ArticlePLoS computational biology2020
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed.
- Autoinhibition of untimely DNA binding by structural disorder in the full-length peroxisome proliferator-activated receptors (PPARs).Nature communications · 2026Article
- Guidelines for Comparing Circular Dichroism Spectroscopy and Molecular Dynamics Simulations for Biomolecules.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
- Probing the Structural Dynamics of the Unbound MAX Protein: Insights from Well-Tempered Metadynamics.Journal of chemical information and modeling · 2026Article
- Linking Structure and Topology in Single-Chain Nanoparticles Using Simulations and Scattering Data.ACS polymers Au · 2025Article
- Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition.Biophysical journal · 2025Article
- Article
- Optimal weights and priors in simultaneous fitting of multiple small-angle scattering datasets.Journal of applied crystallography · 2025Article
- Applications of visualization technology in the structural sciences.Structural dynamics (Melville, N.Y.) · 2025Article
- Martini3-IDP: improved Martini 3 force field for disordered proteins.Nature communications · 2025Article
- Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry.Nanoscale · 2025Article
- Effects of All-Atom and Coarse-Grained Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of a Tau K18 Monomer.Journal of chemical information and modeling · 2024Article
- Asymmetric fluctuation of overlapping dinucleosome studied by cryoelectron microscopy and small-angle X-ray scattering.PNAS nexus · 2024Article
- Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.Nature communications · 2024Article
- Hierarchical Assembly of Single-Stranded RNA.Journal of chemical theory and computation · 2024Article
- Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation.Biophysical journal · 2023Article
- Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation.Science (New York, N.Y.) · 2023Article
- SANS Spectra with PLUMED: Implementation and Application to Metainference.Journal of chemical information and modeling · 2023Article
- Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties.European biophysics journal : EBJ · 2023Article
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6 authors.
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Abstract
Many proteins contain multiple folded domains separated by flexible linkers, and the ability to describe the structure and conformational heterogeneity of such flexible systems pushes the limits of structural biology. Using the three-domain protein TIA-1 as an example, we here combine coarse-grained molecular dynamics simulations with previously measured small-angle scattering data to study the conformation of TIA-1 in solution. We show that while the coarse-grained potential (Martini) in itself leads to too compact conformations, increasing the strength of protein-water interactions results in ensembles that are in very good agreement with experiments. We show how these ensembles can be refined further using a Bayesian/Maximum Entropy approach, and examine the robustness to errors in the energy function. In particular we find that as long as the initial simulation is relatively good, reweighting against experiments is very robust. We also study the relative information in X-ray and neutron scattering experiments and find that refining against the SAXS experiments leads to improvement in the SANS data. Our results suggest a general strategy for studying the conformation of multi-domain proteins in solution that combines coarse-grained simulations with small-angle X-ray scattering data that are generally most easy to obtain. These results may in turn be used to design further small-angle neutron scattering experiments that exploit contrast variation through 1H/2H isotope substitutions.
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