ArticleThe journal of physical chemistry. B2008
Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix.
Article in The journal of physical chemistry. B, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
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- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
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- Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy.Physical chemistry chemical physics : PCCP · 2024Article
- Nanoscale water-polymer interactions tune macroscopic diffusivity of water in aqueous poly(ethylene oxide) solutions.Chemical science · 2024Article
- Observation of pH-Dependent Residual Structure in the Pmel17 Repeat Domain and the Implication for Its Amyloid Formation.Biochemistry · 2023Article
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- Structural Anomaly in Glasses: Molecular Dynamics Study of Organic Radical in Dibutylphthalate at Different Temperatures.International journal of molecular sciences · 2022Article
- Comparative evaluation of spin-label modeling methods for protein structural studies.Biophysical journal · 2022Article
- Location of the TEMPO moiety of TEMPO-PC in phosphatidylcholine bilayers is membrane phase dependent.Biophysical journal · 2022Article
- Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries.Biophysical journal · 2021Article
- Spin Labeling of Surface Cysteines Using a Bromoacrylaldehyde Spin Label.Applied magnetic resonance · 2021Article
- DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.PLoS computational biology · 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
- Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins.The journal of physical chemistry. B · 2019Article
- Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations.PLoS computational biology · 2019Article
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3 authors.
Funding
Abstract
The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains.
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