ArticleBiophysical journal2012
Identification of minimally interacting modules in an intrinsically disordered protein.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Conformational transition of a polycationic hinge domain contributes to DNA binding.Biophysical chemistry · 2026Article
- Node features of chromosome structure networks and their connections to genome annotation.Computational and structural biotechnology journal · 2024Article
- Article
- Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation.Biophysical chemistry · 2021Article
- Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor.ACS omega · 2020Article
- Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework.Nucleic acids research · 2018Article
- CONAN: A Tool to Decode Dynamical Information from Molecular Interaction Maps.Biophysical journal · 2018Article
- CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences.The Journal of chemical physics · 2015Article
- Reads meet rotamers: structural biology in the age of deep sequencing.Current opinion in structural biology · 2015Review
- The role of semidisorder in temperature adaptation of bacterial FlgM proteins.Biophysical journal · 2013Article
- Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics.Chemical physics · 2013Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The conformational characterization of intrinsically disordered proteins (IDPs) is complicated by their conformational heterogeneity and flexibility. If an IDP could somehow be divided into smaller fragments and reconstructed later, theoretical and spectroscopic studies could probe its conformational variability in detail. Here, we used replica molecular-dynamics simulations and network theory to explore whether such a divide-and-conquer strategy is feasible for α-synuclein, a prototypical IDP. We characterized the conformational variability of α-synuclein by conducting >100 unbiased all-atom molecular-dynamics simulations, for a total of >10 μs of trajectories. In these simulations, α-synuclein formed a heterogeneous ensemble of collapsed coil states in an aqueous environment. These states were stabilized by heterogeneous contacts between sequentially distant regions. We find that α-synuclein contains residual secondary structures in the collapsed states, and the heterogeneity in the collapsed state makes it feasible to split α-synuclein into sequentially contiguous minimally interacting fragments. This study reveals previously unknown characteristics of α-synuclein and provides a new (to our knowledge) approach for studying other IDPs.
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