  • Chodera, John D.; Swope, William C.; Pitera, Jed W.
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 1
  • DOI: 10.1021/ct0502864

Single Molecule AFM Force Spectroscopy Analysis of Alpha-Synuclein Misfolding
journal, January 2013


The fold of  -synuclein fibrils
journal, June 2008

  • Vilar, M.; Chou, H. -T.; Luhrs, T.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 25
  • DOI: 10.1073/pnas.0712179105

Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
journal, January 2005

  • Dedmon, Matthew M.; Lindorff-Larsen, Kresten; Christodoulou, John
  • Journal of the American Chemical Society, Vol. 127, Issue 2
  • DOI: 10.1021/ja044834j

VMD: Visual molecular dynamics
journal, February 1996


    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.