ArticleThe journal of physical chemistry. B2015
Simulating the distance distribution between spin-labels attached to proteins.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 53 citations in OpenAlex.
- Hidden protein disorder: Deciphering the structural organisation and dynamics of a non-canonical CP12 from the diatom Thalassiosira pseudonana.The FEBS journal · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Alternating access of a bacterial homolog of neurotransmitter: sodium symporters determined from AlphaFold2 ensembles and DEER spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Review
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT.Nature communications · 2023Article
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling.PLoS computational biology · 2023Article
- Comparative evaluation of spin-label modeling methods for protein structural studies.Biophysical journal · 2022Article
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.Journal of the American Chemical Society · 2021Article
- An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling.Frontiers in molecular biosciences · 2021Article
- Linkage between Proximal and Distal Movements of P450cam Induced by Putidaredoxin.Biochemistry · 2020Article
- Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories.Scientific reports · 2020Article
- Atomistic Models from Orientation and Distance Constraints Using EPR of a Bifunctional Spin Label.Biophysical journal · 2019Article
- Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP.The Journal of general physiology · 2019Article
- A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.International journal of molecular sciences · 2019Article
- Refinement of Highly Flexible Protein Structures using Simulation-Guided Spectroscopy.Angewandte Chemie (International ed. in English) · 2018Article
- Sodium and proton coupling in the conformational cycle of a MATE antiporter fromProceedings of the National Academy of Sciences of the United States of America · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
EPR/DEER spectroscopy is playing an increasingly important role in the characterization of the conformational states of proteins. In this study, force field parameters for the bifunctional spin-label (RX) used in EPR/DEER are parametrized and tested with molecular dynamics (MD) simulations. The dihedral angles connecting the Cα atom of the backbone to the nitroxide ring moiety of the RX spin-label attached to i and i + 4 positions in a polyalanine α-helix agree very well with those observed in the X-ray crystallography. Both RXi,i+4 and RXi,i+3 are more rigid than the monofunctional spin-label (R1) commonly used in EPR/DEER, while RXi,i+4 is more rigid and causes less distortion in a protein backbone than RXi,i+3. Simplified dummy spin-label models with a single effective particle representing the RXi,i+3 and RXi,i+4 are also developed and parametrized from the all-atom simulations. MD simulations with dummy spin-labels (MDDS) provide distance distributions that can be directly compared to distance distributions obtained from EPR/DEER to rapidly assess if a hypothetical three-dimensional (3D) structural model is consistent with experiment. The dummy spin-labels can also be used in the restrained-ensemble MD (re-MD) simulations to carry out structural refinement of 3D models. Applications of this methodology to T4 lysozyme, KCNE1, and LeuT are shown to provide important insights about their conformational dynamics.
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