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Visualizing gaussian-chain like structural models of human α-synuclein in monomeric pre-fibrillar state: Solution SAXS data and modeling analysis

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Dey, Madhumita, Gupta, Arpit, Badmalia, Maulik D., Ashish, Sharma, Deepak·2025·International Journal of Biological Macromolecules
DOI 10.1016/j.ijbiomac.2024.138614

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Abstract

Here, using small angle X-ray scattering (SAXS) data profile as reference, we attempted to visualize conformational ensemble accessible prefibrillar monomeric state of α-synuclein in solution. In agreement with previous reports, our analysis also confirmed that α-synuclein molecules adopted disordered shape profile under non-associating conditions. Chain-ensemble modeling protocol with dummy residues provided two weighted averaged clusters of semi-extended shapes. Further, Ensemble Optimization Method (EOM) computed mole fractions of semi-extended "twisted" conformations which might co-exist in solution. Since these were only C α traces of the models, ALPHAFOLD2 server was used to search for all-atom models. Comparison with experimental data showed all predicted models disagreed equally, as individuals. Finally, we employed molecular dynamics simulations and normal mode analysis-based search coupled with SAXS data to seek better agreeing models. Overall, our analysis concludes that a shifting equilibrium of curved models with low α-helical content best-represents non-associating monomeric α-synuclein.

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Metadata

Authors
Dey, M., Gupta, A., Badmalia, M. D., Ashish, & Sharma, D.
Affiliations
Institute of Microbial Technology (IN)
Corresponding author
  • Ashish
  • Sharma, Deepak
ORCID
Venue
International Journal of Biological Macromolecules
Publisher
Elsevier BV
Published
2025-02
Volume
288
Pages
138614
ISSN
0141-8130 (ISSN-L)
DOI
10.1016/j.ijbiomac.2024.138614
OpenAlex
W4405316207
Cited by
5
References
4
Citations by year
2026: 1 · 2025: 3
FWCI
0.68
Type
journal article
Language
en
Open access
Licence
Locations
  • International Journal of Biological Macromolecules (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
  • CSIR - Institute of Microbial Technology (50/2023)
  • Council of Scientific & Industrial Research
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Health Sciences › Medicine › Clinical Neurology › Parkinson's Disease Mechanisms and Treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
alpha-synuclein, conformational ensembles, Gaussian chain model, twisted conformation, solution structure, molecular dynamics, normal mode analysis, protein disorder
MeSH terms
Humans, Models, Molecular, Protein Conformation, Solutions, X-Ray Diffraction, Normal Distribution, alpha-Synuclein, Scattering, Small Angle, Molecular Dynamics Simulation

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CoChat. (2026). Citation check: Visualizing gaussian-chain like structural models of human α-synuclein in monomeric pre-fibrillar state: Solution SAXS data and modeling analysis. https://app.cochat.ai/papers/10.1016/j.ijbiomac.2024.138614
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Dey, M., Gupta, A., Badmalia, M. D., Ashish, & Sharma, D. (2025). Visualizing gaussian-chain like structural models of human α-synuclein in monomeric pre-fibrillar state: Solution SAXS data and modeling analysis. International Journal of Biological Macromolecules. https://doi.org/10.1016/j.ijbiomac.2024.138614